Synthesis of a drug delivery vehicle for cancer treatment utilizing DNA-functionalized gold nanoparticles

NASA Astrophysics Data System (ADS)

Brann, Tyler

The treatment of cancer with chemotherapeutic agents has made great strides in the last few decades but still introduces major systemic side effects. The potent drugs needed to kill cancer cells often cause irreparable damage to otherwise healthy organs leading to further morbidity and mortality. A therapy with intrinsic selective properties and/or an inducible activation has the potential to change the way cancer can be treated. Gold nanoparticles (GNPs) are biocompatible and chemically versatile tools that can be readily functionalized to serve as molecular vehicles. The ability of these particles to strongly absorb light with wavelengths in the therapeutic window combined with the heating effect of surface plasmon resonance makes them uniquely suited for noninvasive heating in biologic applications. Specially designed DNA aptamers have shown their ability to serve as drug carriers through intercalation as well as directly acting as therapeutic agents. By combining these separate molecules a multifaceted drug delivery vehicle can be created with great potential as a selective and controllable treatment for cancer. Oligonucleotide-coated GNPs have been created using spherical GNPs but little work has been reported using gold nanoplates in this way. Using the Diasynth method gold nanoplates were produced to absorb strongly in the therapeutic near infrared (nIR) window. These particles were functionalized with two DNA oligonucleotides: one serving as an intercalation site for doxorubicin, and another, AS1411, serving directly as an anticancer targeting/therapeutic agent. These functional particles were fully synthesized and processed along with confirmation of DNA functionalization and doxorubicin intercalation. Doxorubicin is released via denaturation of the DNA structure into which doxorubicin is intercalated upon the heating of the gold nanoplate well above the DNA melting temperature. This temperature increase, due to light stimulation of surface plasmon resonance, was measured during laser application. Successful release of doxorubicin via laser application was measured with fluorescence measurements providing proof that the doxorubicin was successfully intercalated and released.

Unveiling the Mode of Interaction of Berberine Alkaloid in Different Supramolecular Confined Environments: Interplay of Surface Charge between Nano-Confined Charged Layer and DNA.

PubMed

Kundu, Niloy; Roy, Arpita; Banik, Debasis; Sarkar, Nilmoni

2016-02-18

In this Article, we demonstrate a detailed characterization of binding interaction of berberine chloride (BBCl) with calf-thymus DNA (CT-DNA) in buffer solution as well as in two differently charged reverse micelles (RMs). The photophyscial properties of this alkaloid have been modulated within these microheterogeneous bioassemblies. The mode of binding of this alkaloid with DNA is of debate to date. However, fluorescence spectroscopic measurements, circular dichroism (CD) measurement, and temperature-dependent study unambiguously establish that BBCl partially intercalates into the DNA base pairs. The nonplanarity imposed by partial saturation in their structure causes the nonclassical types of intercalation into DNA. Besides the intercalation, electrostatic interactions also play a significant role in the binding between BBCl and DNA. DNA structure turns into a condensed form after encapsulation into RMs, which is followed by the CD spectra and microscopy study. The probe location and dynamics in the nanopool of the RMs depended on the electrostatic interaction between the charged surfactants and cationic berberine. The structural alteration of CT-DNA from B form to condensed form and the interplay of surface charge between RMs and DNA determine the interaction between the alkaloid and DNA in RMs. Time-resolved study and fluorescence anisotropy measurements successfully provide the binding interaction of BBCl in the nanopool of the RMs in the absence and in the presence of DNA. This study motivates us to judge further the potential applicability of this alkaloid in other biological systems or other biomimicking organized assemblies.

Assessment of amsacrine binding with DNA using UV-visible, circular dichroism and Raman spectroscopic techniques.

PubMed

Jangir, Deepak Kumar; Dey, Sanjay Kumar; Kundu, Suman; Mehrotra, Ranjana

2012-09-03

Proper understanding of the mechanism of binding of drugs to their targets in cell is a fundamental requirement to develop new drug therapy regimen. Amsacrine is a rationally designed anticancer drug, used to treat leukemia and lymphoma. Binding with cellular DNA is a crucial step in its mechanism of cytotoxicity. Despite numerous studies, DNA binding properties of amsacrine are poorly understood. Its reversible binding with DNA does not permit X-ray crystallography or NMR spectroscopic evaluation of amsacrine-DNA complexes. In the present work, interaction of amsacrine with calf thymus DNA is investigated at physiological conditions. UV-visible, FT-Raman and circular dichroism spectroscopic techniques were employed to determine the binding mode, binding constant, sequence specificity and conformational effects of amsacrine binding to native calf thymus DNA. Our results illustrate that amsacrine interacts with DNA by and large through intercalation between base pairs. Binding constant of the amsacrine-DNA complex was found to be K=1.2±0.1×10(4) M(-1) which is indicative of moderate type of binding of amsacrine to DNA. Raman spectroscopic results suggest that amsacrine has a binding preference of intercalation between AT base pairs of DNA. Minor groove binding is also observed in amsacrine-DNA complexes. These results are in good agreement with in silico investigation of amsacrine binding to DNA and thus provide detailed insight into DNA binding properties of amsacrine, which could ultimately, renders its cytotoxic efficacy. Copyright © 2012 Elsevier B.V. All rights reserved.

Process to Selectively Distinguish Viable from Non-Viable Bacterial Cells

NASA Technical Reports Server (NTRS)

LaDuc, Myron T.; Bernardini, Jame N.; Stam, Christina N.

2010-01-01

The combination of ethidium monoazide (EMA) and post-fragmentation, randomly primed DNA amplification technologies will enhance the analytical capability to discern viable from non-viable bacterial cells in spacecraft-related samples. Intercalating agents have been widely used since the inception of molecular biology to stain and visualize nucleic acids. Only recently, intercalating agents such as EMA have been exploited to selectively distinguish viable from dead bacterial cells. Intercalating dyes can only penetrate the membranes of dead cells. Once through the membrane and actually inside the cell, they intercalate DNA and, upon photolysis with visible light, produce stable DNA monoadducts. Once the DNA is crosslinked, it becomes insoluble and unable to be fragmented for post-fragmentation, randomly primed DNA library formation. Viable organisms DNA remains unaffected by the intercalating agents, allowing for amplification via post-fragmentation, randomly primed technologies. This results in the ability to carry out downstream nucleic acid-based analyses on viable microbes to the exclusion of all non-viable cells.

Photoinduced Electron Transfer between Psoralens and DNA: Influence of DNA Sequence and Substitution.

PubMed

Fröbel, Sascha; Levi, Lucilla; Ulamec, Sabine M; Gilch, Peter

2016-05-04

Psoralens are heterocyclic compounds which are, among other uses, used to treat skin deseases in the framework of PUVA therapy. In the dark, they intercalate into DNA and can form photoadducts with thymines upon UV-A excitation, which harms the affected cells. We have recently discovered that after excitation of intercalated psoralens, an efficient photoinduced electron transfer (PET) from DNA occurs. Here, the PET is studied in detail by means of femtosecond transient absorption spectroscopy. Using DNA samples that contain either only GC or AT base pairs, we show that only guanine donates the electrons. Additionally, the substituent effects on PET are studied relying on three different psoralen derivatives. The substitution alters spectroscopic and electrochemical properties of the psoralens, which are determined by cyclic voltammetry and steady state spectroscopy. These experiments allow us to estimate the PET energetics, which are in line with the measured kinetics. Implications for the applications of psoralens are discussed. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Comparative analysis of topoisomerase IB inhibition and DNA intercalation by flavonoids and similar compounds: structural determinates of activity

PubMed Central

2004-01-01

Flavonoids and other polyphenolic compounds have been shown to inhibit human topoisomerase IB (topo I) through both inhibition of relaxation activity and through stabilization of the cleavable complex (poisoning). Some flavonoids have also been shown to intercalate DNA, and an association of topoisomerase inhibition with intercalation has been noted. We surveyed 34 polyphenolic compounds, primarily flavonoid glycones and aglycones, for their ability to inhibit topo I and to intercalate DNA using an in vitro gel electrophoresis method. We show that the most potent topo I poisons are the flavones and flavonols, and that these generally, but not always, are found to be DNA intercalators. There was no clear correlation, however, of topo-I-poisoning activity with the degree of DNA unwinding. Surprisingly, both DNA intercalation and topo I poisoning were shown to occur with some flavone glycones, including the C-glycosylflavone orientin. Inhibition of relaxation activity by flavonoids was found to be difficult to quantify and was most likely to be due to non-specific inhibition through flavonoid aggregation. As part of a structure–activity analysis, we also investigated the acid–base chemistry of flavonoids and determined that many flavonoids show acid–base activity with a pKa in the physiological pH region. For this reason, subtle pH changes can have significant effects on solution activity of flavonoids and their concomitant biological activity. In addition, these effects may be complicated by pH-dependent aggregation and oxidative degradation. Finally, we develop a simple model for the intercalation of flavonoids into DNA and discuss possible consequences of intercalation and topoisomerase inhibition on a number of cellular processes. PMID:15312049

Intercalation and de-intercalation pathway of proflavine through the minor and major grooves of DNA: roles of water and entropy.

PubMed

Sasikala, Wilbee D; Mukherjee, Arnab

2013-05-07

DNA intercalation is a clinically relevant biophysical process due to its potential to inhibit the growth and survival of tumor cells and microbes through the arrest of the transcription and replication processes. Extensive kinetic and thermodynamic studies have followed since the discovery of the intercalative binding mode. However, the molecular mechanism and the origin of the thermodynamic and kinetic profile of the process are still not clear. Here we have constructed the free energy landscape of intercalation, de-intercalation and dissociation from both the major and minor grooves of DNA using extensive all-atom metadynamics simulations, capturing both the free energy barriers and stability in close agreement with fluorescence kinetic experiments. In the intercalated state, an alternate orientation of proflavine is found with an almost equal stability compared to the crystal orientation, however, separated by a 5.0 kcal mol(-1) barrier that decreases as the drug approaches the groove edges. This study provides a comprehensive picture in comparison with experiments, which indicates that the intercalation and de-intercalation of proflavine happen through the major groove side, although the effective intercalation barrier increases because the path of intercalation goes through the stable (abortive) minor groove bound state, making the process a millisecond long one in excellent agreement with the experiments. The molecular origin of the higher barrier for the intercalation from the minor groove side is attributed to the desolvation energy of DNA and the loss of entropy, while the barrier from the major groove, in the absence of desolvation energy, is primarily entropic.

Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA and lengthen linear DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Verebová, Valéria; Adamcik, Jozef; Danko, Patrik

2014-01-31

Highlights: • Anthraquinones quinizarin and danthron unwind negatively supercoiled DNA. • Anthraquinones quinizarin and danthron lengthen linear DNA. • Anthraquinones quinizarin and danthron possess middle binding affinity to DNA. • Anthraquinones quinizarin and danthron interact with DNA by intercalating mode. - Abstract: The intercalating drugs possess a planar aromatic chromophore unit by which they insert between DNA bases causing the distortion of classical B-DNA form. The planar tricyclic structure of anthraquinones belongs to the group of chromophore units and enables anthraquinones to bind to DNA by intercalating mode. The interactions of simple derivatives of anthraquinone, quinizarin (1,4-dihydroxyanthraquinone) and danthron (1,8-dihydroxyanthraquinone),more » with negatively supercoiled and linear DNA were investigated using a combination of the electrophoretic methods, fluorescence spectrophotometry and single molecule technique an atomic force microscopy. The detection of the topological change of negatively supercoiled plasmid DNA, unwinding of negatively supercoiled DNA, corresponding to appearance of DNA topoisomers with the low superhelicity and an increase of the contour length of linear DNA in the presence of quinizarin and danthron indicate the binding of both anthraquinones to DNA by intercalating mode.« less

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. III. Synthesis and investigation of properties of oligonucleotides, bearing bifunctional non-nucleotide insert].

PubMed

Kupriushkin, M S; Pyshnyĭ, D V

2012-01-01

Non-nucleotide phosporamidites were synthetized, having branched backbone with different position of functional groups. Obtained phosphoramidite monomers contain intercalator moiety--6-chloro-2-methoxyacridine, and additional hydroxyl residue protected with dimethoxytrityl group or with tert-butyldimethylsilyl group for post-synthetic modification. Synthesized oligothymidilates contain one or more modified units in different positions of sequence. Melting temperature and thermodynamic parameters of formation of complementary duplexes formed by modified oligonucleotides was defined (change in enthalpy and entropy). The introduction of intercalating residue causes a significant stabilization of DNA duplexes. It is shown that the efficiency of the fluorescence of acridine residue in the oligonucleotide conjugate significantly changes upon hybridization with DNA.

Antiproliferative, DNA intercalation and redox cycling activities of dioxonaphtho[2,3-d]imidazolium analogs of YM155: A structure-activity relationship study.

PubMed

Ho, Si-Han Sherman; Sim, Mei-Yi; Yee, Wei-Loong Sherman; Yang, Tianming; Yuen, Shyi-Peng John; Go, Mei-Lin

2015-11-02

The anticancer agent YM155 is widely investigated as a specific survivin suppressant. More recently, YM155 was found to induce DNA damage and this has raised doubts as to whether survivin is its primary target. In an effort to assess the contribution of DNA damage to the anticancer activity of YM155, several analogs were prepared and evaluated for antiproliferative activity on malignant cells, participation in DNA intercalation and free radical generation by redox cycling. The intact positively charged scaffold was found to be essential for antiproliferative activity and intercalation but was less critical for redox cycling where the minimal requirement was a pared down bicyclic quinone. Side chain requirements at the N(1) and N(3) positions of the scaffold were more alike for redox cycling and intercalation than antiproliferative activity, underscoring yet again, the limited structural overlaps for these activities. Furthermore, antiproliferative activities were poorly correlated to DNA intercalation and redox cycling. Potent antiproliferative activity (IC50 9-23 nM), exceeding that of YM155, was found for a minimally substituted methyl analog AB7. Like YM155 and other dioxonaphthoimidazoliums, AB7 was a modest DNA intercalator but with weak redox cycling activity. Thus, the capacity of this scaffold to inflict direct DNA damage leading to cell death may not be significant and YM155 should not be routinely classified as a DNA damaging agent. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Mitochondrial nucleoid clusters protect newly synthesized mtDNA during Doxorubicin- and Ethidium Bromide-induced mitochondrial stress

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alán, Lukáš, E-mail: lukas.alan@fgu.cas.cz; Špaček

Mitochondrial DNA (mtDNA) is compacted in ribonucleoprotein complexes called nucleoids, which can divide or move within the mitochondrial network. Mitochondrial nucleoids are able to aggregate into clusters upon reaction with intercalators such as the mtDNA depletion agent Ethidium Bromide (EB) or anticancer drug Doxorobicin (DXR). However, the exact mechanism of nucleoid clusters formation remains unknown. Resolving these processes may help to elucidate the mechanisms of DXR-induced cardiotoxicity. Therefore, we addressed the role of two key nucleoid proteins; mitochondrial transcription factor A (TFAM) and mitochondrial single-stranded binding protein (mtSSB); in the formation of mitochondrial nucleoid clusters during the action of intercalators.more » We found that both intercalators cause numerous aberrations due to perturbing their native status. By blocking mtDNA replication, both agents also prevented mtDNA association with TFAM, consequently causing nucleoid aggregation into large nucleoid clusters enriched with TFAM, co-existing with the normal nucleoid population. In the later stages of intercalation (> 48 h), TFAM levels were reduced to 25%. In contrast, mtSSB was released from mtDNA and freely distributed within the mitochondrial network. Nucleoid clusters mostly contained nucleoids with newly replicated mtDNA, however the nucleoid population which was not in replication mode remained outside the clusters. Moreover, the nucleoid clusters were enriched with p53, an anti-oncogenic gatekeeper. We suggest that mitochondrial nucleoid clustering is a mechanism for protecting nucleoids with newly replicated DNA against intercalators mediating genotoxic stress. These results provide new insight into the common mitochondrial response to mtDNA stress and can be implied also on DXR-induced mitochondrial cytotoxicity. - Highlights: • The mechanism for mitochondrial nucleoid clustering is proposed. • DNA intercalators (Doxorubicin or Ethidium Bromide) prevent TFAM binding to mtDNA. • Replicating nucleoids are less prone to DNA intercalator and preserve more TFAM. • Nucleoid clusters mostly contain nucleoids with newly replicated mtDNA. • Recently replicated nucleoids are protected in clusters by increased TFAM and p53.« less

Exploring DNA binding and nucleolytic activity of few 4-aminoantipyrine based amino acid Schiff base complexes: A comparative approach

NASA Astrophysics Data System (ADS)

Raman, N.; Sakthivel, A.; Pravin, N.

A series of novel Co(II), Cu(II), Ni(II) and Zn(II) complexes were synthesized from Schiff base(s), obtained by the condensation of 4-aminoantipyrine with furfural and amino acid (glycine(L1)/alanine(L2)/valine(L3)) and respective metal(II) chloride. Their structural features and other properties were explored from the analytical and spectral methods. The binding behaviors of the complexes to calf thymus DNA were investigated by absorption spectra, viscosity measurements and cyclic voltammetry. The intrinsic binding constants for the above synthesized complexes are found to be in the order of 102 to 105 indicating that most of the synthesized complexes are good intercalators. The binding constant values (Kb) clearly indicate that valine Schiff-base complexes have more intercalating ability than alanine and glycine Schiff-base complexes. The results indicate that the complexes bind to DNA through intercalation and act as efficient cleaving agents. The in vitro antibacterial and antifungal assay indicates that these complexes are good antimicrobial agents against various pathogens. The IC50 values of [Ni(L1)2] and [Zn(L1)2] complexes imply that these complexes have preferable ability to scavenge hydroxyl radical.

Spermine Attenuates the Action of the DNA Intercalator, Actinomycin D, on DNA Binding and the Inhibition of Transcription and DNA Replication

PubMed Central

Chen, Jeremy J. W.; Wu, Wen-Lin; Yuann, Jeu-Ming P.; Su, Wang-Lin; Chuang, Show-Mei; Hou, Ming-Hon

2012-01-01

The anticancer activity of DNA intercalators is related to their ability to intercalate into the DNA duplex with high affinity, thereby interfering with DNA replication and transcription. Polyamines (spermine in particular) are almost exclusively bound to nucleic acids and are involved in many cellular processes that require nucleic acids. Until now, the effects of polyamines on DNA intercalator activities have remained unclear because intercalation is the most important mechanism employed by DNA-binding drugs. Herein, using actinomycin D (ACTD) as a model, we have attempted to elucidate the effects of spermine on the action of ACTD, including its DNA-binding ability, RNA and DNA polymerase interference, and its role in the transcription and replication inhibition of ACTD within cells. We found that spermine interfered with the binding and stabilization of ACTD to DNA. The presence of increasing concentrations of spermine enhanced the transcriptional and replication activities of RNA and DNA polymerases, respectively, in vitro treated with ActD. Moreover, a decrease in intracellular polyamine concentrations stimulated by methylglyoxal-bis(guanylhydrazone) (MGBG) enhanced the ACTD-induced inhibition of c-myc transcription and DNA replication in several cancer cell lines. The results indicated that spermine attenuates ACTD binding to DNA and its inhibition of transcription and DNA replication both in vitro and within cells. Finally, a synergistic antiproliferative effect of MGBG and ACTD was observed in a cell viability assay. Our findings will be of significant relevance to future developments in combination with cancer therapy by enhancing the anticancer activity of DNA interactors through polyamine depletion. PMID:23144800

Spermine attenuates the action of the DNA intercalator, actinomycin D, on DNA binding and the inhibition of transcription and DNA replication.

PubMed

Wang, Sheng-Yu; Lee, Alan Yueh-Luen; Lee, Yueh-Luen; Lai, Yi-Hua; Chen, Jeremy J W; Wu, Wen-Lin; Yuann, Jeu-Ming P; Su, Wang-Lin; Chuang, Show-Mei; Hou, Ming-Hon

2012-01-01

The anticancer activity of DNA intercalators is related to their ability to intercalate into the DNA duplex with high affinity, thereby interfering with DNA replication and transcription. Polyamines (spermine in particular) are almost exclusively bound to nucleic acids and are involved in many cellular processes that require nucleic acids. Until now, the effects of polyamines on DNA intercalator activities have remained unclear because intercalation is the most important mechanism employed by DNA-binding drugs. Herein, using actinomycin D (ACTD) as a model, we have attempted to elucidate the effects of spermine on the action of ACTD, including its DNA-binding ability, RNA and DNA polymerase interference, and its role in the transcription and replication inhibition of ACTD within cells. We found that spermine interfered with the binding and stabilization of ACTD to DNA. The presence of increasing concentrations of spermine enhanced the transcriptional and replication activities of RNA and DNA polymerases, respectively, in vitro treated with ActD. Moreover, a decrease in intracellular polyamine concentrations stimulated by methylglyoxal-bis(guanylhydrazone) (MGBG) enhanced the ACTD-induced inhibition of c-myc transcription and DNA replication in several cancer cell lines. The results indicated that spermine attenuates ACTD binding to DNA and its inhibition of transcription and DNA replication both in vitro and within cells. Finally, a synergistic antiproliferative effect of MGBG and ACTD was observed in a cell viability assay. Our findings will be of significant relevance to future developments in combination with cancer therapy by enhancing the anticancer activity of DNA interactors through polyamine depletion.

Stereochemical model for proflavin intercalation in A-DNA.

PubMed Central

Alden, C J; Arnott, S

1977-01-01

Linked-atom molecular modelling was employed to determine the steric and torsional requirements for intercalation of proflavine into a double-stranded region of DNA compatible with adjacent regions of cohelical A-DNA. The optimum intercalation conformation is characterized by the dihedral angles xi and psi becoming trans, with all sugars retaining the characteristics C3'-endo pucker. This extended conformation results in virtually no helical unwinding, suggesting it may be an appropriate model for an intercalative intermediary in mutagenesis by virtue of its similarity to standard helical DNA. PMID:593890

Metal complexes as DNA intercalators.

PubMed

Liu, Hong-Ke; Sadler, Peter J

2011-05-17

DNA has a strong affinity for many heterocyclic aromatic dyes, such as acridine and its derivatives. Lerman in 1961 first proposed intercalation as the source of this affinity, and this mode of DNA binding has since attracted considerable research scrutiny. Organic intercalators can inhibit nucleic acid synthesis in vivo, and they are now common anticancer drugs in clinical therapy. The covalent attachment of organic intercalators to transition metal coordination complexes, yielding metallointercalators, can lead to novel DNA interactions that influence biological activity. Metal complexes with σ-bonded aromatic side arms can act as dual-function complexes: they bind to DNA both by metal coordination and through intercalation of the attached aromatic ligand. These aromatic side arms introduce new modes of DNA binding, involving mutual interactions of functional groups held in close proximity. The biological activity of both cis- and trans-diamine Pt(II) complexes is dramatically enhanced by the addition of σ-bonded intercalators. We have explored a new class of organometallic "piano-stool" Ru(II) and Os(II) arene anticancer complexes of the type [(η(6)-arene)Ru/Os(XY)Cl](+). Here XY is, for example, ethylenediamine (en), and the arene ligand can take many forms, including tetrahydroanthracene, biphenyl, or p-cymene. Arene-nucleobase stacking interactions can have a significant influence on both the kinetics and thermodynamics of DNA binding. In particular, the cytotoxic activity, conformational distortions, recognition by DNA-binding proteins, and repair mechanisms are dependent on the arene. A major difficulty in developing anticancer drugs is cross-resistance, a phenomenon whereby a cell that is resistant to one drug is also resistant to another drug in the same class. These new complexes are non-cross-resistant with cisplatin towards cancer cells: they constitute a new class of anticancer agents, with a mechanism of action that differs from the anticancer drug cisplatin and its analogs. The Ru-arene complexes with dual functions are more potent towards cancer cells than their nonintercalating analogs. In this Account, we focus on recent studies of dual-function organometallic Ru(II)- and Os(II)-arene complexes and the methods used to detect arene-DNA intercalation. We relate these interactions to the mechanism of anticancer activity and to structure-activity relationships. The interactions between these complexes and DNA show close similarities to those of covalent polycyclic aromatic carcinogens, especially to N7-alkylating intercalation compounds. However, Ru-arene complexes exhibit some new features. Classical intercalation and base extrusion next to the metallated base is observed for {(η(6)-biphenyl)Ru(ethylenediamine)}(2+) adducts of a 14-mer duplex, while penetrating arene intercalation occurs for adducts of the nonaromatic bulky intercalator {(η(6)-tetrahydroanthracene)Ru(ethylenediamine)}(2+) with a 6-mer duplex. The introduction of dual-function Ru-arene complexes introduces new mechanisms of antitumor activity, novel mechanisms for attack on DNA, and new concepts for developing structure- activity relationships. We hope this discussion will stimulate thoughtful and focused research on the design of anticancer chemotherapeutic agents using these unique approaches.

Sanguinarine interacts with chromatin, modulates epigenetic modifications, and transcription in the context of chromatin.

PubMed

Selvi B, Ruthrotha; Pradhan, Suman Kalyan; Shandilya, Jayasha; Das, Chandrima; Sailaja, Badi Sri; Shankar G, Naga; Gadad, Shrikanth S; Reddy, Ashok; Dasgupta, Dipak; Kundu, Tapas K

2009-02-27

DNA-binding anticancer agents cause alteration in chromatin structure and dynamics. We report the dynamic interaction of the DNA intercalator and potential anticancer plant alkaloid, sanguinarine (SGR), with chromatin. Association of SGR with different levels of chromatin structure was enthalpy driven with micromolar dissociation constant. Apart from DNA, it binds with comparable affinity with core histones and induces chromatin aggregation. The dual binding property of SGR leads to inhibition of core histone modifications. Although it potently inhibits H3K9 methylation by G9a in vitro, H3K4 and H3R17 methylation are more profoundly inhibited in cells. SGR inhibits histone acetylation both in vitro and in vivo. It does not affect the in vitro transcription from DNA template but significantly represses acetylation-dependent chromatin transcription. SGR-mediated repression of epigenetic marks and the alteration of chromatin geography (nucleography) also result in the modulation of global gene expression. These data, conclusively, show an anticancer DNA binding intercalator as a modulator of chromatin modifications and transcription in the chromatin context.

Why Do Silver Trimers Intercalated in DNA Exhibit Unique Nonlinear Properties That Are Promising for Applications?

PubMed

Bonačić-Koutecký, Vlasta; Perić, Martina; Sanader, Željka

2018-05-17

Our investigation of one-photon absorption (OPA) and nonlinear optical (NLO) properties such as two-photon absorption (TPA) of silver trimer intercalated in DNA based on TDDFT approach allowed us to propose a mechanism responsible for large TPA cross sections of such NLO-phores. We present a concept that illustrates the key role of quantum cluster as well as of nucleotide bases from the immediate neighborhood. For this purpose, different surroundings consisting of guanine-cytosine and adenine-thymine such as (GCGC) and (ATAT) have been investigated that are exhibiting substantially different values of TPA cross sections. This has been confirmed by extending the immediate surroundings as well as using the two-layer quantum mechanics/molecular mechanics (QM/MM) approach. We focus on the cationic closed-shell system and illustrate that the neutral open-shell system shifts OPA spectra into the NIR regime, which is suitable for applications. Thus, in this contribution, we propose novel NLO-phores inducing large TPA cross sections, opening the route for multiphoton imaging.

Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: investigating the fundamental forces of DNA-intercalator interactions.

PubMed

Hohenstein, Edward G; Parrish, Robert M; Sherrill, C David; Turney, Justin M; Schaefer, Henry F

2011-11-07

Symmetry-adapted perturbation theory (SAPT) provides a means of probing the fundamental nature of intermolecular interactions. Low-orders of SAPT (here, SAPT0) are especially attractive since they provide qualitative (sometimes quantitative) results while remaining tractable for large systems. The application of density fitting and Laplace transformation techniques to SAPT0 can significantly reduce the expense associated with these computations and make even larger systems accessible. We present new factorizations of the SAPT0 equations with density-fitted two-electron integrals and the first application of Laplace transformations of energy denominators to SAPT. The improved scalability of the DF-SAPT0 implementation allows it to be applied to systems with more than 200 atoms and 2800 basis functions. The Laplace-transformed energy denominators are compared to analogous partial Cholesky decompositions of the energy denominator tensor. Application of our new DF-SAPT0 program to the intercalation of DNA by proflavine has allowed us to determine the nature of the proflavine-DNA interaction. Overall, the proflavine-DNA interaction contains important contributions from both electrostatics and dispersion. The energetics of the intercalator interaction are are dominated by the stacking interactions (two-thirds of the total), but contain important contributions from the intercalator-backbone interactions. It is hypothesized that the geometry of the complex will be determined by the interactions of the intercalator with the backbone, because by shifting toward one side of the backbone, the intercalator can form two long hydrogen-bonding type interactions. The long-range interactions between the intercalator and the next-nearest base pairs appear to be negligible, justifying the use of truncated DNA models in computational studies of intercalation interaction energies.

Large-scale symmetry-adapted perturbation theory computations via density fitting and Laplace transformation techniques: Investigating the fundamental forces of DNA-intercalator interactions

NASA Astrophysics Data System (ADS)

Hohenstein, Edward G.; Parrish, Robert M.; Sherrill, C. David; Turney, Justin M.; Schaefer, Henry F.

2011-11-01

Symmetry-adapted perturbation theory (SAPT) provides a means of probing the fundamental nature of intermolecular interactions. Low-orders of SAPT (here, SAPT0) are especially attractive since they provide qualitative (sometimes quantitative) results while remaining tractable for large systems. The application of density fitting and Laplace transformation techniques to SAPT0 can significantly reduce the expense associated with these computations and make even larger systems accessible. We present new factorizations of the SAPT0 equations with density-fitted two-electron integrals and the first application of Laplace transformations of energy denominators to SAPT. The improved scalability of the DF-SAPT0 implementation allows it to be applied to systems with more than 200 atoms and 2800 basis functions. The Laplace-transformed energy denominators are compared to analogous partial Cholesky decompositions of the energy denominator tensor. Application of our new DF-SAPT0 program to the intercalation of DNA by proflavine has allowed us to determine the nature of the proflavine-DNA interaction. Overall, the proflavine-DNA interaction contains important contributions from both electrostatics and dispersion. The energetics of the intercalator interaction are are dominated by the stacking interactions (two-thirds of the total), but contain important contributions from the intercalator-backbone interactions. It is hypothesized that the geometry of the complex will be determined by the interactions of the intercalator with the backbone, because by shifting toward one side of the backbone, the intercalator can form two long hydrogen-bonding type interactions. The long-range interactions between the intercalator and the next-nearest base pairs appear to be negligible, justifying the use of truncated DNA models in computational studies of intercalation interaction energies.

AgI -Induced Switching of DNA Binding Modes via Formation of a Supramolecular Metallacycle.

PubMed

Basak, Shibaji; Léon, J Christian; Ferranco, Annaleizle; Sharma, Renu; Hebenbrock, Marian; Lough, Alan; Müller, Jens; Kraatz, Heinz-Bernhard

2018-03-12

The histidine derivative L1 of the DNA intercalator naphthalenediimide (NDI) forms a triangular Ag I complex (C2). The interactions of L1 and of C2 with DNA were studied by circular dichroism (CD) and UV/Vis spectroscopy and by viscosity studies. Different binding modes were observed for L1 and for C2, as the Ag I complex C2 is too large in size to act as an intercalator. If Ag I is added to the NDI molecule that is already intercalated into a duplex, higher order complexes are formed within the DNA duplex and cause disruptions in the helical duplex structure, which leads to a significant decrease in the characteristic CD features of B-DNA. Thus, via addition of a metal we show how a classic and well-known organic intercalator unit can be turned into a partial metallo insertor. We also show how electrochemical impedance spectroscopy (EIS) can be used to probe DNA binding modes on DNA films that are immobilized on gold surfaces. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Intercalation of a Zn(II) complex containing ciprofloxacin drug between DNA base pairs.

PubMed

Shahabadi, Nahid; Asadian, Ali Ashraf; Mahdavi, Mryam

2017-11-02

In this study, an attempt has been made to study the interaction of a Zn(II) complex containing an antibiotic drug, ciprofloxacin, with calf thymus DNA using spectroscopic methods. It was found that Zn(II) complex could bind with DNA via intercalation mode as evidenced by: hyperchromism in UV-Vis spectrum; these spectral characteristics suggest that the Zn(II) complex interacts with DNA most likely through a mode that involves a stacking interaction between the aromatic chromophore and the base pairs of DNA. DNA binding constant (K b = 1.4 × 10 4 M -1 ) from spectrophotometric studies of the interaction of Zn(II) complex with DNA is comparable to those of some DNA intercalative polypyridyl Ru(II) complexes 1.0 -4.8 × 10 4 M -1 . CD study showed stabilization of the right-handed B form of DNA in the presence of Zn(II) complex as observed for the classical intercalator methylene blue. Thermodynamic parameters (ΔH < 0 and ΔS < 0) indicated that hydrogen bond and Van der Waals play main roles in this binding prose. Competitive fluorimetric studies with methylene blue (MB) dye have shown that Zn(II) complex exhibits the ability of this complex to displace with DNA-MB, indicating that it binds to DNA in strong competition with MB for the intercalation.

Charging YOYO-1 on Capillary Wall for Online DNA Intercalation and Integrating This Approach with Multiplex PCR and Bare Narrow Capillary–Hydrodynamic Chromatography for Online DNA Analysis

PubMed Central

2016-01-01

Multiplex polymerase chain reaction (PCR) has been widely utilized for high-throughput pathogen identification. Often, a dye is used to intercalate the amplified DNA fragments, and identifications of the pathogens are carried out by DNA melting curve analysis or gel electrophoresis. Integrating DNA amplification and identification is a logic path toward maximizing the benefit of multiplex PCR. Although PCR and gel electrophoresis have been integrated, replenishing the gels after each run is tedious and time-consuming. In this technical note, we develop an approach to address this issue. We perform multiplex PCR inside a capillary, transfer the amplified fragments to a bare narrow capillary, and measure their lengths online using bare narrow capillary–hydrodynamic chromatography (BaNC-HDC), a new technique recently developed in our laboratory for free-solution DNA separation. To intercalate the DNA with YOYO-1 (a fluorescent dye) for BaNC-HDC, we flush the capillary column with a YOYO-1 solution; positively charged YOYO-1 is adsorbed (or charged) onto the negatively charged capillary wall. As DNA molecules are driven down the column for separation, they react with the YOYO-1 stored on the capillary wall and are online-intercalated with the dye. With a single YOYO-1 charging, the column can be used for more than 40 runs, although the fluorescence signal intensities of the DNA peaks decrease gradually. Although the dye-DNA intercalation occurs during the separation, it does not affect the retention times, separation efficiencies, or resolutions. PMID:25555111

Real-time electrochemical LAMP: a rational comparative study of different DNA intercalating and non-intercalating redox probes.

PubMed

Martin, Alexandra; Bouffier, Laurent; Grant, Kathryn B; Limoges, Benoît; Marchal, Damien

2016-06-20

We present a comparative study of ten redox-active probes for use in real-time electrochemical loop-mediated isothermal amplification (LAMP). Our main objectives were to establish the criteria that need to be fulfilled for minimizing some of the current limitations of the technique and to provide future guidelines in the search for ideal redox reporters. To ensure a reliable comparative study, each redox probe was tested under similar conditions using the same LAMP reaction and the same entirely automatized custom-made real-time electrochemical device (designed for electrochemically monitoring in real-time and in parallel up to 48 LAMP samples). Electrochemical melt curve analyses were recorded immediately at the end of each LAMP reaction. Our results show that there are a number of intercalating and non-intercalating redox compounds suitable for real-time electrochemical LAMP and that the best candidates are those able to intercalate strongly into ds-DNA but not too much to avoid inhibition of the LAMP reaction. The strongest intercalating redox probes were finally shown to provide higher LAMP sensitivity, speed, greater signal amplitude, and cleaner-cut DNA melting curves than the non-intercalating molecules.

Intercalation complex of proflavine with DNA: Structure and dynamics by solid-state NMR

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tang, Pei; Juang, Chilong; Harbison, G.S.

1990-07-06

The structure of the complex formed between the intercalating agent proflavine and fibrous native DNA was studied by one- and two-dimensional high-resolution solid-state nuclear magnetic resonance (NMR). Carbon-13-labeled proflavine was used to show that the drug is stacked with the aromatic ring plane perpendicular to the fiber axis and that it is essentially immobile. Natural abundance carbon-13 NMR of the DNA itself shows that proflavine binding does not change the puckering of the deoxyribose ring. However, phosphorus-31 NMR spectra show profound changes in the orientation of the phosphodiester grouping on proflavine binding, with some of the phosphodiesters tilting almost parallelmore » to the helix axis, and a second set almost perpendicular. The first group to the phosphodiesters probably spans the intercalation sites, whereas the tilting of the second set likely compensates for the unwinding of the DNA by the intercalator.« less

Development of propidium iodide as a fluorescence probe for the on-line screening of non-specific DNA-intercalators in Fufang Banbianlian Injection.

PubMed

Niu, Yanyan; Li, Sensen; Lin, Zongtao; Liu, Meixian; Wang, Daidong; Wang, Hong; Chen, Shizhong

2016-09-09

Fufang Banbianlian Injection (FBI) has been widely used as an anti-inflammatory and anti-tumor prescription. To understand the relationships between its bioactive ingredients and pharmacological efficacies, our previous study has been successfully identified some DNA-binding compounds in FBI using an established on-line screening system, in which 4',6-diamidino-2-phenylindole (DAPI) was developed as a probe. However, DAPI can be only used to screen ATT-specific DNA minor groove binders, leaving the potential active intercalators unknown in FBI. As a continuation of our studies on FBI, here we present a sensitive analytical method for rapid identification and evaluation of DNA-intercalators using propidium iodide (PI) as a fluorescent probe. We have firstly established the technique of high-performance liquid chromatography-diode-array detector-multistage mass spectrometry-deoxyribonucleic acid-propidium iodide-fluorescence detector (HPLC-DAD-MS(n)-DNA-PI-FLD) system. As a result, 38 of 58 previously identified compounds in FBI were DNA-intercalation active. Interestingly, all previously reported DNA-binders also showed intercalative activities, suggesting they are dual-mode DNA-binders. Quantitative study showed that flavonoid glycosides and chlorogenic acids were the main active compounds in FBI, and displayed similar DNA-binding ability using either DAPI or PI. In addition, 13 active compounds were used to establish the structure-activity relationships. In this study, PI was developed into an on-line method for identifying DNA-intercalators for the first time, and thus it will be a useful high-throughput screening technique for other related samples. Copyright © 2016 Elsevier B.V. All rights reserved.

Increasing the Analytical Sensitivity by Oligonucleotides Modified with Para- and Ortho-Twisted Intercalating Nucleic Acids – TINA

PubMed Central

Schneider, Uffe V.; Géci, Imrich; Jøhnk, Nina; Mikkelsen, Nikolaj D.; Pedersen, Erik B.; Lisby, Gorm

2011-01-01

The sensitivity and specificity of clinical diagnostic assays using DNA hybridization techniques are limited by the dissociation of double-stranded DNA (dsDNA) antiparallel duplex helices. This situation can be improved by addition of DNA stabilizing molecules such as nucleic acid intercalators. Here, we report the synthesis of a novel ortho-Twisted Intercalating Nucleic Acid (TINA) amidite utilizing the phosphoramidite approach, and examine the stabilizing effect of ortho- and para-TINA molecules in antiparallel DNA duplex formation. In a thermal stability assay, ortho- and para-TINA molecules increased the melting point (Tm) of Watson-Crick based antiparallel DNA duplexes. The increase in Tm was greatest when the intercalators were placed at the 5′ and 3′ termini (preferable) or, if placed internally, for each half or whole helix turn. Terminally positioned TINA molecules improved analytical sensitivity in a DNA hybridization capture assay targeting the Escherichia coli rrs gene. The corresponding sequence from the Pseudomonas aeruginosa rrs gene was used as cross-reactivity control. At 150 mM ionic strength, analytical sensitivity was improved 27-fold by addition of ortho-TINA molecules and 7-fold by addition of para-TINA molecules (versus the unmodified DNA oligonucleotide), with a 4-fold increase retained at 1 M ionic strength. Both intercalators sustained the discrimination of mismatches in the dsDNA (indicated by ΔTm), unless placed directly adjacent to the mismatch – in which case they partly concealed ΔTm (most pronounced for para-TINA molecules). We anticipate that the presented rules for placement of TINA molecules will be broadly applicable in hybridization capture assays and target amplification systems. PMID:21673988

DNA mismatch-specific targeting and hypersensitivity of mismatch-repair-deficient cells to bulky rhodium(III) intercalators

PubMed Central

Hart, Jonathan R.; Glebov, Oleg; Ernst, Russell J.; Kirsch, Ilan R.; Barton, Jacqueline K.

2006-01-01

Mismatch repair (MMR) is critical to maintaining the integrity of the genome, and deficiencies in MMR are correlated with cancerous transformations. Bulky rhodium intercalators target DNA base mismatches with high specificity. Here we describe the application of bulky rhodium intercalators to inhibit cellular proliferation differentially in MMR-deficient cells compared with cells that are MMR-proficient. Preferential inhibition by the rhodium complexes associated with MMR deficiency is seen both in a human colon cancer cell line and in normal mouse fibroblast cells; the inhibition of cellular proliferation depends strictly on the MMR deficiency of the cell. Furthermore, our assay of cellular proliferation is found to correlate with DNA mismatch targeting by the bulky metallointercalators. It is the Δ-isomer that is active both in targeting base mismatches and in inhibiting DNA synthesis. Additionally, the rhodium intercalators promote strand cleavage at the mismatch site with photoactivation, and we observe that the cellular response is enhanced with photoactivation. Targeting DNA mismatches may therefore provide a cell-selective strategy for chemotherapeutic design. PMID:17030786

1,8-Naphthalimide: A Potent DNA Intercalator and Target for Cancer Therapy.

PubMed

Tandon, Runjhun; Luxami, Vijay; Kaur, Harsovin; Tandon, Nitin; Paul, Kamaldeep

2017-10-01

The poor pharmacokinetics, side effects and particularly the rapid emergence of drug resistance compromise the efficiency of clinically used anticancer drugs. Therefore, the discovery of novel and effective drugs is still an extremely primary mission. Naphthalimide family is one of the highly active anticancer drug based upon effective intercalator with DNA. In this article, we review the discovery and development of 1,8-naphthalimide moiety, and, especially, pay much attention to the structural modifications and structure activity relationships. The review demonstrates how modulation of the moiety affecting naphthalimide compound for DNA binding that is achieved to afford a profile of antitumor activity. The DNA binding of imide and ring substitution at naphthalimide, bisnaphthalimide, naphthalimide-metal complexes is achieved by molecular recognition through intercalation mode. Thus, this synthetic/natural small molecule can act as a drug when activation or inhibition of DNA function, is required to cure or control the cancer disease. The present study is a review of the advances in 1,8-naphthalimide-related research, with a focus on how such derivatives are intercalated into DNA for their anticancer activities. © 2017 The Chemical Society of Japan & Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

A ruthenium polypyridyl intercalator stalls DNA replication forks, radiosensitizes human cancer cells and is enhanced by Chk1 inhibition

NASA Astrophysics Data System (ADS)

Gill, Martin R.; Harun, Siti Norain; Halder, Swagata; Boghozian, Ramon A.; Ramadan, Kristijan; Ahmad, Haslina; Vallis, Katherine A.

2016-08-01

Ruthenium(II) polypyridyl complexes can intercalate DNA with high affinity and prevent cell proliferation; however, the direct impact of ruthenium-based intercalation on cellular DNA replication remains unknown. Here we show the multi-intercalator [Ru(dppz)2(PIP)]2+ (dppz = dipyridophenazine, PIP = 2-(phenyl)imidazo[4,5-f][1,10]phenanthroline) immediately stalls replication fork progression in HeLa human cervical cancer cells. In response to this replication blockade, the DNA damage response (DDR) cell signalling network is activated, with checkpoint kinase 1 (Chk1) activation indicating prolonged replication-associated DNA damage, and cell proliferation is inhibited by G1-S cell-cycle arrest. Co-incubation with a Chk1 inhibitor achieves synergistic apoptosis in cancer cells, with a significant increase in phospho(Ser139) histone H2AX (γ-H2AX) levels and foci indicating increased conversion of stalled replication forks to double-strand breaks (DSBs). Normal human epithelial cells remain unaffected by this concurrent treatment. Furthermore, pre-treatment of HeLa cells with [Ru(dppz)2(PIP)]2+ before external beam ionising radiation results in a supra-additive decrease in cell survival accompanied by increased γ-H2AX expression, indicating the compound functions as a radiosensitizer. Together, these results indicate ruthenium-based intercalation can block replication fork progression and demonstrate how these DNA-binding agents may be combined with DDR inhibitors or ionising radiation to achieve more efficient cancer cell killing.

A ruthenium polypyridyl intercalator stalls DNA replication forks, radiosensitizes human cancer cells and is enhanced by Chk1 inhibition.

PubMed

Gill, Martin R; Harun, Siti Norain; Halder, Swagata; Boghozian, Ramon A; Ramadan, Kristijan; Ahmad, Haslina; Vallis, Katherine A

2016-08-25

Ruthenium(II) polypyridyl complexes can intercalate DNA with high affinity and prevent cell proliferation; however, the direct impact of ruthenium-based intercalation on cellular DNA replication remains unknown. Here we show the multi-intercalator [Ru(dppz)2(PIP)](2+) (dppz = dipyridophenazine, PIP = 2-(phenyl)imidazo[4,5-f][1,10]phenanthroline) immediately stalls replication fork progression in HeLa human cervical cancer cells. In response to this replication blockade, the DNA damage response (DDR) cell signalling network is activated, with checkpoint kinase 1 (Chk1) activation indicating prolonged replication-associated DNA damage, and cell proliferation is inhibited by G1-S cell-cycle arrest. Co-incubation with a Chk1 inhibitor achieves synergistic apoptosis in cancer cells, with a significant increase in phospho(Ser139) histone H2AX (γ-H2AX) levels and foci indicating increased conversion of stalled replication forks to double-strand breaks (DSBs). Normal human epithelial cells remain unaffected by this concurrent treatment. Furthermore, pre-treatment of HeLa cells with [Ru(dppz)2(PIP)](2+) before external beam ionising radiation results in a supra-additive decrease in cell survival accompanied by increased γ-H2AX expression, indicating the compound functions as a radiosensitizer. Together, these results indicate ruthenium-based intercalation can block replication fork progression and demonstrate how these DNA-binding agents may be combined with DDR inhibitors or ionising radiation to achieve more efficient cancer cell killing.

The effects of linear assembly of two carbazole groups on acid-base and DNA-binding properties of a ruthenium(II) complex.

PubMed

Chen, Xi; Xue, Long-Xin; Ju, Chun-Chuan; Wang, Ke-Zhi

2013-07-01

A novel Ru(II) complex of [Ru(bpy)2(Hbcpip)](ClO4)2 {where bpy=2,2-bipyridine, Hbcpip=2-(4-(9H-3,9'-bicarbazol-9-yl)phenyl)-1H-imidazo[4,5-f][1,10]phenanthroline} is synthesized and characterized. Calf-thymus DNA-binding properties of the complex were studied by UV-vis absorption and luminescence titrations, steady-state emission quenching by [Fe(CN)6](4-), DNA competitive binding with ethidium bromide, thermal denaturation and DNA viscosity measurements. The results indicate that the complex partially intercalated into the DNA with a binding constant of (5.5±1.4)×10(5) M(-1) in buffered 50 mM NaCl. The acid-base properties of the complex were also studied by UV-visible and luminescence spectrophotometric pH titrations, and ground- and excited-state acidity ionization constant values were derived. Copyright © 2013 Elsevier B.V. All rights reserved.

Pico-level DNA sensing by hetero-polymetalate, Na10{Dy2W10O30(µ-S)6}·80H2O, cluster

NASA Astrophysics Data System (ADS)

Dutta, Taposhree; Ganguly, Jhuma; Sarkar, Sabyasachi

2018-04-01

The polyoxometalate dysprosium cluster, (Dy-S-W POM) , Na10[Dy2W10O30(µ-S)6]·80H2O, shows remarkable dsDNA denaturation property. In the presence of 0.22 µmol of this Dy-S-W POM, the melting temperature (Tm) of calf-thymus (CT) dsDNA is decreased to 62.35 °C. Dy-S-W POM shows bleaching of methylene blue (MB). Addition of CT-DNA in the MB bleached solution of Dy-S-W POM apparently intercalates MB. Such trapped MB by CT-DNA responds to its re-oxidation by elemental sulfur formed in the bleaching process involving Dy-S-W POM. This reduction-oxidation property of MB with Dy-S-W POM led to the detection of pico (13.20 pmol) level of DNA even by naked eye, which will be helpful for rapid trace DNA detection in forensic science and DNA-related diagnostics, complimenting time-consuming sophisticated methodology.

Photo-degradation of CT-DNA with a series of carbothioamide ruthenium (II) complexes - Synthesis and structural analysis

NASA Astrophysics Data System (ADS)

Muthuraj, V.; Umadevi, M.

2018-04-01

The present research article is related with the method of preparation, structure and spectroscopic properties of a series of carbothioamide ruthenium (II) complexes with N and S donor ligands namely, 2-((6-chloro-4-oxo-4H-chromen-3-yl)methylene) hydrazine carbothioamide (ClChrTs)/2-((6-methoxy-4-oxo-4H-chromen-3-yl)methylene)hydrazine carbothioamide (MeOChrTS). The synthesized complexes were characterized by several techniques using analytical methods as well as by spectral techniques such as FT-IR, 1HNMR, 13CNMR, ESI mass and thermogravimetry/differential thermal analysis (TG-DTA). The IR spectra shows that the ligand acts as a neutral bidentate with N and S donor atoms. The biological activity of the prepared compounds and metal complexes were tested against cell line of calf-thymus DNA via an intercalation mechanism (MCF-7). In addition, the interaction of Ru(II) complexes and its free ligands with CT-DNA were also investigated by titration with UV-Vis spectra, fluorescence spectra, and Circular dichroism studies. Results suggest that both of the two Ru(II) complexes can bind with calf-thymus DNA via an intercalation mechanism.

Neocarzinostatin as a probe for DNA protection activity--molecular interaction with caffeine.

PubMed

Chin, Der-Hang; Li, Huang-Hsien; Kuo, Hsiu-Maan; Chao, Pei-Dawn Lee; Liu, Chia-Wen

2012-04-01

Neocarzinostatin (NCS), a potent mutagen and carcinogen, consists of an enediyne prodrug and a protein carrier. It has a unique double role in that it intercalates into DNA and imposes radical-mediated damage after thiol activation. Here we employed NCS as a probe to examine the DNA-protection capability of caffeine, one of common dietary phytochemicals with potential cancer-chemopreventive activity. NCS at the nanomolar concentration range could induce significant single- and double-strand lesions in DNA, but up to 75 ± 5% of such lesions were found to be efficiently inhibited by caffeine. The percentage of inhibition was caffeine-concentration dependent, but was not sensitive to the DNA-lesion types. The well-characterized activation reactions of NCS allowed us to explore the effect of caffeine on the enediyne-generated radicals. Postactivation analyses by chromatographic and mass spectroscopic methods identified a caffeine-quenched enediyne-radical adduct, but the yield was too small to fully account for the large inhibition effect on DNA lesions. The affinity between NCS chromophore and DNA was characterized by a fluorescence-based kinetic method. The drug-DNA intercalation was hampered by caffeine, and the caffeine-induced increases in DNA-drug dissociation constant was caffeine-concentration dependent, suggesting importance of binding affinity in the protection mechanism. Caffeine has been shown to be both an effective free radical scavenger and an intercalation inhibitor. Our results demonstrated that caffeine ingeniously protected DNA against the enediyne-induced damages mainly by inhibiting DNA intercalation beforehand. The direct scavenging of the DNA-bound NCS free radicals by caffeine played only a minor role. Copyright © 2011 Wiley Periodicals, Inc.

Effect of marine derived deoxyribonucleic acid on nonlinear optical properties of PicoGreen dye

NASA Astrophysics Data System (ADS)

Pradeep, C.; Mathew, S.; Nithyaja, B.; Radhakrishnan, P.; Nampoori, V. P. N.

2013-06-01

We have investigated the effect of DNA on nonlinear absorption of PicoGreen dye using single beam open aperture Z-scan technique in nanosecond regime. We observed reverse saturable absorption at 532 nm for PicoGreen without DNA. In the presence of DNA, the sample begins to behave like saturable absorbers and this effect increased as the concentration of DNA was increased. The dye-intercalated DNA showed SA characteristics near the focus but exhibited RSA characteristics at the focus. Theoretical analysis has been performed using a two-photon absorption model based on nonlinear absorption coefficient and saturation intensity. Such tailoring of optical nonlinear absorption in PicoGreen makes it a potential candidate for photonic application.

Experimental and computational studies on the effects of valganciclovir as an antiviral drug on calf thymus DNA.

PubMed

Shahabadi, Nahid; Pourfoulad, Mehdi; Moghadam, Neda Hosseinpour

2017-01-02

DNA-binding properties of an antiviral drug, valganciclovir (valcyte) was studied by using emission, absorption, circular dichroism, viscosity, differential pulse voltammetry, fluorescence techniques, and computational studies. The drug bound to calf thymus DNA (ct-DNA) in a groove-binding mode. The calculated binding constant of UV-vis, K a , is comparable to groove-binding drugs. Competitive fluorimetric studies with Hoechst 33258 showed that valcyte could displace the DNA-bound Hoechst 33258. The drug could not displace intercalated methylene blue from DNA double helix. Furthermore, the induced detectable changes in the CD spectrum of ct-DNA as well as changes in its viscosity confirm the groove-binding mode. In addition, an integrated molecular docking was employed to further investigate the binding interactions between valcyte and calf thymus DNA.

Insights into finding a mismatch through the structure of a mispaired DNA bound by a rhodium intercalator

PubMed Central

Pierre, Valérie C.; Kaiser, Jens T.; Barton, Jacqueline K.

2007-01-01

We report the 1.1-Å resolution crystal structure of a bulky rhodium complex bound to two different DNA sites, mismatched and matched in the oligonucleotide 5′-(dCGGAAATTCCCG)2-3′. At the AC mismatch site, the structure reveals ligand insertion from the minor groove with ejection of both mismatched bases and elucidates how destabilized mispairs in DNA may be recognized. This unique binding mode contrasts with major groove intercalation, observed at a matched site, where doubling of the base pair rise accommodates stacking of the intercalator. Mass spectral analysis reveals different photocleavage products associated with the two binding modes in the crystal, with only products characteristic of mismatch binding in solution. This structure, illustrating two clearly distinct binding modes for a molecule with DNA, provides a rationale for the interrogation and detection of mismatches. PMID:17194756

Spectroscopic and electrochemical studies of the interaction between oleuropein, the major bio-phenol in olives, and salmon sperm DNA

NASA Astrophysics Data System (ADS)

Mohamadi, Maryam; Afzali, Daryoush; Esmaeili-Mahani, Saeed; Mostafavi, Ali; Torkzadeh-Mahani, Masoud

2015-09-01

Interaction of oleuropein, the major bio-phenol in olive leaf and fruit, with salmon sperm double-stranded DNA was investigated by employing electronic absorption titrations, fluorescence quenching spectroscopy, competitive fluorescence spectroscopy, thermal denaturation and voltammetric studies. Titration of oleuropein with the DNA caused a hypochromism accompanied with a red shift indicating an intercalative mode of interaction. Binding constant of 1.4 × 104 M-1 was obtained for this interaction. From the curves of fluorescence titration of oleuropein with the DNA, binding constant and binding sites were calculated to be 8.61 × 103 M-1 and 1.05, respectively. Competitive studies with ethidium bromide (a well-known DNA intercalator) showed that the bio-phenol could take the place of ethidium bromide in the DNA intercalation sites. The interaction of oleuropein with DNA was also studied electrochemically. In the presence of the DNA, the anodic and cathodic peak currents of oleuropein decreased accompanied with increases in peak-to-peak potential separation and formal potential, indicating the intercalation of oleuropein into the DNA double helix. Moreover, melting temperature of the DNA was found to increase in the presence of oleuropein, indicating the stabilization of the DNA double helix due to an intercalative interaction.

Photoinduced Oxidative DNA Damage Revealed by an Agarose Gel Nicking Assay: A Biophysical Chemistry Laboratory Experiment

NASA Astrophysics Data System (ADS)

Shafirovich, Vladimir; Singh, Carolyn; Geacintov, Nicholas E.

2003-11-01

Oxidative damage of DNA molecules associated with electron-transfer reactions is an important phenomenon in living cells, which can lead to mutations and contribute to carcinogenesis and the aging processes. This article describes the design of several simple experiments to explore DNA damage initiated by photoinduced electron-transfer reactions sensitized by the acridine derivative, proflavine (PF). A supercoiled DNA agarose gel nicking assay is employed as a sensitive probe of DNA strand cleavage. A low-cost experimental and computer-interfaced imaging apparatus is described allowing for the digital recording and analysis of the gel electrophoresis results. The first experiment describes the formation of direct strand breaks in double-stranded DNA induced by photoexcitation of the intercalated PF molecules. The second experiment demonstrates that the addition of the well-known electron acceptor, methylviologen, gives rise to a significant enhancement of the photochemical DNA strand cleavage effect. This occurs by an electron transfer step to methylviologen that renders the inital photoinduced charge separation between photoexcited PF and DNA irreversible. The third experiment demonstrates that the action spectrum of the DNA photocleavage matches the absorption spectrum of DNA-bound, intercalated PF molecules, which differs from that of free PF molecules. This result demonstrates that the photoinduced DNA strand cleavage is initiated by intercalated rather than free PF molecules.

Dynamics of DNA/intercalator complexes

NASA Astrophysics Data System (ADS)

Schurr, J. M.; Wu, Pengguang; Fujimoto, Bryant S.

1990-05-01

Complexes of linear and supercoiled DNAs with different intercalating dyes are studied by time-resolved fluorescence polarization anisotropy using intercalated ethidium as the probe. Existing theory is generalized to take account of excitation transfer between intercalated ethidiums, and Forster theory is shown to be valid in this context. The effects of intercalated ethidium, 9-aminoacridine, and proflavine on the torsional rigidity of linear and supercoiled DNAs are studied up to rather high binding ratios. Evidence is presented that metastable secondary structure persists in dye-relaxed supercoiled DNAs, which contradicts the standard model of supercoiled DNAs.

Molecular mechanism of direct proflavine-DNA intercalation: evidence for drug-induced minimum base-stacking penalty pathway.

PubMed

Sasikala, Wilbee D; Mukherjee, Arnab

2012-10-11

DNA intercalation, a biophysical process of enormous clinical significance, has surprisingly eluded molecular understanding for several decades. With appropriate configurational restraint (to prevent dissociation) in all-atom metadynamics simulations, we capture the free energy surface of direct intercalation from minor groove-bound state for the first time using an anticancer agent proflavine. Mechanism along the minimum free energy path reveals that intercalation happens through a minimum base stacking penalty pathway where nonstacking parameters (Twist→Slide/Shift) change first, followed by base stacking parameters (Buckle/Roll→Rise). This mechanism defies the natural fluctuation hypothesis and provides molecular evidence for the drug-induced cavity formation hypothesis. The thermodynamic origin of the barrier is found to be a combination of entropy and desolvation energy.

An intercalation-locked parallel-stranded DNA tetraplex

DOE PAGES

Tripathi, S.; Zhang, D.; Paukstelis, P. J.

2015-01-27

DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC BrUCGGA BrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A basemore » pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H– 1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

Synthesis, crystal structure, DFT calculation and DNA binding studies of new water-soluble derivatives of dppz

NASA Astrophysics Data System (ADS)

Aminzadeh, Mohammad; Eslami, Abbas; Kia, Reza; Aleeshah, Roghayeh

2017-10-01

Diquaternarization of dipyrido-[2,3-a:2‧,3‧-c]-phenazine,(dppz) and its analogous dipyrido-[2,3-a:2‧,3‧-c]-dimethylphenazine,(dppx) using 1,3-dibromopropane afford new water-soluble derivatives of phenazine, propylene-bipyridyldiylium-phenazine (1) and propylene-bipyridyldiylium-dimethylphenazine (2). The compounds have been characterized by means of FT-IR, NMR, elemental analysis and conductometric measurements and their structure were determined by X-ray crystallography. The experimental studies on the compounds have been accompanied computationally by Density Functional Theory (DFT) calculations. The DNA binding properties of both compounds to calf thymus DNA (ctDNA) were investigated by UV-Vis absorption and emission methods. The expanded UV-Vis spectral data matrix was analyzed by multivariate curve resolution-alternating least squares (MCR-ALS) technique to obtain the concentration profile and pure spectra of all reaction species which existed in the interaction procedure. Multivariate curve resolution may help us to give a better understanding of the 1(Cl)2-ctDNA and 2(Cl)2-ctDNA interaction mechanism. The results suggest that both compounds bind tightly to DNA through intercalation mechanism and the DNA binding affinity of 2 is slightly lower than that of 1 due to steric hindrance of the methyl group. Also, thermal denaturation studies reveal that these compounds show strong affinity for binding with calf thymus DNA. The thermodynamic parameters of the DNA binding process were obtained from the temperature dependence of the binding constants and the results showed that binding of both compounds to DNA is an enthalpically driven process that is in agreement with proposed DNA intercalation capability of these compounds.

Synthesis and electrical characterization of magnetic bilayer graphene intercalate.

PubMed

Kim, Namdong; Kim, Kwang S; Jung, Naeyoung; Brus, Louis; Kim, Philip

2011-02-09

We report synthesis and transport properties of the minimal graphite intercalation compound, a ferric chloride (FeCl(3))(n) island monolayer inside bilayer graphene. Chemical doping by the intercalant is simultaneously probed by micro-Raman spectroscopy and Hall measurements. Quantum oscillations of conductivity originate from microscopic domains of intercalated and unintercalated regions. A slight upturn in resistance related to magnetic transition is observed. Two-dimensional intercalation in bilayer graphene opens new possibilities to engineer two-dimensional properties of intercalates.

Improved DNA hybridization parameters by Twisted Intercalating Nucleic Acid (TINA).

PubMed

Schneider, Uffe Vest

2012-01-01

This thesis establishes oligonucleotide design rules and applications of a novel group of DNA stabilizing molecules collectively called Twisted Intercalating Nucleic Acid - TINA. Three peer-reviewed publications form the basis for the thesis. One publication describes an improved and rapid method for determination of DNA melting points and two publications describe the effects of positioning TINA molecules in parallel triplex helix and antiparallel duplex helix forming DNA structures. The third publication establishes that TINA molecules containing oligonucleotides improve an antiparallel duplex hybridization based capture assay's analytical sensitivity compared to conventionel DNA oligonucleotides. Clinical microbiology is traditionally based on pathogenic microorganisms' culture and serological tests. The introduction of DNA target amplification methods like PCR has improved the analytical sensitivity and total turn around time involved in clinical diagnostics of infections. Due to the relatively weak hybridization between the two strands of double stranded DNA, a number of nucleic acid stabilizing molecules have been developed to improve the sensitivity of DNA based diagnostics through superior binding properties. A short introduction is given to Watson-Crick and Hoogsteen based DNA binding and the derived DNA structures. A number of other nucleic acid stabilizing molecules are described. The stabilizing effect of TINA molecules on different DNA structures is discussed and considered in relation to other nucleic acid stabilizing molecules and in relation to future use of TINA containing oligonucleotides in clinical diagnostics and therapy. In conclusion, design of TINA modified oligonucleotides for antiparallel duplex helixes and parallel triplex helixes follows simple purpose dependent rules. TINA molecules are well suited for improving multiplex PCR assays and can be used as part of novel technologies. Future research should test whether combinations of TINA molecules and other nucleic acid stabilizing molecules can increase analytical sensitivity whilst maintaining nucleobase mismatch discrimination in triplex helix based diagnostic assays.

Combination probes with intercalating anchors and proximal fluorophores for DNA and RNA detection

PubMed Central

Qiu, Jieqiong; Wilson, Adam; El-Sagheer, Afaf H.; Brown, Tom

2016-01-01

A new class of modified oligonucleotides (combination probes) has been designed and synthesised for use in genetic analysis and RNA detection. Their chemical structure combines an intercalating anchor with a reporter fluorophore on the same thymine nucleobase. The intercalator (thiazole orange or benzothiazole orange) provides an anchor, which upon hybridisation of the probe to its target becomes fluorescent and simultaneously stabilizes the duplex. The anchor is able to communicate via FRET to a proximal reporter dye (e.g. ROX, HEX, ATTO647N, FAM) whose fluorescence signal can be monitored on a range of analytical devices. Direct excitation of the reporter dye provides an alternative signalling mechanism. In both signalling modes, fluorescence in the unhybridised probe is switched off by collisional quenching between adjacent intercalator and reporter dyes. Single nucleotide polymorphisms in DNA and RNA targets are identified by differences in the duplex melting temperature, and the use of short hybridization probes, made possible by the stabilisation provided by the intercalator, enhances mismatch discrimination. Unlike other fluorogenic probe systems, placing the fluorophore and quencher on the same nucleobase facilitates the design of short probes containing multiple modifications. The ability to detect both DNA and RNA sequences suggests applications in cellular imaging and diagnostics. PMID:27369379

Effects of TiO2 crystal structure on the luminescence quenching of [Ru(bpy)2(dppz)]2 +-intercalated into DNA

NASA Astrophysics Data System (ADS)

Chen, Linlin; Wang, Yi; Huang, Minggao; Li, Xiaodan; Zhu, Licai; Li, Hong

2017-06-01

The intercalation of [Ru(bpy)2(dppz)]2 + labeled as Ru(II) (bpy = 2,2‧-bipyridine and dppz = dipyrido[3,2,-a:2‧,3‧-c]phenazine) into herring sperm DNA leads to the formation of emissive Ru(II)-DNA dyads, which can be quenched by TiO2 nanoparticles (NPs) and sol-gel silica matrices at heterogeneous interfaces. The calcinations temperature exhibits a remarkable influence on the luminescence quenching of the Ru(II)-DNA dyads by TiO2 NPs. With increasing calcinations temperature in the range from 200 to 850 °C, the anatase-to-rutile TiO2 crystal structure transformation increases the average particle size and hydrodynamic diameter of TiO2 and DNA@TiO2. The anatase TiO2 has the stronger ability to unbind the Ru(II)-DNA dyads than the rutile TiO2 at room temperature. The TiO2 NPs and sol-gel silica matrices can quench the luminescence of the Ru(II) complex intercalated into DNA by selectively capturing the negatively DNA and positively charged Ru(II) complex to unbind the dyads, respectively. This present results provide new insights into the luminescence quenching and competitive binding of dye-labeled DNA dyads by inorganic NPs.

Synthesis, characterization and biological evaluation of novel α, β unsaturated amides.

PubMed

Esmailzadeh, K; Housaindokht, M R; Moradi, A; Esmaeili, A A; Sharifi, Z

2016-05-15

Three derivatives of α,β unsaturated amides have been successfully synthesized via Ugi-four component (U-4CR) reaction. The interactions of the amides with calf thymus deoxyribonucleic acid (ct-DNA) have been investigated in the Tris-HCl buffer (pH=7.4) using viscometric, spectroscopic, thermal denaturation studies, and also molecular docking. By UV-Vis absorption spectroscopy studies, adding CT-DNA to the compound solution caused the hypochromism indicates that there are interactions between the compounds and DNA base pairs. In competitive fluorescence with methylene blue as an intercalator probe, adding compounds to DNA-MB solution caused an increase in emission spectra of the complex. This could be because of compound replacing, with similar binding mode of MB, between the DNA base pairs due to release of bonded MB molecules from DNA-MB complex. Thermal denaturation studies and viscometric experiments also indicated that all three investigated compounds bind to CT-DNA by non-classical intercalation mode. Additionally, molecular docking technique predicted partial intercalation binding mode for the compounds. Also, the highest binding energy was obtained for compound 5a. These results are in agreement with results obtained by empirical methods. Copyright © 2016 Elsevier B.V. All rights reserved.

Electrochemical studies of DNA interaction and antimicrobial activities of MnII, FeIII, CoII and NiII Schiff base tetraazamacrocyclic complexes

NASA Astrophysics Data System (ADS)

Kumar, Anuj; Vashistha, Vinod Kumar; Tevatia, Prashant; Singh, Randhir

2017-04-01

Tetraazamacrocyclic complexes of MnII, FeIII, CoII and NiII have been synthesized by template method. These tetraazamacrocycles have been analyzed with various techniques like molar conductance, IR, UV-vis, mass spectral and cyclic voltammetric studies. On the basis of all these studies, octahedral geometry has been assigned to these tetraazamacrocyclic complexes. The DNA binding properties of these macrocyclic complexes have been investigated by electronic absorption spectra, fluorescence spectra, cyclic voltammetric and differential pulse voltammetric studies. The cyclic voltammetric data showed that ipc and ipa were effectively decreased in the presence of calf thymus DNA, which is a strong evidence for the interaction of these macrocyclic complexes with the calf thymus DNA (ct-DNA). The heterogeneous electron transfer rate constant found in the order: KCoII > KNiII > KMnII which indicates that CoII macrocyclic complex has formed a strong intercalated intermediate. The Stern-Volmer quenching constant (KSV) and voltammetric binding constant were found in the order KSV(CoII) > KSV(NiII) > KSV(MnII) and K+(CoII) > K+(NiII) > K+(MnII) which shows that CoII macrocyclic complex exhibits the high interaction affinity towards ct-DNA by the intercalation binding. Biological studies of the macrocyclic complexes compared with the standard drug like Gentamycin, have shown antibacterial activities against E. coli, P. aeruginosa, B. cereus, S. aureus and antifungal activity against C. albicans.

C-1311 (Symadex), a potential anti-cancer drug, intercalates into DNA between A and G moieties. NMR-derived and MD-refined stereostructure of the d(GAGGCCTC)2:C-1311 complex

NASA Astrophysics Data System (ADS)

Laskowski, Tomasz; Borzyszkowska, Julia; Grynda, Jakub; Mazerski, Jan

2017-08-01

Imidazoacridinone C-1311 (Symadex®) is an antitumor agent which has been recommended for Phase II clinical trials a few years ago. Previously, it was shown experimentally that during the initial stage of its action C-1311 forms stable intercalation complexes with DNA duplexes. Herein, a NMR-derived stereostructure of d(GAGGCCTC)2:C-1311 complex was reported. The ligand was found locating itself between A and G moieties, forming symmetrical DNA:drug 1:2 mol/mol complex. Intercalation site was located upon the DNA-ligand proton/proton dipolar couplings observed in the NOESY spectrum and the performed MD simulations. NMR-derived stereostructure was hence refined by restrained MD using distance restraints obtained from the NOESY data and the result was compared with MD-derived structure of the proposed complex, obtained from the calculations performed with distance restraints applied only for hydrogen bonds in the terminal GC base pairs. The results of both simulations were coherent. Basing on the observed C-1311's intercalation sites and on our previous results concerning the d(CGATCG)2:C-1311 complex, we stated that AG/GA sequences are the preferred binding sites of imidazoacridinone C-1311.

New porphyrins bearing positively charged peripheral groups linked by a sulfonamide group to meso-tetraphenylporphyrin: interactions with calf thymus DNA.

PubMed

Manono, Janet; Marzilli, Patricia A; Marzilli, Luigi G

2009-07-06

New water-soluble cationic meso-tetraarylporphyrins (TArP, Ar = 4-C(6)H(4)) and some metal derivatives have been synthesized and characterized. One main goal was to assess if N-methylpyridinium (N-Mepy) groups must be directly attached to the porphyrin core for intercalative binding of porphyrins to DNA. The new porphyrins have the general formula, [T(R(2)R(1)NSO(2)Ar)P]X(4/8) (R(1) = CH(3) or H and R(2) = N-Mepy-n-CH(2) with n = 2, 3, or 4; or R(1) = R(2) = Et(3)NCH(2)CH(2)). Interactions of selected porphyrins and metalloporphyrins (Cu(II), Zn(II)) with calf thymus DNA were investigated by visible circular dichroism (CD), absorption, and fluorescence spectroscopies. The DNA-induced changes in the porphyrin Soret region (a positive induced CD feature and, at high DNA concentration, increases in the Soret band and fluorescence intensities) indicate that the new porphyrins interact with DNA in an outside, non-self-stacking binding mode. Several new metalloporphyrins did not increase DNA solution viscosity and thus do not intercalate, confirming the conclusion drawn from spectroscopic studies. Porphyrins known to intercalate typically bear two or more N-Mepy groups directly attached to the porphyrin ring, such as the prototypical meso-tetra(N-Mepy)porphyrin tetracation (TMpyP(4)). The distances between the nitrogens of the N-Mepy group are estimated to be approximately 11 A (cis) and 16 A (trans) for the relatively rigid TMpyP(4). For the new flexible porphyrin, [T(N-Mepy-4-CH(2)(CH(3))NSO(2)Ar)P]Cl(4), the distances between the nitrogens are estimated to be able to span the range from approximately 9 to approximately 25 A. Thus, the N-Mepy groups in the new porphyrins can adopt the same spacing as in known intercalators such as TMpyP(4). The absence of intercalation by the new porphyrins indicates that the propensity for the N-Mepy group to facilitate DNA intercalation of cationic porphyrins requires direct attachment of N-Mepy groups to the porphyrin core.

Multivalent Lipid--DNA Complexes: Distinct DNA Compaction Regimes

NASA Astrophysics Data System (ADS)

Evans, Heather M.; Ahmad, A.; Ewert, K.; Safinya, C. R.

2004-03-01

Cationic liposomes (CL), while intrinsically advantageous in comparison to viruses, still have limited success for gene therapy and require more study. CL spontaneously self-assemble with DNA via counterion release, forming small particles approximately 200nm in diameter. X-ray diffraction reveals CL-DNA structures that are typically a multilamellar organization of lipids with DNA intercalated between the layers. We explore the structural properties of CL-DNA complexes formed with new multivalent lipids (Ewert et al, J. Med. Chem. 2002; 45:5023) that range from 2+ to 16+. Contrary to a simple prediction for the DNA interaxial spacing d_DNA based on a geometrical space-filling model, these lipids show dramatic DNA compaction, down to d_DNA ˜ 25 ÅVariations in the membrane charge density, σ _M, lead to distinct spacing regimes. We propose that this DNA condensation is controlled by a unique locking mechanism between the DNA double helix and the large, multivalent lipid head groups. Funded by NSF DMR-0203755 and NIH GM-59288.

Alternate-strand triple-helix formation by the 3'-3'-linked oligodeoxynucleotides with the intercalators at the junction point.

PubMed

Ueno, Y; Mikawa, M; Hoshika, S; Takeba, M; Kitade, Y; Matsuda, A

2001-01-01

3'-3'-Linked oligodeoxynucleotides (ODNs) with the anthraquinonyl group at the junction point were synthesized on a DNA synthesizer using a controlled pore glass (CPG), which has pentaerythritol carrying the intercalator at one of the four hydroxymethyl groups. Stability of the triplexes with the target duplexes was studied by thermal denaturation. The 3'-3'-linked ODNs with the anthraquinonyl group enhanced the thermal stability of the triplexes when compared with those without the intercalator and the unmodified nonamer. The inhibitory activity of the 3'-3'-linked ODNs against the cleavage of the target DNA by the restriction enzyme Hind III was tested. It was found that the 3'-3'-linked ODN with the anthraquinonyl group at the junction point inhibited the cleavage by the enzyme more effectively than the nonamer and the 3'-3'-linked ODN without the intercalator.

A multi-spectroscopic and molecular docking approach to investigate the interaction of antiviral drug oseltamivir with ct-DNA.

PubMed

Moghadam, Neda Hosseinpour; Salehzadeh, Sadegh; Shahabadi, Nahid; Golbedaghi, Reza

2017-07-03

The possible interaction between the antiviral drug oseltamivir and calf thymus DNA at physiological pH was studied by spectrophotometry, competitive spectrofluorimetry, differential pulse voltammogram (DPV), circular dichroism spectroscopy (CD), viscosity measurements, salt effect, and computational studies. Intercalation of oseltamivir between the base pairs of DNA was shown by a sharp increase in specific viscosity of DNA and a decrease of the peak current and a positive shift in differential pulse voltammogram. Competitive fluorescence experiments were performed using neutral red (NR) as a probe for the intercalation binding mode. The studies showed that oseltamivir is able to release the NR.

A new triple system DNA-Nanosilver-Berberine for cancer therapy

NASA Astrophysics Data System (ADS)

Grebinyk, Anna; Yashchuk, Valeriy; Bashmakova, Nataliya; Gryn, Dmytro; Hagemann, Tobias; Naumenko, Antonina; Kutsevol, Nataliya; Dandekar, Thomas; Frohme, Marcus

2018-03-01

The isoquinoline quaternary alkaloid Berberine possesses a variety of pharmacological properties that suggests its promising application for an anticancer delivery system design utilizing its ability to intercalate DNA. In the current work, we have investigated the effects of Berberine on the human T cell leukemia cell line in vitro. Fluorescent microscopy of leukemic cells revealed Berberine nuclear localization. The results showed that Berberine inhibited leukemic cell growth in a time- and dose-dependent manner, that was associated with reactive oxygen species production intensification and caspase 3/7 activity increase with followed apoptosis induction. Berberine was used as a toxic and phototoxic agent for triple system synthesis along with DNA as a carrier and nanosilver as a plasmonic accelerator of Berberine electronic transitions and high energy emission absorbent centers. The proposed method allows to obtain the complex of DNA with Berberine molecules and silver nanoparticles. The optical properties of free components as well as their various combinations, including the final triple system DNA-Nanosilver-Berberine, were investigated. Obtained results support the possibility to use the triple system DNA-Nanosilver-Berberine as an alternative therapeutic agent for cancer treatment.

Interaction of proflavine with DNA studied by colloid surface enhanced resonance Raman spectroscopy

NASA Astrophysics Data System (ADS)

Koglin, E.; Séquaris, J.-M.

1986-03-01

The interaction of the mutagenic highly fluourescing proflavine (3,6-diaminoacridine: PF) dye with calf thymus DNA has been studied by Surface Enhanced Resonance Raman Scattering (SERRS). Since the Ag-colloids almost completely quenche the strong fluorescence it is possible to obtain excellent vibrational spectra in a wide frequency range providing valuable information about the intercalation. The intercalation does not affect the vibrational frequencies of the proflavine dye. On the other hand, intensity changes are observed in some of the ring- and NH 2-modes of proflavine upon intercalation. This Raman hypochromism is characteristic for ring stacking interactions and in the SERRS spetroscopy for an additional effects of the dye orientation to the surface.

The effect of novel rhenium compounds on lymphosarcoma, PC-3 prostate and myeloid leukemia cancer cell lines and an investigation on the DNA binding properties of one of these compounds through electronic spectroscopy

PubMed Central

Parson, Carl; Smith, Valerie; Krauss, Christopher; Banerjee, Hirendra N.; Reilly, Christopher; Krause, Jeanette A.; Wachira, James M.; Giri, Dipak; Winstead, Angela; Mandal, Santosh K.

2014-01-01

Despite the tremendous success of cisplatin and other platinum-based anticancer drugs, severe toxicity and resistance to tumors limit their applications. It is believed that the coordination (formation of covalent bond) of the metal (platinum) to the nitrogen bases of DNA cause the ruptures of the cancer as well as normal cells. A search for anticancer drugs with different modes of action resulted in the synthesis of variety of novel compounds. Many of them are in clinical trials now. Recently we synthesized a series of novel rhenium pentylcarbonato compounds (PC1–PC6). The rhenium atom in each compound is coordinated (bonded) to a planar polypyridyl aromatic ligand, thereby forcing each compound to intercalate between the DNA bases. We have investigated the DNA binding properties of one of the PC-series of compounds (PC6) using electronic spectroscopy. The UV absorption titration of PC6 with DNA shows hypochromic effect with concomitant bathochromic shift of the charge transfer band at 290 nm. These results suggest that the compound PC6 binds to DNA through intercalation. It is therefore likely that the other PC-series of compounds will behave in a similar manner. Thus it is expected that these compounds will exhibit negligible or no side effect. We have observed that the PC-series of compounds are strong cytotoxic agents against lymphosarcoma (average GI50 ≈ 2±2.6 µM), PC-3 prostate (average GI50 ≈ 3±2.8 µM) and myeloid leukemia (average GI50 ≈ 3±2.8 µM) cancer cell lines. The average GI50 values of the PC-series of compounds are 2–3 less than the corresponding GI50 values of cisplatin. Also each of the PC-series of compounds exhibits less toxicity than cisplatin in the glomerular mesangial cells. PMID:25221731

Structure and dynamics of proflavine association around DNA.

PubMed

Sasikala, Wilbee D; Mukherjee, Arnab

2016-04-21

Proflavine is a small molecule that intercalates into DNA and, thereby, acts as an anticancer agent. Intercalation of proflavine is shown to be a two-step process in which the first step is believed to be the formation of a pre-intercalative outside bound state. Experimental studies so far have been unable to capture the nature of the outside bound state. However, the sub-millisecond timescale observed in fluorescence kinetic experiments is often attributed to the binding of proflavine outside of DNA. Here, we have performed molecular dynamics simulations with multiple proflavine molecules to study the structure and dynamics of the formation of the outside bound state of DNA at different ion concentrations. We observed that the timescale of the outside bound state formation is, at least, five orders of magnitude faster (in nanoseconds) than the experimentally reported timescale (sub-milliseconds) attributed to binding outside DNA. Moreover, we also observed the stacked arrangement of proflavine all around DNA, which is different from the experimentally predicted stacking arrangement perpendicular to the helical axis of DNA in the close vicinity of the phosphate groups. This study, therefore, provides insight into the molecular structure and dynamics of the pre-intercalative outside bound state and will help in understanding the overall intercalation mechanism.

Probing the DNA kink structure induced by the hyperthermophilic chromosomal protein Sac7d

PubMed Central

Chen, Chin-Yu; Ko, Tzu-Ping; Lin, Ting-Wan; Chou, Chia-Cheng; Chen, Chun-Jung; Wang, Andrew H.-J.

2005-01-01

Sac7d, a small, abundant, sequence-general DNA-binding protein from the hyperthermophilic archaeon Sulfolobus acidocaldarius, causes a single-step sharp kink in DNA (∼60°) via the intercalation of both Val26 and Met29. These two amino acids were systematically changed in size to probe their effects on DNA kinking. Eight crystal structures of five Sac7d mutant–DNA complexes have been analyzed. The DNA-binding pattern of the V26A and M29A single mutants is similar to that of the wild-type, whereas the V26A/M29A protein binds DNA without side chain intercalation, resulting in a smaller overall bending (∼50°). The M29F mutant inserts the Phe29 side chain orthogonally to the C2pG3 step without stacking with base pairs, inducing a sharp kink (∼80°). In the V26F/M29F-GCGATCGC complex, Phe26 intercalates deeply into DNA bases by stacking with the G3 base, whereas Phe29 is stacked on the G15 deoxyribose, in a way similar to those used by the TATA box-binding proteins. All mutants have reduced DNA-stabilizing ability, as indicated by their lower Tm values. The DNA kink patterns caused by different combinations of hydrophobic side chains may be relevant in understanding the manner by which other minor groove-binding proteins interact with DNA. PMID:15653643

Multiply Intercalator-Substituted Cu(II) Cyclen Complexes as DNA Condensers and DNA/RNA Synthesis Inhibitors.

PubMed

Hormann, Jan; Malina, Jaroslav; Lemke, Oliver; Hülsey, Max J; Wedepohl, Stefanie; Potthoff, Jan; Schmidt, Claudia; Ott, Ingo; Keller, Bettina G; Brabec, Viktor; Kulak, Nora

2018-05-07

Many drugs that are applied in anticancer therapy such as the anthracycline doxorubicin contain DNA-intercalating 9,10-anthraquinone (AQ) moieties. When Cu(II) cyclen complexes were functionalized with up to three (2-anthraquinonyl)methyl substituents, they efficiently inhibited DNA and RNA synthesis resulting in high cytotoxicity (selective for cancer cells) accompanied by DNA condensation/aggregation phenomena. Molecular modeling suggests an unusual bisintercalation mode with only one base pair between the two AQ moieties and the metal complex as a linker. A regioisomer, in which the AQ moieties point in directions unfavorable for such an interaction, had a much weaker biological activity. The ligands alone and corresponding Zn(II) complexes (used as redox inert control compounds) also exhibited lower activity.

[Increasing the resolution of chromosome analysis using pyrido[1,2alpha]benzimidazoles].

PubMed

Rachinskaia, O A; Popov, K V; Ryzvanovich, G A; Bol'sheva, N L; Begunov, R S; Iurkevich, O Iu; Zelenin, A V; Muravlenko, O V

2012-10-01

We studied the influence of three derivatives of pyrido[1,2alpha]benzimidazoles (PBIs), which have DNA-intercalating properties, on plant mitotic chromosome condensation, in order to increase the resolution of chromosome analysis. The efficiency of the influence of these agents was assessed using the median chromosome length on chromosome slides, as well as by the number and size of chromosome DAPI bands. We used the third chromosome of Linum grandiflorum Desf. in these experiments. The chromosome was identified on the slides using its DAPI band pattern and a molecular marker, viz., the 5S rDNA site, which is located in the proximal region of the long arm of the chromosome. The influence of the well-known 9-aminoacridine (9-AMA) DNA intercalator, which is widely used in karyotype studies of short-chromosome organisms, was used as a control in all of the experiments. It was found that the influence of each of the three PBIs in the study on the root meristem of L. grandiflorum resulted in an increase in the median length of the third chromosome, the linear centromeric DAPI band size, and the number ofintercalary DAPI bands. All three PBIs acted more efficiently than 9-AMA. The median chromosome length was increased by 15-40% and the number of intercalary bands increased by 1.5-3 times after PBI treatment, as compared to 9-AMA treatment. At the same time, 7-CF3-PBI, in a similar manner to 9-AMA, did not change the relative size of the centromeric DAPI band, while 7-NH2-PBI and 7-CF3-9-NH2-PBI gradually increased this parameter. It is concluded that these substances can be used as intercalating agents in cytogenetic studies in order to increase the resolution of chromosome analysis.

The intercalation chemistry of layered iron chalcogenide superconductors

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vivanco, Hector K.; Rodriguez, Efrain E., E-mail: efrain@umd.edu

The iron chalcogenides FeSe and FeS are superconductors composed of two-dimensional sheets held together by van der Waals interactions, which makes them prime candidates for the intercalation of various guest species. We review the intercalation chemistry of FeSe and FeS superconductors and discuss their synthesis, structure, and physical properties. Before we review the latest work in this area, we provide a brief background on the intercalation chemistry of other inorganic materials that exhibit enhanced superconducting properties upon intercalation, which include the transition metal dichalcogenides, fullerenes, and layered cobalt oxides. From past studies of these intercalated superconductors, we discuss the rolemore » of the intercalates in terms of charge doping, structural distortions, and Fermi surface reconstruction. We also briefly review the physical and chemical properties of the host materials—mackinawite-type FeS and β-FeSe. The three types of intercalates for the iron chalcogenides can be placed in three categories: 1.) alkali and alkaline earth cations intercalated through the liquid ammonia technique; 2.) cations intercalated with organic amines such as ethylenediamine; and 3.) layered hydroxides intercalated during hydrothermal conditions. A recurring theme in these studies is the role of the intercalated guest in electron doping the chalcogenide host and in enhancing the two-dimensionality of the electronic structure by spacing the FeSe layers apart. We end this review discussing possible new avenues in the intercalation chemistry of transition metal monochalcogenides, and the promise of these materials as a unique set of new inorganic two-dimensional systems.« less

Plant Flavone Apigenin Binds to Nucleic Acid Bases and Reduces Oxidative DNA Damage in Prostate Epithelial Cells

PubMed Central

Bhaskaran, Natarajan; Gupta, Sanjay

2014-01-01

Oxidative stress has been linked to prostate carcinogenesis as human prostate tissue is vulnerable to oxidative DNA damage. Apigenin, a dietary plant flavone, possesses anti-proliferative and anticancer effects; however, its antioxidant properties have not been fully elucidated. We investigated sub-cellular distribution of apigenin, it’s binding to DNA and protective effects against H2O2-induced DNA damage using transformed human prostate epithelial RWPE-1 cells and prostate cancer LNCaP, PC-3 and DU145 cells. Exposure of cells to apigenin exhibited higher accumulation in RWPE-1 and LNCaP cells, compared to PC-3 and DU145 cells. The kinetics of apigenin uptake in LNCaP cells was estimated with a Km value of 5 µmole/L and Vmax of 190 pmoles/million cells/h. Sub-cellular fractionation demonstrated that nuclear matrix retains the highest concentration of apigenin (45.3%), followed by cytosol (23.9%), nuclear membranes (17.9%) and microsomes (12.9%), respectively. Spectroscopic analysis of apigenin with calf-thymus DNA exhibited intercalation as the dominant binding mode to DNA duplex. Apigenin exposure resulted in significant genoprotective effects in H2O2-stressed RWPE-1 cells by reduction in reactive oxygen species levels. In addition, apigenin exposure suppressed the formation of 8-hydroxy-2′ deoxyguanosine and protected exposed cells from apoptosis. Our studies demonstrate that apigenin is readily taken up by normal prostatic epithelial cells and prostate cancer cells, and is incorporated into their nuclei, where its intercalation with nucleic acid bases may account for its antioxidant and chemopreventive activities. PMID:24614817

Plant flavone apigenin binds to nucleic acid bases and reduces oxidative DNA damage in prostate epithelial cells.

PubMed

Sharma, Haripaul; Kanwal, Rajnee; Bhaskaran, Natarajan; Gupta, Sanjay

2014-01-01

Oxidative stress has been linked to prostate carcinogenesis as human prostate tissue is vulnerable to oxidative DNA damage. Apigenin, a dietary plant flavone, possesses anti-proliferative and anticancer effects; however, its antioxidant properties have not been fully elucidated. We investigated sub-cellular distribution of apigenin, it's binding to DNA and protective effects against H2O2-induced DNA damage using transformed human prostate epithelial RWPE-1 cells and prostate cancer LNCaP, PC-3 and DU145 cells. Exposure of cells to apigenin exhibited higher accumulation in RWPE-1 and LNCaP cells, compared to PC-3 and DU145 cells. The kinetics of apigenin uptake in LNCaP cells was estimated with a Km value of 5 µmole/L and Vmax of 190 pmoles/million cells/h. Sub-cellular fractionation demonstrated that nuclear matrix retains the highest concentration of apigenin (45.3%), followed by cytosol (23.9%), nuclear membranes (17.9%) and microsomes (12.9%), respectively. Spectroscopic analysis of apigenin with calf-thymus DNA exhibited intercalation as the dominant binding mode to DNA duplex. Apigenin exposure resulted in significant genoprotective effects in H2O2-stressed RWPE-1 cells by reduction in reactive oxygen species levels. In addition, apigenin exposure suppressed the formation of 8-hydroxy-2' deoxyguanosine and protected exposed cells from apoptosis. Our studies demonstrate that apigenin is readily taken up by normal prostatic epithelial cells and prostate cancer cells, and is incorporated into their nuclei, where its intercalation with nucleic acid bases may account for its antioxidant and chemopreventive activities.

Binding mechanism of PicoGreen to DNA characterized by magnetic tweezers and fluorescence spectroscopy.

PubMed

Wang, Ying; Schellenberg, Helene; Walhorn, Volker; Toensing, Katja; Anselmetti, Dario

2017-09-01

Fluorescent dyes are broadly used in many biotechnological applications to detect and visualize DNA molecules. However, their binding to DNA alters the structural and nanomechanical properties of DNA and, thus, interferes with associated biological processes. In this work we employed magnetic tweezers and fluorescence spectroscopy to investigate the binding of PicoGreen to DNA at room temperature in a concentration-dependent manner. PicoGreen is an ultrasensitive quinolinium nucleic acid stain exhibiting hardly any background signal from unbound dye molecules. By means of stretching and overwinding single, torsionally constrained, nick-free double-stranded DNA molecules, we acquired force-extension and supercoiling curves which allow quantifying DNA contour length, persistence length and other thermodynamical binding parameters, respectively. The results of our magnetic tweezers single-molecule binding study were well supported through analyzing the fluorescent spectra of stained DNA. On the basis of our work, we could identify a concentration-dependent bimodal binding behavior, where, apparently, PicoGreen associates to DNA as an intercalator and minor-groove binder simultaneously.

Anthocyanin Interactions with DNA: Intercalation, Topoisomerase I Inhibition and Oxidative Reactions

PubMed Central

Webb, Michael R.; Min, Kyungmi; Ebeler, Susan E.

2009-01-01

Anthocyanins and their aglycone anthocyanidins are pigmented flavonoids found in significant amounts in many commonly consumed foods. They exhibit a complex chemistry in aqueous solution, which makes it difficult to study their chemistry under physiological conditions. Here we used a gel electrophoresis assay employing supercoiled DNA plasmid to examine the ability of these compounds (1) to intercalate DNA, (2) to inhibit human topoisomerase I through both inhibition of plasmid relaxation activity (catalytic inhibition) and stabilization of the cleavable DNA-topoisomerase complex (poisoning), and (3) to inhibit or enhance oxidative single-strand DNA nicking. We found no evidence of DNA intercalation by anthocyan(id)ins in the physiological pH range for any of the compounds used in this study—cyanidin chloride, cyanidin 3-O-glucoside, cyanidin 3,5-O-diglucoside, malvidin 3-O-glucoside and luteolinidin chloride. The anthocyanins inhibited topoisomerase relaxation activity only at high concentrations (> 50 μM) and we could find no evidence of topoisomerase I cleavable complex stabilization by these compounds. However, we observed that all of the anthocyan(id)ins used in this study were capable of inducing significant oxidative DNA strand cleavage (nicking) in the presence of 1 mM DTT (dithiothreitol), while the free radical scavenger, DMSO, at concentrations typically used in similar studies, completely inhibited DNA nicking. Finally, we propose a mechanism to explain the anthocyan(id)in induced oxidative DNA cleavage observed under our experimental conditions. PMID:19924259

Effect of DNA-CTMA complex on optical properties of LDS 821 dye

NASA Astrophysics Data System (ADS)

Udayan, Sony; Ramachandran, Vijesh Kavumoottil; Sebastian, Mathew; Chandran, Pradeep; Nampoori, Vadakkedath Parameswaran Narayanan; Thomas, Sheenu

2017-07-01

We have investigated the fluorescence behavior of LDS 821 dye (Styryl 9 M) with deoxyribonucleic acid attached with cetyltrimethyl-ammonium (DNA-CTMA). Optical absorption studies confirm the intercalation of the dye molecules with DNA-CTMA. Fluorescence studies show an enhancement of fluorescence intensity of dye with DNA-CTMA, which suggest the reduction of TICT states of the dye molecule. The FWHM of the fluorescence spectrum increases from 95 nm to 161 nm indicating the formation of new energy levels when DNA-CTMA forms a complex with LDS 821 dye. Fluorescence lifetime measurements shows that lifetime of LDS 821 varies from 507ps to 953 ps with the addition of DNA-CTMA, which also confirms the deactivation of TICT states of dye molecule. Results show that the incorporation of DNA-CTMA with LDS 821 dye improves the optical characteristics of LDS 821 dye and therefore, can be used as a good fluorescence probe for DNA visualization as well as in lasing applications.

Interactions of vitamin K3 with herring-sperm DNA using spectroscopy and electrochemistry.

PubMed

Huang, Jianhang; Wang, Xingming; Fei, Dan; Ding, Lisheng

2010-10-01

By means of ultraviolet-visible (UV-Vis) and fluorescence spectra, the binding ratio between vitamin K(3) and herring-sperm DNA in a physiological pH environment (pH = 7.40) was determined as n(K3):n(DNA) = 2:1, and the binding constants of vitamin K(3) binding to DNA at different temperatures were determined as K(θ)(298K) = 1.28 × 10(5) L·mol(-1) and K(θ)(310K) = 7.19 × 10(4) L·mol(-1), which were confirmed using the double reciprocal method are Δ(r)H(m)(θ) = -3.57 × 10(4) J·mol(-1), Δ(r)G(m)(θ) = -2.92 × 10(4) J·mol(-1), and Δ(r)S(m)(θ) = 217.67 J·mol(-1)K(-1). The driving power of this process was enthalpy. An intercalation binding of the vitamin K(3) with DNA was supported by a competitive experiment using acridine orange (AO) as a spectral probe. By combination analysis of the Scatchard method and cyclic voltammetry, we suggested that the interaction mode between vitamin K(3) and herring-sperm DNA would be a mixed mode. The quinonoid, duality fused-ring of vitamin K(3) can intercalate into the base pairs of DNA, and there is an electrostatic binding along with intercalation binding.

Physics and chemistry of MoS2 intercalation compounds

NASA Technical Reports Server (NTRS)

Woollam, J. A.; Somoano, R. B.

1977-01-01

An investigation is made of the physics and chemistry of MoS2 intercalation compounds. These compounds may be separated into two groups according to their stoichiometry, structure and superconducting properties. The first group consists of Na, Ca, and Sr intercalates, and the second group consists of K, Rb, and Cs intercalates. Particular attention is given to the structure of the electronic energy band and to the normal state and superconducting properties of these compounds.

Ethidium and proflavine binding to a 2',5'-linked RNA duplex.

PubMed

Horowitz, Eric D; Hud, Nicholas V

2006-12-06

Despite over 40 years of physical investigations, fundamental questions persist regarding the energetics of RNA and DNA intercalation. The dramatic unwinding of a nucleic acid duplex upon intercalation immediately suggests that the nucleic acid backbone should play a significant role in dictating the free energy of intercalation. However, the contribution of the backbone to intercalation free energy is difficult to appreciate given the intertwined energetics associated with intercalation (e.g., pi-pi stacking and solvent effects). Fluorescence titrations were used to determine the association constants of two known intercalators, proflavine and ethidium, for duplex 2',5'-linked RNA. Proflavine was found to bind 2',5' RNA with an association constant 25-fold greater than that measured for standard, 3',5'-linked RNA. In contrast, ethidium binds 2',5' RNA less favorably than standard RNA.

Cytotoxic activity of proflavine diureas: synthesis, antitumor, evaluation and DNA binding properties of 1',1''-(acridin-3,6-diyl)-3',3''-dialkyldiureas.

PubMed

Kozurková, Mária; Sabolová, Danica; Janovec, Ladislav; Mikes, Jaromír; Koval', Ján; Ungvarský, Ján; Stefanisinová, Miroslava; Fedorocko, Peter; Kristian, Pavol; Imrich, Ján

2008-04-01

The synthesis of novel 1',1''-(acridin-3,6-diyl)-3',3''-dialkyldiureas was reported. Their biological activity to inhibit cell proliferation was assessed by a MTT assay on two cell lines, HeLa and HCT-116, at micromolar concentration. 1',1''-(Acridin-3,6-diyl)-3',3''-dihexyldiurea hydrochloride was active on a HCT-116 cell line with an IC(50) value of 3.1 microM. The interaction of these compounds with calf thymus DNA was investigated by a variety of spectroscopic techniques including UV-vis, fluorescence and CD spectroscopy. From spectrofluorimetric titrations, binding constants for the DNA-drug complexes were determined (K=0.9-4.2x10(5) M(-1)). Antiproliferative activity of synthesized derivatives might be related to their intercalation into DNA.

NMR solution structure of an N2-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: Intercalation from the minor groove with ruptured Watson-Crick base pairing

PubMed Central

Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin H.; Cai, Yuqin; Rodriguez, Fabian A.; Sayer, Jane M.; Jerina, Donald M.; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E.

2012-01-01

The most potent tumorigen identified among the polycyclic aromatic hydrocarbons (PAH) is the non-planar fjord region dibenzo[a,l]pyrene (DB[a,l]P). It is metabolically activated in vivo through the widely-studied diol epoxide (DE) pathway to form covalent adducts with DNA bases, predominantly guanine and adenine. The (+)-11S,12R,13R,14S DE enantiomer forms adducts via its C14-position with the exocyclic amino group of guanine. Here, we present the first NMR solution structure of a DB[a,l]P-derived adduct, the 14R (+)-trans-anti-DB[a,l]P–N2-dG (DB[a,l]P-dG) lesion in double-stranded DNA. In contrast to the stereochemically identical benzo[a]pyrene-derived N2-dG adduct (B[a]P-dG) in which the B[a]P rings reside in the B-DNA minor groove on the 3’-side of the modifed deoxyguanosine, in the DB[a,l]P-derived adduct the DB[a,l]P rings intercalate into the duplex on the 3’-side of the modified base from the sterically crowded minor groove. Watson-Crick base pairing of the modified guanine with the partner cytosine is broken, but these bases retain some stacking with the bulky DB[a,l]P ring system. This new theme in PAH DE - DNA adduct conformation differs from: (1) the classical intercalation motif where Watson-Crick base-pairing is intact at the lesion site, and (2) the base-displaced intercalation motif in which the damaged base and its partner are extruded from the helix . The structural considerations that lead to the intercalated conformation of the DB[a,l]P-dG lesion in contrast to the minor groove alignment of the B[a]P-dG adduct, and the implications of the DB[a,l]P-dG conformational motif for the recognition of such DNA lesions by the human nucleotide excision repair apparatus, are discussed. PMID:23121427

Nuclear magnetic resonance solution structure of an N(2)-guanine DNA adduct derived from the potent tumorigen dibenzo[a,l]pyrene: intercalation from the minor groove with ruptured Watson-Crick base pairing.

PubMed

Tang, Yijin; Liu, Zhi; Ding, Shuang; Lin, Chin H; Cai, Yuqin; Rodriguez, Fabian A; Sayer, Jane M; Jerina, Donald M; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E

2012-12-04

The most potent tumorigen identified among the polycyclic aromatic hydrocarbons (PAH) is the nonplanar fjord region dibenzo[a,l]pyrene (DB[a,l]P). It is metabolically activated in vivo through the widely studied diol epoxide (DE) pathway to form covalent adducts with DNA bases, predominantly guanine and adenine. The (+)-11S,12R,13R,14S DE enantiomer forms adducts via its C14 position with the exocyclic amino group of guanine. Here, we present the first nuclear magnetic resonance solution structure of a DB[a,l]P-derived adduct, the 14R-(+)-trans-anti-DB[a,l]P-N(2)-dG (DB[a,l]P-dG) lesion in double-stranded DNA. In contrast to the stereochemically identical benzo[a]pyrene-derived N(2)-dG adduct (B[a]P-dG) in which the B[a]P rings reside in the B-DNA minor groove on the 3'-side of the modifed deoxyguanosine, in the DB[a,l]P-derived adduct the DB[a,l]P rings intercalate into the duplex on the 3'-side of the modified base from the sterically crowded minor groove. Watson-Crick base pairing of the modified guanine with the partner cytosine is broken, but these bases retain some stacking with the bulky DB[a,l]P ring system. This new theme in PAH DE-DNA adduct conformation differs from (1) the classical intercalation motif in which Watson-Crick base pairing is intact at the lesion site and (2) the base-displaced intercalation motif in which the damaged base and its partner are extruded from the helix. The structural considerations that lead to the intercalated conformation of the DB[a,l]P-dG lesion in contrast to the minor groove alignment of the B[a]P-dG adduct, and the implications of the DB[a,l]P-dG conformational motif for the recognition of such DNA lesions by the human nucleotide excision repair apparatus, are discussed.

Ultraviolet-induced sister chromatid exchanges in V-79 cells with normal and BrdUrd-substituted DNA and the influence of intercalating substances and cysteine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Speit, G.; Mehnert, K.; Wolf, M.

1982-06-01

The influence of intercalating substances (proflavine, ethidium bromide) and of an SH compound (L-cysteine) on uv-induced sister chromatid exchanges (SCEs) was investigated in V-79 cells with normal and BrdUrd-substituted DNA. The results are discussed in relation to the primary damages leading to SCE induction produced by uv irradiation. The data indicate that neither the pyrimidine dimers nor DNA single-strand breaks are the primary cause of SCE induction, and that the damages leading to SCEs by uv irradiation differ from those which cause chromosome aberrations.

Small molecule-mediated duplex formation of nucleic acids with 'incompatible' backbones.

PubMed

Cafferty, Brian J; Musetti, Caterina; Kim, Keunsoo; Horowitz, Eric D; Krishnamurthy, Ramanarayanan; Hud, Nicholas V

2016-04-07

Proflavine, a known intercalator of DNA and RNA, promotes duplex formation by nucleic acids with natural and non-natural backbones that otherwise form duplexes with low thermal stability, and even some that show no sign of duplex formation in the absence of proflavine. These findings demonstrate the potential for intercalators to be used as cofactors for the assembly of rationally designed nucleic acid structures, and could provide fundamental insights regarding intercalation of natural nucleic acid duplexes.

A molecular model for proflavine-DNA intercalation.

PubMed Central

Neidle, S; Pearl, L H; Herzyk, P; Berman, H M

1988-01-01

A molecular model has been derived for the intercalation of proflavine into the CpG site of the decamer duplex of d(GATACGATAC). The starting geometry of the intercalation site was taken from previous crystallographic studies on the d(CpG)-proflavine complex, and molecular mechanics used to obtain a stereochemically acceptable structure. This has widened grooves compared to standard A- or B- double helices, as well as distinct conformational, roll, twist and tilt features. PMID:3174439

Design of copper DNA intercalators with leishmanicidal activity.

PubMed

Navarro, Maribel; Cisneros-Fajardo, Efrén José; Sierralta, Aníbal; Fernández-Mestre, Mercedes; Silva, Pedro; Arrieche, Dwight; Marchán, Edgar

2003-04-01

The complexes [Cu(dppz)(NO(3))]NO(3) (1), [Cu(dppz)(2)(NO(3))]NO(3) (2), [Cu(dpq)(NO(3))]NO(3) (3), and [Cu(dpq)(2)(NO(3))]NO(3) (4) were synthesized and characterized by elemental analysis, FAB-mass spectrometry, EPR, UV, and IR spectroscopies, and molar conductivity. DNA interaction studies showed that intercalation is an important way of interacting with DNA for these complexes. The biological activity of these copper complexes was evaluated on Leishmania braziliensis promastigotes, and the results showed leishmanicidal activity. Preliminary ultrastructural studies with the most active complex (2) at 1 h revealed parasite swelling and binucleated cells. This finding suggests that the leishmanicidal activity of the copper complexes could be associated with their interaction with the parasitic DNA.

Modeling intercalated PAH metabolites: Explanation for the stereochemical and shape selectivity of B-DNA for bay-region carcinogens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Szentpaly, L.V.; Shamovsky, I.L.

1996-12-31

The equilibrium structures of 22 intercalation complexes of different metabolites of polycyclic aromatic hydrocarbons (PAH) with the dG{sub 2}{lg_bullet}dC{sub 2} dinucleotide are obtained by AMBER and FLEX molecular modeling. The triol carbocations of highly potent carcinogens are stereochemically compatible with the dinucleotide and B-DNA. Their intercalation complexes are found (1) to be stabilized by two hydrogen bonds between DH groups of the triol cation and the N(3) atoms of the adjacent guanine residues, (2) to be {open_quotes}preorganized{close_quotes} for covalent bonding to the N(2) amino group of quanine, (3) to display only minor conformational changes with respect to the uncomplexed dinucleotidemore » in B-DNA. A new explanation for the stereochemical and shape selectivity in the initiation of cancer by PAHa is presented. The molecular mechanics study is sugmented by HF/6-31G{sup I} calculations on the conformations of phenanthrene triol carbocation.« less

CyDNA: synthesis and replication of highly Cy-dye substituted DNA by an evolved polymerase.

PubMed

Ramsay, Nicola; Jemth, Ann-Sofie; Brown, Anthony; Crampton, Neal; Dear, Paul; Holliger, Philipp

2010-04-14

DNA not only transmits genetic information but can also serve as a versatile supramolecular scaffold. Here we describe a strategy for the synthesis and replication of DNA displaying hundreds of substituents using directed evolution of polymerase function by short-patch compartmentalized self-replication (spCSR) and the widely used fluorescent dye labeled deoxinucleotide triphosphates Cy3-dCTP and Cy5-dCTP as substrates. In just two rounds of spCSR selection, we have isolated a polymerase that allows the PCR amplification of double stranded DNA fragments up to 1kb, in which all dC bases are substituted by its fluorescent dye-labeled equivalent Cy3- or Cy5-dC. The resulting "CyDNA" displays hundreds of aromatic heterocycles on the outside of the DNA helix and is brightly colored and highly fluorescent. CyDNA also exhibits significantly altered physicochemical properties compared to standard B-form DNA, including loss of silica and intercalating dye binding, resistance to cleavage by some endonucleases, an up to 40% increased apparent diameter as judged by atomic force microscopy and organic phase partitioning during phenol extraction. CyDNA also displays very bright fluorescence enabling significant signal gains in microarray and microfluidic applications. CyDNA represents a step toward a long-term goal of the encoded synthesis of DNA-based polymers of programmable and evolvable sequence and properties.

Studies on DNA binding behaviour of biologically active transition metal complexes of new tetradentate N2O2 donor Schiff bases: inhibitory activity against bacteria.

PubMed

Sobha, S; Mahalakshmi, R; Raman, N

2012-06-15

A series of Cu(II), Ni(II) and Zn(II) complexes of the type ML have been synthesized with Schiff bases derived from o-acetoacetotoluidide, 2-hydroxybenzaldehyde and o-phenylenediamine/1,4-diaminobutane. The complexes are insoluble in common organic solvents but soluble in DMF and DMSO. The measured molar conductance values in DMSO indicate that the complexes are non-electrolytic in nature. All the six metal complexes have been fully characterized with the help of elemental analyses, molecular weights, molar conductance values, magnetic moments and spectroscopic data. The analytical data helped to elucidate the structure of the metal complexes. The Schiff bases are found to act as tetradentate ligands using N(2)O(2) donor set of atoms leading to a square-planar geometry for the complexes around all the metal ions. The binding properties of metal complexes with DNA were investigated by absorption spectra, viscosity measurements and cyclic voltammetry. Detailed analysis reveals that the metal complexes intercalate into the DNA base stack as intercalators. All the metal complexes cleave the pUC19 DNA in presence of H(2)O(2.) The Schiff bases and their complexes have been screened for their antibacterial activity against five bacterial strains (Staphylococcus aureus, Pseudomonas aeruginosa, Escherichia coli, Staphylococcus epidermidis, Klebsiella pneumoniae) by disk diffusion method. All the metal complexes have potent biocidal activity than the free ligands. Copyright © 2012 Elsevier B.V. All rights reserved.

Electrochemical DNA biosensor for detection of porcine oligonucleotides using ruthenium(II) complex as intercalator label redox

DOE Office of Scientific and Technical Information (OSTI.GOV)

Halid, Nurul Izni Abdullah; Hasbullah, Siti Aishah; Heng, Lee Yook

2014-09-03

A DNA biosensor detection of oligonucleotides via the interactions of porcine DNA with redox active complex based on the electrochemical transduction is described. A ruthenium(II) complex, [Ru(bpy){sub 2}(PIP)]{sup 2+}, (bpy = 2,2′bipyridine, PIP = 2-phenylimidazo[4,5-f[[1,10-phenanthroline]) as DNA label has been synthesized and characterized by 1H NMR and mass spectra. The study was carried out by covalent bonding immobilization of porcine aminated DNA probes sequences on screen printed electrode (SPE) modified with succinimide-acrylic microspheres and [Ru(bpy){sub 2}(PIP)]{sup 2+} was used as electrochemical redox intercalator label to detect DNA hybridization event. Electrochemical detection was performed by cyclic voltammetry (CV) and differential pulsemore » voltammetry (DPV) over the potential range where the ruthenium (II) complex was active. The results indicate that the interaction of [Ru(bpy){sub 2}(PIP)]{sup 2+} with hybridization complementary DNA has higher response compared to single-stranded and mismatch complementary DNA.« less

CyDNA: Synthesis and Replication of Highly Cy-Dye Substituted DNA by an Evolved Polymerase

PubMed Central

2010-01-01

DNA not only transmits genetic information but can also serve as a versatile supramolecular scaffold. Here we describe a strategy for the synthesis and replication of DNA displaying hundreds of substituents using directed evolution of polymerase function by short-patch compartmentalized self-replication (spCSR) and the widely used fluorescent dye labeled deoxinucleotide triphosphates Cy3-dCTP and Cy5-dCTP as substrates. In just two rounds of spCSR selection, we have isolated a polymerase that allows the PCR amplification of double stranded DNA fragments up to 1kb, in which all dC bases are substituted by its fluorescent dye-labeled equivalent Cy3- or Cy5-dC. The resulting “CyDNA” displays hundreds of aromatic heterocycles on the outside of the DNA helix and is brightly colored and highly fluorescent. CyDNA also exhibits significantly altered physicochemical properties compared to standard B-form DNA, including loss of silica and intercalating dye binding, resistance to cleavage by some endonucleases, an up to 40% increased apparent diameter as judged by atomic force microscopy and organic phase partitioning during phenol extraction. CyDNA also displays very bright fluorescence enabling significant signal gains in microarray and microfluidic applications. CyDNA represents a step toward a long-term goal of the encoded synthesis of DNA-based polymers of programmable and evolvable sequence and properties. PMID:20235594

NLP-1: a DNA intercalating hypoxic cell radiosensitizer and cytotoxin

DOE Office of Scientific and Technical Information (OSTI.GOV)

Panicucci, R.; Heal, R.; Laderoute, K.

The 2-nitroimidazole linked phenanthridine, NLP-1 (5-(3-(2-nitro-1-imidazoyl)-propyl)-phenanthridinium bromide), was synthesized with the rationale of targeting the nitroimidazole to DNA via the phenanthridine ring. The drug is soluble in aqueous solution (greater than 25 mM) and stable at room temperature. It binds to DNA with a binding constant 1/30 that of ethidium bromide. At a concentration of 0.5 mM, NLP-1 is 8 times more toxic to hypoxic than aerobic cells at 37 degrees C. This concentration is 40 times less than the concentration of misonidazole, a non-intercalating 2-nitroimidazole, required for the same degree of hypoxic cell toxicity. The toxicity of NLP-1 ismore » reduced at least 10-fold at 0 degrees C. Its ability to radiosensitize hypoxic cells is similar to misonidazole at 0 degrees C. Thus the putative targeting of the 2-nitroimidazole, NLP-1, to DNA, via its phenanthridine group, enhances its hypoxic toxicity, but not its radiosensitizing ability under the present test conditions. NLP-1 represents a lead compound for intercalating 2-nitroimidazoles with selective toxicity for hypoxic cells.« less

Solution structure and thermodynamics of 2',5' RNA intercalation.

PubMed

Horowitz, Eric D; Lilavivat, Seth; Holladay, Benjamin W; Germann, Markus W; Hud, Nicholas V

2009-04-29

As a means to explore the influence of the nucleic acid backbone on the intercalative binding of ligands to DNA and RNA, we have determined the solution structure of a proflavine-bound 2',5'-linked octamer duplex with the sequence GCCGCGGC. This structure represents the first NMR structure of an intercalated RNA duplex, of either backbone structural isomer. By comparison with X-ray crystal structures, we have identified similarities and differences between intercalated 3',5' and 2',5'-linked RNA duplexes. First, the two forms of RNA have different sugar pucker geometries at the intercalated nucleotide steps, yet have the same interphosphate distances. Second, as in intercalated 3',5' RNA, the phosphate backbone angle zeta at the 2',5' RNA intercalation site prefers to be in the trans conformation, whereas unintercalated 2',5' and 3',5' RNA prefer the -gauche conformation. These observations provide new insights regarding the transitions required for intercalation of a phosphodiester-ribose backbone and suggest a possible contribution of the backbone to the origin of the nearest-neighbor exclusion principle. Thermodynamic studies presented for intercalation of both structural RNA isomers also reveal a surprising sensitivity of intercalator binding enthalpy and entropy to the details of RNA backbone structure.

[Ru(phen)2DPPZ]2+ is in contact with DNA bases when it forms a luminescent complex with single-stranded oligonucleotides.

PubMed

Moon, Seok Joon; Kim, Jong Moon; Choi, Ji Youn; Kim, Seog K; Lee, Je Seung; Jang, Ho G

2005-05-01

The luminescence intensity of the Delta- and Lambda-enantiomer of [Ru(phen)2DPPZ]2+ ([Ru(phenanthroline)2 dipyrido[3,2-a:2',3'-c]phenazine]2+) complex enhanced upon binding to double stranded DNA, which has been known as "light switch effect". The enhancement of the luminescence required the intercalation of the large ligand between DNA base pairs. In this study, we report the enhancement in the luminescence intensity when the metal complexes bind to single stranded oligonucleotides, indicating that the "light switch effect" does not require intercalation of the large DPPZ ligand. Oligonucleotides may provide a hydrophobic cavity for the [Ru(phen)2DPPZ]2+ complex to prevent the quenching by the water molecule. In the cavity, the metal complex is in contact with DNA bases as is evidenced by the observation that the excited energy of the DNA bases transfer to the bound metal complex. However, the contact of the metal complex with DNA bases is different from the stacking of DPPZ in the intercalation pocket. In addition to the normal two luminescence lifetimes, a short lifetime in the range of 1-2 ns was found for both the delta- and lambda-enantiomer of [Ru(phen)2DPPZ]2+ when complexed with single stranded oligonucleotides, which may be assigned to the metal complex that is outside of the cavity, interacting with phosphate groups of DNA.

Analysis of Oligonucleotide DNA Binding and Sedimentation Properties of Montmorillonite Clay Using Ultraviolet Light Spectroscopy

PubMed Central

Beall, Gary W.; Sowersby, Drew S.; Roberts, Rachel D.; Robson, Michael H.; Lewis, L. Kevin

2009-01-01

Smectite clays such as montmorillonite form complexes with a variety of biomolecules, including the nucleic acids DNA and RNA. Most previous studies of DNA adsorption onto clay have relied upon spectrophotometric analysis after separation of free nucleic acids from bound complexes by centrifugation. In the current work we demonstrate that such studies produce a consistent error due to (a) incomplete sedimentation of montmorillonite and (b) strong absorbance of the remaining clay at 260 nm. Clay sedimentation efficiency was strongly dependent upon cation concentration (Na+ or Mg2+) and on the level of dispersion of the original suspension. An improved clay:DNA adsorption assay was developed and utilized to assess the impact of metal counterions on binding of single-stranded DNA to montmorillonite. X-ray diffraction demonstrated, for the first time, formation of intercalated structures consistent with orientation of the DNA strands parallel to the clay surface. Observed gallery spacings were found to closely match values calculated utilizing atomistic modeling techniques. PMID:19061334

Synthesis, DNA Binding, and Antiproliferative Activity of Novel Acridine-Thiosemicarbazone Derivatives

PubMed Central

de Almeida, Sinara Mônica Vitalino; Lafayette, Elizabeth Almeida; Gomes da Silva, Lúcia Patrícia Bezerra; Amorim, Cézar Augusto da Cruz; de Oliveira, Tiago Bento; Gois Ruiz, Ana Lucia Tasca; de Carvalho, João Ernesto; de Moura, Ricardo Olímpio; Beltrão, Eduardo Isidoro Carneiro; de Lima, Maria do Carmo Alves; de Carvalho Júnior, Luiz Bezerra

2015-01-01

In this work, the acridine nucleus was used as a lead-compound for structural modification by adding different substituted thiosemicarbazide moieties. Eight new (Z)-2-(acridin-9-ylmethylene)-N-phenylhydrazinecarbothioamide derivatives (3a–h) were synthesized, their antiproliferative activities were evaluated, and DNA binding properties were performed with calf thymus DNA (ctDNA) by electronic absorption and fluorescence spectroscopies. Both hyperchromic and hypochromic effects, as well as red or blue shifts were demonstrated by addition of ctDNA to the derivatives. The calculated binding constants ranged from 1.74 × 104 to 1.0 × 106 M−1 and quenching constants from −0.2 × 104 to 2.18 × 104 M−1 indicating high affinity to ctDNA base pairs. The most efficient compound in binding to ctDNA in vitro was (Z)-2-(acridin-9-ylmethylene)-N-(4-chlorophenyl) hydrazinecarbothioamide (3f), while the most active compound in antiproliferative assay was (Z)-2-(acridin-9-ylmethylene)-N-phenylhydrazinecarbothioamide (3a). There was no correlation between DNA-binding and in vitro antiproliferative activity, but the results suggest that DNA binding can be involved in the biological activity mechanism. This study may guide the choice of the size and shape of the intercalating part of the ligand and the strategic selection of substituents that increase DNA-binding or antiproliferative properties. PMID:26068233

Doxorubicin hinders DNA condensation promoted by the protein bovine serum albumin (BSA).

PubMed

Lima, C H M; de Paula, H M C; da Silva, L H M; Rocha, M S

2017-12-01

In this work, we have studied the interaction between the anticancer drug doxorubicin (doxo) and condensed DNA, using optical tweezers. To perform this task, we use the protein bovine serum albumin (BSA) in the working buffer to mimic two key conditions present in the real intracellular environment: the condensed state of the DNA and the abundant presence of charged macromolecules in the surrounding medium. In particular, we have found that, when doxo is previously intercalated in disperse DNA, the drug hinders the DNA condensation process upon the addition of BSA in the buffer. On the other hand, when bare DNA is firstly condensed by BSA, doxo is capable to intercalate and to unfold the DNA condensates at relatively high concentrations. In addition, a specific interaction between BSA and doxo was verified, which significantly changes the chemical equilibrium of the DNA-doxo interaction. Finally, the presence of BSA in the buffer stabilizes the double-helix structure of the DNA-doxo complexes, preventing partial DNA denaturation induced by the stretching forces. © 2017 Wiley Periodicals, Inc.

Binding mode and thermodynamic studies on the interaction of the anticancer drug dacarbazine and dacarbazine-Cu(II) complex with single and double stranded DNA.

PubMed

Temerk, Yassien; Ibrahim, Hossieny

2014-07-01

The binding mode and thermodynamic characteristics of the anticancer drug dacarbazine (Dac) with double and single stranded DNA were investigated in the absence and presence of Cu(II) using cyclic voltammetry, square wave voltammetry and fluorescence spectroscopy. The interaction of Dac and Dac-Cu(II) complex with dsDNA indicated their intercalation into the base stacking domain of dsDNA double helix and the strength of interaction is independent on the ionic strength. The interaction of Dac with dsDNA in the presence of Cu(II) leads to a much stronger intercalation. The interaction mode of Dac molecules with ssDNA is electrostatic attraction via negative phosphate on the exterior of the ssDNA with Dac. The binding constants, stoichiometric coefficients and thermodynamic parameters of Dac and Dac-Cu(II) complex with dsDNA and ssDNA were evaluated. Comparison of the mode interaction of Dac with dsDNA and ssDNA was discussed. The decrease of peak current of Dac was proportional to DNA concentration, which was applied for determination of dsDNA and ssDNA concentration. Copyright © 2014 Elsevier B.V. All rights reserved.

Unexpected DNA affinity and sequence selectivity through core rigidity in guanidinium-based minor groove binders.

PubMed

Nagle, Padraic S; McKeever, Caitriona; Rodriguez, Fernando; Nguyen, Binh; Wilson, W David; Rozas, Isabel

2014-09-25

In this paper we report the design and biophysical evaluation of novel rigid-core symmetric and asymmetric dicationic DNA binders containing 9H-fluorene and 9,10-dihydroanthracene cores as well as the synthesis of one of these fluorene derivatives. First, the affinity toward particular DNA sequences of these compounds and flexible core derivatives was evaluated by means of surface plasmon resonance and thermal denaturation experiments finding that the position of the cations significantly influence the binding strength. Then their affinity and mode of binding were further studied by performing circular dichroism and UV studies and the results obtained were rationalized by means of DFT calculations. We found that the fluorene derivatives prepared have the ability to bind to the minor groove of certain DNA sequences and intercalate to others, whereas the dihydroanthracene compounds bind via intercalation to all the DNA sequences studied here.

Modulating the electronic and magnetic properties of bilayer borophene via transition metal atoms intercalation: from metal to half metal and semiconductor

NASA Astrophysics Data System (ADS)

Zhang, Xiuyun; Sun, Yi; Ma, Liang; Zhao, Xinli; Yao, Xiaojing

2018-07-01

Borophene, a two-dimensional monolayer made of boron atoms, has attracted wide attention due to its appealing properties. Great efforts have been devoted to fine tuning its electronic and magnetic properties for desired applications. Herein, we theoretically investigate the versatile electronic and magnetic properties of bilayer borophene (BLB) intercalated by 3d transition metal (TM) atoms, TM@BLBs (TM = Ti-Fe), using ab initio calculations. Four allotropes of AA-stacking (α 1-, β-, β 12- and χ 3-) BLBs with different intercalation concentrations of TM atoms are considered. Our results show that the TM atoms are strongly bonded to the borophene layers with fairly large binding energies, around 6.31 ∼ 15.44 eV per TM atom. The BLBs with Cr and Mn intercalation have robust ferromagnetism, while for the systems decorated with Fe atoms, fruitful magnetic properties, such as nonmagnetic, ferromagnetic or antiferromagnetic, are identified. In particular, the α 1- and β-BLBs intercalated by Mn or Fe atom can be transformed into a semiconductor, half metal or graphene-like semimetal. Moreover, some heavily doped TM@BLBs expose high Curie temperatures above room temperature. The attractive properties of TM@BLBs entail an efficient way to modulate the electronic and magnetic properties of borophene sheets for advanced applications.

Intercalation of XR5944 with the estrogen response element is modulated by the tri-nucleotide spacer sequence between half-sites

PubMed Central

Sidell, Neil; Mathad, Raveendra I.; Shu, Feng-jue; Zhang, Zhenjiang; Kallen, Caleb B.; Yang, Danzhou

2011-01-01

DNA-intercalating molecules can impair DNA replication, DNA repair, and gene transcription. We previously demonstrated that XR5944, a DNA bis-intercalator, specifically blocks binding of estrogen receptor-α (ERα) to the consensus estrogen response element (ERE). The consensus ERE sequence is AGGTCAnnnTGACCT, where nnn is known as the tri-nucleotide spacer. Recent work has shown that the tri-nucleotide spacer can modulate ERα-ERE binding affinity and ligand-mediated transcriptional responses. To further understand the mechanism by which XR5944 inhibits ERα-ERE binding, we tested its ability to interact with consensus EREs with variable tri-nucleotide spacer sequences and with natural but non-consensus ERE sequences using one dimensional nuclear magnetic resonance (1D 1H NMR) titration studies. We found that the tri-nucleotide spacer sequence significantly modulates the binding of XR5944 to EREs. Of the sequences that were tested, EREs with CGG and AGG spacers showed the best binding specificity with XR5944, while those spaced with TTT demonstrated the least specific binding. The binding stoichiometry of XR5944 with EREs was 2:1, which can explain why the spacer influences the drug-DNA interaction; each XR5944 spans four nucleotides (including portions of the spacer) when intercalating with DNA. To validate our NMR results, we conducted functional studies using reporter constructs containing consensus EREs with tri-nucleotide spacers CGG, CTG, and TTT. Results of reporter assays in MCF-7 cells indicated that XR5944 was significantly more potent in inhibiting the activity of CGG- than TTT-spaced EREs, consistent with our NMR results. Taken together, these findings predict that the anti-estrogenic effects of XR5944 will depend not only on ERE half-site composition but also on the tri-nucleotide spacer sequence of EREs located in the promoters of estrogen-responsive genes. PMID:21333738

Synthesis, characterization, DNA-binding study and anticancer properties of ternary metal(II) complexes of edda and an intercalating ligand.

PubMed

Ng, Chew Hee; Kong, King Chow; Von, Sze Tin; Balraj, Pauline; Jensen, Paul; Thirthagiri, Eswary; Hamada, Hirokazu; Chikira, Makoto

2008-01-28

A series of ternary metal(ii) complexes {M(phen)(edda); 1a (Cu), 1b (Co), 1c (Zn), 1d (Ni); H(2)edda = N,N(')-ethylenediaminediacetic acid} of N,N'-ethylene-bridged diglycine and 1,10-phenanthroline were synthesized and characterized by elemental analysis, FTIR, UV-visible spectroscopy and magnetic susceptibility measurement. The interaction of these complexes with DNA was investigated using CD and EPR spectroscopy. MTT assay results of 1a-1c , screened on MCF-7 cancer cell lines, show that synergy between the metal and ligands results in significant enhancement of their antiproliferative properties. Preliminary results from apoptosis and cell cycle analyses with flow cytometry are reported. seems to be able to induce cell cycle arrest at G(0)/G(1). The crystal structure of 1a is also included.

Synergetic effects of K + and Mg 2+ ion intercalation on the electrochemical and actuation properties of the two-dimensional Ti 3 C 2 MXene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Qiang; Come, Jeremy; Naguib, Michael

2017-01-01

Two-dimensional materials, such as MXenes, are attractive candidates for energy storage and electrochemical actuators due to their high volume changes upon ion intercalation. Of special interest for boosting energy storage is the intercalation of multivalent ions such as Mg 2+, which suffers from sluggish intercalation and transport kinetics due to its ion size. By combining traditional electrochemical characterization techniques with electrochemical dilatometry and contact resonance atomic force microscopy, the synergetic effects of the pre-intercalation of K +ions are demonstrated to improve the charge storage of multivalent ions, as well as tune the mechanical and actuation properties of the Ti 3Cmore » 2MXene. Our results have important implications for quantitatively understanding the charge storage processes in intercalation compounds and provide a new path for studying the mechanical evolution of energy storage materials.« less

B1-induced caspase-independent apoptosis in MCF-7 cells is mediated by down-regulation of Bcl-2 via p53 binding to P2 promoter TATA box

DOE Office of Scientific and Technical Information (OSTI.GOV)

Liang Xin; Xu Ke; Xu Yufang

The Bcl-2 family contains a panel of proteins which are conserved regulators of apoptosis in mammalian cells, like the anti-apoptotic protein Bcl-2. According to its significant role in altering susceptibility to apoptosis, the deciphering of the mechanism of Bcl-2 expression modulation may be crucial for identifying therapeutics strategies for cancer. Treatment with naphthalimide-based DNA intercalators, including M2-A and R16, generally leads to a decrease in Bcl-2 intracellular amounts. Whereas the interest for these chemotherapeutics is accompanied by advances in the fundamental understanding of their anticancer properties, the molecular mechanism underlying changes in Bcl-2 expression remains poorly understood. We report heremore » that p53 contributes to Bcl-2 down-regulation induced by B1, a novel naphthalimide-based DNA intercalating agent. Indeed, the decrease in Bcl-2 protein levels observed during B1-induced apoptosis was correlated to the decrease in mRNA levels, as a result of the inhibition of Bcl-2 transcription and promoter activity. In this context, we evaluated p53 contribution in the Bcl-2 transcriptional down-regulation. We found a significant increase of p53 binding to P{sub 2} promoter TATA box in MCF7 cells by chromatin immunoprecipitation. These data suggest that B1-induced caspase-independent apoptosis in MCF-7 cells is associated with the activation of p53 and the down-regulation of Bcl-2. Our study strengthens the links between p53 and Bcl-2 at a transcriptional level, upon naphthalimide-based DNA intercalator treatment. - Research Highlights: > B1 induced apoptosis in MCF-7 cells, following a transcriptional decrease in Bcl-2. > B1 treatment triggered p53 activation and leads to a p53-dependent down-regulation of Bcl-2. > B1 induced significant increase of p53 binding to Bcl-2 P{sub 2} promoter TATA box.« less

Single Fluorescence Channel-based Multiplex Detection of Avian Influenza Virus by Quantitative PCR with Intercalating Dye

PubMed Central

Ahberg, Christian D.; Manz, Andreas; Neuzil, Pavel

2015-01-01

Since its invention in 1985 the polymerase chain reaction (PCR) has become a well-established method for amplification and detection of segments of double-stranded DNA. Incorporation of fluorogenic probe or DNA intercalating dyes (such as SYBR Green) into the PCR mixture allowed real-time reaction monitoring and extraction of quantitative information (qPCR). Probes with different excitation spectra enable multiplex qPCR of several DNA segments using multi-channel optical detection systems. Here we show multiplex qPCR using an economical EvaGreen-based system with single optical channel detection. Previously reported non quantitative multiplex real-time PCR techniques based on intercalating dyes were conducted once the PCR is completed by performing melting curve analysis (MCA). The technique presented in this paper is both qualitative and quantitative as it provides information about the presence of multiple DNA strands as well as the number of starting copies in the tested sample. Besides important internal control, multiplex qPCR also allows detecting concentrations of more than one DNA strand within the same sample. Detection of the avian influenza virus H7N9 by PCR is a well established method. Multiplex qPCR greatly enhances its specificity as it is capable of distinguishing both haemagglutinin (HA) and neuraminidase (NA) genes as well as their ratio. PMID:26088868

Toward efficient Zn(II)-based artificial nucleases.

PubMed

Boseggia, Elisa; Gatos, Maddalena; Lucatello, Lorena; Mancin, Fabrizio; Moro, Stefano; Palumbo, Manlio; Sissi, Claudia; Tecilla, Paolo; Tonellato, Umberto; Zagotto, Giuseppe

2004-04-14

A series of cis-cis-triaminocyclohexane Zn(II) complex-anthraquinone intercalator conjugates, designed in such a way to allow their easy synthesis and modification, have been investigated as hydrolytic cleaving agents for plasmid DNA. The ligand structure comprises a triaminocyclohexane platform linked by means of alkyl spacers of different length (from C(4) to C(8)) to the anthraquinone group which may intercalate the DNA. At a concentration of 5 microM, the complex of the derivative with a C(8) alkyl spacer induces the hydrolytic stand scission of supercoiled DNA with a rate of 4.6 x 10(-6) s(-1) at pH 7 and 37 degrees C. The conjugation of the metal complex with the anthraquinone group leads to a 15-fold increase of the cleavage efficiency when compared with the anthraquinone lacking Zn-triaminocyclohexane complex. The straightforward synthetic procedure employed, allowing a systematic change of the spacer length, made possible to gain more insight on the role of the intercalating group in determining the reactivity of the systems. Comparison of the reactivity of the different complexes shows a remarkable increase of the DNA cleaving efficiency with the length of the spacer. In the case of too-short spacers, the advantages due to the increased DNA affinity are canceled due to the incorrect positioning of the reactive group, thus leading to cleavage inhibition.

Electronic properties of carbon fibers intercalated with copper chloride

NASA Technical Reports Server (NTRS)

Oshima, H.; Natarajan, V.; Woollam, J. A.; Yavrouian, A.; Haugland, E. J.; Tsuzuku, T.

1984-01-01

Copper chloride intercalated pitch-based carbon fibers are found to have electrical resistivities as low as 12.9 micro-ohm-cm, and are air- and thermally-stable at and above room temperature. This is therefore a good candidate system for conductor application. In addition, Shubnikov-deHaas quantum oscillatory effects were found, and electronic properties of the intercalated fiber are studied using magnetic fields to 20 tesla.

Antiviral and Anticancer Optimization Studies of the DNA-binding Marine Natural Product Aaptamine

PubMed Central

Bowling, John J.; Pennaka, Hari K.; Ivey, Kelly; Wahyuono, Subagus; Kelly, Michelle; Schinazi, Raymond F.; Valeriote, Frederick A.; Graves, David E.; Hamann, Mark T.

2016-01-01

Aaptamine has potent cytotoxicity that may be explained by its ability to intercalate DNA. Aaptamine was evaluated for its ability to bind to DNA to validate DNA binding as the primary mechanism of cytotoxicity. Based on UV–vis absorbance titration data, the Kobs for aaptamine was 4.0 (±0.2) × 103 which was essentially equivalent to the known DNA intercalator N-[2-(diethylamino)ethyl]-9-aminoacridine-4-carboxamide. Semi-synthetic core modifications were performed to improve the general structural diversity of known aaptamine analogs and vary its absorption characteristics. Overall, 26 aaptamine derivatives were synthesized which consisted of a simple homologous range of mono and di-N-alkylations as well as some 9-O-sulfonylation and bis-O-isoaaptamine dimer products. Each product was evaluated for activity in a variety of whole cell and viral assays including a unique solid tumor disk diffusion assay. Details of aaptamine's DNA-binding activity and its derivatives’ whole cell and viral assay results are discussed. PMID:18251774

Mechanistic aspects of thioflavin-T self-aggregation and DNA binding: evidence for dimer attack on DNA grooves.

PubMed

Biancardi, A; Biver, T; Burgalassi, A; Mattonai, M; Secco, F; Venturini, M

2014-10-07

Thioflavin-T (TFT) is a fluorescent marker widely employed in biomedical research but the mechanism of its binding to polynucleotides has been poorly understood. This paper presents a study of the mechanisms of TFT self-aggregation and binding to DNA. Relaxation kinetics of TFT solutions show that the cyanine undergoes dimerization followed by dimer isomerisation. The interaction of TFT with DNA has been investigated using static methods, such as spectrophotometric and spectrofluorometric titrations under different conditions (salt content, temperature), fluorescence quenching, viscometric experiments and the T-jump relaxation method. The combined use of these techniques enabled us to show that the TFT monomer undergoes intercalation between the DNA base pairs and external binding according to a branched mechanism. Moreover, it has also been observed that, under dye excess conditions, the TFT dimer binds to the DNA grooves. The molecular structures of intercalated TFT and the groove-bound TFT dimer are obtained by performing QM/MM MD simulations.

Development of an Automated DNA Detection System Using an Electrochemical DNA Chip Technology

NASA Astrophysics Data System (ADS)

Hongo, Sadato; Okada, Jun; Hashimoto, Koji; Tsuji, Koichi; Nikaido, Masaru; Gemma, Nobuhiro

A new compact automated DNA detection system Genelyzer™ has been developed. After injecting a sample solution into a cassette with a built-in electrochemical DNA chip, processes from hybridization reaction to detection and analysis are all operated fully automatically. In order to detect a sample DNA, electrical currents from electrodes due to an oxidization reaction of electrochemically active intercalator molecules bound to hybridized DNAs are detected. The intercalator is supplied as a reagent solution by a fluid supply unit of the system. The feasibility test proved that the simultaneous typing of six single nucleotide polymorphisms (SNPs) associated with a rheumatoid arthritis (RA) was carried out within two hours and that all the results were consistent with those by conventional typing methods. It is expected that this system opens a new way to a DNA testing such as a test for infectious diseases, a personalized medicine, a food inspection, a forensic application and any other applications.

Crystal structure of a four-stranded intercalated DNA: d(C4)

NASA Technical Reports Server (NTRS)

Chen, L.; Cai, L.; Zhang, X.; Rich, A.

1994-01-01

The crystal structure of d(C4) solved at 2.3-A resolution reveals a four-stranded molecule composed of two interdigitated or intercalated duplexes. The duplexes are held together by hemiprotonated cytosine-cytosine base pairs and are parallel stranded, but the two duplexes point in opposite directions. The molecule has a slow right-handed twist of 12.4 degrees between covalently linked cytosine base pairs, and the base stacking distance is 3.1 A. This is in general agreement with the NMR studies. A biological role for DNA in this conformation is suggested.

Interaction of cationic phthalocyanines with DNA. Importance of the structure of the substituents.

PubMed

López Zeballos, N C; Gauna, G A; García Vior, M C; Awruch, J; Dicelio, L E

2014-07-05

The interaction of novel zinc (II) cationic phthalocyanines with CT-DNA was studied using absorption and fluorescence spectroscopy, as well as thermal denaturation profiles. Results showed an electrostatic interaction between the phthalocyanines and CT-DNA. The properties of these phthalocyanines were compared taking the structure of the macrocycle peripheral substituents into account. 2,9(10),16(17),23(24)-tetrakis[(N-butyl-N-methylammonium)ethylsulfanyl]phthalocyaninatozinc(II) tetraiodide (Pc6) had a greater affinity for the CT-DNA helix than its bioisoster 2,9(10),16(17),23(24)-tetrakis[(N-dibutyl-N-methylammonium)ethoxy]phthalocyaninatozinc(II) tetraiodide (Pc7). 2,9(10),16(17),23(24)-tetrakis[(2-trimethylammonium)ethyl-sulfanyl]phthalocyaninatozinc(II) tetraiodide (Pc13) also carried a sulfur atom like Pc6, but linked to bulky substituents such as trimethylammonium groups. The planar aromatic region of the cationic phthalocyanines in this study appears to be unable to facilitate their intercalation with CT-DNA. Copyright © 2014 Elsevier B.V. All rights reserved.

Studies on interaction of norbixin with DNA: Multispectroscopic and in silico analysis

NASA Astrophysics Data System (ADS)

Anantharaman, Amrita; Priya, Rajendra Rao; Hemachandran, Hridya; Sivaramakrishna, Akella; Babu, Subramanian; Siva, Ramamoorthy

2015-06-01

The interaction of food colorant norbixin with calf thymus DNA (CTDNA) was investigated through UV-Visible spectroscopy, Fourier Transform Infrared (FTIR), Circular Dichroism (CD), Nuclear Magnetic Resonance (NMR), DNA melting studies, electrophoretic analysis, histological staining technique and molecular docking studies. The results indicated that norbixin interacted with CTDNA by partial intercalation mode. The binding constant (K) of norbixin with CTDNA was calculated to be 5.08 × 105 Mol-1 L. FTIR and CD studies were coupled with 1H NMR spectra revealed that norbixin intercalates partially and binds to the groove's, phosphate group, deoxyribose sugar of DNA and also induces conformational transition of B-form to A-form DNA. Agarose gel electrophoretic and histological staining technique results further prove that, norbixin specifically binds to the DNA in the cell. Moreover, molecular docking studies on the specific binding of norbixin with CTDNA have exhibited lowest conformation energy score of -3.2. Therefore, this food colorant has the ability to interact with DNA and it could emerge as a promising class of natural DNA targeted therapeutic.

Spectroscopic and viscometric elucidation of the interaction between a potential chloride channel blocker and calf-thymus DNA: the effect of medium ionic strength on the binding mode.

PubMed

Ganguly, Aniruddha; Ghosh, Soumen; Guchhait, Nikhil

2015-01-07

The present study demonstrates a detailed characterization of the binding interaction of a potential chloride channel blocker 9-methyl anthroate (9-MA) with calf-thymus DNA. The modulated photophysical properties of the emissive molecule within the microheterogeneous bio-assembly have been spectroscopically exploited to monitor the drug-DNA binding interaction. Experimental results based on fluorescence and absorption spectroscopy aided with DNA-melting, viscometric and circular dichroism studies unambiguously establish the binding mode between the drug and DNA to be principally intercalative. Concomitantly, a discernible dependence of the mode of binding between the concerned moieties on the ionic strength of the medium is noteworthy. A dip-and-rise characteristic of the rotational relaxation profile of the drug within the DNA environment has been argued to be originating from a substantial difference in the lifetime as well as amplitude of the free and DNA bound drug molecule. In view of the prospective biological applications of the drug, the issue of facile dissociation of the intercalated drug from the DNA helix via a simple detergent-sequestration technique has also been unveiled. The utility of the present work resides in exploring the potential applicability of the fluorescence properties of 9-MA for studying its interactions with other relevant biological or biomimicking targets.

Binding of DNA-binding alkaloids berberine and palmatine to tRNA and comparison to ethidium: Spectroscopic and molecular modeling studies

NASA Astrophysics Data System (ADS)

Islam, Md. Maidul; Pandya, Prateek; Chowdhury, Sebanti Roy; Kumar, Surat; Kumar, Gopinatha Suresh

2008-11-01

The interaction of two natural protoberberine plant alkaloids berberine and palmatine with tRNA phe was studied using various biophysical techniques and molecular modeling and the data were compared with the binding of the classical DNA intercalator, ethidium. Circular dichroic studies revealed that the tRNA conformation was moderately perturbed on binding of the alkaloids. The cooperative binding of both the alkaloids and ethidium to tRNA was revealed from absorbance and fluorescence studies. Fluorescence quenching studies advanced a conclusion that while berberine and palmatine are partially intercalated, ethidium is fully intercalated on the tRNA molecule. The binding of the alkaloids as well as ethidium stabilized the tRNA melting, and the binding constant evaluated from the averaged optical melting temperature data was in agreement with fluorescence spectral-binding data. Differential scanning calorimetry revealed that the tRNA melting showed three close transitions that were affected on binding of these small molecules. Molecular docking calculations performed showed the preferred regions of binding of these small molecules on the tRNA. Taken together, the results suggest that the binding of the alkaloids berberine and palmatine on the tRNA structure appears to be mostly by partial intercalation while ethidium intercalates fully on the tRNA. These results further advance our knowledge on the molecular aspects on the interaction of these alkaloids to tRNA.

Preparation of nanostructured and nanosheets of MoS2 oxide using oxidation method.

PubMed

Amini, Majed; Ramazani S A, Ahmad; Faghihi, Morteza; Fattahpour, Seyyedfaridoddin

2017-11-01

Molybdenum disulfide (MoS 2 ), a two-dimensional transition metal has a 2D layered structure and has recently attracted attention due to its novel catalytic properties. In this study, MoS 2 has been successfully intercalated using chemical and physical intercalation techniques, while enhancing its surface properties. The final intercalated MoS 2 is of many interests because of its low-dimensional and potential properties in in-situ catalysis. In this research, we report different methods to intercalate the layers of MoS 2 successfully using acid-treatment, ultrasonication, oxidation and thermal shocking. The other goal of this study is to form SO bonds mainly because of expected enhanced in-situ catalytic operations. The intercalated MoS 2 is further characterized using analyses such as Fourier Transform Infrared Spectroscopy (FTIR), Raman, Contact Angle, X-ray diffraction (XRD), Field Emission Scanning Electron Microscope (FESEM), Energy Dispersive X-Ray Microanalysis (EDAX), Transmission electron microscopy (TEM), and BET. Copyright © 2017. Published by Elsevier B.V.

Design of a Sensitive and Selective Electrochemical Aptasensor for the Determination of the Complementary cDNA of miRNA-145 Based on the Intercalation and Electrochemical Reduction of Doxorubicin.

PubMed

Mohamadi, Maryam; Mostafavi, Ali; Torkzadeh-Mahani, Masoud

2017-11-01

The aim of this research was the determination of a microRNA (miRNA) using a DNA electrochemical aptasensor. In this biosensor, the complementary complementary DNA (cDNA) of miRNA-145 (a sense RNA transcript) was the target strand and the cDNA of miRNA-145 was the probe strand. Both cDNAs can be the product of the reverse transcriptase-polymerase chain reaction of miRNA. The proposed aptasensor's function was based on the hybridization of target strands with probes immobilized on the surface of a working electrode and the subsequent intercalation of doxorubicin (DOX) molecules functioning as the electroactive indicators of any double strands that formed. Electrochemical transduction was performed by measuring the cathodic current resulting from the electrochemical reduction of the intercalated molecules at the electrode surface. In the experiment, because many DOX molecules accumulated on each target strand on the electrode surface, amplification was inherently easy, without a need for enzymatic or complicated amplification strategies. The proposed aptasensor also had the excellent ability to regenerate as a result of the melting of the DNA duplex. Moreover, the use of DNA probe strands obviated the challenges of working with an RNA probe, such as sensitivity to RNase enzyme. In addition to the linear relationship between the electrochemical signal and the concentration of the target strands that ranged from 2.0 to 80.0 nM with an LOD of 0.27 nM, the proposed biosensor was clearly capable of distinguishing between complementary (target strand) and noncomplementary sequences. The presented biosensor was successfully applied for the quantification of DNA strands corresponding to miRNA-145 in human serum samples.

Amsacrine as a Topoisomerase II Poison: Importance of Drug-DNA Interactions†

PubMed Central

Ketron, Adam C.; Denny, William A.; Graves, David E.; Osheroff, Neil

2012-01-01

Amsacrine (m-AMSA) is an anticancer agent that displays activity against refractory acute leukemias as well as Hodgkin’s and non-Hodgkin’s lymphomas. The drug is comprised of an intercalative acridine moiety coupled to a 4’-amino-methanesulfon-m-anisidide head group. m-AMSA is historically significant in that it was the first drug demonstrated to function as a topoisomerase II poison. Although m-AMSA was designed as a DNA binding agent, the ability to intercalate does not appear to be the sole determinant of drug activity. Therefore, to more fully analyze structure-function relationships and the role of DNA binding in the action of m-AMSA, we analyzed a series of derivatives for the ability to enhance DNA cleavage mediated by human topoisomerase IIα and topoisomerase IIβ and to intercalate DNA. Results indicate that the 3’-methoxy (m-AMSA) positively affects drug function, potentially by restricting the rotation of the head group in a favorable orientation. Shifting the methoxy to the 2’-position (o-AMSA), which abrogates drug function, appears to increase rotational freedom of the head group and may impair interactions of the 1’-substituent or other portions of the head group within the ternary complex. Finally, the non-intercalative m-AMSA head group enhanced enzyme-mediated DNA cleavage when it was detached from the acridine moiety, albeit with 100-fold lower affinity. Taken together, our results suggest that much of the activity and specificity of m-AMSA as a topoisomerase II poison is embodied in the head group, while DNA intercalation is used primarily to increase the affinity of m-AMSA for the topoisomerase II-DNA cleavage complex. PMID:22304499

Modulating the electronic and magnetic properties of bilayer borophene via transition metal atoms intercalation: from metal to half metal and semiconductor.

PubMed

Zhang, Xiuyun; Sun, Yi; Ma, Liang; Zhao, Xinli; Yao, Xiaojing

2018-07-27

Borophene, a two-dimensional monolayer made of boron atoms, has attracted wide attention due to its appealing properties. Great efforts have been devoted to fine tuning its electronic and magnetic properties for desired applications. Herein, we theoretically investigate the versatile electronic and magnetic properties of bilayer borophene (BLB) intercalated by 3d transition metal (TM) atoms, TM@BLBs (TM = Ti-Fe), using ab initio calculations. Four allotropes of AA-stacking (α 1 -, β-, β 12 - and χ 3 -) BLBs with different intercalation concentrations of TM atoms are considered. Our results show that the TM atoms are strongly bonded to the borophene layers with fairly large binding energies, around 6.31 ∼ 15.44 eV per TM atom. The BLBs with Cr and Mn intercalation have robust ferromagnetism, while for the systems decorated with Fe atoms, fruitful magnetic properties, such as nonmagnetic, ferromagnetic or antiferromagnetic, are identified. In particular, the α 1 - and β-BLBs intercalated by Mn or Fe atom can be transformed into a semiconductor, half metal or graphene-like semimetal. Moreover, some heavily doped TM@BLBs expose high Curie temperatures above room temperature. The attractive properties of TM@BLBs entail an efficient way to modulate the electronic and magnetic properties of borophene sheets for advanced applications.

Theory of electron transfer and molecular state in DNA

NASA Astrophysics Data System (ADS)

Endres, Robert Gunter

2002-09-01

In this thesis, a mechanism for long-range electron transfer in DNA and a systematic search for high conductance DNA are developed. DNA is well known for containing the genetic code of all living species. On the other hand, there are some experimental indications that DNA can mediate effectively long-range electron transfer leading to the concept of chemistry at a distance. This can be important for DNA damage and healing. In the first part of the thesis, a possible mechanism for long-range electron transfer is introduced. The weak distance dependent electron transfer was experimentally observed using transition metal intercalators for donor and acceptor. In our model calculations, the transfer is mediated by the molecular analogue of a Kondo bound state well known from solid state physics of mixed-valence rare-earth compounds. We believe this is quite realistic, since localized d orbitals of the transition metal ions could function as an Anderson impurity embedded in a reservoir of rather delocalized molecular orbitals of the intercalator ligands and DNA pi orbitals. The effective Anderson model is solved with a physically intuitive variational ansatz as well as with the essentially exact DMRG method. The electronic transition matrix element, which is important because it contains the donor-acceptor distance dependence, is obtained with the Mulliken-Hush algorithm as well as from Born-Oppenheimer potential energy surfaces. Our possible explanation of long-range electron transfer is put in context to other more conventional mechanisms which also could lead to similar behavior. Another important issue of DNA is its possible use for nano-technology. Although DNA's mechanical properties are excellent, the question whether it can be conducting and be used for nano-wires is highly controversial. Experimentally, DNA shows conducting, semi-conducting and insulating properties. Motivated by these wide ranging experimental results on the conductivity of DNA, we have embarked on a theoretical effort to ascertain what conditions might induce such remarkable behavior. We use a combination of an ab initio density functional theory method and a parameterized Huckel-Slater-Koster model. Our focus here is to examine whether any likely DNA structures or environments can yield reduced activation gaps to conduction or enhanced electronic overlaps. In particular, we study a hypothetical stretched ribbon structure, A-, and B-form DNA, and the effects of counterions and humidity. Unlike solids, DNA and other molecules are considered soft condensed matter. Hence, we study the influence of vibrations upon the electronic structure of DNA. We calculate parameters for charge transfer rates between adjacent bases. We find good agreement between our estimated rates and recent experimental data assuming that torsional vibrations limit the charge transfer most significantly.

Studies on the interaction of apigenin with calf thymus DNA by spectroscopic methods

NASA Astrophysics Data System (ADS)

Zhang, Shufang; Sun, Xuejun; Kong, Rongmei; Xu, Mingming

2015-02-01

The interaction between apigenin and calf thymus deoxyribonucleic acid (ctDNA) in a pH 7.4 Tris-HCl buffer solution was investigated by UV-Vis spectroscopy, fluorescence spectroscopy, DNA melting techniques, and viscosity measurements. It was found that apigenin molecules could intercalate into the base pairs of DNA, forming a apigenin-DNA complex with a binding constant of K310K = 6.4 × 104 L mol-1. The thermodynamic parameters enthalpy change (ΔH), entropy change (ΔS) and Gibbs free energy (ΔG) were calculated to be 7.36 × 104 J mol-1, 329 J K-1 mol-1 and -2.84 × 104 J mol-1 at 310 K, respectively. Hydrophobic interaction was the predominant intermolecular force in stabilizing the apigenin-DNA complex. Thermal denaturation study suggested that the stabilization of the ctDNA helix was increased when the apigenin binding to ctDNA as indicated by the increase in thermal denaturation temperature of ctDNA at around 5.0 °C in the presence of apigenin. Spectroscopic techniques together with melting techniques and viscosity determination provided evidences of intercalation mode of binding for the interaction between apigenin and ctDNA.

Structure-function correlation of chloroquine and analogues as transgene expression enhancers in nonviral gene delivery.

PubMed

Cheng, Jianjun; Zeidan, Ryan; Mishra, Swaroop; Liu, Aijie; Pun, Suzie H; Kulkarni, Rajan P; Jensen, Gregory S; Bellocq, Nathalie C; Davis, Mark E

2006-11-02

To understand how chloroquine (CQ) enhances transgene expression in polycation-based, nonviral gene delivery systems, a number of CQ analogues with variations in the aliphatic amino side chain or in the aromatic ring are synthesized and investigated. Our studies indicate that the aliphatic amino moiety of CQ is essential to provide increased gene expression. Further, the enhancements are more dramatically affected by changes to the aromatic ring and are positively correlated to the strength of intercalation between DNA and the CQ analogues. Quinacrine (QC), a CQ analogue with a fused acridinyl structure that can strongly intercalate DNA, enhances transfection similarly to CQ at a concentration 10 times lower, while N(4)-(4-pyridinyl)-N(1),N(1)-diethyl-1,4-pentanediamine (CP), a CQ analogue that has a weakly intercalating pyridinyl ring, shows no effect on gene expression. Subtle change on the 7-substituent of the chloroquine aromatic structure can also greatly affect the ability of the CQ analogues to enhance transgene expression. Transfection in the presence of N(4)-(7-trifluoromethyl-4-quinolinyl)-N(1),N(1)-diethyl-1,4-pentanediamin e (CQ7a) shows expression efficiency 10 times higher than in the presence of CQ at same concentration, while transfection in the presence of N(4)-(4-quinolinyl)-N(1),N(1)-diethyl-1,4-pentanediamine (CQ7b) does not reveal any enhancing effects on expression. Through a number of comparative studies with CQ and its analogues, we conclude that there are at least three mechanistic features of CQ that lead to the enhancement in gene expression: (i) pH buffering in endocytic vesicles, (ii) displacement of polycations from the nucleic acids in polyplexes, and (iii) alteration of the biophysical properties of the released nucleic acid.

Activation of cGAS-dependent antiviral responses by DNA intercalating agents

PubMed Central

Pépin, Geneviève; Nejad, Charlotte; Thomas, Belinda J.; Ferrand, Jonathan; McArthur, Kate; Bardin, Philip G.; Williams, Bryan R.G.; Gantier, Michael P.

2017-01-01

Acridine dyes, including proflavine and acriflavine, were commonly used as antiseptics before the advent of penicillins in the mid-1940s. While their mode of action on pathogens was originally attributed to their DNA intercalating activity, work in the early 1970s suggested involvement of the host immune responses, characterized by induction of interferon (IFN)-like activities through an unknown mechanism. We demonstrate here that sub-toxic concentrations of a mixture of acriflavine and proflavine instigate a cyclic-GMP-AMP (cGAMP) synthase (cGAS)-dependent type-I IFN antiviral response. This pertains to the capacity of these compounds to induce low level DNA damage and cytoplasmic DNA leakage, resulting in cGAS-dependent cGAMP-like activity. Critically, acriflavine:proflavine pre-treatment of human primary bronchial epithelial cells significantly reduced rhinovirus infection. Collectively, our findings constitute the first evidence that non-toxic DNA binding agents have the capacity to act as indirect agonists of cGAS, to exert potent antiviral effects in mammalian cells. PMID:27694309

Improved stability and electrophoretic properties of preformed fluorescent cationic dye-DNA complexes in a taps-tetrapentylammonium buffer in agarose slab gels.

PubMed

Zeng, Z; Clark, S M; Mathies, R A; Glazer, A N

1997-10-01

High-resolution capillary electrophoresis sizing of preformed complexes of bis-intercalating fluorescent dyes with double-stranded DNA has been demonstrated using hydroxyethylcellulose and 3-[tris-(hydroxymethyl) methylamino]-1-propanesulfonic acid-tetrapentylammonium (Taps-NPe+4) buffers (S. M. Clark and R. A. Mathies, Anal. Chem. 69, 1355-1363, 1997). Such capillary electrophoresis separations were unattainable in conventional buffers containing other cations such as Tris+, Na+, and NH+4. We report here the behavior of preformed double-stranded DNA-dye complexes on agarose slab gel electrophoresis in 40 mM Taps-NPe+4, 1 mM H2EDTA, pH 8.2. Upon electrophoresis in this buffer (a) complexes formed at DNA base pairs:dye ratios ranging from 100:1 to 5:1 show the same mobility; (b) the half-lives of DNA-dye complexes with monointercalators are two- to threefold longer than those in commonly used Tris buffers; (c) there is little dye transfer between labeled and unlabeled DNA molecules; and (d) precise two-color sizing of preformed restriction fragment-dye complexes with fluorescent bisintercalators is achieved.

Composite material of DNA and cyclodextrin-immobilized poly(ethyleneimine): Accumulation of harmful compounds from multi-component solution.

PubMed

Yamada, Masanori; Hori, Minako; Tabuchi, Shinya

2010-08-01

Water-soluble beta-cyclodextrin-immobilized poly(ethyleneimine) (PEICD) was synthesized by the grafting of beta-cyclodextrin to the branched poly(ethyleneimine). In an aqueous solution, this PEICD polymer could encapsulate bisphenol A, known to be a harmful compound. Additionally, the stability constant of bisphenol A to the PEICD polymer was 1.1 x 10(4)M(-1). However, the water-solubility of PEICD has been making it difficult to utilize it as an environmental material. Therefore, we prepared the DNA-PEICD composite material by mixing the double-stranded DNA and PEICD. This DNA-PEICD composite material was extremely stable in water and possessed both properties of the intercalation into the double-stranded DNA and the encapsulation into the CD cavity. As a result, this material can accumulate various harmful compounds, such as dioxin- and polychlorobiphenyl (PCB)-derivatives and bisphenol A, from a multi-component solution. Therefore, the DNA-PEICD composite material may have the potential to be used as an environmental material. Copyright 2010 Elsevier B.V. All rights reserved.

Effect of lightning strike on bromine intercalated graphite fiber/epoxy composites

NASA Technical Reports Server (NTRS)

Gaier, James R.; Slabe, Melissa E.; Brink, Norman O.

1991-01-01

Laminar composites were fabricated from pristine and bromine intercalated pitch based graphite fibers. It was found that laminar composites could be fabricated using either pristine or intercalated graphite fibers using standard fabrication techniques. The intercalated graphite fiber composites had electrical properties which were markedly improved over both the corresponding pitch based and polyacrylonitrile (PAN) based composites. Despite composites resistivities more than an order of magnitude lower for pitch based fiber composites, the lightning strike resistance was poorer than that of the Pan based fiber composites. This leads to the conclusion that the mechanical properties of the pitch fibers are more important than electrical or thermal properties in determining the lightning strike resistance. Based on indicated lightning strike tolerance for high elongation to failure materials, the use of vapor grown, rather than pitch based graphite fibers appears promising.

Structure and spectroscopic investigations of a bi-dentate N‧-[(4-ethylphenyl)methylidene]-4-hydroxybenzohydrazide and its Co(II), Ni(II), Cu(II) and Cd(II) complexes: Insights relevant to biological properties

NASA Astrophysics Data System (ADS)

Gopal Reddy, N. B.; Krishna, P. Murali; Shantha Kumar, S. S.; Patil, Yogesh P.; Nethaji, Munirathinam

2017-06-01

The present paper describes the synthesis of novel ligand, N‧-[(4-ethylphenyl)methylidene]-4-hydroxy benzohydrazide (HL) and its Co(II), Ni(II), Cu(II) and Cd(II) complexes. The ligand (HL) crystallizes in orthorhombic lattice in P212121 space group with a = 7.9941 (7) Å, b = 11.6154 (10) Å, c = 15.2278 (13) Å, α = β = γ = 90°. Spectroscopic data gives the strong evidence that ligand is coordinated through azomethine nitrogen and enolic oxygen with metal ion. The DNA binding studies revealed that the complexes bind to CT-DNA via intercalation/electrostatic interaction. All the targeted compounds showed more pronounced DNA cleavage activity in the presence of H2O2 and also inhibit the growth of in vitro antibacterial activity against Gram-positive and Gram-negative bacteria.

π-Stacking between Casiopeinas® and DNA bases.

PubMed

Galindo-Murillo, Rodrigo; Hernandez-Lima, Joseelyne; González-Rendón, Mayra; Cortés-Guzmán, Fernando; Ruíz-Azuara, Lena; Moreno-Esparza, Rafael

2011-08-28

Casiopeínas® are copper complexes with the general formula [Cu(N-N)(N-O)]NO(3) and [Cu(N-N)(O-O)]NO(3) where N-N denotes a substituted bipyridine or phenanthroline, N-O indicates α-aminoacidate or peptide and O-O represents acetylacetonate or salicylaldehyde. This family of compounds has been evaluated in vitro and in vivo showing cytotoxic, genotoxic, and antineoplastic activity. The action mechanism is still not completely elucidated, but the possibility exists that these compounds interact with DNA by intercalation due to the aromatic moiety. In this work we found, using the properties of the electron density of a π-complex model base-Casiopeína®-base, that the stacking mechanism between Casiopeínas® and DNA bases is due to an electron density deficiency of the ligand of the Casiopeína® which is compensated for by an electron transfer from adenines by a π-π interaction.

Alkali metal intercalated fullerene-like MS(2) (M = W, Mo) nanoparticles and their properties.

PubMed

Zak, Alla; Feldman, Yishay; Lyakhovitskaya, Vera; Leitus, Gregory; Popovitz-Biro, Ronit; Wachtel, Ellen; Cohen, Hagai; Reich, Shimon; Tenne, Reshef

2002-05-01

Layered metal disulfides-MS(2) (M = Mo, W) in the form of fullerene-like nanoparticles and in the form of platelets (crystallites of the 2H polytype) have been intercalated by exposure to alkali metal (potassium and sodium) vapor using a two-zone transport method. The composition of the intercalated systems was established using X-ray energy dispersive spectrometer and X-ray photoelectron spectroscopy (XPS). The alkali metal concentration in the host lattice was found to depend on the kind of sample and the experimental conditions. Furthermore, an inhomogeneity of the intercalated samples was observed. The product consisted of both nonintercalated and intercalated phases. X-ray diffraction analysis and transmission electron microscopy of the samples, which were not exposed to the ambient atmosphere, showed that they suffered little change in their lattice parameters. On the other hand, after exposure to ambient atmosphere, substantial increase in the interplanar spacing (3-5 A) was observed for the intercalated phases. Insertion of one to two water molecules per intercalated metal atom was suggested as a possible explanation for this large expansion along the c-axis. Deintercalation of the hydrated alkali atoms and restacking of the MS(2) layers was observed in all the samples after prolonged exposure to the atmosphere. Electric field induced deintercalation of the alkali metal atoms from the host lattice was also observed by means of the XPS technique. Magnetic moment measurements for all the samples indicate a diamagnetic to paramagnetic transition after intercalation. Measurements of the transport properties reveal a semiconductor to metal transition for the heavily K intercalated 2H-MoS(2). Other samples show several orders of magnitude decrease in resistivity and two- to five-fold decrease in activation energies upon intercalation. These modifications are believed to occur via charge transfer from the alkali metal to the conduction band of the host lattice. Recovery of the pristine compound properties (diamagnetism and semiconductivity) was observed as a result of deintercalation.

Superconducting selenides intercalated with organic molecules: synthesis, crystal structure, electric and magnetic properties, superconducting properties, and phase separation in iron based-chalcogenides and hybrid organic-inorganic superconductors

NASA Astrophysics Data System (ADS)

Krzton-Maziopa, Anna; Pesko, Edyta; Puzniak, Roman

2018-06-01

Layered iron-based superconducting chalcogenides intercalated with molecular species are the subject of intensive studies, especially in the field of solid state chemistry and condensed matter physics, because of their intriguing chemistry and tunable electric and magnetic properties. Considerable progress in the research, revealing superconducting inorganic–organic hybrid materials with transition temperatures to superconducting state, T c, up to 46 K, has been brought in recent years. These novel materials are synthesized by low-temperature intercalation of molecular species, such as solvates of alkali metals and nitrogen-containing donor compounds, into layered FeSe-type structure. Both the chemical nature as well as orientation of organic molecules between the layers of inorganic host, play an important role in structural modifications and may be used for fine tuning of superconducting properties. Furthermore, a variety of donor species compatible with alkali metals, as well as the possibility of doping also in the host structure (either on Fe or Se sites), makes this system quite flexible and gives a vast array of new materials with tunable electric and magnetic properties. In this review, the main aspects of intercalation chemistry are discussed with a particular attention paid to the influence of the unique nature of intercalating species on the crystal structure and physical properties of the hybrid inorganic–organic materials. To get a full picture of these materials, a comprehensive description of the most effective chemical and electrochemical methods, utilized for synthesis of intercalated species, with critical evaluation of their strong and weak points, related to feasibility of synthesis, phase purity, crystal size and morphology of final products, is included as well.

Physical nature of ethidium and proflavine interactions with nucleic acid bases in the intercalation plane.

PubMed

Langner, Karol M; Kedzierski, Pawel; Sokalski, W Andrzej; Leszczynski, Jerzy

2006-05-18

On the basis of the crystallographic structures of three nucleic acid intercalation complexes involving ethidium and proflavine, we have analyzed the interaction energies between intercalator chromophores and their four nearest bases, using a hybrid variation-perturbation method at the second-order Møller-Plesset theory level (MP2) with a 6-31G(d,p) basis set. A total MP2 interaction energy minimum precisely reproduces the crystallographic position of the ethidium chromophore in the intercalation plane between UA/AU bases. The electrostatic component constitutes the same fraction of the total energy for all three studied structures. The multipole electrostatic interaction energy, calculated from cumulative atomic multipole moments (CAMMs), was found to converge only after including components above the fifth order. CAMM interaction surfaces, calculated on grids in the intercalation planes of these structures, reasonably reproduce the alignment of intercalators in crystal structures; they exhibit additional minima in the direction of the DNA grooves, however, which also need to be examined at higher theory levels if no crystallographic data are given.

Electrochemical detection of synthetic DNA and native 16S rRNA fragments on a microarray using a biotinylated intercalator as coupling site for an enzyme label.

PubMed

Zimdars, Andreas; Gebala, Magdalena; Hartwich, Gerhard; Neugebauer, Sebastian; Schuhmann, Wolfgang

2015-10-01

The direct electrochemical detection of synthetic DNA and native 16S rRNA fragments isolated from Escherichia coli is described. Oligonucleotides are detected via selective post-labeling of double stranded DNA and DNA-RNA duplexes with a biotinylated intercalator that enables high-specific binding of a streptavidin/alkaline phosphatase conjugate. The alkaline phosphatase catalyzes formation of p-aminophenol that is subsequently oxidized at the underlying gold electrode and hence enables the detection of complementary hybridization of the DNA capture strands due to the enzymatic signal amplification. The hybridization assay was performed on microarrays consisting of 32 individually addressable gold microelectrodes. Synthetic DNA strands with sequences representing six different pathogens which are important for the diagnosis of urinary tract infections could be detected at concentrations of 60 nM. Native 16S rRNA isolated from the different pathogens could be detected at a concentration of 30 fM. Optimization of the sensing surface is described and influences on the assay performance are discussed. Copyright © 2015 Elsevier B.V. All rights reserved.

Transition Metal Intercalators as Anticancer Agents—Recent Advances

PubMed Central

Deo, Krishant M.; Pages, Benjamin J.; Ang, Dale L.; Gordon, Christopher P.; Aldrich-Wright, Janice R.

2016-01-01

The diverse anticancer utility of cisplatin has stimulated significant interest in the development of additional platinum-based therapies, resulting in several analogues receiving clinical approval worldwide. However, due to structural and mechanistic similarities, the effectiveness of platinum-based therapies is countered by severe side-effects, narrow spectrum of activity and the development of resistance. Nonetheless, metal complexes offer unique characteristics and exceptional versatility, with the ability to alter their pharmacology through facile modifications of geometry and coordination number. This has prompted the search for metal-based complexes with distinctly different structural motifs and non-covalent modes of binding with a primary aim of circumventing current clinical limitations. This review discusses recent advances in platinum and other transition metal-based complexes with mechanisms of action involving intercalation. This mode of DNA binding is distinct from cisplatin and its derivatives. The metals focused on in this review include Pt, Ru and Cu along with examples of Au, Ni, Zn and Fe complexes; these complexes are capable of DNA intercalation and are highly biologically active. PMID:27809241

Effect of adsorbed/intercalated anionic dyes into the mechanical properties of PVA: layered zinc hydroxide nitrate nanocomposites.

PubMed

Marangoni, Rafael; Mikowski, Alexandre; Wypych, Fernando

2010-11-15

Zinc hydroxide nitrate (ZHN) was adsorbed with anions of blue dyes (Chicago sky blue, CSB; Evans blue, EB; and Niagara blue, NB) and intercalated with anions of orange dyes (Orange G, OG; Orange II, OII; methyl orange, MO). Transparent, homogeneous and colored nanocomposite films were obtained by casting after dispersing the pigments (dye-intercalated/adsorbed into LHSs) into commercial poly(vinyl alcohol) (PVA). The films were characterized by XRD, UV-Vis spectroscopy, and mechanical testing. The mechanical properties of the PVA compounded with the dye-intercalated/adsorbed ZHN were evaluated, and reasonable increases in Young's modulus and ultimate tensile strength were observed, depending on the amount and choice of layered filler. These results demonstrate the possibility of using a new class of layered hydroxide salts intercalated and adsorbed with anionic dyes to prepare multifunctional polymer nanocomposite materials. Copyright © 2010 Elsevier Inc. All rights reserved.

Fish DNA-modified clays: Towards highly flame retardant polymer nanocomposite with improved interfacial and mechanical performance.

PubMed

Zabihi, Omid; Ahmadi, Mojtaba; Khayyam, Hamid; Naebe, Minoo

2016-12-05

Deoxyribonucleic Acid (DNA) has been recently found to be an efficient renewable and environmentally-friendly flame retardant. In this work, for the first time, we have used waste DNA from fishing industry to modify clay structure in order to increase the clay interactions with epoxy resin and take benefit of its additional thermal property effect on thermo-physical properties of epoxy-clay nanocomposites. Intercalation of DNA within the clay layers was accomplished in a one-step approach confirmed by FT-IR, XPS, TGA, and XRD analyses, indicating that d-space of clay layers was expanded from ~1.2 nm for pristine clay to ~1.9 nm for clay modified with DNA (d-clay). Compared to epoxy nanocomposite containing 2.5%wt of Nanomer I.28E organoclay (m-clay), it was found that at 2.5%wt d-clay loading, significant enhancements of ~14%, ~6% and ~26% in tensile strength, tensile modulus, and fracture toughness of epoxy nanocomposite can be achieved, respectively. Effect of DNA as clay modifier on thermal performance of epoxy nanocomposite containing 2.5%wt d-clay was evaluated using TGA and cone calorimetry analysis, revealing significant decreases of ~4000 kJ/m 2 and ~78 kW/m 2 in total heat release and peak of heat release rate, respectively, in comparison to that containing 2.5%wt of m-clay.

Fish DNA-modified clays: Towards highly flame retardant polymer nanocomposite with improved interfacial and mechanical performance

NASA Astrophysics Data System (ADS)

Zabihi, Omid; Ahmadi, Mojtaba; Khayyam, Hamid; Naebe, Minoo

2016-12-01

Deoxyribonucleic Acid (DNA) has been recently found to be an efficient renewable and environmentally-friendly flame retardant. In this work, for the first time, we have used waste DNA from fishing industry to modify clay structure in order to increase the clay interactions with epoxy resin and take benefit of its additional thermal property effect on thermo-physical properties of epoxy-clay nanocomposites. Intercalation of DNA within the clay layers was accomplished in a one-step approach confirmed by FT-IR, XPS, TGA, and XRD analyses, indicating that d-space of clay layers was expanded from ~1.2 nm for pristine clay to ~1.9 nm for clay modified with DNA (d-clay). Compared to epoxy nanocomposite containing 2.5%wt of Nanomer I.28E organoclay (m-clay), it was found that at 2.5%wt d-clay loading, significant enhancements of ~14%, ~6% and ~26% in tensile strength, tensile modulus, and fracture toughness of epoxy nanocomposite can be achieved, respectively. Effect of DNA as clay modifier on thermal performance of epoxy nanocomposite containing 2.5%wt d-clay was evaluated using TGA and cone calorimetry analysis, revealing significant decreases of ~4000 kJ/m2 and ~78 kW/m2 in total heat release and peak of heat release rate, respectively, in comparison to that containing 2.5%wt of m-clay.

Fish DNA-modified clays: Towards highly flame retardant polymer nanocomposite with improved interfacial and mechanical performance

PubMed Central

Zabihi, Omid; Ahmadi, Mojtaba; Khayyam, Hamid; Naebe, Minoo

2016-01-01

Deoxyribonucleic Acid (DNA) has been recently found to be an efficient renewable and environmentally-friendly flame retardant. In this work, for the first time, we have used waste DNA from fishing industry to modify clay structure in order to increase the clay interactions with epoxy resin and take benefit of its additional thermal property effect on thermo-physical properties of epoxy-clay nanocomposites. Intercalation of DNA within the clay layers was accomplished in a one-step approach confirmed by FT-IR, XPS, TGA, and XRD analyses, indicating that d-space of clay layers was expanded from ~1.2 nm for pristine clay to ~1.9 nm for clay modified with DNA (d-clay). Compared to epoxy nanocomposite containing 2.5%wt of Nanomer I.28E organoclay (m-clay), it was found that at 2.5%wt d-clay loading, significant enhancements of ~14%, ~6% and ~26% in tensile strength, tensile modulus, and fracture toughness of epoxy nanocomposite can be achieved, respectively. Effect of DNA as clay modifier on thermal performance of epoxy nanocomposite containing 2.5%wt d-clay was evaluated using TGA and cone calorimetry analysis, revealing significant decreases of ~4000 kJ/m2 and ~78 kW/m2 in total heat release and peak of heat release rate, respectively, in comparison to that containing 2.5%wt of m-clay. PMID:27917901

Preparation and enhanced properties of polyaniline/grafted intercalated ZnAl-LDH nanocomposites

NASA Astrophysics Data System (ADS)

Hu, Jinlong; Gan, Mengyu; Ma, Li; Zhang, Jun; Xie, Shuang; Xu, Fenfang; Shen, JiYue Zheng Xiaoyu; Yin, Hui

2015-02-01

The polymeric nanocomposites (PANI/AD-LDH) were prepared by in situ polymerization based on polyaniline (PANI) and decavanadate-intercalated and γ-aminopropyltriethoxysilane (APTS)-grafted ZnAl-layered double hydroxide (AD-LDH). FTIR and XRD studies confirm the grafting of APTS with decavanadate-intercalated LDH (D-LDH). The extent of grafting (wt%) has also been estimated on the basis of the residue left in nitrogen atmosphere at 800 °C in TGA. SEM and XPS studies show the partial exfoliation of grafted LDH in the PANI matrix and the interfacial interaction between PANI and grafted LDH, respectively. The grafted intercalated layered double hydroxide in reinforcing the properties of the PANI nanocomposites has also been investigated by open circuit potential (OCP), tafel polarization curves (TAF), electrochemical impendence spectroscopy (EIS), salt spray test and TGA-DTA. The experimental results indicate that the PANI/AD-LDH has a higher thermal stability and anticorrosion properties relative to the PANI.

A review on acridinylthioureas and its derivatives: biological and cytotoxic activity.

PubMed

Kožurková, Mária; Sabolová, Danica; Kristian, Pavol

2017-10-01

Acridines possess two characteristics that have led many researchers to consider the agents interesting targets for future development as potential farmacophores: the planar acridine skeleton, which is able to intercalate into DNA, and the intense fluorescence of the agents. This review offers a study of the multifunctional character of acridines and the synthesis of novel acridine derivatives, with particular focus being placed on isothiocyanates and their congeners, e.g. thioureas, isothioureas, quaternary ammonium salts and platinum/gold conjugates. The review provides an overview of the structure, spectral properties, DNA binding and biological activity of acridinylthiourea congeners. These acridinylthiourea derivatives display significant cytotoxic activities against different types of cancer cell lines at micromolar concentrations. Copyright © 2017 John Wiley & Sons, Ltd. Copyright © 2017 John Wiley & Sons, Ltd.

The fluorescence resonance energy transfer (FRET) gate: a time-resolved study.

PubMed

Xu, Qing-Hua; Wang, Shu; Korystov, Dmitry; Mikhailovsky, Alexander; Bazan, Guillermo C; Moses, Daniel; Heeger, Alan J

2005-01-18

The two-step energy-transfer process in a self-assembled complex comprising a cationic conjugated polymer (CCP) and a dsDNA is investigated by using pump-dump-emission spectroscopy and time-correlated single-photon counting; energy is transferred from the CCP to an ethidium bromide (EB) molecule intercalated into the dsDNA through a fluorescein molecule linked to one terminus of the DNA. Time-dependent anisotropy measurements indicate that the inefficient direct energy transfer from the CCP to the intercalated EB results from the near orthogonality of their transition moments. These measurements also show that the transition moment of the fluorescein spans a range of angular distributions and lies between that of the CCP and EB. Consequently, the fluorescein acts as a fluorescence resonance energy-transfer gate to relay the excitation energy from the CCP to the EB.

The fluorescence resonance energy transfer (FRET) gate: A time-resolved study

PubMed Central

Xu, Qing-Hua; Wang, Shu; Korystov, Dmitry; Mikhailovsky, Alexander; Bazan, Guillermo C.; Moses, Daniel; Heeger, Alan J.

2005-01-01

The two-step energy-transfer process in a self-assembled complex comprising a cationic conjugated polymer (CCP) and a dsDNA is investigated by using pump-dump-emission spectroscopy and time-correlated single-photon counting; energy is transferred from the CCP to an ethidium bromide (EB) molecule intercalated into the dsDNA through a fluorescein molecule linked to one terminus of the DNA. Time-dependent anisotropy measurements indicate that the inefficient direct energy transfer from the CCP to the intercalated EB results from the near orthogonality of their transition moments. These measurements also show that the transition moment of the fluorescein spans a range of angular distributions and lies between that of the CCP and EB. Consequently, the fluorescein acts as a fluorescence resonance energy-transfer gate to relay the excitation energy from the CCP to the EB. PMID:15642946

Stable loop in the crystal structure of the intercalated four-stranded cytosine-rich metazoan telomere

NASA Technical Reports Server (NTRS)

Kang, C.; Berger, I.; Lockshin, C.; Ratliff, R.; Moyzis, R.; Rich, A.

1995-01-01

In most metazoans, the telomeric cytosine-rich strand repeating sequence is d(TAACCC). The crystal structure of this sequence was solved to 1.9-A resolution. Four strands associate via the cytosine-containing parts to form a four-stranded intercalated structure held together by C.C+ hydrogen bonds. The base-paired strands are parallel to each other, and the two duplexes are intercalated into each other in opposite orientations. One TAA end forms a highly stabilized loop with the 5' thymine Hoogsteen-base-paired to the third adenine. The 5' end of this loop is in close proximity to the 3' end of one of the other intercalated cytosine strands. Instead of being entirely in a DNA duplex, this structure suggests the possibility of an alternative conformation for the cytosine-rich telomere strands.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Tripathi, S.; Zhang, D.; Paukstelis, P. J.

DNA has proved to be an excellent material for nanoscale construction because complementary DNA duplexes are programmable and structurally predictable. However, in the absence of Watson–Crick pairings, DNA can be structurally more diverse. Here, we describe the crystal structures of d(ACTCGGATGAT) and the brominated derivative, d(AC BrUCGGA BrUGAT). These oligonucleotides form parallel-stranded duplexes with a crystallographically equivalent strand, resulting in the first examples of DNA crystal structures that contains four different symmetric homo base pairs. Two of the parallel-stranded duplexes are coaxially stacked in opposite directions and locked together to form a tetraplex through intercalation of the 5'-most A–A basemore » pairs between adjacent G–G pairs in the partner duplex. The intercalation region is a new type of DNA tertiary structural motif with similarities to the i-motif. 1H– 1H nuclear magnetic resonance and native gel electrophoresis confirmed the formation of a parallel-stranded duplex in solution. Finally, we modified specific nucleotide positions and added d(GAY) motifs to oligonucleotides and were readily able to obtain similar crystals. This suggests that this parallel-stranded DNA structure may be useful in the rational design of DNA crystals and nanostructures.« less

DNA Polyplexes as Combinatory Drug Carriers of Doxorubicin and Cisplatin: An In Vitro Study

PubMed Central

Kang, Han Chang; Cho, Hana; Bae, You Han

2015-01-01

Double helix nucleic acids were used as a combination drug carrier for doxorubicin (DOX), which physically intercalates with DNA double helices, and cisplatin (CDDP), which binds to DNA without an alkylation reaction. DNA interacting with DOX, CDDP, or both was complexed with positively charged, endosomolytic polymers. Compared with the free drug, the polyplexes (100 ~ 170 nm in size) delivered more drug into the cytosol and the nucleus and demonstrated similar or superior (up to a 7-fold increase) in vitro cell-killing activity. Additionally, the gene expression activities of most of the chemical drug-loaded plasmid DNA (pDNA) polyplexes were not impaired by the physical interactions between the nucleic acid and DOX/CDDP. When a model reporter pDNA (luciferase) was employed, it expressed luciferase protein at 0.7- ~ 1.4-fold the amount expressed by the polyplex with no bound drugs (a control), which indicated the fast translocation of the intercalated or bound drugs from the “carrier DNA” to the “nuclear DNA” of target cells. The proposed concept may offer the possibility of versatile combination therapies of genetic materials and small molecule drugs that bind to nucleic acids to treat various diseases. PMID:26132975

Alkali metal intercalates of molybdenum disulfide.

NASA Technical Reports Server (NTRS)

Somoano, R. B.; Hadek, V.; Rembaum, A.

1973-01-01

Study of some of the physicochemical properties of compounds obtained by subjecting natural molybdenite and single crystals of molybdenum disulfide grown by chemical vapor transport to intercalation with the alkali group of metals (Li, Na, K, Rb, and Cs) by means of the liquid ammonia technique. Reported data and results include: (1) the intercalation of the entire alkali metal group, (2) stoichiometries and X-ray data on all of the compounds, and (3) superconductivity data for all the intercalation compounds.

Investigation of the complex structure, comparative DNA-binding and DNA cleavage of two water-soluble mono-nuclear lanthanum(III) complexes and cytotoxic activity of chitosan-coated magnetic nanoparticles as drug delivery for the complexes

NASA Astrophysics Data System (ADS)

Asadi, Zahra; Nasrollahi, Neda; Karbalaei-Heidari, Hamidreza; Eigner, Vaclav; Dusek, Michal; Mobaraki, Nabiallah; Pournejati, Roya

2017-05-01

Two water-soluble mono-nuclear macrocyclic lanthanum(III) complexes of 2,6-diformyl-4-methylphenol with 1,3-diamino-2-propanol (C1) or 1,3-propylenediamine (C2) were synthesized and characterized by UV-Vis, FT-IR, 13C and 1H NMR spectroscopy and elemental analysis. C1 complex was structurally characterized by single-crystal X-ray diffraction, which revealed that the complex was mononuclear and ten-coordinated. The coordination sites around lanthanum(III) were occupied with a five-dentate ligand, two bidentate nitrates, and one water molecule. The interaction of complexes with DNA was studied in buffered aqueous solution at pH 7.4. UV-Vis absorption spectroscopy, emission spectroscopy, circular dichroism (CD) and viscometric measurements provided clear evidence of the intercalation mechanism of binding. The obtained intrinsic binding constants (Kb) 9.3 × 103 and 1.2 × 103 M- 1 for C1 and C2, respectively confirmed that C1 is better intercalator than C2. The DNA docking studies suggested that the complexes bind with DNA in a groove binding mode with the binding affinity of C1 > C2. Moreover, agarose gel electrophoresis study of the DNA-complex for both compounds revealed that the C1 intercalation cause ethidium bromide replacement in a competitive manner which confirms the suggested mechanism of binding. Finally, the anticancer experiments for the treated cancerous cell lines with both synthesized compounds show that these hydrophilic molecules need a suitable carrier to pass through the hydrophobic nature of cell membrane efficiently.

Spectroscopic and thermodynamic insights into the interaction between proflavine and human telomeric G-quadruplex DNA.

PubMed

Kumar, Vivek; Sengupta, Abhigyan; Gavvala, Krishna; Koninti, Raj Kumar; Hazra, Partha

2014-09-25

The G-quadruplex (GQ-DNA), an alternative structure motif of DNA, has emerged as a novel and exciting target for anticancer drug discovery. GQ-DNA formed in the presence of monovalent cations (Na(+)/K(+)) by human telomeric DNA is a point of interest due to their direct relevance for cellular aging and abnormal cell growths. Small molecules that selectively target and stabilize G-quadruplex structures are considered to be potential therapeutic anticancer agents. Herein, we probe G-quadruplex and proflavine (a well-known DNA intercalator, hence acting as an anticarcinogen) association through steady state and time-resolved fluorescence spectroscopy to explore the effect of stabilization of GQ-DNA by this well-known DNA intercalator. The structural modifications of G-quadruplex upon binding are highlighted through circular dichroism (CD) spectra. Moreover, a detailed insight into the thermodynamics of this interaction has been provided though isothermal titration calorimetry (ITC) studies. The thermodynamic parameters obtained from ITC help to gain knowledge about the nature as well as the driving forces of binding. This present study shows that proflavine (PF) can act as a stabilizer of telomeric GQ-DNA through an entropically as well as enthalpically feasible process with high binding affinity and thereby can be considered as a potential telomerase inhibitor.

Layered zinc hydroxide nanocones: synthesis, facile morphological and structural modification, and properties

NASA Astrophysics Data System (ADS)

Ma, Wei; Ma, Renzhi; Liang, Jianbo; Wang, Chengxiang; Liu, Xiaohe; Zhou, Kechao; Sasaki, Takayoshi

2014-10-01

Layered zinc hydroxide nanocones intercalated with DS- have been synthesized for the first time via a convenient synthetic approach, using homogeneous precipitation in the presence of urea and sodium dodecyl sulfate (SDS). SDS plays a significant role in controlling the morphologies of as-synthesized samples. Conical samples intercalated with various anions were transformed through an anion-exchange route in ethanol solution, and the original conical structure was perfectly maintained. Additionally, these DS--inserted nanocones can be transformed into square-like nanoplates in aqueous solution at room temperature, fulfilling the need for different morphology-dependent properties. Corresponding ZnO nanocones and nanoplates have been further obtained through the thermal calcination of NO3--intercalating zinc hydroxide nanocones/nanoplates. These ZnO nanostructures with different morphologies exhibit promising photocatalytic properties.Layered zinc hydroxide nanocones intercalated with DS- have been synthesized for the first time via a convenient synthetic approach, using homogeneous precipitation in the presence of urea and sodium dodecyl sulfate (SDS). SDS plays a significant role in controlling the morphologies of as-synthesized samples. Conical samples intercalated with various anions were transformed through an anion-exchange route in ethanol solution, and the original conical structure was perfectly maintained. Additionally, these DS--inserted nanocones can be transformed into square-like nanoplates in aqueous solution at room temperature, fulfilling the need for different morphology-dependent properties. Corresponding ZnO nanocones and nanoplates have been further obtained through the thermal calcination of NO3--intercalating zinc hydroxide nanocones/nanoplates. These ZnO nanostructures with different morphologies exhibit promising photocatalytic properties. Electronic supplementary information (ESI) available: Typical SEM images, TGA curves and XRD patterns of as-prepared samples. See DOI: 10.1039/c4nr04166f

Solution structure of a DNA complex with the fluorescent bis-intercalator TOTO determined by NMR spectroscopy.

PubMed

Spielmann, H P; Wemmer, D E; Jacobsen, J P

1995-07-11

We have used two-dimensional 1H NMR spectroscopy to determine the solution structure of the DNA oligonucleotide d(5'-CGCTAGCG-3')2 complexed with the bis-intercalating dye 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)bis[4-(3-methyl -2,3- dihydrobenzo-1,3-thiazolyl-2-methylidene)qui nolinium] tetraiodide (TOTO). The determination of the structure was based on total relaxation matrix analysis of the NOESY cross-peak intensities using the program MARDIGRAS. Improved procedures to consider the experimental "noise" in NOESY spectra during these calculations have been employed. The NOE-derived distance restraints were applied in restrained molecular dynamics calculations. Twenty final structures each were generated for the TOTO complex from both A-form and B-form dsDNA starting structures. The root-mean-square (rms) deviation of the coordinates for the 40 structures of the complex was 1.45 A. The local DNA structure is distorted in the complex. The helix is unwound by 60 degrees and has an overall helical repeat of 12 base pairs, caused by bis-intercalation of TOTO. The poly(propylenamine) linker chain is located in the minor groove of dsDNA. Calculations indicate that the benzothiazole ring system is twisted relative to the quinoline in the uncomplexed TOTO molecule. The site selectivity of TOTO for the CTAG-CTAG site is explained by its ability to adapt to the base pair propeller twist of dsDNA to optimize stacking and the hydrophobic interaction between the thymidine methyl group and the benzothiazole ring. There is a 3000-fold fluorescence enhancement upon binding of TOTO to dsDNA. Rotation about the cyanine methine bonds is possible in free TOTO, allowing relaxation nonradiatively. When bound to dsDNA, the benzothiazole ring and the quinolinium ring are clamped by the nucleobases preventing this rotation, and the chromophore loses excitation energy by fluorescence instead.

Hybrid anticancer 1,2-diazine derivatives with multiple mechanism of action. Part 3.

PubMed

Antoci, Vasilichia; Mantu, Dorina; Cozma, Danut Gabriel; Usru, Cornelia; Mangalagiu, Ionel I

2014-01-01

Antitumour chemotherapy is nowadays a very active field of research, DNA targeting drugs being the most widely used group in therapy. The design, synthesis and anticancer activity of a new class of anticancer derivatives with pyrrolo-1,2-diazine and benzoquinone skeleton is presented. The synthesis is direct and efficient, involving an alkylation followed by a [3+2] dipolar cycloaddition. The penta- and tetra-cyclic pyrrolo-1,2-diazine were evaluated for their in vitro anticancer activity against an NCI 60 human tumour cell line panel. The pentacyclic-1,2-diazine exhibit a significant anticancer activity against Non-Small Cell Lung Cancer NCI-H460, Leukemia MOLT-4, Leukemia CCRF-CEM and Breast Cancer MCF7. We hypothesize that these molecules will exert their anticancer activity through multiple mechanisms of action: intercalating the DNA, inhibiting the topoisomerase enzymes and, destroying the DNA strands via electron transfer mechanism. However, the intercalation with the DNA seems to prevail in competition with the others mechanisms. Copyright © 2013 Elsevier Ltd. All rights reserved.

Activation of cGAS-dependent antiviral responses by DNA intercalating agents.

PubMed

Pépin, Geneviève; Nejad, Charlotte; Thomas, Belinda J; Ferrand, Jonathan; McArthur, Kate; Bardin, Philip G; Williams, Bryan R G; Gantier, Michael P

2017-01-09

Acridine dyes, including proflavine and acriflavine, were commonly used as antiseptics before the advent of penicillins in the mid-1940s. While their mode of action on pathogens was originally attributed to their DNA intercalating activity, work in the early 1970s suggested involvement of the host immune responses, characterized by induction of interferon (IFN)-like activities through an unknown mechanism. We demonstrate here that sub-toxic concentrations of a mixture of acriflavine and proflavine instigate a cyclic-GMP-AMP (cGAMP) synthase (cGAS)-dependent type-I IFN antiviral response. This pertains to the capacity of these compounds to induce low level DNA damage and cytoplasmic DNA leakage, resulting in cGAS-dependent cGAMP-like activity. Critically, acriflavine:proflavine pre-treatment of human primary bronchial epithelial cells significantly reduced rhinovirus infection. Collectively, our findings constitute the first evidence that non-toxic DNA binding agents have the capacity to act as indirect agonists of cGAS, to exert potent antiviral effects in mammalian cells. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Electrochemical and spectroscopic studies of the interaction of proflavine with DNA.

PubMed

Aslanoglu, Mehmet

2006-03-01

The interaction of proflavine with herring sperm DNA has been investigated by cyclic voltammetry and UV-Vis spectroscopy as well as viscosity measurements. Shifts in the peak potentials in cyclic voltammetry, spectral changes in UV absorption titration, an increase in viscosity of DNA and the results of the effect of ionic strength on the binding constant strongly support the intercalation of proflavine into the DNA double helix. The binding constant for the interaction between proflavine and DNA was K = 2.32 (+/- 0.41) x 10(4) M(-1) and the binding site size was 2.07 (+/- 0.1) base pairs, estimated in voltammetric measurements. The value of the binding site size was determined to be closer to that expected for a planar intercalating agent. The standard Gibbs free-energy change is ca. -24.90 kJ/mol at 25 degrees C, indicating the spontaneity of the binding interaction. The binding constant determined by UV absorption measurements was K = 2.20 (+/- 0.48) x 10(4) M(-1), which is very close to the value determined by cyclic voltammetry assuming that the binding equilibrium is static.

Photoconductivity in DNA-Porphyrin Complexes

NASA Astrophysics Data System (ADS)

Myint, Peco; Oxford, Emma; Nyazenga, Collence; Smith, Walter; Qi, Zhengqing; Johnson, A. T.

2015-03-01

We have measured the photoconductivity of λ - DNA that is modified by intercalating a porphyrin compound, meso-tetrakis(N-methyl-4-pyridiniumyl)porphyrin (TMPyP), into its base stacks. Intercalation was verified by a red shift and hypochromism of the Soret absorption peak. The DNA/porphyrin strands were then deposited onto oxidized silicon substrates which had been patterned with interdigitated electrodes, and blown dry. Electrical measurements were carried out under nitrogen, using illumination from a 445 nm laser; this wavelength falls within the absorption peak of the DNA/porphyrin complexes. When initially measured under dry nitrogen, the complexes show no photoconductivity or dark conductivity. However, at relative humidities of 30% and above, we do observe dark conductivity, and also photoconductivity that grows with time. Photoconductivity gets larger at higher relative humidity. Remarkably, when the humidity is lowered again, some photoconductivity is now observed, indicating a change that persists for more than 24 hours. It may be that the humidity alters the structure of the DNA, perhaps allowing for better alignment of the bases. This work was supported by NSF Grant BMAT-1306170.

Development of New Elastomers and Elastic Nanocomposites from Plant Oils

NASA Astrophysics Data System (ADS)

Zhu, Lin; Wool, Richard

2006-03-01

Economic and environmental concerns lead to the development of new polymers from renewable resources. In this research, new elastomers were synthesized from plant oil based resins. Acrylated oleic methyl ester (AOME), synthesized from high oleic triglycerides, can readily undergo free radical polymerization and form a linear polymer. To achieve the elastic properties, different strategies have been developed to generate an elastic network and control the crosslink density. The elastomers are reinforced by nanoclays. The intercalated state has a network structure similar to thermoplastic elastomers in which the hard segments aggregate to give ordered crystalline domains. The selected organically modified clay and AOME matrix have similar solubility parameters, therefore intercalation of the monomer/polymer into the clay layers occurs and the nano-scale multilayered structure is stable. In situ intercalation and solution intercalation were used to prepare the elastic nanocomposites. Dramatic improvement in mechanical properties was observed. Changes of tensile strength, strain, Young's modulus and fracture energy were related to the clay concentration. The fracture surface was studied to further understand clay effects on the mechanical properties. Self-Healing of the intercalated nanobeams, thermal stability, biocompatibility and biodegradability of this new elastomer were also explored.

Spectroscopic studies of STZ-induced methylated-DNA in both in vivo and in vitro conditions

NASA Astrophysics Data System (ADS)

Bathaie, S. Z.; Sedghgoo, F.; Jafarnejad, A.; Farzami, B.; Khayatian, M.

2008-12-01

Alkylating agents after formation of DNA adduct not only posses their harmful role on living cells but also can transfer this information to the next generation. Different techniques have been introduced to study the alkylated DNA, most of which are specific and designed for investigation of specific target DNA. But the exact differences between spectroscopic and functional properties of alkylated DNA are not seen in the literature. In the present study DNA was methylated using streptozotocin (STZ) by both in vitro and in vivo protocols, then methylated-DNA was investigated by various techniques. Our results show that (1) the binding of ethidium bromide as an intercalating dye decreases to methylated-DNA in comparison with normal DNA, (2) CD spectra of methylated-DNA show changes including a decrease in the positive band at 275 nm and a shift from 258 nm crossover to a longer wavelength, which is caused by reduction of water around it, due to the presence of additional hydrophobic methyl groups, (3) the stability of methylated-DNA against DTAB as a denaturant is decreased and (4) the enzyme-like activity of methylated-DNA in an electron transfer reaction is reduced. In conclusion, additional methyl groups not only protrude water around DNA, but also cause the loss of hydrogen bonding, loosening of conformation, preventing desired interactions and thus normal function of DNA.

DNA origami as an in vivo drug delivery vehicle for cancer therapy.

PubMed

Zhang, Qian; Jiang, Qiao; Li, Na; Dai, Luru; Liu, Qing; Song, Linlin; Wang, Jinye; Li, Yaqian; Tian, Jie; Ding, Baoquan; Du, Yang

2014-07-22

Many chemotherapeutics used for cancer treatments encounter issues during delivery to tumors in vivo and may have high levels of systemic toxicity due to their nonspecific distribution. Various materials have been explored to fabricate nanoparticles as drug carriers to improve delivery efficiency. However, most of these materials suffer from multiple drawbacks, such as limited biocompatibility and inability to engineer spatially addressable surfaces that can be utilized for multifunctional activity. Here, we demonstrate that DNA origami possessed enhanced tumor passive targeting and long-lasting properties at the tumor region. Particularly, the triangle-shaped DNA origami exhibits optimal tumor passive targeting accumulation. The delivery of the known anticancer drug doxorubicin into tumors by self-assembled DNA origami nanostructures was performed, and this approach showed prominent therapeutic efficacy in vivo. The DNA origami carriers were prepared through the self-assembly of M13mp18 phage DNA and hundreds of complementary DNA helper strands; the doxorubicin was subsequently noncovalently intercalated into these nanostructures. After conducting fluorescence imaging and safety evaluation, the doxorubicin-containing DNA origami exhibited remarkable antitumor efficacy without observable systemic toxicity in nude mice bearing orthotopic breast tumors labeled with green fluorescent protein. Our results demonstrated the potential of DNA origami nanostructures as innovative platforms for the efficient and safe drug delivery of cancer therapeutics in vivo.

An electrochemical sensor based on polyaniline for monitoring hydroquinone and its damage on DNA.

PubMed

Tang, Wenwei; Zhang, Min; Li, Weihao; Zeng, Xinping

2014-09-01

A dsDNA/PANI/CTS/GCE biosensor was constructed by using the biocompatible chitosan (CTS) and the polyaniline (PANI) with excellent electric catalytic properties and large specific surface areas. The electrochemical behavior of hydroquinone on biosensor and its DNA-damaging mechanisms were investigated. Results showed that the redox peak current was remarkably increased after glassy carbon electrode (GCE) was modified by PANI/CTS. The dsDNA damage by hydroquinone was concentration dependent, and increased along with the increase of hydroquinone oxidation peak current and the reduction of dsDNA guanine oxidation peak current. The linear detection range of hydroquinone with dsDNA/PANI/CTS/GCE was 1.25×10(-6)-3.2×10(-4) M, and the detection limit was 9.65×10(-7) M. It was confirmed by the UV method that applying dsDNA/PANI/CTS/GCE to monitor hydroquinone was accurate and reliable. In addition, it could be deduced that the mode of interaction between the hydroquinone and dsDNA was intercalation. The electrochemical oxidation of hydroquinone on the dsDNA/PANI/CTS/GCE electrode was an adsorption-controlled irreversible and a two-electron two-proton transfer process. Copyright © 2014 Elsevier B.V. All rights reserved.

Evaluation of new iodinated acridine derivatives for targeted radionuclide therapy of melanoma using 125I, an Auger electron emitter.

PubMed

Gardette, Maryline; Papon, Janine; Bonnet, Mathilde; Desbois, Nicolas; Labarre, Pierre; Wu, Ting-Dee; Miot-Noirault, Elisabeth; Madelmont, Jean-Claude; Guerquin-Kern, Jean-Luc; Chezal, Jean-Michel; Moins, Nicole

2011-12-01

The increasing incidence of melanoma and the lack of effective therapy on the disseminated form have led to an urgent need for new specific therapies. Several iodobenzamides or analogs are known to possess specific affinity for melanoma tissue. New heteroaromatic derivatives have been designed with a cytotoxic moiety and termed DNA intercalating agents. These compounds could be applied in targeted radionuclide therapy using (125)I, which emits Auger electrons and gives high-energy, localized irradiation. Two iodinated acridine derivatives have been reported to present an in vivo kinetic profile conducive to application in targeted radionuclide therapy. The aim of the present study was to perform a preclinical evaluation of these compounds. The DNA intercalating property was confirmed for both compounds. After radiolabeling with (125)I, the two compounds induced in vitro a significant radiotoxicity to B16F0 melanoma cells. Nevertheless, the acridine compound appeared more radiotoxic than the acridone compound. While cellular uptake was similar for both compounds, SIMS analysis and in vitro protocol showed a stronger affinity for melanin with acridone derivative, which was able to induce a predominant scavenging process in the melanosome and restrict access to the nucleus. In conclusion, the acridine derivative with a higher nuclear localization appeared a better candidate for application in targeted radionuclide therapy using (125)I.

Drug-DNA interactions at single molecule level: A view with optical tweezers

NASA Astrophysics Data System (ADS)

Paramanathan, Thayaparan

Studies of small molecule--DNA interactions are essential for developing new drugs for challenging diseases like cancer and HIV. The main idea behind developing these molecules is to target and inhibit the reproduction of the tumor cells and infected cells. We mechanically manipulate single DNA molecule using optical tweezers to investigate two molecules that have complex and multiple binding modes. Mononuclear ruthenium complexes have been extensively studied as a test for rational drug design. Potential drug candidates should have high affinity to DNA and slow dissociation kinetics. To achieve this, motifs of the ruthenium complexes are altered. Our collaborators designed a dumb-bell shaped binuclear ruthenium complex that can only intercalate DNA by threading through its bases. Studying the binding properties of this complex in bulk studies took hours. By mechanically manipulating a single DNA molecule held with optical tweezers, we lower the barrier to thread and make it fast compared to the bulk experiments. Stretching single DNA molecules with different concentration of drug molecules and holding it at a constant force allows the binding to reach equilibrium. By this we can obtain the equilibrium fractional ligand binding and length of DNA at saturated binding. Fitting these results yields quantitative measurements of the binding thermodynamics and kinetics of this complex process. The second complex discussed in this study is Actinomycin D (ActD), a well studied anti-cancer agent that is used as a prototype for developing new generations of drugs. However, the biophysical basis of its activity is still unclear. Because ActD is known to intercalate double stranded DNA (dsDNA), it was assumed to block replication by stabilizing dsDNA in front of the replication fork. However, recent studies have shown that ActD binds with even higher affinity to imperfect duplexes and some sequences of single stranded DNA (ssDNA). We directly measure the on and off rates by stretching the DNA molecule to a certain force and holding it at constant force while adding the drug and then while washing off the drug. Our finding resolves the long lasting controversy of ActD binding modes, clearly showing that both the dsDNA binding and ssDNA binding converge to the same single mode. The result supports the hypothesis that the primary characteristic of ActD that contributes to its biological activity is its ability to inhibit cellular replication by binding to transcription bubbles and causing cell death.

Effect of a Dual Charge on the DNA-Conjugated Redox Probe on DNA Sensing by Short Hairpin Beacons Tethered to Gold Electrodes.

PubMed

Kékedy-Nagy, László; Shipovskov, Stepan; Ferapontova, Elena E

2016-08-16

Charges of redox species can critically affect both the interfacial state of DNA and electrochemistry of DNA-conjugated redox labels and, as a result, the electroanalytical performance of those systems. Here, we show that the kinetics of electron transfer (ET) between the gold electrode and methylene blue (MB) label conjugated to a double-stranded (ds) DNA tethered to gold strongly depend on the charge of the MB molecule, and that affects the performance of genosensors exploiting MB-labeled hairpin DNA beacons. Positively charged MB binds to dsDNA via electrostatic and intercalative/groove binding, and this binding allows the DNA-mediated electrochemistry of MB intercalated into the duplex and, as a result, a complex mode of the electrochemical signal change upon hairpin hybridization to the target DNA, dominated by the "on-off" signal change mode at nanomolar levels of the analyzed DNA. When MB bears an additional carboxylic group, the negative charge provided by this group prevents intimate interactions between MB and DNA, and then the ET in duplexes is limited by the diffusion of the MB-conjugated dsDNA (the phenomenon first shown in Farjami , E. ; Clima , L. ; Gothelf , K. ; Ferapontova , E. E. Anal. Chem. 2011 , 83 , 1594 ) providing the robust "off-on" nanomolar DNA sensing. Those results can be extended to other intercalating redox probes and are of strategic importance for design and development of electrochemical hybridization sensors exploiting DNA nanoswitchable architectures.

The structure of drug-deoxydinucleoside phosphate complex; generalized conformational behavior of intercalation complexes with RNA and DNA fragments.

PubMed Central

Shieh, H S; Berman, H M; Dabrow, M; Neidle, S

1980-01-01

A 2:2 complex of proflavine and deoxycytidylyl-3', 5'-guanosine has been crystallized and its structure determined by x-ray crystallography. The two dinucleoside phosphate strands form self complementary duplexes with Watson Crick hydrogen bonds. One proflavin is asymmetrically intercalated between the base pairs and the other is stacked above them. The conformations of the nucleotides are unusual in that one strand has C3',C2'endomixed sugar puckering and the other has C3',C3' endo deoxyribose sugars. These results show that the conformation of the 3'sugar is of secondary importance to the intercalated geometry. PMID:7355129

Spectroscopic studies of the interaction between pirimicarb and calf thymus DNA.

PubMed

Zhang, Guowen; Hu, Xing; Pan, Junhui

2011-02-01

The interaction between pirimicarb and calf thymus DNA in physiological buffer (pH 7.4) was investigated with the use of Neutral Red (NR) dye as a spectral probe by UV-vis absorption, fluorescence and circular dichroism (CD) spectroscopy, as well as viscosity measurements and DNA melting techniques. The results revealed that an intercalation binding should be the interaction mode of pirimicarb to DNA. CD spectra indicated that pirimicarb induced conformational changes of DNA. The binding constants of pirimicarb with DNA were obtained by the fluorescence quenching method. The thermodynamic parameters, enthalpy change (ΔHθ) and entropy change (ΔSθ) were calculated to be -52.13±2.04 kJ mol(-1) and -108.8±6.72 J mol(-1) K(-1) according to the van't Hoff equation, which suggested that hydrogen bonds and van der Waals forces might play a major role in the binding of pirimicarb to DNA. Further, the alternative least squares (ALS) method was applied to resolve a complex two-way array of the absorption spectra data, which provided simultaneously the concentration information for the three reaction components, pirimicarb, NR and DNA-NR. This ALS analysis indicated that the intercalation of pirimicarb into the DNA by substituting for NR in the DNA-NR complex. Copyright © 2010 Elsevier B.V. All rights reserved.

Intercalation of aflatoxin B sub 1 in two oligodeoxynucleotide adducts: Comparative sup 1 H NMR analysis of d(ATC sup AFB GAT)ter dot d(ATCGAT) and d(AT sup ATB GCAT) sub 2

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gopalakrishnan, S.; Harris, T.M.; Stone, M.P.

8,9-Dihydro-8-(N7-guanyl-(d(ATCGAT)))-9-hydroxyaflatoxin B{sub 1}{center dot}d(ATCGAT) and 8,9-dihydro-8-(N7-guanyl-(d(ATGCAT)))-9-hydroxyafltoxin B{sub 1}{center dot}8,9-dihydro-8-(N7-guanyl-(d(ATGCAT)))-9-hydroxyaflatoxin B{sub 1} were prepared by direct addition of aflatoxin B{sub 1} 8,9-expoxide to d(ATCGAT){sub 2} and d(ATGCAT){sub 2}, respectively. {sup 1}H NOE experiments, nonselective {sup 1}H T{sub 1} relaxation measurements, and {sup 1}H chemical shift perturbations demonstrate that in both modified oligodeoxynucleotides the aflatoxin moiety is intercalated above the 5{prime}-face of the modified guanine. The oligodeoxynucleotides remain right-handed, and perturbation of the B-DNA structure is localized adjacent to the adducted guanine. Aflatoxin-oligodeoxynucleotide {sup 1}H NOEs are observed between aflatoxin and the 5{prime}-neighbor base pair and include both the major groove andmore » the minor groove. The protons at C8 and C9 of the aflatoxin terminal furan ring exhibit slower spin-lattice relaxation as compared to other oligodeoxynucleotide protons, which supports the conclusion that they face into the major groove. Increased shielding is observed for aflatoxin protons. The difference in reaction stoichiometry is consistent with an intercalated transition-state complex between aflatoxin B{sub 1} 8,9-epoxide and B-DNA. Intercalation provides excellent positioning for nucleophilic attack by guanine N7 on aflatoxin B{sub 1} 8,9-epoxide, which probably accounts for the observed efficiency of adduct formation despite the relatively low DNA binding affinity observed for aflatoxin B{sub 1}.« less

Thermodynamic and spectroscopic investigations of TMPyP4 association with guanine- and cytosine-rich DNA and RNA repeats of C9orf72.

PubMed

Alniss, Hasan; Zamiri, Bita; Khalaj, Melisa; Pearson, Christopher E; Macgregor, Robert B

2018-01-22

An expansion of the hexanucleotide repeat (GGGGCC)n·(GGCCCC)n in the C9orf72 promoter has been shown to be the cause of Amyotrophic lateral sclerosis and frontotemporal dementia (ALS-FTD). The C9orf72 repeat can form four-stranded structures; the cationic porphyrin (TMPyP4) binds and distorts these structures. Isothermal titration calorimetry (ITC), and circular dichroism (CD) were used to study the binding of TMPyP4 to the C-rich and G-rich DNA and RNA oligos containing the hexanucleotide repeat at pH 7.5 and 0.1 M K + . The CD spectra of G-rich DNA and RNA TMPyP4 complexes showed features of antiparallel and parallel G-quadruplexes, respectively. The shoulder at 260 nm in the CD spectrum becomes more intense upon formation of complexes between TMPyP4 and the C-rich DNA. The peak at 290 nm becomes more intense in the c-rich RNA molecules, suggesting induction of an i-motif structure. The ITC data showed that TMPyP4 binds at two independent sites for all DNA and RNA molecules. For DNA, the data are consistent with TMPyP4 stacking on the terminal tetrads and intercalation. For RNA, the thermodynamics of the two binding modes are consistent with groove binding and intercalation. In both cases, intercalation is the weaker binding mode. These findings are considered with respect to the structural differences of the folded DNA and RNA molecules and the energetics of the processes that drive site-specific recognition by TMPyP4; these data will be helpful in efforts to optimize the specificity and affinity of the binding of porphyrin-like molecules. Copyright © 2018 Elsevier Inc. All rights reserved.

Intercalated graphite fiber composites as EMI shields in aerospace structures

NASA Technical Reports Server (NTRS)

Gaier, James R.

1990-01-01

The requirements for electromagnetic interference (EMI) shielding in aerospace structures are complicated over that of ground structures by their weight limitations. As a result, the best EMI shielding materials must blend low density, high strength, and high elastic modulus with high shielding ability. In addition, fabrication considerations including penetrations and joints play a major role. The EMI shielding properties are calculated for shields formed from pristine and intercalated graphite fiber/epoxy composites and compared to preliminary experimental results and to shields made from aluminum. Calculations indicate that EMI shields could be fabricated from intercalated graphite composites which would have less than 12 percent of the mass of conventional aluminum shields, based on mechanical properties and shielding properties alone.

Imaging chromatin nanostructure with binding-activated localization microscopy based on DNA structure fluctuations

PubMed Central

Szczurek, Aleksander; Klewes, Ludger; Xing, Jun; Gourram, Amine; Birk, Udo; Knecht, Hans; Dobrucki, Jurek W.; Mai, Sabine

2017-01-01

Abstract Advanced light microscopy is an important tool for nanostructure analysis of chromatin. In this report we present a general concept for Single Molecule localization Microscopy (SMLM) super-resolved imaging of DNA-binding dyes based on modifying the properties of DNA and the dye. By careful adjustment of the chemical environment leading to local, reversible DNA melting and hybridization control over the fluorescence signal of the DNA-binding dye molecules can be introduced. We postulate a transient binding as the basis for our variation of binding-activated localization microscopy (BALM). We demonstrate that several intercalating and minor-groove binding DNA dyes can be used to register (optically isolate) only a few DNA-binding dye signals at a time. To highlight this DNA structure fluctuation-assisted BALM (fBALM), we applied it to measure, for the first time, nanoscale differences in nuclear architecture in model ischemia with an anticipated structural resolution of approximately 50 nm. Our data suggest that this approach may open an avenue for the enhanced microscopic analysis of chromatin nano-architecture and hence the microscopic analysis of nuclear structure aberrations occurring in various pathological conditions. It may also become possible to analyse nuclear nanostructure differences in different cell types, stages of development or environmental stress conditions. PMID:28082388

PMA-PhyloChip DNA Microarray to Elucidate Viable Microbial Community Structure

NASA Technical Reports Server (NTRS)

Venkateswaran, Kasthuri J.; Stam, Christina N.; Andersen, Gary L.; DeSantis, Todd

2011-01-01

Since the Viking missions in the mid-1970s, traditional culture-based methods have been used for microbial enumeration by various NASA programs. Viable microbes are of particular concern for spacecraft cleanliness, for forward contamination of extraterrestrial bodies (proliferation of microbes), and for crew health/safety (viable pathogenic microbes). However, a "true" estimation of viable microbial population and differentiation from their dead cells using the most sensitive molecular methods is a challenge, because of the stability of DNA from dead cells. The goal of this research is to evaluate a rapid and sensitive microbial detection concept that will selectively estimate viable microbes. Nucleic acid amplification approaches such as the polymerase chain reaction (PCR) have shown promise for reducing time to detection for a wide range of applications. The proposed method is based on the use of a fluorescent DNA intercalating agent, propidium monoazide (PMA), which can only penetrate the membrane of dead cells. The PMA-quenched reaction mixtures can be screened, where only the DNA from live cells will be available for subsequent PCR reaction and microarray detection, and be identified as part of the viable microbial community. An additional advantage of the proposed rapid method is that it will detect viable microbes and differentiate from dead cells in only a few hours, as opposed to less comprehensive culture-based assays, which take days to complete. This novel combination approach is called the PMA-Microarray method. DNA intercalating agents such as PMA have previously been used to selectively distinguish between viable and dead bacterial cells. Once in the cell, the dye intercalates with the DNA and, upon photolysis under visible light, produces stable DNA adducts. DNA cross-linked in this way is unavailable for PCR. Environmental samples suspected of containing a mixture of live and dead microbial cells/spores will be treated with PMA, and then incubated in the dark. Thereafter, the sample is exposed to visible light for five minutes, so that the DNA from dead cells will be cross-linked. Following this PMA treatment step, the sample is concentrated by centrifugation and washed (to remove excessive PMA) before DNA is extracted. The 16S rRNA gene fragments will be amplified by PCR to screen the total microbial community using PhyloChip DNA microarray analysis. This approach will detect only the viable microbial community since the PMA intercalated DNA from dead cells would be unavailable for PCR amplification. The total detection time including PCR reaction for low biomass samples will be a few hours. Numerous markets may use this technology. The food industry uses spore detection to validate new alternative food processing technologies, sterility, and quality. Pharmaceutical and medical equipment companies also detect spores as a marker for sterility. This system can be used for validating sterilization processes, water treatment systems, and in various public health and homeland security applications.

[Affinity between CrIII and purified DNA, studied by competition with an intercalating agent: ethidium bromide].

PubMed

Vecchio, D; Balbi, C; Russo, P; Parodi, S; Santi, L

1981-05-30

The affinity between CrIII and purified calf- thymus DNA was studied at neutral pH by competition with ethidium bromide. Competition results indicated an affinity between CrIII and DNA of the order of 10(5) 1/mole. These results are in good agreement with previous results CrIII - DNA affinity was studied by the independent method of equilibrium dialysis and chromium dosage by atomic spectrometry.

Structural and thermal properties of inorganic-organic montmorillonite: Implications for their potential environmental applications.

PubMed

Rathnayake, Suramya I; Xi, Yunfei; Frost, Ray L; Ayoko, Godwin A

2015-12-01

Inorganic-organic clays (IOCs), clays intercalated with both organic cations such as cationic surfactants and inorganic cations such as metal hydroxy polycations have the properties of both organic and pillared clays, and thereby the ability to remove both inorganic and organic contaminants from water simultaneously. In this study, IOCs were synthesised using three different methods with different surfactant concentrations. Octadecyltrimethylammonium bromide (ODTMA) and hydroxy aluminium ([Al13O4(OH)24(H2O)12](7+) or Al13) are used as the organic and inorganic modifiers (intercalation agents). According to the results, the interlayer distance, the surfactant loading amount and the Al/Si ratio of IOCs strictly depend on the intercalation method and the intercalation agent ratio. Interlayers of IOCs synthesised by intercalating ODTMA before Al13 and IOCs synthesised by simultaneous intercalation of ODTMA and Al13 were increased with increasing the ODTMA concentration used in the synthesis procedure and comparatively high loading amounts could be observed in them. In contrast, Al/Si decreased with increasing ODTMA concentration in these two types of IOCs. The results suggest that Al-pillars can be fixed within the interlayers by calcination and any increment in the amount of ODTMA used in the synthesis procedure did not affect the interlayer distance of the IOCs. Overall the study provides valuable insights into the structure and properties of the IOCs and their potential environmental applications. Copyright © 2015 Elsevier Inc. All rights reserved.

Probing the recognition surface of a DNA triplex: binding studies with intercalator-neomycin conjugates.

PubMed

Xue, Liang; Xi, Hongjuan; Kumar, Sunil; Gray, David; Davis, Erik; Hamilton, Paris; Skriba, Michael; Arya, Dev P

2010-07-06

Thermodynamic studies on the interactions between intercalator-neomycin conjugates and a DNA polynucleotide triplex [poly(dA).2poly(dT)] were conducted. To draw a complete picture of such interactions, naphthalene diimide-neomycin (3) and anthraquinone-neomycin (4) conjugates were synthesized and used together with two other analogues, previously synthesized pyrene-neomycin (1) and BQQ-neomycin (2) conjugates, in our investigations. A combination of experiments, including UV denaturation, circular dichroism (CD) titration, differential scanning calorimetry (DSC), and isothermal titration calorimetry (ITC), revealed that all four conjugates (1-4) stabilized poly(dA).2poly(dT) much more than its parent compound, neomycin. UV melting experiments clearly showed that the temperature (T(m3-->2)) at which poly(dA).2poly(dT) dissociated into poly(dA).poly(dT) and poly(dT) increased dramatically (>12 degrees C) in the presence of intercalator-neomycin conjugates (1-4) even at a very low concentration (2 muM). In contrast to intercalator-neomycin conjugates, the increment of T(m3-->2) of poly(dA).2poly(dT) induced by neomycin was negligible under the same conditions. The binding preference of intercalator-neomycin conjugates (1-4) to poly(dA).2poly(dT) was also confirmed by competition dialysis and a fluorescent intercalator displacement assay. Circular dichroism titration studies revealed that compounds 1-4 had slightly larger binding site size ( approximately 7-7.5) with poly(dA).2poly(dT) as compared to neomycin ( approximately 6.5). The thermodynamic parameters of these intercalator-neomycin conjugates with poly(dA).2poly(dT) were derived from an integrated van't Hoff equation using the T(m3-->2) values, the binding site size numbers, and other parameters obtained from DSC and ITC. The binding affinity of all tested ligands with poly(dA).2poly(dT) increased in the following order: neomycin < 1 < 3 < 4 < 2. Among them, the binding constant [(2.7 +/- 0.3) x 10(8) M(-1)] of 2 with poly(dA).2poly(dT) was the highest, almost 1000-fold greater than that of neomycin. The binding of compounds 1-4 with poly(dA).2poly(dT) was mostly enthalpy-driven and gave negative DeltaC(p) values. The results described here suggest that the binding affinity of intercalator-neomycin conjugates for poly(dA).2poly(dT) increases as a function of the surface area of the intercalator moiety.

Effects of electrostatic screening on the conformation of single DNA molecules confined in a nanochannel

NASA Astrophysics Data System (ADS)

Zhang, Ce; Zhang, Fang; van Kan, Jeroen A.; van der Maarel, Johan R. C.

2008-06-01

Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range of 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with fluorescence microscopy as a function of the ionic strength and composition of the buffer as well as the DNA intercalation level by the YOYO-1 dye. The data were interpreted with the scaling theory for a wormlike polymer in good solvent, including the effects of confinement, charge, and self-avoidance. It was found that the elongation of the DNA molecules with decreasing ionic strength can be interpreted in terms of an increase of the persistence length. Self-avoidance effects on the extension are moderate, due to the small correlation length imposed by the channel cross-sectional diameter. Intercalation of the dye results in an increase of the DNA contour length and a partial neutralization of the DNA charge, but besides effects of electrostatic origin it has no significant effect on the bare bending rigidity. In the presence of divalent cations, the DNA molecules were observed to contract, but they do not collapse into a condensed structure. It is proposed that this contraction results from a divalent counterion mediated attractive force between the segments of the DNA molecule.

Molecular spectroscopic studies on the interaction of ferulic acid with calf thymus DNA

NASA Astrophysics Data System (ADS)

Zhang, Shufang; Sun, Xuejun; Qu, Fengli; Kong, Rongmei

2013-08-01

The interaction between ferulic acid and calf thymus deoxyribonucleic acid (ctDNA) under physiological conditions (Tris-HCl buffer solutions, pH 7.4) was investigated by UV-Vis spectroscopy, fluorescence spectroscopy, DNA melting techniques, and viscosity measurements. Results indicated that a complex of ferulic acid with ctDNA was formed with a binding constant of K290K = 7.60 × 104 L mol-1 and K310K = 4.90 × 104 L mol-1. The thermodynamic parameters enthalpy change (ΔH°), entropy change (ΔS°) and Gibbs free energy (ΔG°) were calculated to be -1.69 × 104 J mol-1, 35.36 J K-1 mol-1 and -2.79 × 104 J mol-1 at 310 K, respectively. The acting forces between ferulic acid and DNA mainly included hydrophobic interaction and hydrogen bonds. Acridine orange displacement studies revealed that ferulic acid can substitute for AO probe in the AO-DNA complex which was indicative of intercalation binding. Thermal denaturation study suggested that the interaction of ferulic acid with DNA could result in the increase of the denaturation temperature, which indicated that the stabilization of the DNA helix was increased in the presence of ferulic acid. Spectroscopic techniques together with melting techniques and viscosity determination provided evidences of intercalation mode of binding for the interaction between ferulic acid and ctDNA.

DNA/RNA binding and anticancer/antimicrobial activities of polymer-copper(II) complexes

NASA Astrophysics Data System (ADS)

Lakshmipraba, Jagadeesan; Arunachalam, Sankaralingam; Riyasdeen, Anvarbatcha; Dhivya, Rajakumar; Vignesh, Sivanandham; Akbarsha, Mohammad Abdulkader; James, Rathinam Arthur

2013-05-01

Water soluble polymer-copper(II) complexes with various degrees of coordination in the polymer chain were synthesized and characterized by elemental analysis, IR, UV-visible and EPR spectra. The DNA/RNA binding behavior of these polymer-copper(II) complexes was examined by UV-visible absorption, emission and circular dichroism spectroscopic methods, and cyclic voltammetry techniques. The binding of the polymer-copper(II) complexes with DNA/RNA was mainly through intercalation but some amount of electrostatic interaction was also observed. This binding capacity increased with the degree of coordination of the complexes. The polymer-copper(II) complex having the highest degree of coordination was subjected to analysis of cytotoxic and antimicrobial properties. The cytotoxicity study indicated that the polymer-copper(II) complexes affected the viability of MCF-7 mammary carcinoma cells, and the cells responded to the treatment with mostly through apoptosis although a few cells succumbed to necrosis. The antimicrobial screening showed activity against some human pathogens.

DNA sensing by a Eu-binding peptide containing a proflavine unit.

PubMed

Ancel, Laetitia; Gateau, Christelle; Lebrun, Colette; Delangle, Pascale

2013-01-18

Synthesis of a lanthanide-binding peptide (LBP) for the detection of double-stranded DNA is presented. A proflavine moiety was introduced into a high affinity LBP involving two unnatural chelating amino acids in the Ln ion coordination. The Eu(3+)-LBP complex is demonstrated to bind to ct-DNA and to sensitize Eu luminescence. The DNA binding process is effectively detected via the Eu-centered luminescence thanks to the intimate coupling between the LBP scaffold and DNA intercalating unit.

Cytotoxicity and DNA interaction of brucine and strychnine-Two alkaloids of semen strychni.

PubMed

Liu, Fei; Wang, Xiaolin; Han, Xu; Tan, Xiaoxin; Kang, Weijun

2015-01-01

The cytotoxicities of the two alkaloids strychnine and brucine from the seed of Strychnos nux-vomica and their interaction with DNA were investigated. A 3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyl-tetrasolium bromide (MTT) assay was used to examine the growth inhibitory effects of these alkaloids on Vero cells after 24, 48 and 72h of incubation. The cytotoxicities of strychnine and brucine were found to be time- and concentration-dependent. Strychnine was determined to be more toxic to Vero cells than brucine. At the same time, the interactions of strychnine and brucine with DNA were investigated using neutral red (NR) dye as a probe by UV-vis spectroscopy, fluorescence spectroscopy, and an examination of the ionic strength effect, and the effects of alkaloids on DNA melting were also examined. The results indicated that a DNA-brucine mixture but not a DNA-strychnine mixture could be extracted from Vero cells after treatment with brucine and strychnine, respectively. Brucine competitively intercalated into the DNA double-helix causing fluorescence quenching of the DNA-NR system. UV absorption spectroscopy and the melting temperature (Tm) curve also provided evidence that brucine interacted with DNA through intercalation. Furthermore, the results of the ionic strength effect experiment suggested that electrostatic interactions between brucine and phosphate groups in the DNA backbone might also play an important role in the binding of brucine to DNA. Copyright © 2015 Elsevier B.V. All rights reserved.

Small molecule glycoconjugates with anticancer activity.

PubMed

Pastuch-Gawołek, Gabriela; Malarz, Katarzyna; Mrozek-Wilczkiewicz, Anna; Musioł, Marta; Serda, Maciej; Czaplinska, Barbara; Musiol, Robert

2016-04-13

Glycoconjugates are combinations of sugar moieties with organic compounds. Due to their biological resemblance, such structures often have properties that are desirable for drugs. In this study we designed and synthesised several glycoconjugates from small molecular quinolines and substituted gluco- and galactopyranosyl amines. Although the parent quinoline compounds were inactive in affordable concentrations, the glycoconjugates that were obtained appeared to be cytotoxic against cancer cells at the micromolar level. When combined with copper ions, their activity increased even further. Their mechanism of action is connected to the formation of reactive oxygen species and the intercalation of DNA. Copyright © 2016 Elsevier Masson SAS. All rights reserved.

[Features of binding of proflavine to DNA at different DNA-ligand concentration ratios].

PubMed

Berezniak, E G; gladkovskaia, N A; Khrebtova, A S; Dukhopel'nikov, E V; Zinchenko, A V

2009-01-01

The binding of proflavine to calf thymus DNA has been studied using the methods of differential scanning calorimetry and spectrophotometry. It was shown that proflavine can interact with DNA by at least 3 binding modes. At high DNA-ligand concentration ratios (P/D), proflavine intercalates into both GC- and AT-sites, with a preference to GC-rich sequences. At low P/D ratios proflavine interacts with DNA by the external binding mode. From spectrophotometric concentration dependences, the parameters of complexing of proflavine with DNA were calculated. Thermodynamic parameters of DNA melting were calculated from differential scanning calorimetry data.

Label-free detection of kanamycin based on a G-quadruplex DNA aptamer-based fluorescent intercalator displacement assay

NASA Astrophysics Data System (ADS)

Xing, Yun-Peng; Liu, Chun; Zhou, Xiao-Hong; Shi, Han-Chang

2015-01-01

This work was the first to report that the kanamycin-binding DNA aptamer (5'-TGG GGG TTG AGG CTA AGC CGA-3') can form stable parallel G-quadruplex DNA (G4-DNA) structures by themselves and that this phenomenon can be verified by nondenaturing polyacrylamide gel electrophoresis and circular dichroism spectroscopy. Based on these findings, we developed a novel label-free strategy for kanamycin detection based on the G4-DNA aptamer-based fluorescent intercalator displacement assay with thiazole orange (TO) as the fluorescence probe. In the proposed strategy, TO became strongly fluorescent upon binding to kanamycin-binding G4-DNA. However, the addition of kanamycin caused the displacement of TO from the G4-DNA-TO conjugate, thereby resulting in decreased fluorescent signal, which was inversely related to the kanamycin concentration. The detection limit of the proposed assay decreased to 59 nM with a linear working range of 0.1 μM to 20 μM for kanamycin. The cross-reactivity against six other antibiotics was negligible compared with the response to kanamycin. A satisfactory recovery of kanamycin in milk samples ranged from 80.1% to 98.0%, confirming the potential of this bioassay in the measurement of kanamycin in various applications. Our results also served as a good reference for developing similar fluorescent G4-DNA-based bioassays in the future.

Hexagonal boron nitride intercalated multi-layer graphene: a possible ultimate solution to ultra-scaled interconnect technology

NASA Astrophysics Data System (ADS)

Li, Yong-Jun; Sun, Qing-Qing; Chen, Lin; Zhou, Peng; Wang, Peng-Fei; Ding, Shi-Jin; Zhang, David Wei

2012-03-01

We proposed intercalation of hexagonal boron nitride (hBN) in multilayer graphene to improve its performance in ultra-scaled interconnects for integrated circuit. The effect of intercalated hBN layer in bilayer graphene is investigated using non-equilibrium Green's functions. We find the hBN intercalated bilayer graphene exhibit enhanced transport properties compared with pristine bilayer ones, and the improvement is attributed to suppression of interlayer scattering and good planar bonding condition of inbetween hBN layer. Based on these results, we proposed a via structure that not only benefits from suppressed interlayer scattering between multilayer graphene, but also sustains the unique electrical properties of graphene when many graphene layers are stacking together. The ideal current density across the structure can be as high as 4.6×109 A/cm2 at 1V, which is very promising for the future high-performance interconnect.

Novel water soluble morpholine substituted Zn(II) phthalocyanine: Synthesis, characterization, DNA/BSA binding, DNA photocleavage and topoisomerase I inhibition.

PubMed

Barut, Burak; Demirbaş, Ümit; Özel, Arzu; Kantekin, Halit

2017-12-01

In this study, novel peripherally tetra 3-morpholinophenol substituted zinc(II) phthalocyanine (4) and its water soluble form quaternized zinc(II) phthalocyanine (ZnQ) were synthesized for the first time. These novel compounds were characterized by a combination of different spectroscopic techniques such as FT-IR, 1 H NMR, 13 C NMR, UV-vis and mass. The DNA binding of ZnQ was investigated using UV-vis absorption titration, competitive ethidium bromide, thermal denaturation and viscosity experiments that the ZnQ bound to CT-DNA via intercalation mode. ZnQ indicated photocleavage activity on supercoiled pBR322 plasmid DNA via formation of singlet oxygen under irradiation at 700nm. Besides, the topoisomerase I inhibitory effect experiments showed that ZnQ inhibited topoisomerase I enzyme in a concentration-dependent manner. The bovine serum albumin (BSA) binding experiments indicated that ZnQ bound to proteins through a static quenching mechanism. All of these results claim that ZnQ has potential agent for photodynamic therapy owing to its nucleic acid interactions and photobiological or photochemical properties. Copyright © 2017 Elsevier B.V. All rights reserved.

Detection of sequence variation in parasite ribosomal DNA by electrophoresis in agarose gels supplemented with a DNA-intercalating agent.

PubMed

Zhu, X Q; Chilton, N B; Gasser, R B

1998-05-01

This study evaluated the use of a commercially available DNA intercalating agent (Resolver Gold) in agarose gels for the direct detection of sequence variation in ribosomal DNA (rDNA). This agent binds preferentially to AT sequence motifs in DNA. Regions of nuclear rDNA, known to provide genetic markers for the identification of species of parasitic ascarid nematodes (order Ascaridida), were amplified by polymerase chain reaction (PCR) and subjected to electrophoresis in standard agarose gels versus gels supplemented with Resolver Gold. Individual taxa examined could not be distinguished reliably based on the size of their amplicons in standard agarose gels, whereas they could be readily delineated based on mobility using Resolver Gold-supplemented gels. The latter was achieved because of differences (approximately 0.1-8.2%) in the AT content of the fragments among different taxa, which were associated with significant interspecific differences (approximately 11-39%) in the rDNA sequences employed. There was a tendency for fragments with higher AT content to migrate slower in supplemented agarose gels compared with those of lower AT content. The results indicate the usefulness of this electrophoretic approach to rapidly screen for sequence variability within or among PCR-amplified rDNA fragments of similar sizes but differing AT contents. Although evaluated on rDNA of parasites, the approach has potential to be applied to a range of genes of different groups of infectious organisms.

Modification of thermal and electronic properties of bilayer graphene by using slow Na+ ions

NASA Astrophysics Data System (ADS)

Ryu, Mintae; Lee, Paengro; Kim, Jingul; Park, Heemin; Chung, Jinwook

2016-12-01

Bilayer graphene (BLG) has an extensive list of industrial applications in graphene-based nanodevices such as energy storage devices, flexible displays, and thermoelectric devices. By doping slow Na+ ions on Li-intercalated BLG, we find significantly improved thermal and electronic properties of BLG by using angle-resolved photoemission and high-resolution core level spectroscopy (HRCLS) with synchrotron photons. Our HRCLS data reveal that the adsorbed Na+ ions on a BLG produced by Li-intercalation through single layer graphene (SLG) spontaneously intercalate below the BLG, and substitute Li atoms to form Na-Si bonds at the SiC interface while preserving the same phase of BLG. This is in sharp contrast with no intercalation of Na+ ions on SLG though neutral Na atoms intercalate. The Na+-induced BLG is found to be stable upon heating up to T = 400 °C, but returns to SLG when heated at T d = 500 °C. The evolution of the π-bands upon doping the Na+ ions followed by thermal annealing shows that the carrier concentration of the π-band may be artificially controlled without damaging the Dirac nature of the π-electrons. The doubled desorption temperature from that (T d = 250 °C) of the Na-intercalated SLG together with the electronic stability of the Na+-intercalated BLG may find more practical and effective applications in advancing graphene-based thermoelectric devices and anode materials for rechargeable batteries.

Synthesis and Catalytic Performance of Gold Intercalated in the Walls of Mesoporous Silica.

PubMed

Ji, Yazhou; Caskey, Christopher; Richards, Ryan M

2015-07-09

As a promising catalytically active nano reactor, gold nanoparticles intercalated in mesoporous silica (GMS) were successfully synthesized and properties of the materials were investigated. We used a one pot sol-gel approach to intercalate gold nano particles in the walls of mesoporous silica. To start with the synthesis, P123 was used as template to form micelles. Then TESPTS was used as a surface modification agent to intercalate gold nano particles. Following this process, TEOS was added in as a silica source which underwent a polymerization process in acid environment. After hydrothermal processing and calcination, the final product was acquired. Several techniques were utilized to characterize the porosity, morphology and structure of the gold intercalated mesoporous silica. The results showed a stable structure of mesoporous silica after gold intercalation. Through the oxidation of benzyl alcohol as a benchmark reaction, the GMS materials showed high selectivity and recyclability.

Synthesis and Catalytic Performance of Gold Intercalated in the Walls of Mesoporous Silica

PubMed Central

Ji, Yazhou; Caskey, Christopher; Richards, Ryan M.

2015-01-01

As a promising catalytically active nano reactor, gold nanoparticles intercalated in mesoporous silica (GMS) were successfully synthesized and properties of the materials were investigated. We used a one pot sol-gel approach to intercalate gold nano particles in the walls of mesoporous silica. To start with the synthesis, P123 was used as template to form micelles. Then TESPTS was used as a surface modification agent to intercalate gold nano particles. Following this process, TEOS was added in as a silica source which underwent a polymerization process in acid environment. After hydrothermal processing and calcination, the final product was acquired. Several techniques were utilized to characterize the porosity, morphology and structure of the gold intercalated mesoporous silica. The results showed a stable structure of mesoporous silica after gold intercalation. Through the oxidation of benzyl alcohol as a benchmark reaction, the GMS materials showed high selectivity and recyclability. PMID:26274058

Ab initio density functional theory investigation of Li-intercalated silicon carbide nanotube bundles

NASA Astrophysics Data System (ADS)

Moradian, Rostam; Behzad, Somayeh; Chegel, Raad

2009-06-01

We present the results of ab initio density functional theory calculations on the energetic, and geometric and electronic structure of Li-intercalated ( 6,6) silicon carbide nanotube (SiCNT) bundles. Our results show that intercalation of lithium leads to the significant changes in the geometrical structure. The most prominent effect of Li intercalation on the electronic band structure is a shift of the Fermi energy which occurs as a result of charge transfer from lithium to the SiCNTs. All the Li-intercalated ( 6,6) SiCNT bundles are predicted to be metallic representing a substantial change in electronic properties relative to the undoped bundle, which is a wide band gap semiconductor. Both inside of the nanotube and the interstitial space are susceptible for intercalation. The present calculations suggest that the SiCNT bundle is a promising candidate for the anode material in battery applications.

Kinetic and thermodynamic hysteresis imposed by intercalation of proflavine in ferrocene-modified double-stranded DNA.

PubMed

Gebala, Magdalena; La Mantia, Fabio; Schuhmann, Wolfgang

2013-07-22

Surface-confined immobilized redox species often do not show the expected zero peak separation in slow-scan cyclic voltammograms. This phenomenon is frequently associated to experimental drawbacks and hence neglected. However, a nonzero peak separation, which is common to many electrochemical systems with high structural flexibility, can be rationally assigned to a thermodynamic hysteresis. To study this phenomenon, a surface-confined redox species was used. Specifically, a DNA strand which is tagged with ferrocene (Fc) moieties at its 5' end and its complementary capture probe is thiolated at the 3' end was self-assembled in a monolayer at a Au electrode with the Fc moieties being located at the bottom plane of the double-stranded DNA (dsDNA). The DNA-bound Fc undergoes rapid electron transfer with the electrode surface as evaluated by fast scan cyclic voltammetry. The electron transfer is sensitive to the ion transport along the DNA strands, a phenomenon which is modulated upon specific intercalation of proflavine into surface-bound dsDNA. The electron transfer rate of the Fc(0/+) redox process is influenced by the cationic permselectivity of the DNA monolayer. In addition to the kinetic hindrance, a thermodynamic effect correlated with changes in the activity coefficients of the Fc(0/+) moieties near the gold-dsDNA interface is observed and discussed as source of the observed hysteresis causing the non-zero peak separation in the voltammograms. Copyright © 2013 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Molecular spectroscopic studies on the interaction of ferulic acid with calf thymus DNA.

PubMed

Zhang, Shufang; Sun, Xuejun; Qu, Fengli; Kong, Rongmei

2013-08-01

The interaction between ferulic acid and calf thymus deoxyribonucleic acid (ctDNA) under physiological conditions (Tris-HCl buffer solutions, pH 7.4) was investigated by UV-Vis spectroscopy, fluorescence spectroscopy, DNA melting techniques, and viscosity measurements. Results indicated that a complex of ferulic acid with ctDNA was formed with a binding constant of K(290K)=7.60×10(4) L mol(-1) and K(310K)=4.90×10(4) L mol(-1). The thermodynamic parameters enthalpy change (ΔH°), entropy change (ΔS°) and Gibbs free energy (ΔG°) were calculated to be -1.69×10(4) J mol(-1), 35.36 J K(-1) mol(-1) and -2.79×10(4) J mol(-1) at 310 K, respectively. The acting forces between ferulic acid and DNA mainly included hydrophobic interaction and hydrogen bonds. Acridine orange displacement studies revealed that ferulic acid can substitute for AO probe in the AO-DNA complex which was indicative of intercalation binding. Thermal denaturation study suggested that the interaction of ferulic acid with DNA could result in the increase of the denaturation temperature, which indicated that the stabilization of the DNA helix was increased in the presence of ferulic acid. Spectroscopic techniques together with melting techniques and viscosity determination provided evidences of intercalation mode of binding for the interaction between ferulic acid and ctDNA. Copyright © 2013 Elsevier B.V. All rights reserved.

Metallization and superconductivity in Ca-intercalated bilayer MoS2

NASA Astrophysics Data System (ADS)

Szczȱśniak, R.; Durajski, A. P.; Jarosik, M. W.

2017-12-01

A two-dimensional molybdenum disulfide (MoS2) has attracted significant interest recently due to its outstanding physical, chemical and optoelectronic properties. In this paper, using the first-principles calculations, the dynamical stability, electronic structure and superconducting properties of Ca-intercalated bilayer MoS2 are investigated. The calculated electron-phonon coupling constant implies that the stable form of investigated system is a strong-coupling superconductor (λ = 1.05) with a low value of critical temperature (TC = 13.3 K). Moreover, results obtained within the framework of the isotropic Migdal-Eliashberg formalism proved that Ca-intercalated bilayer MoS2 exhibits behavior that goes beyond the scope of the conventional BCS theory.

Nanogold-functionalized DNAzyme concatamers with redox-active intercalators for quadruple signal amplification of electrochemical immunoassay.

PubMed

Zhou, Jun; Lai, Wenqiang; Zhuang, Junyang; Tang, Juan; Tang, Dianping

2013-04-10

A novel and in situ amplified immunoassay strategy with quadruple signal amplification was designed for highly efficient electrochemical detection of low-abundance proteins (carcinoembryonic antigen, CEA, as a model) by using nanogold-functionalized DNAzyme concatamers with redox-active intercalators. To construct such an in situ amplification system, streptavidin-labeled gold nanoparticles (AuNP-SA) were initially used for the labelling of initiator strands (S0) and detection antibody (mAb2) with a large ratio (mAb2-AuNP-S0), and then two auxiliary DNA strands S1 and S2 were designed for in situ propagation of DNAzyme concatamers with the hemin/G-quadruplex format. The quadruple signal amplification was implemented by using the avidin-biotin chemistry, nanogold labels, DNA concatamers, and DNAzymes. In the presence of target CEA, the sandwiched immunocomplex was formed between the immobilized primary antibodies on the electrode and the conjugated detection antibodies on the mAb2-AuNP-S0. The carried S0 initiator strands could progress a chain reaction of hybridization events between alternating S1/S2 DNA strands to form a nicked double-helix. Upon addition of hemin, the hemin-binding aptamers could be bound to form the hemin/G-quadruplex-based DNAzymes. The formed double-helix DNA polymers could cause the intercalation of numerous electroactive methylene blue molecules. During the electrochemical measurement, the formed DNAzymes could catalyze the reduction of H2O2 in the solution to amplify the electrochemical signal of the intercalated methylene blue. Under optimal conditions, the electrochemical immunoassay exhibited a wide dynamic range of 1.0 fg mL(-1) to 20 ng mL(-1) toward CEA standards with a low detection limit of 0.5 fg mL(-1). Intra-assay and inter-assay coefficients of variation (CV) were less than 8.5% and 11.5%, respectively. No significant differences at the 0.05 significance level were encountered in the analysis of 14 clinical serum specimens between the developed immunoassay and commercialized electrochemiluminescent (ECL) method for detection of CEA.

Selenium nanoparticles synthesized in aqueous extract of Allium sativum perturbs the structural integrity of Calf thymus DNA through intercalation and groove binding.

PubMed

Ezhuthupurakkal, Preedia Babu; Polaki, Lokeswara Rao; Suyavaran, Arumugam; Subastri, Ariraman; Sujatha, Venugopal; Thirunavukkarasu, Chinnasamy

2017-05-01

Biomedical application of selenium nanoparticles (SeNPs) demands the eco-friendly composite for synthesis of SeNPs. The present study reports an aqueous extract of Allium sativum (AqEAS) plug-up the current need. Modern spectroscopic, microscopic and gravimetric techniques were employed to characterize the synthesized nanoparticles. Characterization studies revealed the formation of crystalline spherical shaped SeNPs. FTIR spectrum brings out the presence of different functional groups in AqEAS, which influence the SeNPs formation and stabilization. Furthermore the different aspects of the interaction between SeNPs and CT-DNA were scrutinized by various spectroscopic and cyclic voltametric studies. The results reveals the intercalation and groove binding mode of interaction of SeNPs with stacked base pair of CT-DNA. The Stern-Volmer quenching constant (K SV ) were found to be 7.02×10 6 M- 1 (ethidium bromide), 4.22×10 6 M- 1 (acridine orange) and 7.6×10 6 M- 1 (Hoechst) indicating strong binding of SeNPs with CT-DNA. The SeNPs - CT-DNA interactions were directly visualized by atomic force microscopy. The present study unveils the cost effective, innocuous, highly stable SeNPs intricate mechanism of DNA interaction, which will be a milestone in DNA targeted chemotherapy. Copyright © 2017 Elsevier B.V. All rights reserved.

Quercetin-Iron Complex: Synthesis, Characterization, Antioxidant, DNA Binding, DNA Cleavage, and Antibacterial Activity Studies.

PubMed

Raza, Aun; Xu, Xiuquan; Xia, Li; Xia, Changkun; Tang, Jian; Ouyang, Zhen

2016-11-01

Quercetin-iron (II) complex was synthesized and characterized by elemental analysis, ultraviolet-visible spectrophotometry, fourier transform infrared spectroscopy, mass spectrometry, proton nuclear magnetic resonance spectroscopy, thermogravimetry and differential scanning calorimetry, scanning electron micrography and molar conductivity. The low molar conductivity value investigates the non-electrolyte nature of the complex. The elemental analysis and other physical and spectroscopic methods reveal the 1:2 stoichiometric ratio (metal:ligand) of the complex. Antioxidant study of the quercetin and its metal complex against 2, 2-di-phenyl-1-picryl hydrazyl radical showed that the complex has much more radical scavenging activity than free quercetin. The interaction of quercetin-iron (II) complex with DNA was determined using ultraviolet visible spectra, fluorescence spectra and agarose gel electrophoresis. The results showed that quercetin-iron (II) complex can intercalate moderately with DNA, quench a strong intercalator ethidium bromide and compete for the intercalative binding sites. The complex showed significant cleavage of pBR 322 DNA from supercoiled form to nicked circular form and these cleavage effects were dose-dependent. Moreover, the mechanism of DNA cleavage indicated that it was an oxidative cleavage pathway. These results revealed the potential nuclease activity of complex to cleave DNA. In addition, antibacterial activity of complex on E.coli and S. aureus was also investigated. The results showed that complex has higher antibacterial activity than ligand.

Factors affecting nucleolytic efficiency of some ternary metal complexes with DNA binding and recognition domains. Crystal and molecular structure of Zn(phen)(edda).

PubMed

Seng, Hoi-Ling; Ong, Han-Kiat Alan; Rahman, Raja Noor Zaliha Raja Abd; Yamin, Bohari M; Tiekink, Edward R T; Tan, Kong Wai; Maah, Mohd Jamil; Caracelli, Ignez; Ng, Chew Hee

2008-11-01

The binding selectivity of the M(phen)(edda) (M=Cu, Co, Ni, Zn; phen=1,10-phenanthroline, edda=ethylenediaminediacetic acid) complexes towards ds(CG)(6), ds(AT)(6) and ds(CGCGAATTCGCG) B-form oligonucleotide duplexes were studied by CD spectroscopy and molecular modeling. The binding mode is intercalation and there is selectivity towards AT-sequence and stacking preference for A/A parallel or diagonal adjacent base steps in their intercalation. The nucleolytic properties of these complexes were investigated and the factors affecting the extent of cleavage were determined to be: concentration of complex, the nature of metal(II) ion, type of buffer, pH of buffer, incubation time, incubation temperature, and the presence of hydrogen peroxide or ascorbic acid as exogenous reagents. The fluorescence property of these complexes and its origin were also investigated. The crystal structure of the Zn(phen)(edda) complex is reported in which the zinc atom displays a distorted trans-N(4)O(2) octahedral geometry; the crystal packing features double layers of complex molecules held together by extensive hydrogen bonding that inter-digitate with adjacent double layers via pi...pi interactions between 1,10-phenanthroline residues. The structure is compared with that of the recently described copper(II) analogue and, with the latter, included in molecular modeling.

Fluorochrome-functionalized magnetic nanoparticles for high-sensitivity monitoring of the polymerase chain reaction by magnetic resonance.

PubMed

Alcantara, David; Guo, Yanyan; Yuan, Hushan; Goergen, Craig J; Chen, Howard H; Cho, Hoonsung; Sosnovik, David E; Josephson, Lee

2012-07-09

Easy to find: magnetic nanoparticles bearing fluorochromes (red) that intercalate with DNA (green) form microaggregates with DNA generated by the polymerase chain reaction (PCR). These aggregates can be detected at low cycle numbers by magnetic resonance (MR). Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Lithium ion intercalation in thin crystals of hexagonal TaSe2 gated by a polymer electrolyte

NASA Astrophysics Data System (ADS)

Wu, Yueshen; Lian, Hailong; He, Jiaming; Liu, Jinyu; Wang, Shun; Xing, Hui; Mao, Zhiqiang; Liu, Ying

2018-01-01

Ionic liquid gating has been used to modify the properties of layered transition metal dichalcogenides (TMDCs), including two-dimensional (2D) crystals of TMDCs used extensively recently in the device work, which has led to observations of properties not seen in the bulk. The main effect comes from the electrostatic gating due to the strong electric field at the interface. In addition, ionic liquid gating also leads to ion intercalation when the ion size of the gate electrolyte is small compared to the interlayer spacing of TMDCs. However, the microscopic processes of ion intercalation have rarely been explored in layered TMDCs. Here, we employed a technique combining photolithography device fabrication and electrical transport measurements on the thin crystals of hexagonal TaSe2 using multiple channel devices gated by a polymer electrolyte LiClO4/Polyethylene oxide (PEO). The gate voltage and time dependent source-drain resistances of these thin crystals were used to obtain information on the intercalation process, the effect of ion intercalation, and the correlation between the ion occupation of allowed interstitial sites and the device characteristics. We found a gate voltage controlled modulation of the charge density waves and a scattering rate of charge carriers. Our work suggests that ion intercalation can be a useful tool for layered materials engineering and 2D crystal device design.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osiry, H.; Cano, A.; Lemus-Santana, A.A.

This contribution discusses the intercalation of imidazole and its 2-ethyl derivative, and pyridine in 2D copper nitroprusside. In the interlayer region, neighboring molecules remain interacting throu gh their dipole and quadrupole moments, which supports the solid 3D crystal structure. The crystal structure of this series of intercalation compounds was solved and refined from powder X-ray diffraction patterns complemented with spectroscopic information. The intermolecular interactions were studied from the refined crystal structures and low temperature magnetic measurements. Due to strong attractive forces between neighboring molecules, the resulting π–π cloud overlapping enables the ferromagnetic coupling between metal centers on neighboring layers, which wasmore » actually observed for the solids containing imidazole and pyridine as intercalated molecules. For these two solids, the magnetic data were properly described with a model of six neighbors. For the solid containing 2-ethylimidazole and for 2D copper nitroprusside, a model of four neighbors in a plane is sufficient to obtain a reliable data fitting. - Highlights: • Intercalation of organic molecules in 2D copper (II) nitroprusside. • Molecular properties of intercalation compounds of 2D copper (II) nitroprusside. • Magnetic properties of hybrid inorganic–organic solids. • Hybrid inorganic–organic 3D framework.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xia Shengjie; Ni Zheming; Xu Qian

Zn/Al layered double hydroxides (LDHs) were intercalated with the anionic antihypertensive drugs Enalpril, Lisinopril, Captopril and Ramipril by using coprecipitation or ion-exchange technique. TG-MS analyses suggested that the thermal stability of Ena{sup -}, Lis{sup -} (arranged with monolayer, resulted from X-ray diffraction (XRD) and Fourier transform infrared spectra (FT-IR) analysis was enhanced much more than Cap{sup -} and Ram{sup -} (arranged with bilayer). The release studies show that the release rate of all samples markedly decreased in both pH 4.25 and 7.45. However, the release time of Ena{sup -}, Lis{sup -} were much longer compared with Cap{sup -}, Ram{sup -}more » in both pH 4.25 and 7.45, it is possible that the intercalated guests, arranged with monolayer in the interlayer, show lesser repulsive force and strong affinity with the LDH layers. And the release data followed both the Higuchi-square-root law and the first-order equation well. Based on the analysis of batch release, intercalated structural models as well as the TG-DTA results, we conclude that for drug-LDH, stronger the affinity between intercalated anions and the layers is, better the thermal property and the stability to the acid attack of drug-LDH, and the intercalated anions are easier apt to monolayer arrangement within the interlayer, were presented. - Graphical abstract: A series of antihypertensive drugs including Enalpril, Lisinopril, Captopril and Ramipril were intercalated into Zn/Al-NO{sub 3}-LDHs successfully by coprecipitation or ion-exchange technique. We focus on the structure, thermal property and low/controlled release property of as-synthesized drug-LDH composite intended for the possibility of applying these LDH-antihypertensive nanohybrids in drug delivery and controlled release systems.« less

Electrochemical tuning of vertically aligned MoS2 nanofilms and its application in improving hydrogen evolution reaction

PubMed Central

Wang, Haotian; Lu, Zhiyi; Xu, Shicheng; Kong, Desheng; Cha, Judy J.; Zheng, Guangyuan; Hsu, Po-Chun; Yan, Kai; Bradshaw, David; Prinz, Fritz B.; Cui, Yi

2013-01-01

The ability to intercalate guest species into the van der Waals gap of 2D layered materials affords the opportunity to engineer the electronic structures for a variety of applications. Here we demonstrate the continuous tuning of layer vertically aligned MoS2 nanofilms through electrochemical intercalation of Li+ ions. By scanning the Li intercalation potential from high to low, we have gained control of multiple important material properties in a continuous manner, including tuning the oxidation state of Mo, the transition of semiconducting 2H to metallic 1T phase, and expanding the van der Waals gap until exfoliation. Using such nanofilms after different degree of Li intercalation, we show the significant improvement of the hydrogen evolution reaction activity. A strong correlation between such tunable material properties and hydrogen evolution reaction activity is established. This work provides an intriguing and effective approach on tuning electronic structures for optimizing the catalytic activity. PMID:24248362

The electronic properties of SWNTs intercalated by electron acceptors

NASA Astrophysics Data System (ADS)

Chernysheva, M. V.; Kiseleva, E. A.; Verbitskii, N. I.; Eliseev, A. A.; Lukashin, A. V.; Tretyakov, Yu. D.; Savilov, S. V.; Kiselev, N. A.; Zhigalina, O. M.; Kumskov, A. S.; Krestinin, A. V.; Hutchison, J. L.

2008-05-01

Here we report synthesis of Chal@SWNT nanocomposites (where Chal=S, Se and Te) and the impact of the intercalated electron-acceptor compounds on the electronic properties of SWNTs. The chalcogens were introduced to the channels of single-walled carbon nanotubes by molten media technique via impregnation of pre-opened SWNTs with melted guest compounds in vacuum. HRTEM imaging confirms the filling of nanotube channels by continuous nanostructures of corresponding chalcogens. The strong influence of incorporated matter on the electronic properties of the SWNTs was detected by Raman spectroscopy.

Toxicity, mutagenicity and transport in Saccharomyces cerevisiae of three popular DNA intercalating fluorescent dyes.

PubMed

Sayas, Enric; García-López, Federico; Serrano, Ramón

2015-09-01

We have compared the toxicity, mutagenicity and transport in Saccharomyces cerevisiae of three DNA-intercalating fluorescent dyes widely used to stain DNA in gels. Safety data about ethidium bromide (EtBr) are contradictory, and two compounds of undisclosed structure (Redsafe and Gelred) have been proposed as safe alternatives. Our results indicate that all three compounds inhibit yeast growth, with Gelred being the most inhibitory and also the only one causing cell death. EtBr and Gelred, but not Redsafe, induce massive formation of petite (non-respiratory) mutants, but only EtBr induces massive loss of mitochondrial DNA. All three compounds increase reversion of a chromosomal point mutation (lys2-801(amber) ), with Gelred being the most mutagenic and Redsafe the least. These dyes are all cationic and are probably taken by cells through non-selective cation channels. We could measure the glucose-energized transport of EtBr and Gelred inside the cells, while uptake of Redsafe was below our detection limit. We conclude that although all three compounds are toxic and mutagenic in the yeast system, Redsafe is the safest for yeast, probably because of very limited uptake by these cells. Copyright © 2015 John Wiley & Sons, Ltd.

Structural, conformational and thermodynamic aspects of groove-directed-intercalation of flavopiridol into DNA.

PubMed

Ray, Bhumika; Agarwal, Shweta; Lohani, Neelam; Rajeswari, Moganty R; Mehrotra, Ranjana

2016-11-01

Certain plant-derived alkaloids and flavonoids have shown propitious cytotoxic acitvity against different types of cancer, having deoxyribose nucleic acid (DNA) as their main cellular target. Flavopiridol, a semi-synthetic derivative of rohitukine (a natural compound isolated from Dysoxylum binectariferum plant), has attained much attention owing to its anticancer potential against various haematological malignancies and solid tumours. This work focuses on investigating interaction between flavopiridol and DNA at molecular level in order to decipher its underlying mechanism of action, which is not well understood. To define direct influence of flavopiridol on the structural, conformational and thermodynamic aspects of DNA, various spectroscopic and calorimetric techniques have been used. ATR-FTIR and SERS spectral outcomes indicate a novel insight into groove-directed-intercalation of flavopiridol into DNA via direct binding with nitrogenous bases guanine (C6=O6) and thymine (C2=O2) in DNA groove together with slight external binding to its sugar-phosphate backbone. Circular dichroism spectral analysis of flavopiridol-DNA complexes suggests perturbation in native B-conformation of DNA and its transition into C-form, which may be localized up to a few base pairs of DNA. UV-visible spectroscopic results illustrate dual binding mode of flavopiridol when interacts with DNA having association constant, Ka = 1.18 × 10(4) M(-1). This suggests moderate type of interaction between flavopiridol and DNA. Further, UV melting analysis also supports spectroscopic outcomes. Thermodynamically, flavopiridol-DNA complexation is an enthalpy-driven exothermic process. These conclusions drawn from this study could be helpful in unveiling mechanism of cytoxicity induced by flavopiridol that can be further applied in the development of flavonoid-based new chemotherapeutics with more specificity and better efficacy.

DNA Binding, Cleavage and Antibacterial Activity of Mononuclear Cu(II), Ni(II) and Co(II) Complexes Derived from Novel Benzothiazole Schiff Bases.

PubMed

Vamsikrishna, Narendrula; Kumar, Marri Pradeep; Tejaswi, Somapangu; Rambabu, Aveli; Shivaraj

2016-07-01

A series of novel bivalent metal complexes M(L1)2 and M(L2)2 where M = Cu(II), Ni(II), Co(II) and L1 = 2-((benzo [d] thiazol-6-ylimino)methyl)-4-bromophenol [BTEMBP], L2 = 1-((benzo [d] thiazol-6-ylimino)methyl) naphthalen-2-ol [BTEMNAPP] were synthesized. All the compounds have been characterized by elemental analysis, SEM, Mass, (1)H NMR, (13)C NMR, UV-Vis, IR, ESR, spectral data and magnetic susceptibility measurements. Based on the analytical and spectral data four-coordinated square planar geometry is assigned to all the complexes. DNA binding properties of these complexes have been investigated by electronic absorption spectroscopy, fluorescence and viscosity measurements. It is observed that these binary complexes strongly bind to calf thymus DNA by an intercalation mode. DNA cleavage efficacy of these complexes was tested in presence of H2O2 and UV light by gel electrophoresis and found that all the complexes showed better nuclease activity. Finally the compounds were screened for antibacterial activity against few pathogens and found that the complexes have potent biocidal activity than their free ligands.

KlenTaq polymerase replicates unnatural base pairs by inducing a Watson-Crick geometry.

PubMed

Betz, Karin; Malyshev, Denis A; Lavergne, Thomas; Welte, Wolfram; Diederichs, Kay; Dwyer, Tammy J; Ordoukhanian, Phillip; Romesberg, Floyd E; Marx, Andreas

2012-07-01

Many candidate unnatural DNA base pairs have been developed, but some of the best-replicated pairs adopt intercalated structures in free DNA that are difficult to reconcile with known mechanisms of polymerase recognition. Here we present crystal structures of KlenTaq DNA polymerase at different stages of replication for one such pair, dNaM-d5SICS, and show that efficient replication results from the polymerase itself, inducing the required natural-like structure.

Targeting radiosensitizers to DNA by attachment of an intercalating group: Nitroimidazole-linked phenanthridines

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cowan, D.S.; Panicucci, R.; McClelland, R.A.

The nitroimidazole-linked phenanthridine series of compounds (NLP-1, 2, and 3) were synthesized under the assumption that it should be possible to enhance the molar efficiency of 2-nitroimidazoles as hypoxic cell radiosensitizers and cytotoxins by targeting them to their likely site of action, DNA. The targeting group chosen was the phenanthridine moiety, the major component of the classical DNA intercalating compound, ethidium bromide. The sole difference between the compounds is the length of the hydrocarbon chain linking the nitroimidazole to the phenanthridine. The phenanthridine group with a three-carbon side chain, P-1, was also synthesized to allow studies on the effect ofmore » the targeting group by itself. The ability of the compounds to bind to DNA is inversely proportional to their linker chain length with binding constant values ranging from approximately 1 {times} 10(5) mol-1 for NLP-2 to 6 {times} 10(5) mol-1 for NLP-3. The NLP compounds show selective toxicity to hypoxic cells at 37 degrees C at external drug concentrations 10-40 times lower than would be required for untargeted 2-nitroimidazoles such as misonidazole in vitro. Toxicity to both hypoxic and aerobic cells is dependent on the linker chain: the shorter the chain, the greater the toxicity. In addition, the NLP compounds radiosensitize hypoxic cells at external drug concentrations as low as 0.05 mM with almost the full oxygen effect being observed at a concentration of 0.5 mM. These concentrations are 10-100 times lower than would be required for similar radiosensitization using misonidazole. Radiosensitizing ability is independent of linker chain length. The present compounds represent prototypes for further studies of the efficacy and mechanism of action of 2-nitroimidazoles targeted to DNA by linkage to an intercalating group.« less

Optical tracking of organically modified silica nanoparticles as DNA carriers: A nonviral, nanomedicine approach for gene delivery

NASA Astrophysics Data System (ADS)

Roy, Indrajit; Ohulchanskyy, Tymish Y.; Bharali, Dhruba J.; Pudavar, Haridas E.; Mistretta, Ruth A.; Kaur, Navjot; Prasad, Paras N.

2005-01-01

This article reports a multidisciplinary approach to produce fluorescently labeled organically modified silica nanoparticles as a nonviral vector for gene delivery and biophotonics methods to optically monitor intracellular trafficking and gene transfection. Highly monodispersed, stable aqueous suspensions of organically modified silica nanoparticles, encapsulating fluorescent dyes and surface functionalized by cationic-amino groups, are produced by micellar nanochemistry. Gel-electrophoresis studies reveal that the particles efficiently complex with DNA and protect it from enzymatic digestion of DNase 1. The electrostatic binding of DNA onto the surface of the nanoparticles, due to positively charged amino groups, is also shown by intercalating an appropriate dye into the DNA and observing the Förster (fluorescence) resonance energy transfer between the dye (energy donor) intercalated in DNA on the surface of nanoparticles and a second dye (energy acceptor) inside the nanoparticles. Imaging by fluorescence confocal microscopy shows that cells efficiently take up the nanoparticles in vitro in the cytoplasm, and the nanoparticles deliver DNA to the nucleus. The use of plasmid encoding enhanced GFP allowed us to demonstrate the process of gene transfection in cultured cells. Our work shows that the nanomedicine approach, with nanoparticles acting as a drug-delivery platform combining multiple optical and other types of probes, provides a promising direction for targeted therapy with enhanced efficacy as well as for real-time monitoring of drug action. nonviral vector | ORMOSIL nanoparticles | confocal microscopy

A novel quantitative electrochemical method to monitor DNA double-strand breaks caused by a DNA cleavage agent at a DNA sensor.

PubMed

Banasiak, Anna; Cassidy, John; Colleran, John

2018-06-01

To date, DNA cleavage, caused by cleavage agents, has been monitored mainly by gel and capillary electrophoresis. However, these techniques are time-consuming, non-quantitative and require gel stains. In this work, a novel, simple and, importantly, a quantitative method for monitoring the DNA nuclease activity of potential anti-cancer drugs, at a DNA electrochemical sensor, is presented. The DNA sensors were prepared using thiol-modified oligonucleotides that self-assembled to create a DNA monolayer at gold electrode surfaces. The quantification of DNA double-strand breaks is based on calculating the DNA surface coverage, before and after exposure to a DNA cleavage agent. The nuclease properties of a model DNA cleavage agent, copper bis-phenanthroline ([Cu II (phen) 2 ] 2+ ), that can cleave DNA in a Fenton-type reaction, were quantified electrochemically. The DNA surface coverage decreased on average by 21% after subjecting the DNA sensor to a nuclease assay containing [Cu II (phen) 2 ] 2+ , a reductant and an oxidant. This percentage indicates that 6 base pairs were cleaved in the nuclease assay from the immobilised 30 base pair strands. The DNA cleavage can be also induced electrochemically in the absence of a chemical reductant. [Cu II (phen) 2 ] 2+ intercalates between DNA base pairs and, on application of a suitable potential, can be reduced to [Cu I (phen) 2 ] + , with dissolved oxygen acting as the required oxidant. This reduction process is facilitated through DNA strands via long-range electron transfer, resulting in DNA cleavage of 23%. The control measurements for both chemically and electrochemically induced cleavage revealed that DNA strand breaks did not occur under experimental conditions in the absence of [Cu II (phen) 2 ] 2+ . Copyright © 2018 Elsevier B.V. All rights reserved.

Manipulation of Dirac cones in metal-intercalated epitaxial graphene

NASA Astrophysics Data System (ADS)

Wang, Cai-Zhuang; Kim, Minsung; Tringides, Michael; Ho, Kai-Ming

Graphene is one of the most attractive materials from both fundamental and practical points of view due to its characteristic Dirac cones. The electronic property of graphene can be modified through the interaction with substrate or another graphene layer as illustrated in few-layer epitaxial graphene. Recently, metal intercalation became an effective method to manipulate the electronic structure of graphene by modifying the coupling between the constituent layers. In this work, we show that the Dirac cones of epitaxial graphene can be manipulated by intercalating rare-earth metals. We demonstrate that rare-earth metal intercalated epitaxial graphene has tunable band structures and the energy levels of Dirac cones as well as the linear or quadratic band dispersion can be controlled depending on the location of the intercalation layer and density. Our results could be important for applications and characterizations of the intercalated epitaxial graphene. Supported by the U.S. DOE-BES under Contract No. DE-AC02-07CH11358.

Synthesis of reduced graphene oxide intercalated ZnO quantum dots nanoballs for selective biosensing detection

NASA Astrophysics Data System (ADS)

Chen, Jing; Zhao, Minggang; Li, Yingchun; Fan, Sisi; Ding, Longjiang; Liang, Jingjing; Chen, Shougang

2016-07-01

ZnO quantum dots (QDs), reduced graphene oxide (rGO) and multi-walled carbon nanotubes (MWCNTs) are always used in sensors due to their excellent electrochemical characteristics. In this work, ZnO QDs were intercalated by rGO sheets with cross-linked MWCNTs to construct intercalation nanoballs. A MWCNTs/rGO/ZnO QDs 3D hierarchical architecture was fabricated on supporting Ni foam, which exhibited excellent mechanical, kinetic and electrochemical properties. The intercalation construction can introduce strong interfacial effects to improve the surface electronic state. The selectively determinate of uric acid, dopamine, and ascorbic acid by an electrode material using distinct applied potentials was realized.

Interaction of indole-papaverine with DNA in solutions of various ionic strength

NASA Astrophysics Data System (ADS)

Travkina, V. I.; Moroshkina, E. B.; Osinnikova, D. N.

2017-11-01

Interaction of synthetic alkaloid of isoquinoline series, which is an analogue of the biologically active compound papaverine, was studied by spectral, microcalorimetric, optical and hydrodynamic methods at different ionic strengths of medium. It was found that the investigated compound may interact with DNA in various ways depending on the ratio of ligand - DNA concentrations and ionic strength of solution (μ). When μ = 0.001, indole-papaverine intercalates into the double helix of DNA. The increase of μ resulted in a decrease of the affinity of the compound to DNA and a change its binding method.

Major versus minor groove DNA binding of a bisarginylporphyrin hybrid molecule: A molecular mechanics investigation

NASA Astrophysics Data System (ADS)

Gresh, Nohad; Perrée-fauvet, Martine

1999-03-01

On the basis of theoretical computations, we have recently synthesised [Perrée-Fauvet, M. and Gresh, N., Tetrahedron Lett., 36 (1995) 4227] a bisarginyl conjugate of a tricationic porphyrin (BAP), designed to target, in the major groove of DNA, the d(GGC GCC)2 sequence which is part of the primary binding site of the HIV-1 retrovirus site [Wain-Hobson, S. et al., Cell, 40 (1985) 9]. In the theoretical model, the chromophore intercalates at the central d(CpG)2 step and each of the arginyl arms targets O6/N7belonging to guanine bases flanking the intercalation site. Recent IR and UV-visible spectroscopic studies have confirmed the essential features of these theoretical predictions [Mohammadi, S. et al., Biochemistry, 37 (1998) 6165]. In the present study, we compare the energies of competing intercalation modes of BAP to several double-stranded oligonucleotides, according to whether one, two or three N- methylpyridinium rings project into the major groove. Correspondingly, three minor groove binding modes were considered, the arginyl arms now targeting N3, O2 sites belonging to the purine or pyrimidine bases flanking the intercalation site. This investigation has shown that: (i) in both the major and minor grooves, the best-bound complexes have the three N-methylpyridinium rings in the groove opposite to that of the phenyl group bearing the arginyl arms; (ii) major groove binding is preferred over minor groove binding by a significant energy (29 kcal/mol); and (iii) the best-bound sequence in the major groove is d(GGC GCC)2 with two successive guanines upstream from the intercalation. On the other hand, due to the flexibility of the arginyl arms, other GC-rich sequences have close binding energies, two of them being less stable than it by less than 8 kcal/mol. These results serve as the basis for the design of derivatives of BAP with enhanced sequence selectivities in the major groove.

Interactions of tetracationic porphyrins with DNA and their effects on DNA cleavage

NASA Astrophysics Data System (ADS)

Lebedeva, Natalya Sh.; Yurina, Elena S.; Gubarev, Yury A.; Syrbu, Sergey A.

2018-06-01

The interaction of tetracationic porphyrins with DNA was studied using UV-Vis absorption, fluorescence spectroscopy and viscometry, and the particle sizes were determined. Аs cationic porphyrins, two isomer porphyrins, 3,3‧,3″,3‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP3) and 4,4‧,4″,4‴-(5,10,15,20-Porphyrintetrayl)tetrakis(1-methylpyridinium) (TMPyP4), were studied. They differ in the position of NCH3+ group in phenyl ring of the porphyrins and hence, in degree of freedom of rotation of the phenyl rings about the central macrocycle. It was found that intercalated complexes are formed at DNA/porphyrin molar ratios (R) of 2.2 and 3.9 for TMPyP3 и TMPyP4, respectively. Decreasing R up to 0.4 and 0.8 for TMPyP3 и TMPyP4, respectively, leads mainly to formation of outside complexes due to π-π stacking between the porphyrin chromophores interacting electrostatically with phosphate framework of DNA. Each type of the obtained complexes was characterized using Scatchard approach. It was ascertained that the affinity of TMPyP4 to DNA is stronger than TMPyP3, meanwhile the wedge effect of the latter is higher. The differences between the porphyrin isomers become more evident at irradiation of their complexes with DNA. It was established that irradiation of the intercalated complexes results in DNA fragmentation. In the case of TMPyP4, DNA fragments of different size are formed. The irradiation of the outside DNA/porphyrin complexes leads to cleavage of DNA (TMPyP3 and TMPyP4) and partial destruction of the complex due to photolysis of the porphyrin (TMPyP3).

Mononuclear zinc(II) complexes of 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols: Synthesis, structural characterization, DNA binding and cheminuclease activities

NASA Astrophysics Data System (ADS)

Ravichandran, J.; Gurumoorthy, P.; Karthick, C.; Kalilur Rahiman, A.

2014-03-01

Four new zinc(II) complexes [Zn(HL1-4)Cl2] (1-4), where HL1-4 = 2-((2-(piperazin-1-yl)ethylimino)methyl)-4-substituted phenols, have been isolated and fully characterized using various spectro-analytical techniques. The X-ray crystal structure of complex 4 shows the distorted trigonal-bipyramidal coordination geometry around zinc(II) ion. The crystal packing is stabilized by intermolecular NH⋯O hydrogen bonding interaction. The complexes display no d-d electronic band in the visible region due to d10 electronic configuration of zinc(II) ion. The electrochemical properties of the synthesized ligands and their complexes exhibit similar voltammogram at reduction potential due to electrochemically innocent Zn(II) ion, which evidenced that the electron transfer is due to the nature of the ligand. Binding interaction of complexes with calf thymus DNA was studied by UV-Vis absorption titration, viscometric titration and cyclic voltammetry. All complexes bind with CT DNA by intercalation, giving the binding affinity in the order of 2 > 1 ≫ 3 > 4. The prominent cheminuclease activity of complexes on plasmid DNA (pBR322 DNA) was observed in the absence and presence of H2O2. Oxidative pathway reveals that the underlying mechanism involves hydroxyl radical.

Intercalation and controlled release properties of vitamin C intercalated layered double hydroxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Xiaorui, E-mail: gxr_1320@sina.com; School of Chemistry and Chemical Engineering, Southeast University, Nanjing 211189; Chemistry Research Laboratory, University of Oxford, Mansfield Road, Oxford OX1 3TA

Two drug-inorganic composites involving vitamin C (VC) intercalated in Mg–Al and Mg–Fe layered double hydroxides (LDHs) have been synthesized by the calcination–rehydration (reconstruction) method. Powder X-ray diffraction (XRD), Fourier transform infrared (FTIR), and UV–vis absorption spectroscopy indicate a successful intercalation of VC into the interlayer galleries of the LDH host. Studies of VC release from the LDHs in deionised water and in aqueous CO{sub 3}{sup 2−} solutions imply that Mg{sub 3}Al–VC LDH is a better controlled release system than Mg{sub 3}Fe–VC LDH. Analysis of the release profiles using a number of kinetic models suggests a solution-dependent release mechanism, and amore » diffusion-controlled deintercalation mechanism in deionised water, but an ion exchange process in CO{sub 3}{sup 2−} solution. - Graphical abstract: Vitamin C anions have been intercalated in the interlayer space of layered double hydroxide and released in CO{sub 3}{sup 2−} solution and deionised water. - Highlights: • Vitamin C intercalated Mg–Al and Mg–Fe layered double hydroxides were prepared. • Release property of vitamin C in aqueous CO{sub 3}{sup 2−} solution is better. • Avrami-Erofe’ev and first-order models provide better fit for release results. • Diffusion-controlled and ion exchange processes occur in deionised water. • An ion exchange process occurs in CO{sub 3}{sup 2−} solution.« less

Oxidation of a critical methionine modulates DNA binding of the Drosophila melanogaster high mobility group protein, HMG-D.

PubMed

Dow, L K; Changela, A; Hefner, H E; Churchill, M E

1997-09-15

HMG-D is a major high mobility group chromosomal protein present during early embryogenesis in Drosophila melanogaster. During overexpression and purification of HMG-D from E. coli, a key DNA binding residue, methionine 13, undergoes oxidation to methionine sulfoxide. Oxidation of this critical residue decreases the affinity of HMG-D for DNA by three-fold, altering the structure of the HMG-D-DNA complex without affecting the structure of the free protein. This work shows that minor modification of DNA intercalating residues may be used to fine tune the DNA binding affinity of HMG domain proteins.

Torsional Rigidity of Positively and Negatively Supercoiled DNA

NASA Astrophysics Data System (ADS)

Selvin, Paul R.; Cook, David N.; Pon, Ning G.; Bauer, William R.; Klein, Melvin P.; Hearst, John E.

1992-01-01

Time-correlated single-photon counting of intercalated ethidium bromide was used to measure the torsion constants of positively supercoiled, relaxed, and negatively supercoiled pBR322 DNA, which range in superhelix density from +0.042 to -0.123. DNA behaves as coupled, nonlinear torsional pendulums under superhelical stress, and the anharmonic term in the Hamiltonian is approximately 15 percent for root-mean-square fluctuations in twist at room temperature. At the level of secondary structure, positively supercoiled DNA is significantly more flexible than negatively supercoiled DNA. These results exclude certain models that account for differential binding affinity of proteins to positively and negatively supercoiled DNA.

Intercalated Nanocomposites Based on High-Temperature Superconducting Ceramics and Their Properties

PubMed Central

Tonoyan, Anahit; Schiсk, Christoph; Davtyan, Sevan

2009-01-01

High temperature superconducting (SC) nanocomposites based on SC ceramics and various polymeric binders were prepared. Regardless of the size of the ceramics’ grains, the increase of their amount leads to an increase of resistance to rupture and modulus and a decrease in limiting deformation, whereas an increase in the average ceramic grain size worsens resistance properties. The SC, thermo-chemical, mechanical and dynamic-mechanical properties of the samples were investigated. Superconducting properties of the polymer ceramic nanocomposites are explained by intercalation of macromolecule fragments into the interstitial layer of the ceramics’ grains. This phenomenon leads to a change in the morphological structure of the superconducting nanocomposites.

Linear and circular dichroism characterization of thionine binding mode with DNA polynucleotides

NASA Astrophysics Data System (ADS)

Tuite, Eimer Mary; Nordén, Bengt

2018-01-01

The binding mode of thionine (3,7-diamino-5-phenothiazinium) with alternating and non-alternating DNA polynucleotides at low binding ratios was conclusively determined using linear and circular dichroism spectroscopies. The binding to [poly(dG-dC)]2 and poly(dG)·poly(dC) was purely intercalative and was insensitive to ionic strength. Intercalative binding to [poly(dA-dT)]2 is observed at low ionic strength, but a shift of some dye to an non-intercalative mode is observed as the background salt concentration increases. With poly(dA)·poly(dT), intercalative binding is unfavourable, although some dye molecules may intercalate at low ionic strength, and groove binding is strongly promoted with increasing concentration of background salt. However, stacking with bases is observed with single-stranded poly(dA) and with triplex poly(dT)*poly(dA)·poly(dT) which suggests that the unusual structure of poly(dA)·poly(dT) precludes intercalation. Thionine behaves similarly to the related dye methylene blue, and small differences may be attributed either to the ability of thionine to form H-bonds that stabilize intercalation or to its improved stacking interactions in the basepair pocket on steric grounds.

Technological hurdles to the application of intercalated graphite fibers

NASA Technical Reports Server (NTRS)

Gaier, James R.

1988-01-01

Before intercalated graphite fibers can be developed as an effective power material, there are several technological hurdles which must be overcome. These include the environmental stability, homogeneity and bulk properties, connection procedures, and costs. Strides were made within the last several years in stability and homogeneity of intercalated graphite fibers. Bulk properties and connection procedures are areas of active research now. Costs are still prohibitive for all but the most demanding applications. None of these problems, however, appear to be unsolvable, and their solution may result in wide spread GOC application. The development of a relatively simple technology application, such as EMI shielding, would stimulate the solution of scale-up problems. Once this technology is developed, then more demanding applications, such as power bus bars, may be possible.

Methylene blue binding to DNA with alternating AT base sequence: minor groove binding is favored over intercalation.

PubMed

Rohs, Remo; Sklenar, Heinz

2004-04-01

The results presented in this paper on methylene blue (MB) binding to DNA with AT alternating base sequence complement the data obtained in two former modeling studies of MB binding to GC alternating DNA. In the light of the large amount of experimental data for both systems, this theoretical study is focused on a detailed energetic analysis and comparison in order to understand their different behavior. Since experimental high-resolution structures of the complexes are not available, the analysis is based on energy minimized structural models of the complexes in different binding modes. For both sequences, four different intercalation structures and two models for MB binding in the minor and major groove have been proposed. Solvent electrostatic effects were included in the energetic analysis by using electrostatic continuum theory, and the dependence of MB binding on salt concentration was investigated by solving the non-linear Poisson-Boltzmann equation. We find that the relative stability of the different complexes is similar for the two sequences, in agreement with the interpretation of spectroscopic data. Subtle differences, however, are seen in energy decompositions and can be attributed to the change from symmetric 5'-YpR-3' intercalation to minor groove binding with increasing salt concentration, which is experimentally observed for the AT sequence at lower salt concentration than for the GC sequence. According to our results, this difference is due to the significantly lower non-electrostatic energy for the minor groove complex with AT alternating DNA, whereas the slightly lower binding energy to this sequence is caused by a higher deformation energy of DNA. The energetic data are in agreement with the conclusions derived from different spectroscopic studies and can also be structurally interpreted on the basis of the modeled complexes. The simple static modeling technique and the neglect of entropy terms and of non-electrostatic solute-solvent interactions, which are assumed to be nearly constant for the compared complexes of MB with DNA, seem to be justified by the results.

Rotational strength of dye-helix complexes as studied by a potential model theory

NASA Astrophysics Data System (ADS)

Kamiya, Mamoru

1988-03-01

The fundamental features of the induced optical activity in dye-helix complexes are clarified by the trap potential model. The effect of the potential depth on the induced rotational strength is explained in terms of the relative magnitudes of the wave-phase and helix-phase variations in the path of an electron moving along a restricted helix segment just like an exciton trapped around a dye intercalation site. The potential parameters have been optimized so as to reproduce the ionic strength effect upon the rotational strengths induced in proflavine-DNA intercalation complexes.

Transition metal intercalated bilayer silicene

NASA Astrophysics Data System (ADS)

Pandey, Dhanshree; Kamal, C.; Chakrabarti, Aparna

2018-04-01

We investigate the electronic and magnetic properties of Mn, Fe and Co-intercalated silicene bilayer with AA and AB stacking by using spin polarized density functional theory. The intercalation of Mn increases the gap between the two layers of silicene due to the larger atomic radii of Mn as compared to Fe and Co. Bader charge analysis has been performed to understand the bonding between the TM and Si atoms. This also helps in explaining the magnetic moment possessed by the composite systems after intercalating TM in between the layers of bilayer silicene system. This study reveals that a significant net magnetic moment is observed in cases of Mn-intercalated silicene bilayers, whereas Fe has a very small moment of 0.78 µB in the case of AA stacking configuration only. Co intercalation leads to net zero magnetic moment. Further, we find that Fe and Co marginally favor the AB stacking whereas Mn has a slight preference of the AA over the AB configuration. The composite systems, specifically when intercalated with Fe and Co atoms, favor a hybridization which is far away from sp3-like hybridization along the plane of Si atoms in bilayer silicene.

Interaction study of some macrocyclic inorganic schiff base complexes with calf thymus DNA using spectroscopic and voltammetric methods

NASA Astrophysics Data System (ADS)

Bordbar, Maryam; Tavoosi, Fariba; Yeganeh-Faal, Ali; Zebarjadian, Mohammad Hasan

2018-01-01

The interaction of Cd(II), Zn(II) and Mn(II)-L (4,8-bis(2-pyridylmethyl)-4,8-diazaundecane-1,11-diamine) transition metal complexes with calf thymus DNA (CT-DNA) has been investigated using electronic, fluorescence and circular dichroism (CD) spectroscopy, thermal denaturation and cyclic voltammetry (CV). Based on the UV-Vis study, binding constants of the complexes with CT-DNA were calculated. Changes in the band of the CD spectrum, DNA melting temperature and in the ipa and ipc of the complexes in the presenceCT-DNA, overall, showed that the studied complex exhibited good DNA interaction ability with partial intercalation mode.

Controlled release formulation of an anti-depression drug based on a L-phenylalanate-zinc layered hydroxide intercalation compound

NASA Astrophysics Data System (ADS)

Hashim, Norhayati; Sharif, Sharifah Norain Mohd; Isa, Illyas Md; Hamid, Shahidah Abdul; Hussein, Mohd Zobir; Bakar, Suriani Abu; Mamat, Mazidah

2017-06-01

The intercalation of L-phenylalanate (LP) into the interlayer gallery of zinc layered hydroxide (ZLH) has been successfully executed using a simple direct reaction method. The synthesised intercalation compound, zinc layered hydroxide-L-phenylalanate (ZLH-LP), was characterised using PXRD, FTIR, CHNS, ICP-OES, TGA/DTG, FESEM and TEM. The PXRD patterns of the intercalation compound demonstrate an intense and symmetrical peak, indicating a well-ordered crystalline layered structure. The appearance of an intercalation peak at a low angle of 2θ with a basal spacing of 16.3 Å, signifies the successful intercalation of the L-phenylalanate anion into the interlayer gallery of the host. The intercalation is also validated by FTIR spectroscopy and CHNS elemental analysis. Thermogravimetric analysis confirms that the ZLH-LP intercalation compound has higher thermal stability than the pristine L-phenylalanine. The observed percentage of L-phenylalanate accumulated release varies in each release media, with 84.5%, 79.8%, 63.8% and 61.8% release in phosphate buffer saline (PBS) solution at pH 4.8, deionised water, PBS solution at pH 7.4 and NaCl solution, respectively. The release behaviour of LP from its intercalation compounds in deionised water and PBS solution at pH 4.8 follows pseudo second order, whereas in NaCl solution and PBS solution at pH 7.4, it follows the parabolic diffusion model. This study shows that the synthesised ZLH-LP intercalation compound can be used for the formation of a new generation of materials for targeted drug release with controlled release properties.

The staging mechanism of AlCl4 intercalation in a graphite electrode for an aluminium-ion battery.

PubMed

Bhauriyal, Preeti; Mahata, Arup; Pathak, Biswarup

2017-03-15

Identifying a suitable electrode material with desirable electrochemical properties remains a primary challenge for rechargeable Al-ion batteries. Recently an ultrafast rechargeable Al-ion battery was reported with high charge/discharge rate, (relatively) high discharge voltage and high capacity that uses a graphite-based cathode. Using calculations from first-principles, we have investigated the staging mechanism of AlCl 4 intercalation into bulk graphite and evaluated the stability, specific capacity and voltage profile of AlCl 4 intercalated compounds. Ab initio molecular dynamics is performed to investigate the thermal stability of AlCl 4 intercalated graphite structures. Our voltage profiles show that the first AlCl 4 intercalation step could be a more sluggish step than the successive intercalation steps. However, the diffusion of AlCl 4 is very fast in the expanded graphite host layers with a diffusion barrier of ∼0.01 eV, which justifies the ultrafast charging rate of a graphite based Al-ion battery. And such an AlCl 4 intercalated battery provides an average voltage of 2.01-2.3 V with a maximum specific capacity of 69.62 mA h g -1 , which is excellent for anion intercalated batteries. Our density of states and Bader charge analysis shows that the AlCl 4 intercalation into the bulk graphite is a charging process. Hence, we believe that our present study will be helpful in understanding the staging mechanism of AlCl 4 intercalation into graphite-like layered electrodes for Al-ion batteries, thus encouraging further experimental work.

Effect of metal ion intercalation on the structure of MXene and water dynamics on its internal surfaces

DOE PAGES

Osti, Naresh C.; Naguib, Michael; Ostadhossein, Alireza; ...

2016-03-24

MXenes are a recently discovered class of 2D materials with an excellent potential for energy storage applications. Because MXene surfaces are hydrophilic and attractive interaction forces between the layers are relatively weak, water molecules can spontaneously intercalate at ambient humidity and significantly influence the key properties of this 2D material. Using complementary X-ray and neutron scattering techniques, we demonstrate that intercalation with potassium cations significantly improves structural homogeneity and water stability in MXenes. Furthermore, in agreement with molecular dynamics simulations, intercalated potassium ions reduce the water self-diffusion coefficient by 2 orders of magnitude, suggesting greater stability of hydrated MXene againstmore » changing environmental conditions.« less

Structure-function relationships of new lipids designed for DNA transfection.

PubMed

Dittrich, Matthias; Heinze, Martin; Wölk, Christian; Funari, Sergio S; Dobner, Bodo; Möhwald, Helmuth; Brezesinski, Gerald

2011-08-22

Cationic liposome/DNA complexes can be used as nonviral vectors for direct delivery of DNA-based biopharmaceuticals to damaged cells and tissues. To obtain more effective and safer liposome-based gene transfection systems, two cationic lipids with identical head groups but different chain structures are investigated with respect to their in vitro gene-transfer activity, their cell-damaging characteristics, and their physicochemical properties. The gene-transfer activities of the two lipids are very different. Differential scanning calorimetry and synchrotron small- and wide-angle X-ray scattering give valuable structural insight. A subgel-like structure with high packing density and high phase-transition temperature from gel to liquid-crystalline state are found for lipid 7 (N'-2-[(2,6-diamino-1-oxohexyl)amino]ethyl-2,N-bis(hexadecyl)propanediamide) containing two saturated chains. Additionally, an ordered head-group lattice based on formation of a hydrogen-bond network is present. In contrast, lipid 8 (N'-2-[(2,6-diamino-1-oxohexyl)amino]ethyl-2-hexadecyl-N-[(9Z)-octadec-9-enyl]propanediamide) with one unsaturated and one saturated chain shows a lower phase-transition temperature and a reduced packing density. These properties enhance incorporation of the helper lipid cholesterol needed for gene transfection. Both lipids, either pure or in mixtures with cholesterol, form lamellar phases, which are preserved after addition of DNA. However, the system separates into phases containing DNA and phases without DNA. On increasing the temperature, DNA is released and only a lipid phase without intercalated DNA strands is observed. The conversion temperatures are very different in the two systems studied. The important parameter seems to be the charge density of the lipid membranes, which is a result of different solubility of cholesterol in the two lipid membranes. Therefore, different binding affinities of the DNA to the lipid mixtures are achieved. Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

First Principles Studies for Lithium Intercalation and Diffusion Behaviors in MoS2 treated with the Compressive Sensing Cluster Expansion

NASA Astrophysics Data System (ADS)

Liu, Chi-Ping; Zhou, Fei; Ozolins, Vidvuds

2014-03-01

Molybdenum disulfide (MoS2) is a good candidate electrode material for high capacity energy storage applications, such as lithium ion batteries and supercapacitors. In this work, we investigate lithium intercalation and diffusion kinetics in MoS2 by using first-principles density-functional theory (DFT) calculations. Two different lithium intercalation sites (1-H and 2-T) in MoS2 are found to be stable for lithium intercalation at different van der Waals' (vdW) gap distances. It is found that both thermodynamic and kinetic properties are highly related to the interlayer vdW gap distance, and that the optimal gap distance leads to effective solid-state diffusion in MoS2. Additionally, through the use of compressive sensing, we build accurate cluster expansion models to study the thermodynamic properties of MoS2 at high lithium content by truncating the higher order effective clusters with significant contributions. The results show that compressive sensing cluster expansion is a rigorous and powerful tool for model construction for advanced electrochemical applications in the future.

Selective sodium intercalation into sodium nickel-manganese sulfate for dual Na-Li-ion batteries.

PubMed

Marinova, Delyana M; Kukeva, Rosica R; Zhecheva, Ekaterina N; Stoyanova, Radostina K

2018-05-09

Double sodium transition metal sulfates combine in themselves unique intercalation properties with eco-compatible compositions - a specific feature that makes them attractive electrode materials for lithium and sodium ion batteries. Herein, we examine the intercalation properties of novel double sodium nickel-manganese sulfate, Na2Ni1/2Mn1/2(SO4)2, having a large monoclinic unit cell, through electrochemical and ex situ diffraction and spectroscopic methods. The sulfate salt Na2Ni1/2Mn1/2(SO4)2 is prepared by thermal dehydration of the corresponding hydrate salt Na2Ni1/2Mn1/2(SO4)2·4H2O having a blödite structure. The intercalation reactions on Na2Ni1-xMnx(SO4)2 are studied in two model cells: half-ion cell versus Li metal anode and full-ion cell versus Li4Ti5O12 anode by using lithium (LiPF6 dissolved in EC/DMC) and sodium electrolytes (NaPF6 dissolved in EC:DEC). Based on ex situ XRD and TEM analysis, it is found that sodium intercalation into Na2Ni1/2Mn1/2(SO4)2 takes place via phase separation into the Ni-rich monoclinic phase and Mn-rich alluaudite phase. The redox reactions involving participation of manganese and titanium ions are monitored by ex situ EPR spectroscopy. It has been demonstrated that manganese ions from the sulfate salt are participating in the electrochemical reaction, while the nickel ions remain intact. As a result, a reversible capacity of about 65 mA h g-1 is reached. The selective intercalation properties determine sodium nickel-manganese sulfate as a new electrode material for hybrid lithium-sodium ion batteries that is thought to combine the advantages of individual lithium and sodium batteries.

Synthesis, DNA binding and cytotoxic activity of pyrimido[4',5':4,5]thieno(2,3-b)quinoline with 9-hydroxy-4-(3-diethylaminopropylamino) and 8-methoxy-4-(3-diethylaminopropylamino) substitutions.

PubMed

KiranKumar, Hulihalli N; RohitKumar, Heggodu G; Advirao, Gopal M

2018-01-01

Two new derivatives of pyrimido[4',5';4,5]thieno(2,3-b)quinoline (PTQ), 9-hydroxy-4-(3-diethylaminopropylamino)pyrimido[4',5';4,5]thieno(2,3-b)quinoline (Hydroxy-DPTQ) and 8-methoxy-4-(3-diethylaminopropylamino)pyrimido[4',5';4,5]thieno(2,3-b)quinoline (Methoxy-DPTQ) were synthesized and their DNA binding ability was analyzed using spectroscopy (UV-visible, fluorescence and circular dichroism), ethidium bromide dye displacement assay, melting temperature (T m ) analysis and computational docking studies. The hypochromism in UV-visible spectrum and increased fluorescence emission of Hydroxy-DPTQ and Methoxy-DPTQ in the presence of DNA suggested the molecule-DNA interaction. The association constants calculated from UV-visible and spectral titrations were of the order 10 4 to 10 6 M -1 . Circular dichroism studies corroborated the induced conformational changes in DNA upon addition of molecules. The change in the ellipticity was observed both in negative and positive peak of DNA, thus, suggesting the intercalation of molecules. The observed displacement of ethidium bromide from the DNA and increased T m , upon addition of DNA confirmed the intercalative mode of binding. This was further validated by computational docking, which showed clear intercalation of molecules into the d(GpC)-d(CpG) site of the receptor DNA. Anticancer activities of these molecules are evaluated by using MTT assay. Both molecules showed antiproliferative activity against all the three cancer cells studied, with Hydroxy-DPTQ being more potential molecule among the two. IC 50 value of Hydroxy-DPTQ and Methoxy-DPTQ were in the range of 3-5μM and 130-250μM, respectively. Copyright © 2017 Elsevier B.V. All rights reserved.

Synthesis and characterization of montmorillonite clay intercalated with molecular magnetic compounds

DOE Office of Scientific and Technical Information (OSTI.GOV)

Martins, Marcel G.; Martins, Daniel O.T.A.; Carvalho, Beatriz L.C. de

2015-08-15

In this work montmorillonite (MMT) clay, whose matrix was modified with an ammonium salt (hexadecyltrimethylammonium bromide – CTAB), was employed as an inorganic host for the intercalation of three different molecular magnetic compounds through ion exchange: a nitronyl nitroxide derivative 2-[4-(N-ethyl)-pyridinium]-4,4,5,5-tetramethylimidazoline-1-oxyl-3-oxide (p-EtRad{sup +}) and two binuclear coordination compounds, [Ni(valpn)Ln]{sup 3+}, where H{sub 2}valpn stands for 1,3-propanediyl-bis(2-iminomethylene-6-methoxy-phenol), and Ln=Gd{sup III}; Dy{sup III}. The pristine MMT and the intercalated materials were characterized by X-ray powder diffraction (XRD), infrared spectroscopy (IR), scanning electron microscopy (SEM), thermogravimetric analysis (TGA) and magnetic measurements. The X-ray diffraction data analysis showed an increase of the interlamellar spacemore » of the intercalated MMT, indicating the intercalation of the magnetic compounds. Furthermore, the magnetic properties of the hybrid compounds were investigated, showing similar behavior as the pure magnetic guest species. - Graphical abstract: Montmorillonite clay was employed as inorganic host for the intercalation of three different molecular magnetic compounds through ion exchange - Highlights: • Montmorillonite was employed as a host material. • Three molecular magnetic compounds were intercalated through ion exchange. • The compounds were successful intercalated maintaining the layered structure. • The hybrid materials exhibited similar magnetic behavior as the pure magnetic guest.« less

Metallothionein as a Scavenger of Free Radicals - New Cardioprotective Therapeutic Agent or Initiator of Tumor Chemoresistance?

PubMed

Heger, Zbynek; Rodrigo, Miguel Angel Merlos; Krizkova, Sona; Ruttkay-Nedecky, Branislav; Zalewska, Marta; Del Pozo, Elena Maria Planells; Pelfrene, Aurelie; Pourrut, Bertrand; Stiborova, Marie; Eckschlager, Tomas; Emri, Gabriella; Kizek, Rene; Adam, Vojtech

2016-01-01

Cardiotoxicity is a serious complication of anticancer therapy by anthracycline antibiotics. Except for intercalation into DNA/RNA structure, inhibition of DNA-topoisomerase and histone eviction from chromatin, the main mechanism of their action is iron-mediated formation of various forms of free radicals, which leads to irreversible damage to cancer cells. The most serious adverse effect of anthracyclines is, thus, cardiomyopathy leading to congestive heart failure, which is caused by the same mechanisms. Here, we briefly summarize the basic types of free radicals formed by anthracyclines and the main processes how to scavenge them. From these, the main attention is paid to metallothioneins. These low-molecular cysteine-rich proteins are introduced and their functions and properties are reviewed. Further, their role in detoxification of metals and drugs is discussed. Based on these beneficial roles, their use as a new therapeutic agent against oxidative stress and for cardioprotection is critically evaluated with respect to their ability to increase chemoresistance against some types of commonly used cytostatics.

A TDDFT study of the ruthenium(II) polyazaaromatic complex [Ru(dppz)(phen) 2] 2+ in solution

NASA Astrophysics Data System (ADS)

Fantacci, Simona; De Angelis, Filippo; Sgamellotti, Antonio; Re, Nazzareno

2004-09-01

DFT/TDDFT calculations were performed to investigate the structural, electronic and optical properties of the [Ru(dppz)(phen) 2] 2+ complex in solution. TDDFT calculations in water show two groups of metal-to-ligand charge transfer (MLCT) transitions at ≈450 and 415 nm whose superposition gives account of the broad absorption band experimentally characterized at 440 nm. Also, a group of almost coincident MLCT transitions partially mixed with dppz intraligand π-π ∗ transitions centered at ≈380 nm is found to give rise to the narrow absorption band experimentally found at 380 nm. Our results provide insight into the hypochromic shifts experimentally characterized upon intercalation of the title complex into DNA.

Effects of methyl substitution on DNA binding enthalpies of enantiopure Ru(phenanthroline)2dipyridophenazine2+ complexes.

PubMed

Mårtensson, Anna K F; Lincoln, Per

2018-04-25

Isothermal titration calorimetry (ITC) has been utilized to investigate the effect of methyl substituents on the intercalating dppz ligand of the enantiomers of the parent complex Ru(phen)2dppz2+ (phen = 1,10-phenanthroline; dppz = dipyrido[3,2-a:2',3'-c]phenazine) on DNA binding thermodynamics. The methylated complexes (10-methyl-dppz and 11,12-dimethyl-dppz) have large, concentration-dependent, positive heats of dilution, and a strong endothermic background is also apparent in the ITC-profiles from titration of methylated complexes into poly(dAdT)2, which make direct comparison between complexes difficult. By augmenting a simple cooperative binding model with one equilibrium for complex self-aggregation in solution and one equilibrium for complex aggregation on saturated DNA, it was possible to find an excellent global fit to the experimental data with DNA affinity parameters restricted to be equal for all Δ-enantiomers as well as for all Λ-enantiomers. In general, enthalpic differences, compared to the unsubstituted complex, were small and less than 4 kJ mol-1, except for the heat of intercalation of Δ-10-methyl-dppz (-11,6 kJ mol-1) and Λ-11,12-dimethyl-dppz (+4.3 kJ mol-1).

Label-free electrochemiluminescence biosensor for ultrasensitive detection of telomerase activity in HeLa cells based on extension reaction and intercalation of Ru(phen)3 (2.).

PubMed

Lin, Yue; Yang, Linlin; Yue, Guiyin; Chen, Lifen; Qiu, Bin; Guo, Longhua; Lin, Zhenyu; Chen, Guonan

2016-10-01

Telomerase is one of the most common markers of human malignant tumors, such as uterine, stomach, esophageal, breast, colorectal, laryngeal squamous cell, thyroid, bladder, and so on. It is necessary to develop some sensitive but convenient detection methods for telomerase activity determination. In this study, a label-free and ultrasensitive electrochemiluminescence (ECL) biosensor has been fabricated to detect the activity of telomerase extracted from HeLa cells. Thiolated telomerase substrate (TS) primer was immobilized on the gold electrode surface through gold-sulfur (Au-S) interaction and then elongated by telomerase specifically. Then, it was hybridized with complementary DNA to form double-stranded DNA (dsDNA) fragments on the electrode surface, and Ru(phen)3 (2+) has been intercalated into the dsDNA grooves to act as the ECL probe. The enhanced ECL intensity has a linear relationship with the number of HeLa cells in the range of 5∼5000 and with a detection limit of 2 HeLa cells. The proposed ECL biosensor has high specificity to telomerase in the presence of common interferents. The relative standard deviations (RSDs) were <5 % at 100 HeLa cells. The proposed method provides a convenient approach for telomerase-related cancer screening or diagnosis.

DNA binding studies of Sunset Yellow FCF using spectroscopy, viscometry and electrochemical techniques

NASA Astrophysics Data System (ADS)

Asaadi, Sara; Hajian, Reza

2017-10-01

Color is one of the important factors in food industry. All food companies use synthetic pigments to improve the aesthetic of products. Studies on the interaction between deoxyribonucleic acid (DNA) and food dye molecules is important because DNA is responsible for some processes including replication and transcription of cells, mutations, genetic diseases, and some synthetic chemical nucleases. In this study, the molecular interaction between Sunset Yellow FCF (SY) as a common food coloring additive and calf thymus DNA (ct-DNA) has been studied using UV-Vis spectrophotometry, spectrofluorometry, Fourier transform infrared (FTIR) spectroscopy, cyclic voltammetry and viscometry techniques. The binding constant between ct-DNA and SY in phosphate buffer solution (pH 7.4) was calculated as 2.09 × 103 L mol-1. The non-electrostatic bonding constant (K0t) was almost consistent and the ratio of K0t/Kb increased by increasing the ionic strength in the range of 0.01-0.1 mol L-1 of KCl. This observation shows that, the molecular bonding of SY to ct-DNA is a combination of electrostatic and intercalation interactions. In the electrochemical studies, an oxidation peak at 0.71 V and a reduction peak at about 0.63 V was observed with the peak potential difference (ΔEp) of 0.08 V, showing a reversible process. The oxidation and reduction peaks were significantly decreased in the presence of ct-DNA and the reduction peak current shifted to negative values. In spectrofluorometric study, the fluorescence intensity of SY increased dramatically after successive addition of DNA due to the increasing of molecular surface area and decreasing of impact frequency between solvent and SY-DNA adduct. Moreover, viscometric study shows that the increasing of viscosity for SY solution in the presence of DNA is due to the intercalation mechanism with double strand DNA (ds-DNA).

A rechargeable iodine-carbon battery that exploits ion intercalation and iodine redox chemistry.

PubMed

Lu, Ke; Hu, Ziyu; Ma, Jizhen; Ma, Houyi; Dai, Liming; Zhang, Jintao

2017-09-13

Graphitic carbons have been used as conductive supports for developing rechargeable batteries. However, the classic ion intercalation in graphitic carbon has yet to be coupled with extrinsic redox reactions to develop rechargeable batteries. Herein, we demonstrate the preparation of a free-standing, flexible nitrogen and phosphorus co-doped hierarchically porous graphitic carbon for iodine loading by pyrolysis of polyaniline coated cellulose wiper. We find that heteroatoms could provide additional defect sites for encapsulating iodine while the porous carbon skeleton facilitates redox reactions of iodine and ion intercalation. The combination of ion intercalation with redox reactions of iodine allows for developing rechargeable iodine-carbon batteries free from the unsafe lithium/sodium metals, and hence eliminates the long-standing safety issue. The unique architecture of the hierarchically porous graphitic carbon with heteroatom doping not only provides suitable spaces for both iodine encapsulation and cation intercalation but also generates efficient electronic and ionic transport pathways, thus leading to enhanced performance.Carbon-based electrodes able to intercalate Li + and Na + ions have been exploited for high performing energy storage devices. Here, the authors combine the ion intercalation properties of porous graphitic carbons with the redox chemistry of iodine to produce iodine-carbon batteries with high reversible capacities.

Electron doping through lithium intercalation to interstitial channels in tetrahedrally bonded SiC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sakai, Yuki; Center for Computational Materials, Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712; Oshiyama, Atsushi

2015-11-07

We report on first-principles calculations that clarify the effect of lithium atom intercalation into zinc blende 3C-silicon carbide (3C-SiC) on electronic and structural properties. Lithium atoms inside 3C-SiC are found to donate electrons to 3C-SiC that is an indication of a new way of electron doping through the intercalation. The electrons doped into the conduction band interact with lithium cations and reduce the band spacing between the original valence and conduction bands. We have also found that a silicon monovacancy in 3C-SiC promotes the lithium intercalation, showing that the vacancy generation makes SiC as a possible anode material for lithium-ionmore » battery.« less

New poly(butylene succinate)/layered silicate nanocomposites: preparation and mechanical properties.

PubMed

Ray, Suprakas Sinha; Okamoto, Kazuaki; Maiti, Pralay; Okamoto, Masami

2002-04-01

New poly(butylene succinate) (PBS)/layered silicate nanocomposites have been successfully prepared by simple melt extrusion of PBS and octadecylammonium modified montmorillonite (C18-mmt) at 150 degrees C. The d-spacing of both C18-mmt and intercalated nanocomposites was investigated by wide-angle X-ray diffraction analysis. Bright-field transmission electron microscopic study showed several stacked silicate layers with random orientation in the PBS matrix. The intercalated nanocomposites exhibited remarkable improvement of mechanical properties in both solid and melt states as compared with that of PBS matrix without clay.

An ultrasensitive label-free biosensor for assaying of sequence-specific DNA-binding protein based on amplifying fluorescent conjugated polymer.

PubMed

Liu, Xingfen; Ouyang, Lan; Cai, Xiaohui; Huang, Yanqin; Feng, Xiaomiao; Fan, Quli; Huang, Wei

2013-03-15

Sensitive, reliable, and simple detection of sequence-specific DNA-binding proteins (DBP) is of paramount importance in the area of proteomics, genomics, and biomedicine. We describe herein a novel fluorescent-amplified strategy for ultrasensitive, visual, quantitative, and "turn-on" detection of DBP. A Förster resonance energy transfer (FRET) assay utilizing a cationic conjugated polymer (CCP) and an intercalating dye was designed to detect a key transcription factor, nuclear factor-kappa B (NF-κB), the model target. A series of label-free DNA probes bearing one or two protein-binding sites (PBS) were used to identify the target protein specifically. The binding DBP protects the probe from digestion by exonuclease III, resulting in high efficient FRET due to the high affinity between the intercalating dye and duplex DNA, as well as strong electrostatic interactions between the CCP and DNA probe. By using label-free hairpin DNA or double-stranded DNA containing two PBS as probe, we could detect as low as 1 pg/μL of NF-κB in HeLa nuclear extracts, which is 10000-fold more sensitive than the previously reported methods. The approach also allows naked-eye detection by observing fluorescent color of solutions with the assistance of a hand-held UV lamp. Additionally, a less than 10% relative standard deviation was obtained, which offers a new platform for superior precision, low-cost, and simple detection of DBP. The features of our optical biosensor shows promising potential for early diagnosis of many diseases and high-throughput screening of new drugs targeted to DNA-binding proteins. Copyright © 2012 Elsevier B.V. All rights reserved.

Multifunctional aptamer-based nanoparticles for targeted drug delivery to circumvent cancer resistance.

PubMed

Liu, Juan; Wei, Tuo; Zhao, Jing; Huang, Yuanyu; Deng, Hua; Kumar, Anil; Wang, Chenxuan; Liang, Zicai; Ma, Xiaowei; Liang, Xing-Jie

2016-06-01

By its unique advantages over traditional medicine, nanomedicine has offered new strategies for cancer treatment. In particular, the development of drug delivery strategies has focused on nanoscale particles to improve bioavailability. However, many of these nanoparticles are unable to overcome tumor resistance to chemotherapeutic agents. Recently, new opportunities for drug delivery have been provided by oligonucleotides that can self-assemble into three-dimensional nanostructures. In this work, we have designed and developed functional DNA nanostructures to deliver the chemotherapy drug doxorubicin (Dox) to resistant cancer cells. These nanostructures have two components. The first component is a DNA aptamer, which forms a dimeric G-quadruplex nanostructure to target cancer cells by binding with nucleolin. The second component is double-stranded DNA (dsDNA), which is rich in -GC- base pairs that can be applied for Dox delivery. We demonstrated that Dox was able to efficiently intercalate into dsDNA and this intercalation did not affect the aptamer's three-dimensional structure. In addition, the Aptamer-dsDNA (ApS) nanoparticle showed good stability and protected the dsDNA from degradation in bovine serum. More importantly, the ApS&Dox nanoparticle efficiently reversed the resistance of human breast cancer cells to Dox. The mechanism circumventing doxorubicin resistance by ApS&Dox nanoparticles may be predominantly by cell cycle arrest in S phase, effectively increased cell uptake and decreased cell efflux of doxorubicin. Furthermore, the ApS&Dox nanoparticles could effectively inhibit tumor growth, while less cardiotoxicity was observed. Overall, this functional DNA nanostructure provides new insights into the design of nanocarriers to overcome multidrug resistance through targeted drug delivery. Copyright © 2016 Elsevier Ltd. All rights reserved.

Structural basis of DNA folding and recognition in an AMP-DNA aptamer complex: distinct architectures but common recognition motifs for DNA and RNA aptamers complexed to AMP.

PubMed

Lin, C H; Patel, D J

1997-11-01

Structural studies by nuclear magnetic resonance (NMR) of RNA and DNA aptamer complexes identified through in vitro selection and amplification have provided a wealth of information on RNA and DNA tertiary structure and molecular recognition in solution. The RNA and DNA aptamers that target ATP (and AMP) with micromolar affinity exhibit distinct binding site sequences and secondary structures. We report below on the tertiary structure of the AMP-DNA aptamer complex in solution and compare it with the previously reported tertiary structure of the AMP-RNA aptamer complex in solution. The solution structure of the AMP-DNA aptamer complex shows, surprisingly, that two AMP molecules are intercalated at adjacent sites within a rectangular widened minor groove. Complex formation involves adaptive binding where the asymmetric internal bubble of the free DNA aptamer zippers up through formation of a continuous six-base mismatch segment which includes a pair of adjacent three-base platforms. The AMP molecules pair through their Watson-Crick edges with the minor groove edges of guanine residues. These recognition G.A mismatches are flanked by sheared G.A and reversed Hoogsteen G.G mismatch pairs. The AMP-DNA aptamer and AMP-RNA aptamer complexes have distinct tertiary structures and binding stoichiometries. Nevertheless, both complexes have similar structural features and recognition alignments in their binding pockets. Specifically, AMP targets both DNA and RNA aptamers by intercalating between purine bases and through identical G.A mismatch formation. The recognition G.A mismatch stacks with a reversed Hoogsteen G.G mismatch in one direction and with an adenine base in the other direction in both complexes. It is striking that DNA and RNA aptamers selected independently from libraries of 10(14) molecules in each case utilize identical mismatch alignments for molecular recognition with micromolar affinity within binding-site pockets containing common structural elements.

Implantable hydrogel embedded dark-gold nanoswitch as a theranostic probe to sense and overcome cancer multidrug resistance

PubMed Central

Conde, João; Oliva, Nuria; Artzi, Natalie

2015-01-01

Multidrug resistance (MDR) in cancer cells is a substantial limitation to the success of chemotherapy. Here, we describe facile means to overcome resistance by silencing the multidrug resistance protein 1 (MRP1), before chemotherapeutic drug delivery in vivo with a single local application. Our platform contains hydrogel embedded with dark-gold nanoparticles modified with 5-fluorouracil (5-FU)-intercalated nanobeacons that serve as an ON/OFF molecular nanoswitch triggered by the increased MRP1 expression within the tumor tissue microenvironment. This nanoswitch can sense and overcome MDR prior to local drug release. The nanobeacons comprise a 5-FU intercalated DNA hairpin, which is labeled with a near-infrared (NIR) dye and a dark-quencher. The nanobeacons are designed to open and release the intercalated drug only upon hybridization of the DNA hairpin to a complementary target, an event that restores fluorescence emission due to nanobeacons conformational reorganization. Despite the cross-resistance to 5-FU, more than 90% tumor reduction is achieved in vivo in a triple-negative breast cancer model following 80% MRP1 silencing compared with the continuous tumor growth following only drug or nanobeacon administration. Our approach can be applied to reverse cross-resistance to other chemotherapeutic drugs and restore treatment efficacy. As a universal nanotheranostic probe, this platform can pave the way to early cancer detection and treatment. PMID:25733851

Conformational preferences of DNA following damage by aristolochic acids: Structural and energetic insights into the different mutagenic potential of the ALI and ALII-N(6)-dA adducts.

PubMed

Kathuria, Preetleen; Sharma, Purshotam; Abendong, Minette N; Wetmore, Stacey D

2015-04-21

Aristolochic acids (AAI and AAII), produced by the Aristolochiaceae family of plants, are classified as group I (human) carcinogens by the International Agency for Research on Cancer. These acids are metabolized in cells to yield aristolactams (ALI and ALII, respectively), which further form bulky adducts with the purine nucleobases. Specifically, the adenine lesions are more persistent in cells and have been associated with chronic renal diseases and related carcinogenesis. To understand the structural basis of the nephrotoxicity induced by AAs, the ALI-N(6)-dA and ALII-N(6)-dA lesions are systematically studied using computational methods. Density functional theory calculations indicate that the aristolactam moiety intrinsically prefers a planar conformation with respect to adenine. Nucleoside and nucleotide models suggest that the anti and syn orientations about the glycosidic bond are isoenergetic for both adducts. Molecular dynamics simulations and free energy calculations reveal that the anti base-displaced intercalated conformation is the most stable conformer for both types of AL-N(6)-dA adducted DNA, which agrees with previous experimental work on the ALII-N(6)-dA adduct and thereby validates our approach. Interestingly, this conformer differs from the dominant conformations adopted by other N6-linked adenine lesions, including those derived from polycyclic aromatic hydrocarbons. Furthermore, the second most stable syn base-displaced intercalated conformation lies closer in energy to the anti base-displaced intercalated conformation for ALI-N(6)-dA compared to ALII-N(6)-dA. This indicates that a mixture of conformations may be detectable for ALI-N(6)-dA in DNA. If this enhanced conformational flexibility of double-stranded DNA persists when bound to a lesion-bypass polymerase, this provides a possible structural explanation for the previously observed greater nephrotoxic potential for the ALI versus ALII-N(6)-dA adduct. In addition, the structural characteristics of the preferred conformations of adducted DNA explain the resistance of these adducts to repair and thereby add to our current understanding of the toxicity of AAs within living cells.

In Situ Formation of Decavanadate-Intercalated Layered Double Hydroxide Films on AA2024 and their Anti-Corrosive Properties when Combined with Hybrid Sol Gel Films

PubMed Central

Wu, Junsheng; Peng, Dongdong; He, Yuntao; Du, Xiaoqiong; Zhang, Zhan; Zhang, Bowei; Li, Xiaogang; Huang, Yizhong

2017-01-01

A layered double hydroxide (LDH) film was formed in situ on aluminum alloy 2024 through a urea hydrolysis method, and a decavanadate-intercalated LDH (LDH-V) film fabricated through the dip coating method. The microstructural and morphological characteristics were investigated by scanning electron microscopy (SEM). The corrosion-resistant performance was analyzed by electrochemical impedance spectroscopy (EIS), scanning electrochemical microscopy (SECM), and a salt-spray test (SST).The SEM results showed that a complete and defect-free surface was formed on the LDH-VS film. The anticorrosion results revealed that the LDH-VS film had better corrosion-resistant properties than the LDH-S film, especially long-term corrosion resistance. The mechanism of corrosion protection was proposed to consist of the self-healing effect of the decavanadate intercalation and the shielding effect of the sol-gel film. PMID:28772785

New X-ray insight into oxygen intercalation in epitaxial graphene grown on 4H-SiC(0001)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kowalski, G., E-mail: kowal@fuw.edu.pl; Tokarczyk, M.; Dąbrowski, P.

Efficient control of intercalation of epitaxial graphene by specific elements is a way to change properties of the graphene. Results of several experimental techniques, such as X-ray photoelectron spectroscopy, micro-Raman mapping, reflectivity, attenuated total reflection, X-ray diffraction, and X-ray reflectometry, gave a new insight into the intercalation of oxygen in the epitaxial graphene grown on 4H-SiC(0001). These results confirmed that oxygen intercalation decouples the graphene buffer layer from the 4H-SiC surface and converts it into the graphene layer. However, in contrast to the hydrogen intercalation, oxygen does not intercalate between carbon planes (in the case of few layer graphene) andmore » the interlayer spacing stays constant at the level of 3.35–3.32 Å. Moreover, X-ray reflectometry showed the presence of an oxide layer having the thickness of about 0.8 Å underneath the graphene layers. Apart from the formation of the nonuniform thin oxide layer, generation of defects in graphene caused by oxygen was also evidenced. Last but not least, water islands underneath defected graphene regions in both intercalated and non-intercalated samples were most probably revealed. These water islands are formed in the case of all the samples stored under ambient laboratory conditions. Water islands can be removed from underneath the few layer graphene stacks by relevant thermal treatment or by UV illumination.« less

Preparation, quantitative surface analysis, intercalation characteristics and industrial implications of low temperature expandable graphite

NASA Astrophysics Data System (ADS)

Peng, Tiefeng; Liu, Bin; Gao, Xuechao; Luo, Liqun; Sun, Hongjuan

2018-06-01

Expandable graphite is widely used as a new functional carbon material, especially as fire-retardant; however, its practical application is limited due to the high expansion temperature. In this work, preparation process of low temperature and highly expandable graphite was studied, using natural flake graphite as raw material and KMnO4/HClO4/NH4NO3 as oxidative intercalations. The structure, morphology, functional groups and thermal properties were characterized during expanding process by Fourier transform infrared spectroscopy (FTIR), Raman spectra, thermo-gravimetry differential scanning calorimetry (TG-DSC), X-ray diffraction (XRD), and scanning electron microscope (SEM). The analysis showed that by oxidation intercalation, some oxygen-containing groups were grafted on the edge and within the graphite layer. The intercalation reagent entered the graphite layer to increase the interlayer spacing. After expansion, the original flaky expandable graphite was completely transformed into worm-like expanded graphite. The order of graphite intercalation compounds (GICs) was proposed and determined to be 3 for the prepared expandable graphite, based on quantitative XRD peak analysis. Meanwhile, the detailed intercalation mechanisms were also proposed. The comprehensive investigation paved a benchmark for the industrial application of such sulfur-free expanded graphite.

Spectroscopic studies of the interaction of aspirin and its important metabolite, salicylate ion, with DNA, A·T and G·C rich sequences

NASA Astrophysics Data System (ADS)

Bathaie, S. Z.; Nikfarjam, L.; Rahmanpour, R.; Moosavi-Movahedi, A. A.

2010-12-01

Among different biological effects of acetylsalicylic acid (ASA), its anticancer property is controversial. Since ASA hydrolyzes rapidly to salicylic acid (SA), especially in the blood, interaction of both ASA and SA (as the small molecules) with ctDNA, oligo(dA·dT) 15 and oligo(dG·dC) 15, as a possible mechanism of their action, is investigated here. The results show that the rate of ASA hydrolysis in the absence and presence of ctDNA is similar. The spectrophotometric results indicate that both ASA and SA cooperatively bind to ctDNA. The binding constants ( K) are (1.7 ± 0.7) × 10 3 M -1 and (6.7 ± 0.2) × 10 3 M -1 for ASA and SA, respectively. Both ligands quench the fluorescence emission of ethidium bromide (Et)-ctDNA complex. The Scatchard plots indicate the non-displacement based quenching (non-intercalative binding). The circular dichroism (CD) spectra of ASA- or SA-ctDsNA complexes show the minor distortion of ctDNA structure, with no characteristic peaks for intercalation of ligands. Tm of ctDNA is decreased up to 3 °C upon ASA binding. The CD results also indicate more distortions on oligo(dG·dC) 15 structure due to the binding of both ASA and SA in comparison with oligo(dA·dT) 15. All data indicate the more affinity for SA binding with DNA minor groove in comparison with ASA which has more hydrophobic character.

Graphite fiber intercalation: Basic properties of copper chloride intercalated fibers

NASA Technical Reports Server (NTRS)

Jaworske, D. A.; Miller, J. D.

1986-01-01

In situ resistance measurements were used to follow the intercalation of copper chloride in pitch-based fibers. Subsequent single fiber resistivity measurements reveal a large range of resistivities, from 13 to 160 micro-ohms cm. Additional density measurements reveal a bimodal distribution of mass densities. The dense fibers have lower resistivities and correspond to the stage III compound identified by X-ray diffraction. Neither resistivity nor density correlate with diameter. Both energy dispersive spectroscopy and mass density data suggest that excess chlorine resides in the intercalated fiber, resulting in a stoichiometry of C4.9n CuCl2.5 (where n is the stage number) for the denser fibers. Finally, thermogravimetric analysis shows a 33 percent loss in mass upon heating to 700C. This loss in mass is attributed to loss of both chlorine and carbon.

PicoGreen dye as an active medium for plastic lasers

NASA Astrophysics Data System (ADS)

Pradeep, C.; Vallabhan, C. P. G.; Radhakrishnan, P.; Nampoori, V. P. N.

2015-08-01

Deoxyribonucleic acid lipid complex thin films are used as a host material for laser dyes. We tested PicoGreen dye, which is commonly used for the quantification of single and double stranded DNA, for its applicability as lasing medium. PicoGreen dye exhibits enhanced fluorescence on intercalation with DNA. This enormous fluorescence emission is amplified in a planar microcavity to achieve yellow lasing. Here the role of DNA is not only a host medium, but also as a fluorescence dequencher. With the obtained results we have ample reasons to propose PicoGreen dye as a lasing medium, which can lead to the development of DNA based bio-lasers.

Synthesis and characterization of new unsymmetrical Schiff base Zn (II) and Co (II) complexes and study of their interactions with bovin serum albumin and DNA by spectroscopic techniques.

PubMed

Sedighipoor, Maryam; Kianfar, Ali Hossein; Sabzalian, Mohammad R; Abyar, Fatemeh

2018-06-05

Two novel tetra-coordinated Cobalt(II) and Zinc (II) chelate series with the general formula of [Co (L)·2H 2 O] (1) and [Zn (L)] (2) [L=N-2-hydroxyacetophenon-N'-2-hydroxynaphthaldehyde-1,2 phenylenediimine)] with biologically active Schiff base ligands were synthesized and recognized by elemental analysis and multi-nuclear spectroscopy (IR and 1 H and 13 C NMR); then, their biological activities including DNA and protein interactions were studied. The interaction of the synthesized compounds with bovine serum albumin (BSA) was investigated via fluorescence spectroscopy, showing the affinity of the complexes for these proteins with relatively high binding constant values and the changed secondary BSA structure in the presence of the complexes. The interaction of these compounds with CT-DNA was considered by UV-Vis technique, emission titration, viscosity measurements, helix melting methods, and circular dichroism (CD) spectroscopy, confirming that the complexes were bound to CT-DNA by the intercalation binding mode. Furthermore, the complexes had the capability to displace the DNA-bound MB, as shown by the competitive studies of these complexes with methylene blue (MB), thereby suggesting the intercalation mode for the competition. Finally, the theoretical studies carried out by the docking method were performed to calculate the binding constants and recognize the binding site of the BSA and DNA by the complexes. In addition, in vitro and in silico studies showed that the compounds were degradable by bacterial and fungal biodegradation activities. Copyright © 2018 Elsevier B.V. All rights reserved.

Synthesis and characterization of new unsymmetrical Schiff base Zn (II) and Co (II) complexes and study of their interactions with bovin serum albumin and DNA by spectroscopic techniques

NASA Astrophysics Data System (ADS)

Sedighipoor, Maryam; Kianfar, Ali Hossein; Sabzalian, Mohammad R.; Abyar, Fatemeh

2018-06-01

Two novel tetra-coordinated Cobalt(II) and Zinc (II) chelate series with the general formula of [Co (L)·2H2O] (1) and [Zn (L)] (2) [L = N-2-hydroxyacetophenon-N‧-2-hydroxynaphthaldehyde-1,2 phenylenediimine)] with biologically active Schiff base ligands were synthesized and recognized by elemental analysis and multi-nuclear spectroscopy (IR and 1H and 13C NMR); then, their biological activities including DNA and protein interactions were studied. The interaction of the synthesized compounds with bovine serum albumin (BSA) was investigated via fluorescence spectroscopy, showing the affinity of the complexes for these proteins with relatively high binding constant values and the changed secondary BSA structure in the presence of the complexes. The interaction of these compounds with CT-DNA was considered by UV-Vis technique, emission titration, viscosity measurements, helix melting methods, and circular dichroism (CD) spectroscopy, confirming that the complexes were bound to CT-DNA by the intercalation binding mode. Furthermore, the complexes had the capability to displace the DNA-bound MB, as shown by the competitive studies of these complexes with methylene blue (MB), thereby suggesting the intercalation mode for the competition. Finally, the theoretical studies carried out by the docking method were performed to calculate the binding constants and recognize the binding site of the BSA and DNA by the complexes. In addition, in vitro and in silico studies showed that the compounds were degradable by bacterial and fungal biodegradation activities.

Design, synthesis, molecular modeling and anti-proliferative evaluation of novel quinoxaline derivatives as potential DNA intercalators and topoisomerase II inhibitors.

PubMed

Ibrahim, M K; Taghour, M S; Metwaly, A M; Belal, A; Mehany, A B M; Elhendawy, M A; Radwan, M M; Yassin, A M; El-Deeb, N M; Hafez, E E; ElSohly, M A; Eissa, I H

2018-06-04

New series of [1,2,4]triazolo [4,3-a]quinoxaline and bis([1,2,4]triazolo)[4,3-a:3',4'-c]quinoxaline derivatives have been designed, synthesized and biologically evaluated for their cytotoxic activities against three tumor cell lines (HePG-2, Hep-2 and Caco-2). Compounds 16 e , 21, 25 a and 25 b exhibited the highest activities against the examined cell lines with IC 50 values ranging from 0.29 to 0.90 μM comparable to that of doxorubicin (IC 50 ranging from 0.51 to 0.73 μM). The most active members were further evaluated for their topoisomerase II (Topo II) inhibitory activities and DNA intercalating affinities as potential mechanisms for their anti-proliferative activities. Interestingly, the results of Topo II inhibition and DNA binding assays were consistent with that of the cytotoxicity data, where the most potent anti-proliferative derivatives exhibited good Topo II inhibitory activities and DNA binding affinities, comparable to that of doxorubicin. Moreover, the most active compound 25 a caused cell cycle arrest at G2/M phase and induced apoptosis in Caco-2 cells. In addition, Furthermore, molecular docking studies were performed for the novel compounds against DNA-Topo II complex to investigate their binding patterns. Based on these studies, it was concluded that DNA binding and/or Topo II inhibition may contribute to the observed cytotoxicity of the synthesized compounds. Copyright © 2018. Published by Elsevier Masson SAS.

Progressing single biomolecule force spectroscopy measurements for the screening of DNA binding agents

NASA Astrophysics Data System (ADS)

Zhang, Wenke; Barbagallo, Romina; Madden, Claire; Roberts, Clive J.; Woolford, Alison; Allen, Stephanie

2005-10-01

Recent studies have indicated that the force-extension properties of single molecules of double stranded (ds) DNA are sensitive to the presence of small molecule DNA binding agents, and also to their mode of binding. These observations raise the possibility of using this approach as a highly sensitive tool for the screening of such agents. However, particularly for studies employing the atomic force microscope (AFM), several non-trivial barriers hinder the progress of this approach to the non-specialist arena and hence also the full realization of this possibility. In this paper, we therefore address a series of key reproducibility and metrological issues associated with this type of measurement. Specifically, we present an improved immobilization method that covalently anchors one end (5' end) of a dual labelled (5'-thiol, 3'-biotin) p53 DNA molecule onto a gold substrate via gold-thiol chemistry, whilst the biotinylated 3' end is available for 'pick-up' using a streptavidin modified AFM tip. We also show that co-surface immobilization of DNA with 6-mercapto-1-hexanol (MCH) can also lead to a further increase the measured contour length. We demonstrate the impact of these improved protocols through the observation of the cooperative transition plateau in a DNA fragment of approximately 118 bp, a significantly smaller fragment than previously investigated. The results of a comparative study of the effects of a model minor groove binder (Hoechst 33258) and an intercalating drug (proflavine), alone, as a mixture and under different buffer conditions, are also presented.

DNA binding by a new metallointercalator that contains a proflavine group bearing a hanging chelating unit.

PubMed

Bazzicalupi, Carla; Bencini, Andrea; Bianchi, Antonio; Biver, Tarita; Boggioni, Alessia; Bonacchi, Sara; Danesi, Andrea; Giorgi, Claudia; Gratteri, Paola; Ingraín, Antonio Marchal; Secco, Fernando; Sissi, Claudia; Valtancoli, Barbara; Venturini, Marcella

2008-01-01

The new bifunctional molecule 3,6-diamine-9-[6,6-bis(2-aminoethyl)-1,6-diaminohexyl]acridine (D), which is characterised by both an aromatic moiety and a separate metal-complexing polyamine centre, has been synthesised. The characteristics of D and its ZnII complex ([ZnD]) (protonation and metal-complexing constants, optical properties and self-aggregation phenomena) have been analysed by means of NMR spectroscopy, potentiometric, spectrophotometric and spectrofluorimetric techniques. The equilibria and kinetics of the binding process of D and [ZnD] to calf thymus DNA have been investigated at I=0.11 M (NaCl) and 298.1 K by using spectroscopic methods and the stopped-flow technique. Static measurements show biphasic behaviour for both D-DNA and [ZnD]-DNA systems; this reveals the occurrence of two different binding processes depending on the polymer-to-dye molar ratio (P/D). The binding mode that occurs at low P/D values is interpreted in terms of external binding with a notable contribution from the polyamine residue. The binding mode at high P/D values corresponds to intercalation of the proflavine residue. Stopped-flow, circular dichroism and supercoiled-DNA unwinding experiments corroborate the proposed mechanism. Molecular-modelling studies support the intercalative process and evidence the influence of NH+...O interactions between the protonated acridine nitrogen atom and the oxygen atoms of the polyanion; these interactions play a key role in determining the conformation of DNA adducts.

Antibacterial effect of cationic porphyrazines and anionic phthalocyanine and their interaction with plasmid DNA

NASA Astrophysics Data System (ADS)

Hassani, Leila; Hakimian, Fatemeh; Safaei, Elham; Fazeli, Zahra

2013-11-01

Resistance to antibiotics is a public health issue and identification of new antibacterial agents is one of the most important goals of pharmacological research. Among the novel developed antibacterial agents, porphyrin complexes and their derivatives are ideal candidates for use in medical applications. Phthalocyanines differ from porphyrins by having nitrogen atoms link the individual pyrrol units. The aza analogues of the phthalocyanines (azaPcs) such as tetramethylmetalloporphyrazines are heterocyclic Pc analogues. In this investigation, interaction of an anionic phthalocyanine (Cu(PcTs)) and two cationic tetrapyridinoporphyrazines including [Cu(2,3-tmtppa)]4+ and [Cu(3,4-tmtppa)]4+ complexes with plasmid DNA was studied using spectroscopic and gel electrophoresis methods. In addition, antibacterial effect of the complexes against Gram-positive (Staphylococcus aureus) and Gram-negative (Escherichia coli) bacteria was investigated using dilution test method. The results indicated that both porphyrazines have significant antibacterial properties, but Cu(PcTs) has weak antibacterial effect. Compairing the binding of the phthalocyanine and the porphyrazines to DNA demonstrated that the interaction of cationic porphyrazines is stronger than the anionic phthalocyanine remarkably. The extent of hypochromicity and red shift of absorption spectra indicated preferential intercalation of the two porphyrazine into the base pairs of DNA helix. Gel electrophoresis result implied Cu(2,3-tmtppa) and Cu(3,4-tmtppa) are able to perform cleavage of the plasmid DNA. Consequently, DNA binding and cleavage might be one of the antibacterial mechanisms of the complexes.

Thin-walled nanoscrolls by multi-step intercalation from tubular halloysite-10 Å and its rearrangement upon peroxide treatment

NASA Astrophysics Data System (ADS)

Zsirka, Balázs; Horváth, Erzsébet; Szabó, Péter; Juzsakova, Tatjána; Szilágyi, Róbert K.; Fertig, Dávid; Makó, Éva; Varga, Tamás; Kónya, Zoltán; Kukovecz, Ákos; Kristóf, János

2017-03-01

Surface modification of the halloysite-10 Å mineral with tubular morphology can be achieved by slightly modified procedures developed for the delamination of kaolinite minerals. The resulting delaminated halloysite nanoparticles have unexpected surface/morphological properties that display, new potentials in catalyst development. In this work, a four-step intercalation/delamination procedure is described for the preparation of thin-walled nanoscrolls from the multi-layered hydrated halloysite mineral that consists of (1) intercalation of halloysite with potassium acetate, (2) replacement intercalation with ethylene glycol, (3) replacement intercalation with hexylamine, and (4) delamination with toluene. The intercalation steps were followed by X-ray diffraction, transmission electron microscopy, N2 adsorption-desorption, thermogravimetry, and infrared spectroscopy. Delamination eliminated the crystalline order and the crystallite size along the 'c'-axis, increased the specific surface area, greatly decreased the thickness of the mineral tubes to a monolayer, and shifted the pore diameter toward the micropore region. Unexpectedly, the removal of residual organics from intercalation steps adsorbed at the nanoscroll surface with a peroxide treatment resulted in partial recovery of crystallinity and increase of crystallite size along the 'c'-crystal direction. The d(001) value showed a diffuse pattern at 7.4-7.7 Å due to the rearrangement of the thin-walled nanoscrolls toward the initial tubular morphology of the dehydrated halloysite-7 Å mineral.

Synthesis, spectroscopic, physicochemical and structural characterization of tetrandrine-based macrocycles functionalized with acridine and anthracene groups: DNA binding and anti-proliferative activity.

PubMed

Calvillo-Páez, Viviana; Sotelo-Mundo, Rogerio R; Leyva-Peralta, Mario; Gálvez-Ruiz, Juan Carlos; Corona-Martínez, David; Moreno-Corral, Ramón; Escobar-Picos, Raymundo; Höpfl, Herbert; Juárez-Sánchez, Octavio; Lara, Karen Ochoa

2018-04-25

In this work, we report on the synthesis of two new mono-alkylated tetrandrine derivatives with acridine and anthracene units, MAcT and MAnT. The compounds were fully characterized by physicochemical techniques and single-crystal X-ray diffraction analysis. In addition, both derivatives were studied as nucleotide receptors and double-stranded DNA binders in aqueous phosphate buffer at pH = 7.2 using UV-vis and fluorescence spectroscopy. According to the molecular recognition studies, MAcT and MAnT exhibit high affinity (K ∼ 10 5  M -1 ) and selectivity for ds-DNA, presumably in an intercalation mode. Finally, the anti-proliferative effects of the tetrandrine derivatives on different cancer cell lines were explored, revealing promising activities. Particularly, the mono-anthracene tetrandrine derivative MAnT showed an IC 50 of 2.74 μg/mL on the HeLa cervical cancer cell line, representing a value 3.3 times smaller than that obtained for unsubstituted tetrandrine. Examination of the cytotoxic effects on the HeLa cell line by inverted microscopy suggests that the cell death mechanism consists basically in apoptosis. The molecular modelling of three ds-DNA-MAcT complexes, suggested that the macrocycles may use an intercalation binding mode towards DNA. MAcT is predicted to bind into the major groove of the ds-DNA providing non-covalent interactions such as electrostatic, van der Waals and hydrophobic interactions that lead to selectivity. Overall experimental data supports the mode of action of MAnT and MAcT as cytotoxic compounds against cancer cell lines via a DNA interaction mechanism. Copyright © 2018 Elsevier B.V. All rights reserved.

Interaction of DNA with Simple and Mixed Ligand Copper(II) Complexes of 1,10-Phenanthrolines as Studied by DNA-Fiber EPR Spectroscopy

PubMed Central

Chikira, Makoto; Ng, Chew Hee; Palaniandavar, Mallayan

2015-01-01

The interaction of simple and ternary Cu(II) complexes of 1,10-phenanthrolines with DNA has been studied extensively because of their various interesting and important functions such as DNA cleavage activity, cytotoxicity towards cancer cells, and DNA based asymmetric catalysis. Such functions are closely related to the DNA binding modes of the complexes such as intercalation, groove binding, and electrostatic surface binding. A variety of spectroscopic methods have been used to study the DNA binding mode of the Cu(II) complexes. Of all these methods, DNA-fiber electron paramagnetic resonance (EPR) spectroscopy affords unique information on the DNA binding structures of the complexes. In this review we summarize the results of our DNA-fiber EPR studies on the DNA binding structure of the complexes and discuss them together with the data accumulated by using other measurements. PMID:26402668

Preparation and properties of single-walled nanotubes filled with inorganic compounds

NASA Astrophysics Data System (ADS)

Eliseev, Andrei A.; Kharlamova, M. V.; Chernysheva, M. V.; Lukashin, Alexey V.; Tretyakov, Yuri D.; Kumskov, A. S.; Kiselev, N. A.

2009-09-01

The state-of-the-art methods for filling single-walled carbon nanotubes (SWNTs) are analyzed systematically. In situ and ex situ approaches for filling SWNTs are addressed. They are based on both intercalation of inorganic substances from the gas phase, solution or melts inside SWNTs and the formation of nanocrystals inside the channels as a result of chemical reactions. A comparative evaluation of these methods is performed, and major requirements for successful formation of '1D-crystal@SWNT' nanocomposites are formulated. The functional properties of the intercalated single-walled nanotubes and their possible applications in modern nanotechnologies are discussed.

Phenazine virulence factor binding to extracellular DNA is important for Pseudomonas aeruginosa biofilm formation.

PubMed

Das, Theerthankar; Kutty, Samuel K; Tavallaie, Roya; Ibugo, Amaye I; Panchompoo, Janjira; Sehar, Shama; Aldous, Leigh; Yeung, Amanda W S; Thomas, Shane R; Kumar, Naresh; Gooding, J Justin; Manefield, Mike

2015-02-11

Bacterial resistance to conventional antibiotics necessitates the identification of novel leads for infection control. Interference with extracellular phenomena, such as quorum sensing, extracellular DNA integrity and redox active metabolite release, represents a new frontier to control human pathogens such as Pseudomonas aeruginosa and hence reduce mortality. Here we reveal that the extracellular redox active virulence factor pyocyanin produced by P. aeruginosa binds directly to the deoxyribose-phosphate backbone of DNA and intercalates with DNA nitrogenous base pair regions. Binding results in local perturbations of the DNA double helix structure and enhanced electron transfer along the nucleic acid polymer. Pyocyanin binding to DNA also increases DNA solution viscosity. In contrast, antioxidants interacting with DNA and pyocyanin decrease DNA solution viscosity. Biofilms deficient in pyocyanin production and biofilms lacking extracellular DNA show similar architecture indicating the interaction is important in P. aeruginosa biofilm formation.

Phenazine virulence factor binding to extracellular DNA is important for Pseudomonas aeruginosa biofilm formation

PubMed Central

Das, Theerthankar; Kutty, Samuel K.; Tavallaie, Roya; Ibugo, Amaye I.; Panchompoo, Janjira; Sehar, Shama; Aldous, Leigh; Yeung, Amanda W. S.; Thomas, Shane R.; Kumar, Naresh; Gooding, J. Justin; Manefield, Mike

2015-01-01

Bacterial resistance to conventional antibiotics necessitates the identification of novel leads for infection control. Interference with extracellular phenomena, such as quorum sensing, extracellular DNA integrity and redox active metabolite release, represents a new frontier to control human pathogens such as Pseudomonas aeruginosa and hence reduce mortality. Here we reveal that the extracellular redox active virulence factor pyocyanin produced by P. aeruginosa binds directly to the deoxyribose-phosphate backbone of DNA and intercalates with DNA nitrogenous base pair regions. Binding results in local perturbations of the DNA double helix structure and enhanced electron transfer along the nucleic acid polymer. Pyocyanin binding to DNA also increases DNA solution viscosity. In contrast, antioxidants interacting with DNA and pyocyanin decrease DNA solution viscosity. Biofilms deficient in pyocyanin production and biofilms lacking extracellular DNA show similar architecture indicating the interaction is important in P. aeruginosa biofilm formation. PMID:25669133

Release of the cyano moiety in the crystal structure of N-cyanomethyl-N-(2-methoxyethyl)-daunomycin complexed with d(CGATCG).

PubMed

Saminadin, P; Dautant, A; Mondon, M; Langlois D'estaintot, B; Courseille, C; Précigoux, G

2000-01-01

Doxorubicin is among the most widely used anthracycline in cancer chemotherapy. In an attempt to avoid the cardiotoxicity and drug resistance of doxorubicin therapy, several analogues were synthesized. The cyanomorpholinyl derivative is the most cytotoxic. They differ greatly from their parent compound in their biological and pharmacological properties, inducing cross-links in drug DNA complexes. The present study concerns N-cyanomethyl-N-(2-methoxyethyl)-daunomycin (CMDa), a synthetic analogue of cyanomorpholino-daunomycin. Compared to doxorubicin, CMDa displays a cytotoxic activity on L1210 leukemia cells at higher concentration but is effective on doxorubicin resistant cells. The results of fluorescence quenching experiments as well as the melting temperature (DeltaTm = 7.5 degrees C) studies are consistent with a drug molecule which intercalates between the DNA base pairs and stabilizes the DNA double helix. The crystal structure of CMDa complexed to the hexanucleotide d(CGATCG) has been determined at 1.5 A resolution. The complex crystallizes in the space group P41212 and is similar to other anthracycline-hexanucleotide complexes. In the crystal state, the observed densities indicate the formation of N-hydroxymethyl-N-(2-methoxyethyl)-daunomycin (HMDa) with the release of the cyano moiety without DNA alkylation. The formation of this degradation compound is discussed in relation with other drug modifications when binding to DNA. Comparison with two other drug-DNA crystal structures suggests a correlation between a slight change in DNA conformation and the nature of the amino sugar substituents at the N3' position located in the minor groove.

Polyethylene organo-clay nanocomposites: the role of the interface chemistry on the extent of clay intercalation/exfoliation.

PubMed

Mainil, Michaël; Alexandre, Michaël; Monteverde, Fabien; Dubois, Philippe

2006-02-01

High density polyethylene (HDPE)/clay nanocomposites have been prepared using three different functionalized polyethylene compatibilizers: an ethylene/vinyl acetate copolymer, a polyethylene grafted with maleic anhydride functions and a (styrene-b-ethylene/butylene-b-styrene) block copolymer. The nanocomposites were prepared via two different routes: (1) the dispersion in HDPE of a masterbatch prepared from the compatibilizer and the clay or (2) the direct melt blending of the three components. For each compatibilizer, essentially intercalated nanocomposites were formed as determined by X-ray diffraction and transmission electron microscopy. With the ethylene/vinyl acetate copolymer, a significant delamination of the intercalated clay in thin stacks was observed. This dispersion of thin intercalated stacks within the polymer matrix allowed increasing significantly the stiffness and the flame resistance of the nanocomposite. A positive effect of shear rate and blending time has also been put into evidence, especially for the process based on the masterbatch preparation, improving both the formation of thin stacks of intercalated clay and the mechanical properties and the flame resistance of the formed nanocomposites.

Structural consequences of hydrogen intercalation of epitaxial graphene on SiC(0001)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Emery, Jonathan D., E-mail: jdemery@anl.gov, E-mail: bedzyk@northwestern.edu; Johns, James E.; McBriarty, Martin E.

2014-10-20

The intercalation of various atomic species, such as hydrogen, to the interface between epitaxial graphene (EG) and its SiC substrate is known to significantly influence the electronic properties of the graphene overlayers. Here, we use high-resolution X-ray reflectivity to investigate the structural consequences of the hydrogen intercalation process used in the formation of quasi-free-standing (QFS) EG/SiC(0001). We confirm that the interfacial layer is converted to a layer structurally indistinguishable from that of the overlying graphene layers. This newly formed graphene layer becomes decoupled from the SiC substrate and, along with the other graphene layers within the film, is vertically displacedmore » by ∼2.1 Å. The number of total carbon layers is conserved during the process, and we observe no other structural changes such as interlayer intercalation or expansion of the graphene d-spacing. These results clarify the under-determined structure of hydrogen intercalated QFS-EG/SiC(0001) and provide a precise model to inform further fundamental and practical understanding of the system.« less

Controlling the actuation properties of MXene paper electrodes upon cation intercalation

DOE PAGES

Come, Jeremy E.; Black, Jennifer M.; Naguib, Michael; ...

2015-08-05

Atomic force microscopy was used to monitor the macroscopic deformation in a delaminated Ti₃C₂ paper electrode in-situ, during charge/discharge in a variety of aqueous electrolytes to examine the effect of the cation intercalation on the electrochemical behavior and mechanical response. The results show a strong dependence of the electrode deformation on cation size and charge. The electrode undergoes a large contraction during Li⁺, Na⁺ or Mg²⁺ intercalation, differentiating the Ti₃C₂ paper from conventional electrodes where redox intercalation of ions (e.g. Li⁺) into the bulk phase (e.g. graphite, silicon) results in volumetric expansion. This feature may explain the excellent rate performancemore » and cyclability reported for MXenes. We also demonstrated that the variation of the electromechanical contraction can be easily adjusted by electrolyte exchange, and shows interesting characteristics for the design of actuators based on 2D metal carbides.« less

Intercalated europium metal in epitaxial graphene on SiC

DOE PAGES

Anderson, Nathaniel; Hupalo, Myron; Keavney, David; ...

2017-10-25

X-ray magnetic circular dichroism (XMCD) reveals the magnetic properties of intercalated europium metal under graphene on SiC(0001). Intercalation of Eu nanoclusters (average size 2.5 nm) between graphene and SiC substate are formed by deposition of Eu on epitaxially grown graphene that is subsequently annealed at various temperatures while keeping the integrity of the graphene layer. Using sum-rules analysis of the XMCD of Eu M 4,5 edges at T = 15 K, our samples show paramagnetic-like behavior with distinct anomaly at T ≈ 90 K, which may be related to the Nèel transition, T N = 91 K, of bulk metalmore » Eu. Here, we find no evidence of ferromagnetism due to EuO or antiferromagnetism due to Eu 2 O 3, indicating that the graphene layer protects the intercalated metallic Eu against oxidation over months of exposure to atmospheric environment.« less

Preparation and Characterization of Novel Montmorillonite Nanocomposites

NASA Astrophysics Data System (ADS)

Mansa, Rola

Clay minerals have historically played a consequential role in human health. While the beginnings were rooted in geophagy, a primitive act of consuming earth, the health-related uses of clay minerals have evolved and diversified over time.. As excipients in pharmaceutical formulations, clay minerals can attribute novel properties onto intercalated compounds. Intercalating oxybenzone, a UV filter, within the interlamellar space of montmorillonite is desirable in order to minimize direct contact with skin. Intercalating resveratrol, a compound known for attributing beneficial effects onto human health, may be advantageous since this compound is susceptible to cis-trans isomerisation. The strategy of using alkylammonium--modified clay was undertaken and proved successful for the intercalation of oxybenzone. The field of biopolymer/layered silicate nanocomposites is heavily researched for use in a multitude of applications. Novel montmorillonite nanocomposites were prepared with neutral guar gum and cationic guar gum, using an environmentally friendly process and are fully characterized.

Tunable thermal expansion in framework materials through redox intercalation

PubMed Central

Chen, Jun; Gao, Qilong; Sanson, Andrea; Jiang, Xingxing; Huang, Qingzhen; Carnera, Alberto; Rodriguez, Clara Guglieri; Olivi, Luca; Wang, Lei; Hu, Lei; Lin, Kun; Ren, Yang; Lin, Zheshuai; Wang, Cong; Gu, Lin; Deng, Jinxia; Attfield, J. Paul; Xing, Xianran

2017-01-01

Thermal expansion properties of solids are of fundamental interest and control of thermal expansion is important for practical applications but can be difficult to achieve. Many framework-type materials show negative thermal expansion when internal cages are empty but positive thermal expansion when additional atoms or molecules fill internal voids present. Here we show that redox intercalation offers an effective method to control thermal expansion from positive to zero to negative by insertion of Li ions into the simple negative thermal expansion framework material ScF3, doped with 10% Fe to enable reduction. The small concentration of intercalated Li ions has a strong influence through steric hindrance of transverse fluoride ion vibrations, which directly controls the thermal expansion. Redox intercalation of guest ions is thus likely to be a general and effective method for controlling thermal expansion in the many known framework materials with phonon-driven negative thermal expansion. PMID:28181576

Tunable thermal expansion in framework materials through redox intercalation

NASA Astrophysics Data System (ADS)

Chen, Jun; Gao, Qilong; Sanson, Andrea; Jiang, Xingxing; Huang, Qingzhen; Carnera, Alberto; Rodriguez, Clara Guglieri; Olivi, Luca; Wang, Lei; Hu, Lei; Lin, Kun; Ren, Yang; Lin, Zheshuai; Wang, Cong; Gu, Lin; Deng, Jinxia; Attfield, J. Paul; Xing, Xianran

2017-02-01

Thermal expansion properties of solids are of fundamental interest and control of thermal expansion is important for practical applications but can be difficult to achieve. Many framework-type materials show negative thermal expansion when internal cages are empty but positive thermal expansion when additional atoms or molecules fill internal voids present. Here we show that redox intercalation offers an effective method to control thermal expansion from positive to zero to negative by insertion of Li ions into the simple negative thermal expansion framework material ScF3, doped with 10% Fe to enable reduction. The small concentration of intercalated Li ions has a strong influence through steric hindrance of transverse fluoride ion vibrations, which directly controls the thermal expansion. Redox intercalation of guest ions is thus likely to be a general and effective method for controlling thermal expansion in the many known framework materials with phonon-driven negative thermal expansion.

Intercalated europium metal in epitaxial graphene on SiC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Anderson, Nathaniel; Hupalo, Myron; Keavney, David

X-ray magnetic circular dichroism (XMCD) reveals the magnetic properties of intercalated europium metal under graphene on SiC(0001). Intercalation of Eu nanoclusters (average size 2.5 nm) between graphene and SiC substate are formed by deposition of Eu on epitaxially grown graphene that is subsequently annealed at various temperatures while keeping the integrity of the graphene layer. Using sum-rules analysis of the XMCD of Eu M 4,5 edges at T = 15 K, our samples show paramagnetic-like behavior with distinct anomaly at T ≈ 90 K, which may be related to the Nèel transition, T N = 91 K, of bulk metalmore » Eu. Here, we find no evidence of ferromagnetism due to EuO or antiferromagnetism due to Eu 2 O 3, indicating that the graphene layer protects the intercalated metallic Eu against oxidation over months of exposure to atmospheric environment.« less

Li intercalation in graphite: A van der Waals density-functional study

NASA Astrophysics Data System (ADS)

Hazrati, E.; de Wijs, G. A.; Brocks, G.

2014-10-01

Modeling layered intercalation compounds from first principles poses a problem, as many of their properties are determined by a subtle balance between van der Waals interactions and chemical or Madelung terms, and a good description of van der Waals interactions is often lacking. Using van der Waals density functionals we study the structures, phonons and energetics of the archetype layered intercalation compound Li-graphite. Intercalation of Li in graphite leads to stable systems with calculated intercalation energies of -0.2 to -0.3 eV/Li atom, (referred to bulk graphite and Li metal). The fully loaded stage 1 and stage 2 compounds LiC6 and Li1 /2C6 are stable, corresponding to two-dimensional √{3 }×√{3 } lattices of Li atoms intercalated between two graphene planes. Stage N >2 structures are unstable compared to dilute stage 2 compounds with the same concentration. At elevated temperatures dilute stage 2 compounds easily become disordered, but the structure of Li3 /16C6 is relatively stable, corresponding to a √{7 }×√{7 } in-plane packing of Li atoms. First-principles calculations, along with a Bethe-Peierls model of finite temperature effects, allow for a microscopic description of the observed voltage profiles.

Release behavior and toxicity profiles towards A549 cell lines of ciprofloxacin from its layered zinc hydroxide intercalation compound.

PubMed

Abdul Latip, Ahmad Faiz; Hussein, Mohd Zobir; Stanslas, Johnson; Wong, Charng Choon; Adnan, Rohana

2013-01-01

Layered hydroxides salts (LHS), a layered inorganic compound is gaining attention in a wide range of applications, particularly due to its unique anion exchange properties. In this work, layered zinc hydroxide nitrate (LZH), a family member of LHS was intercalated with anionic ciprofloxacin (CFX), a broad spectrum antibiotic via ion exchange in a mixture solution of water:ethanol. Powder x-ray diffraction (XRD), Fourier transform infrared (FTIR) and thermogravimetric analysis (TGA) confirmed the drug anions were successfully intercalated in the interlayer space of LZH. Specific surface area of the obtained compound was increased compared to that of the host due to the different pore textures between the two materials. CFX anions were slowly released over 80 hours in phosphate-buffered saline (PBS) solution due to strong interactions that occurred between the intercalated anions and the host lattices. The intercalation compound demonstrated enhanced antiproliferative effects towards A549 cancer cells compared to the toxicity of CFX alone. Strong host-guest interactions between the LZH lattice and the CFX anion give rise to a new intercalation compound that demonstrates sustained release mode and enhanced toxicity effects towards A549 cell lines. These findings should serve as foundations towards further developments of the brucite-like host material in drug delivery systems.

Synthesis and DNA interaction of a mixed proflavine-phenanthroline Tröger base.

PubMed

Baldeyrou, Brigitte; Tardy, Christelle; Bailly, Christian; Colson, Pierre; Houssier, Claude; Charmantray, Franck; Demeunynck, Martine

2002-04-01

We report the synthesis of an asymmetric Tröger base containing the two well characterised DNA binding chromophores, proflavine and phenanthroline. The mode of interaction of the hybrid molecule was investigated by circular and linear dichroism experiments and a biochemical assay using DNA topoisomerase I. The data are compatible with a model in which the proflavine moiety intercalates between DNA base pairs and the phenanthroline ring occupies the DNA groove. DNase I cleavage experiments were carried out to investigate the sequence preference of the hybrid ligand and a well resolved footprint was detected at a site encompassing two adjacent 5'-GTC.5-GAC triplets. The sequence preference of the asymmetric molecule is compared to that of the symmetric analogues.

Electronic and Structural Studies of Intercalated Graphite and Buckminsterfullerene.

NASA Astrophysics Data System (ADS)

Kelty, Stephen Paul

Under the direction of Prof. C. M. Lieber, the surface electronic and structural properties of binary MC_{rm x} and ternary rm MM^' C_{x } donor graphite intercalation compounds (GICs) were investigated using scanning tunneling microscopy (STM) and other surface sensitive techniques. The STM images revealed previously unobserved superstructures in the local density of states contours. These new superstructures include a commensurate 4.9 A periodicity (MC_8, where M = Li, K, Rb, Cs, KHg, rm K_2Hg_2 and rm K_2Tl _3). This superstructure has been interpreted as a modulation of the surface density of states due to the underlying commensurate intercalate lattice. Other GICs exhibit longer wavelength incommensurate superstructures, including: 19 A rm (KH_{0.8}C _8), 12 A rm (KH_{0.8 }C_4), 8.9 A rm (KHgC _4) and 7.5 A rm (KTl_ {1.5}C_8) periodicities. The direct -space wavelength of these incommensurate superstructures was found to scale inversely with the amount of charge transferred from the intercalate to the graphite layers. Such a correlation is consistent with the wavelength dependence on Fermi surface expansion of a charge density wave (CDW) state. STM investigations of adsorbed films of colloidal BiI_3, prepared by a solution-phase method, revealed the presence of mono-disperse 10-50 A single-layer particles with atomic resolution. This investigation demonstrated both the validity of the preparative method for the BiI_3 particles and the capability of the STM to atomically resolve small semiconducting particles. The structural and superconducting properties of alkali metal intercalated Buckminsterfullerene (C _{60}) were also investigated. A new preparatory method was developed using heavy metal alloys instead of pure alkali metal. Using these alloys, it was discovered that high superconducting fraction intercalation compounds could be prepared under milder conditions than by using the pure alkali metal. In addition, intercalation of Hg, Tl and Bi alloys of Cs was found to form a superconducting phase which has never been prepared by direct intercalation of Cs metal. Finally, other investigators have empirically derived a linear dependence of T_{ rm c} on lattice constant for intercalated C_{60}. This dependence has been used to model the electron pairing mechanism for the superconducting state. Investigations presented herein indicate that for lattice constants greater than 14.5 A, no further increases in T_{rm c} are observed. This finding places constraints on the above mentioned electron pairing models.

Properties of K,Rb-intercalated C{sub 60} encapsulated inside carbon nanotubes called peapods derived from nuclear magnetic resonance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mahfouz, R.; Bouhrara, M.; Kim, Y.

2015-09-21

We present a detailed experimental study on how magnetic and electronic properties of Rb,K-intercalated C{sub 60} encapsulated inside carbon nanotubes called peapods can be derived from {sup 13}C nuclear magnetic resonance investigations. Ring currents do play a basic role in those systems; in particular, the inner cavities of nanotubes offer an ideal environment to investigate the magnetism at the nanoscale. We report the largest diamagnetic shifts down to −68.3 ppm ever observed in carbon allotropes, which is connected to the enhancement of the aromaticity of the nanotube envelope upon intercalation. The metallization of intercalated peapods is evidenced from the chemical shiftmore » anisotropy and spin-lattice relaxation (T{sub 1}) measurements. The observed relaxation curves signal a three-component model with two slow and one fast relaxing components. We assigned the fast component to the unpaired electrons charged C{sub 60} that show a phase transition near 100 K. The two slow components can be rationalized by the two types of charged C{sub 60} at two different positions with a linear regime following Korringa behavior, which is typical for metallic system and allow us to estimate the density of sate at Fermi level n(E{sub F})« less

Extreme anisotropy and anomalous transport properties of heavily electron doped Lix(NH3)yFe2Se2 single crystals

NASA Astrophysics Data System (ADS)

Sun, Shanshan; Wang, Shaohua; Yu, Rong; Lei, Hechang

2017-08-01

We report the growth of heavily electron doped Li-NH3 intercalated FeSe single crystals that are free of material complexities and allow access to the intrinsic superconducting properties. Lix(NH3)yFe2Se2 single crystals show extremely large electronic anisotropy in both normal and superconducting states. They also exhibit anomalous transport properties in the normal state, which are believed to possibly be related to the anisotropy of relaxation time and/or temperature-dependent electron carrier concentration. Taking into account the great chemical flexibility of intercalants in the system, our findings provide a platform to understanding the origin of superconductivity in FeSe-related superconductors.

Preparation of poly(vinyl alcohol)/kaolinite nanocomposites via in situ polymerization

DOE Office of Scientific and Technical Information (OSTI.GOV)

Jia Xin; Department of Chemistry, Hexi University, Zhangye 734000; Li Yanfeng

2008-03-04

Poly(vinyl alcohol)/kaolinite intercalated nanocomposites (Kao-PVA) were prepared via in situ intercalation radical polymerization. Vinyl acetate (VAc) was intercalated into kaolinite by a displacement method using dimethyl sulfoxide/kaolinite (Kao-DMSO) as the intermediate. Then, PVAc/kaolinite (Kao-PVAc) was obtained via radical polymerization with benzoyl peroxide (BPO) as initiator. Last, PVAc/kaolinite was saponified via direct-hydrolysis with NaOH solution in order to obtain PVA/kaolinite nanocomposites, which was characterized by Fourier-Transformation spectroscopy (FTIR), wide X-ray diffraction (WXRD) and transmission electron microscopy (TEM). Their differential scanning calorimetry (DSC) and thermogravimetric analysis (TGA) results of the obtained PVA/kaolinite suggested that the thermal properties had an obvious improvement.

Preservation of glutamic acid-iron chelate into montmorillonite to efficiently degrade Reactive Blue 19 in a Fenton system under sunlight irradiation at neutral pH

NASA Astrophysics Data System (ADS)

Huang, Zhujian; Wu, Pingxiao; Gong, Beini; Yang, Shanshan; Li, Hailing; Zhu, Ziao; Cui, Lihua

2016-05-01

To further enhance the visible light responsive property and the chemical stability of Fe/clay mineral catalysts, glutamic acid-iron chelate intercalated montmorillonite (G-Fe-Mt) was developed. The physiochemical properties of G-Fe-Mt were investigated by X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), UV-vis diffuse reflectance spectroscopy (DRS), etc. The results showed that glutamic acid-iron chelates were successfully intercalated into the gallery of montmorillonite and the intercalated glutamic acid-iron chelate molecules were well preserved. The product G-Fe-Mt displayed excellent catalytic performance in heterogeneous photo-Fenton reaction under sunlight irradiation at acidic and neutral pH values. The chelation and the visible light responsiveness of glutamic acid produce a synergistic effect leading to greatly enhanced sunlight-Fenton reaction catalyzed by the heterogeneous G-Fe-Mt under neutral pH. G-Fe-Mt is a promising catalyst for advanced oxidation processes.

6,6″-Dimethyl-2,2':6',2″-terpyridine revisited: new fluorescent silver(I) helicates with in vitro antiproliferative activity via selective nucleoli targeting.

PubMed

Fik, Marta A; Gorczyński, Adam; Kubicki, Maciej; Hnatejko, Zbigniew; Fedoruk-Wyszomirska, Agnieszka; Wyszko, Eliza; Giel-Pietraszuk, Małgorzata; Patroniak, Violetta

2014-10-30

6,6″-Dimethyl-2,2':6',2″-terpyridine ligand (L) reacts in equimolar ratio with Ag(I) ions what results in formation of dinuclear double helicates, which differ in terms of framework and complexity in accordance to counterions and solvent applied. Obtained complexes were thoroughly studied in terms of their biological activity, with the positive antiproliferative outcome on three human cancer cell lines: human breast cancer (T47D), human cervical carcinoma (HeLa) and human lung cancer (A-549). Performed DNA binding experiments showed that given Ag(I) species specifically interact with DNA double helix via intercalation and were visualized by confocal microscopy to specifically bind to the nuclei. All newly synthesized helical systems exhibit promising antimicrobial activity against Gram-negative Escherichia coli and Gram-positive Staphylococcus aureus bacterial strains. Spectrophotometric properties were described as fulfilment of structural studies of newly presented complexes confirming their helical structure in solution. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Influence of sodium dodecyl sulfate concentration on the photocatalytic activity and dielectric properties of intercalated sodium dodecyl sulfate into Zn–Cd–Al layered double hydroxide

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahmed, Abdullah Ahmed Ali, E-mail: abdullah2803@gmail.com; Talib, Zainal Abidin; Hussein, Mohd Zobir

2015-02-15

Highlights: • Zn–Cd–Al–LDH–DS were synthesized with different SDS concentrations. • Photocatalytic activity of samples was improved by increasing SDS concentration. • Dielectric response of LDH can be described by anomalous low frequency dispersion. • The dc conductivity values were calculated for Zn–Cd–Al–LDH–DS samples. • ESR spectra exhibited the successful intercalation of DS molecule into LDH gallery. - Abstract: Sodium dodecyl sulfate (SDS) has been successfully intercalated into Zn–Cd–Al–LDH precursor with different SDS concentrations (0.2, 0.3, 0.4, 0.5 and 1 mol L{sup −1}) using the coprecipitation method at (Zn{sup 2+} + Cd{sup 2+})/Al{sup 3+} molar ratio of 13 and pH 8.more » The structural, morphological, texture and composition properties of the synthesized (Zn–Cd–Al–LDH–DS) nanostructure were investigated using powder X-ray diffraction (PXRD), scanning electron microscope (SEM), thermogravimetric analysis (TGA) and Fourier transform infrared (FT-IR), respectively. The photocatalytic activity of these materials was developed by increasing the concentration of intercalated SDS. The absorbance spectra have been used to detect an anion in the LDH interlayer before and after the intercalation process, which confirmed the presence of the dodecyl sulfate (DS{sup −}) anion into LDH gallery after intercalation. The anomalous low frequency dispersion (ALFD) has been used to describe the dielectric response of Zn–Cd–Al–LDH–DS nanostructure using the second type of universal power law. At low frequency, the polarization effect of electrodes caused the rising in dielectric constant and loss values. An important result of the dielectric measurements is the calculated dc conductivity values, which are new in dielectric spectroscopy of LDH materials. An important result of the electron spin resonance (ESR) spectra exhibited the successful intercalation of DS molecule into LDH gallery. The g-factor value was affected by the SDS concentration which indicated changes to the environment around the DS molecule in LDH interlayer.« less

Self-assembled nanoscale DNA-porphyrin complex for artificial light harvesting.

PubMed

Woller, Jakob G; Hannestad, Jonas K; Albinsson, Bo

2013-02-20

Mimicking green plants' and bacteria's extraordinary ability to absorb a vast number of photons and harness their energy is a longstanding goal in artificial photosynthesis. Resonance energy transfer among donor dyes has been shown to play a crucial role on the overall transfer of energy in the natural systems. Here, we present artificial, self-assembled, light-harvesting complexes consisting of DNA scaffolds, intercalated YO-PRO-1 (YO) donor dyes and a porphyrin acceptor anchored to a lipid bilayer, conceptually mimicking the natural light-harvesting systems. A model system consisting of 39-mer duplex DNA in a linear wire configuration with the porphyrin attached in the middle of the wire is primarily investigated. Utilizing intercalated donor fluorophores to sensitize the excitation of the porphyrin acceptor, we obtain an effective absorption coefficient 12 times larger than for direct excitation of the porphyrin. On the basis of steady-state and time-resolved emission measurements and Markov chain simulations, we show that YO-to-YO resonance energy transfer substantially contributes to the overall flow of energy to the porphyrin. This increase is explained through energy migration along the wire allowing the excited state energy to transfer to positions closer to the porphyrin. The versatility of DNA as a structural material is demonstrated through the construction of a more complex, hexagonal, light-harvesting scaffold yielding further increase in the effective absorption coefficient. Our results show that, by using DNA as a scaffold, we are able to arrange chromophores on a nanometer scale and in this way facilitate the assembly of efficient light-harvesting systems.

Synthesis, characterization, DNA/protein interaction and cytotoxicity studies of Cu(II) and Co(II) complexes derived from dipyridyl triazole ligands

NASA Astrophysics Data System (ADS)

Zhang, Wei; Yao, Di; Wei, Yi; Tang, Jie; Bian, He-Dong; Huang, Fu-Ping; Liang, Hong

2016-06-01

Four different transition metal complexes containing dipyridyl triazole ligands, namely [Cu(abpt)2Cl2]·2H2O (1), [Cu(abpt)2(ClO4)2] (2), [Co2(abpt)2(H2O)2Cl2]·Cl2·4H2O (3) and [Co2(Hbpt)2(CH3OH)2(NO3)2] (4) have been designed, synthesized and further structurally characterized by X-ray crystallography, ESI-MS, elemental analysis, IR and Raman spectroscopy. In these complexes, the both ligands act as bidentate ligands with N, N donors. DNA binding interactions with calf thymus DNA (ct-DNA) of the ligand and its complexes 1 ~ 4 were investigated via electronic absorption, fluorescence quenching, circular dichroism and viscosity measurements as well as confocal Laser Raman spectroscopy. The results show these complexes are able to bind to DNA via the non-covalent mode i.e. intercalation and groove binding or electrostatic interactions. The interactions with bovine serum albumin (BSA) were also studied using UV-Vis and fluorescence spectroscopic methods which indicated that fluorescence quenching of BSA by these compounds was the presence of both static and dynamic quenching. Moreover, the in vitro cytotoxic effects of the complexes against four cell lines SK-OV-3, HL-7702, BEL7404 and NCI-H460 showed the necessity of the coordination action on the biological properties on the respective complex and that all four complexes exhibited substantial cytotoxic activity.

A Study on Spectro-Analytical Aspects, DNA - Interaction, Photo-Cleavage, Radical Scavenging, Cytotoxic Activities, Antibacterial and Docking Properties of 3 - (1 - (6 - methoxybenzo [d] thiazol - 2 - ylimino) ethyl) - 6 - methyl - 3H - pyran - 2, 4 - dione and its Metal Complexes.

PubMed

Ravi, Mudavath; Chennam, Kishan Prasad; Ushaiah, B; Eslavath, Ravi Kumar; Perugu, Shyam; Ajumeera, Rajanna; Devi, Ch Sarala

2015-09-01

The focus of the present work is on the design, synthesis, characterization, DNA-interaction, photo-cleavage, radical scavenging, in-vitro cytotoxicity, antimicrobial, docking and kinetic studies of Cu (II), Cd (II), Ce (IV) and Zr (IV) metal complexes of an imine derivative, 3 - (1 - (6 - methoxybenzo [d] thiazol - 2 - ylimino) ethyl) - 6 - methyl - 3H - pyran - 2, 4 - dione. The investigation of metal ligand interactions for the determination of composition of metal complexes, corresponding kinetic studies and antioxidant activity in solution was carried out by spectrophotometric methods. The synthesized metal complexes were characterized by EDX analysis, Mass, IR, (1)H-NMR, (13)C-NMR and UV-Visible spectra. DNA binding studies of metal complexes with Calf thymus (CT) DNA were carried out at room temperature by employing UV-Vis electron absorption, fluorescence emission and viscosity measurement techniques. The results revealed that these complexes interact with DNA through intercalation. The results of in vitro antibacterial studies showed the enhanced activity of chelating agent in metal chelated form and thus inferring scope for further development of new therapeutic drugs. Cell viability experiments indicated that all complexes showed significant dose dependent cytotoxicity in selected cell lines. The molecular modeling and docking studies were carried out with energy minimized structures of metal complexes to identify the receptor to metal interactions.

Selective accumulation of harmful compounds by the DNA-inorganic hybrid-immobilized glass bead.

PubMed

Yamada, Masanori; Hamai, Akari

2009-08-11

Previously, we reported the DNA-inorganic hybrid material including double-stranded DNA by mixing the aqueous DNA solution and silane coupling reagents. Here, we immobilized the DNA-inorganic hybrid material onto the glass bead and prepared the DNA-immobilized glass bead column. The DNA-immobilized glass beads were stable in water and the amount of eluted DNA from the DNA-glass beads did not change for more than 1 week. Additionally, this DNA-immobilized column selectively accumulated the harmful compounds with the planar structure, such as dioxin- and polychlorinated biphenyl (PCB)-derivatives, and these accumulation percentages were 50-70%. Furthermore, the DNA-immobilized glass bead was recycled nine times by the application of ethanol solution and the accumulative ratio was maintained at more than 60% and did not appear to be decreasing. Therefore, these DNA-columns might have a potential for the selective removal and separation of DNA-intercalating molecules and harmful compounds with the planar structure from experimental or industrial drainages.

Modified naphthalene diimide as a suitable tetraplex DNA ligand: application to cancer diagnosis and anti-cancer drug

NASA Astrophysics Data System (ADS)

Takenaka, Shigeori

2017-07-01

It is known that naphthalene diimide carrying two substituents binds to DNA duplex with threading intercalation. Naphthalene diimide carrying ferrocene moieties, ferrocenylnaphthalene diimide (FND), formed a stable complex with DNA duplex and an electrochemical gene detection was achieved with current signal generated from FND bound to the DNA duplex between target DNA and DNA probe immobilized electrode. FND couldn't bind to the mismatched and its surrounding region of DNA duplex and thus FND was applied to the precision detection of single nucleotide polymorphisms (SNPs) using the improved discrimination ability between fully matched and mismatched DNA hybrids and multi-electrode chip. Some of FND derivatives bound to telomere DNA tetraplex stronger than to DNA duplex and was applied to cancer diagnosis as a measure of the elongated telomere DNA with telomerase as a suitable maker of cancer. Furthermore, cyclic naphthalene diimides realized the extremely high preference for DNA tetraplex over DNA duplex. Such molecules will open an effective anti-cancer drug based on telomerase specific inhibitor.

Ab-initio study of superconducting state in intercalated MoSe2 and WSe2 bilayers

NASA Astrophysics Data System (ADS)

Szcześniak, R.; Durajski, A. P.; Jarosik, M. W.

2018-05-01

A two-dimensional systems have attracted significant interest due to their outstanding physical, chemical and optoelectronic properties. This paper focuses on the detailed investigations of the electronic, phononic and superconducting properties of transition-metal dichalcogenide bilayers MSe 2 (M = Mo, W) intercalated by calcium atoms. The first-principles calculations show that (MoSe2)2Ca and (WSe2)2Ca systems exhibit metallic behavior and weak phonon-mediated superconductivity with low critical temperature of 0.51 and 0.30 K, respectively. These results confirm other theoretical predictions and suggest that the investigated materials cannot be a good candidates for a nanoscale superconductors.

Rheological and electrical properties of hybrid nanocomposites of epoxy resins filled with graphite nanoplatelets and carbon black.

PubMed

Truong, Quang-Trung; Lee, Seon-Suk; Lee, Dai-Soo

2011-02-01

Graphite nanoplatelets (GNP) were prepared by microwave irradiation of natural graphites intercalated with ferric chloride in nitromethane (GIC). Intercalated structure of GIC was confirmed by X-ray diffraction patterns. SEM images of GIC after microwave irradiation showed the exfoliation of GIC, the formation of GNPs. Hybrid nanocomposites of bisphenol-A type epoxy resins filled with GNP and a conductive carbon black (CB) were prepared and rheological and electrical properties of the nanocomposites were investigated. Viscosity and electrical surface resistivity of the nanocomposites showed minima at certain mixtures of GNP and CB in the epoxy resins.

In vitro DNA binding studies of therapeutic and prophylactic drug citral.

PubMed

Alam, Md Fazle; Varshney, Supriya; Khan, Masood Alam; Laskar, Amaj Ahmed; Younus, Hina

2018-07-01

The study of drug-DNA interactions is of great importance, as it paves the way towards the design of better therapeutic agents. Here, the interaction of DNA with a therapeutic and prophylactic drug citral has been studied. We have attempted to ascertain the mode of binding of citral with calf thymus DNA (Ct-DNA) through various biophysical techniques. Analysis of the UV-visible absorbance spectra and fluorescence spectra indicated the formation of a complex between citral and Ct-DNA. Competitive binding assays with ethidium bromide (EB), acridine orange (AO) and Hoechst 33258 reflected that citral possibly intercalates within the Ct-DNA. These observations were further confirmed by circular dichroism (CD) spectral analysis, viscosity measurements, DNA melting and molecular docking studies. This study is expected to contribute to a better understanding of molecular mechanisms of citral, and design of new drugs in the future. Copyright © 2018 Elsevier B.V. All rights reserved.

Targeting human c-Myc promoter duplex DNA with actinomycin D by use of multi-way analysis of quantum-dot-mediated fluorescence resonance energy transfer.

PubMed

Gholami, Somayeh; Kompany-Zareh, Mohsen

2013-07-01

Actinomycin D (Act D), an oncogenic c-Myc promoter binder, interferes with the action of RNA polymerase. There is great demand for high-throughput technology able to monitor the activity of DNA-binding drugs. To this end, binding of 7-aminoactinomycin D (7AAD) to the duplex c-Myc promoter was investigated by use of 2D-photoluminescence emission (2D-PLE), and the resulting data were subjected to analysis by use of convenient and powerful multi-way approaches. Fluorescence measurements were performed by use of the quantum dot (QD)-conjugated c-Myc promoter. Intercalation of 7AAD within duplex base pairs resulted in efficient energy transfer from drug to QD via fluorescence resonance energy transfer (FRET). Multi-way analysis of the three-way data array obtained from titration experiments was performed by use of restricted Tucker3 and hard trilinear decomposition (HTD). These techniques enable analysis of high-dimensional and complex data from nanobiological systems which include several spectrally overlapped structures. It was almost impossible to obtain robust and meaningful information about the FRET process for such high overlap data by use of classical analysis. The soft approach had the important advantage over univariate classical methods of enabling us to investigate the source of variance in the fluorescence signal of the DNA-drug complex. It was established that hard trilinear decomposition analysis of FRET-measured data overcomes the problem of rank deficiency, enabling calculation of concentration profiles and pure spectra for all species, including non-fluorophores. The hard modeling approach was also used for determination of equilibrium constants for the hybridization and intercalation equilibria, using nonlinear fit data analysis. The intercalation constant 3.6 × 10(6) mol(-1) L and hybridization stability 1.0 × 10(8) mol(-1) L obtained were in good agreement with values reported in the literature. The analytical concentration of the QD-labeled DNA was determined by use of nonlinear fitting, without using external standard calibration samples. This study was a successful application of multi-way chemometric methods to investigation of nano-biotechnological systems where several overlapped species coexist in solution.

In Situ Multilength-Scale Tracking of Dimensional and Viscoelastic Changes in Composite Battery Electrodes.

PubMed

Dargel, Vadim; Jäckel, Nicolas; Shpigel, Netanel; Sigalov, Sergey; Levi, Mikhael D; Daikhin, Leonid; Presser, Volker; Aurbach, Doron

2017-08-23

Intercalation-induced dimensional changes in a composite battery electrode (comprising a polymeric binder) are one of the major factors limiting electrode cycling performance. Since electrode performance is expressed by the quantities averaged over its entire surface area (e.g., capacity retention, Faradaic efficiency, rate capability), significant efforts have been made to develop a methodology allowing its facile mechanical diagnostics at the same areal scale. Herein we introduce such a generic methodology for a highly sensitive in situ monitoring of intrinsic mechanical properties of composite battery electrodes. The gravimetric, dimensional, viscoelastic, and adhesive changes in the composite electrodes caused by Li-ions intercalation are assessed noninvasively and in real time by electrochemical quartz-crystal microbalance with dissipation monitoring (EQCM-D). Multiharmonic acoustic waves generated by EQCM-D penetrate into thin porous electrodes comprising either rigid or a soft binder resulting in frequency and dissipation changes quantified by analytical acoustic load impedance models. As a first demonstration, we used a composite LiFePO 4 (LFP) electrode containing either polyvinylidene dichloride (PVdF) or Na carboximethyl cellulose (NaCMC) as rigid and viscoelastic binders, respectively, in aqueous electrolytes. The intercalation-induced volume changes of LFP electrode were evaluated from a hydrodynamic correction to the mass effect of the intercalated ions for PVdF, and both components of the effective complex shear modulus (i.e., storage and loss moduli) in case of NaCMC binder have been extracted. The sliding friction coefficients for large particles bound at their bottom to the quartz crystal surface (a measure of the adhesion strength of binders) has also been evaluated. Tracking the mechanical properties of the composite electrodes in different environments and charging/cycling conditions in a self-consistent manner provides all necessary conditions for an optimal selection of the polymeric binders resistant to intercalation-induced volume changes of intercalation particles.

Electronic characterization of silicon intercalated chevron graphene nanoribbons on Au(111).

PubMed

Deniz, O; Sánchez-Sánchez, C; Jaafar, R; Kharche, N; Liang, L; Meunier, V; Feng, X; Müllen, K; Fasel, R; Ruffieux, P

2018-02-08

Electronic and thermal properties of chevron-type graphene nanoribbons can be widely tuned, making them interesting candidates for electronic and thermoelectric applications. Here, we use post-growth silicon intercalation to unambiguously access nanoribbons' energy position of their electronic frontier states. These are otherwise obscured by substrate effects when investigated directly on the growth substrate. In agreement with first-principles calculations we find a band gap of 2.4 eV.

Electroanalytical study of proflavine intercalation in 5-methyl or inosine-containing amplicons.

PubMed

Alexiadou, Despina K; Ioannou, Andrea K; Kouidou-Andreou, Sofia A; Voulgaropoulos, Anastasios N; Girousi, Stella Th

2008-10-01

Amplicons corresponding to the GC-rich p53 exon 5 and its analogues, synthesized by substituting 60% of cytosine by 5-methyl-cytosine, or 60% of guanosine by inosine and GC-poor p53 exon 6 were synthesized and investigated electrochemically, in the presence and absence of proflavine, by differential pulse voltammetry (DPV). Incorporation of base analogues and the thermal stability of the resulting amplicons were tested in the presence of a fluorescent probe (Sybr-Green). Peak current at 1.0 V was lower for methylated than for unmethylated PCR amplicons and was similarly affected by proflavine intercalation. In contrast, considerable peak current differences were observed in the presence of proflavine for unmodified exon 5 v.s. exon 6 or inosine-containing amplicons. Thermal analysis verified the expected shifts in melting temperature (T (m)) due to the base analogue incorporation and GC-content variations. In conclusion, methylated and unmethylated PCR amplicons could be distinguished in model DNA systems using differential pulse voltammetry (DPV) and use of proflavine could serve as an electrochemical probe for identifying different DNA conformations.

In vitro reestablishment of cell-cell contacts in adult rat cardiomyocytes. Functional role of transmembrane components in the formation of new intercalated disk-like cell contacts.

PubMed

Eppenberger, H M; Zuppinger, C

1999-01-01

Primary adult rat cardiomyocytes (ARC)in culture are shown to be a model system for cardiac cell hypertrophy in vitro. ARC undergo a process of morphological transformation and grow only by increase in cell size, however, without loss of the cardiac phenotype. The isolated cells spread and establish new cell-cell contacts, eventually forming a two-dimensional heart tissue-like synchronously beating cell sheet. The reformation of specific cell contacts (intercalated disks) is shown also between ventricular and atrial cardiomyocytes by using antibodies against the gap junction protein connexin-43 and after microinjection into ARC of N-cadherin cDNA fused to reporter green fluorescent protein (GFP) cDNA. The expressed fusion protein allowed the study of live cell cultures and of the dynamics of the adherens junction protein N-cadherin during the formation of new cell-cell contacts. The possible use of the formed ARC cell-sheet cells under microgravity conditions as a test system for the reformation of the cytoskeleton of heart muscle cells is proposed.

Hydroxy double salts loaded with bioactive ions: Synthesis, intercalation mechanisms, and functional performance

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kaassis, Abdessamad Y.A.; Xu, Si-Min; Guan, Shanyue

The intercalation of the anions of diclofenac (Dic), naproxen (Nap), and valproic acid (Val) into three hydroxy double salts (HDSs) has been explored in this work. Experiments were performed with [Co{sub 1.2}Zn{sub 3.8}(OH){sub 8}](NO{sub 3}){sub 2}·2H{sub 2}O (CoZn-NO{sub 3}), [Ni{sub 2}Zn{sub 3}(OH){sub 8}](NO{sub 3}){sub 2}·2H{sub 2}O (NiZn-NO{sub 3}) and [Zn{sub 5}(OH){sub 8}](NO{sub 3}){sub 2}·2H{sub 2}O (Zn-NO{sub 3}). It proved possible to intercalate diclofenac and naproxen into all three HDSs. In contrast, Val could be intercalated into CoZn-NO{sub 3} but when it was reacted with Zn-NO{sub 3} the HDS structure was destroyed, and the product comprised ZnO. Successful intercalation was verifiedmore » by X-ray diffraction, IR spectroscopy, and elemental microanalysis. Molecular dynamics simulations showed the Dic and Nap ions to arrange themselves in an “X” shape in the interlayer space, forming a bilayer. Val was found to adopt a position with its aliphatic groups parallel to the HDS layer, again in a bilayer. In situ time resolved X-ray diffraction experiments revealed that intercalation of Dic and Nap into CoZn-NO{sub 3} and Zn-NO{sub 3} is mechanistically complex, with a number of intermediate phases observed. In contrast, the intercalation of all three guests into NiZn-NO{sub 3} and of Val into CoZn-NO{sub 3} are simple one step reactions proceeding directly from the starting material to the product. The HDS-drug composites were found to have sustained release profiles. - Graphical abstract: Seven new drug intercalates of hydroxy double salts (HDSs) have been prepared and characterised. The intercalation mechanisms have been explored, and the drug release properties of the HDS/drug composites quantified. Display Omitted.« less

Highly Conducting Graphite Epoxy Composite Demonstrated

NASA Technical Reports Server (NTRS)

Gaier, James R.

1999-01-01

Weight savings as high as 80 percent could be achieved if graphite polymer composites could replace aluminum in structures such as electromagnetic interference shielding covers and grounding planes. This could result in significant cost savings, especially for the mobile electronics found in spacecraft, aircraft, automobiles, and hand-held consumer electronics. However, such composites had not yet been fabricated with conductivity sufficient to enable these applications. To address this lack, a partnership of the NASA Lewis Research Center, Manchester College, and Applied Sciences, Inc., fabricated nonmetallic composites with unprecedented electrical conductivity. For these composites, heat-treated, vapor-grown graphite fibers were selected which have a resistivity of about 80 mW-cm, more than 20 times more conductive than typical carbon fibers. These fibers were then intercalated with iodine bromide (IBr). Intercalation is the insertion of guest atoms or molecules between the carbon planes of the graphite fibers. Since the carbon planes are not highly distorted in the process, intercalation has little effect on mechanical and thermal properties. Intercalation does, however, lower the carbon fiber resistivity to less than 10 mW-cm, which is comparable to that of metal fibers. Scaleup of the reaction was required since the initial intercalation experiments would be carried out on 20-mg quantities of fibers, and tens of grams of intercalated fibers would be needed to fabricate even small demonstration composites. The reaction was first optimized through a time and temperature study that yielded fibers with a resistivity of 8.7 2 mW-cm when exposed to IBr vapor at 114 C for 24 hours. Stability studies indicated that the intercalated fibers rapidly lost their conductivity when exposed to temperatures as low as 40 C in air. They were not, however, susceptible to degradation by water vapor in the manner of most graphite intercalation compounds. The 1000-fold scaleup experiments concluded that 114 C was near the optimum temperature, but that the intercalation time needed to be lengthened by a factor of 3.

Genotoxicity of diphenyl diselenide in bacteria and yeast.

PubMed

Rosa, Renato Moreira; Sulzbacher, Krisley; Picada, Jaqueline Nascimento; Roesler, Rafael; Saffi, Jenifer; Brendel, Martin; Henriques, João Antonio Pêgas

2004-10-10

Diphenyl diselenide (DPDS) is an electrophilic reagent used in the synthesis of a variety of pharmacologically active organic selenium compounds. This may increase the risk of human exposure to the chemical at the workplace. We have determined its mutagenic potential in the Salmonella/microsome assay and used the yeast Saccharomyces cerevisiae to assay for putative genotoxicity, recombinogenicity and to determine whether DNA damage produced by DPDS is repairable. Only in exponentially growing cultures was DPDS able to induce frameshift mutations in S. typhimurium and haploid yeast and to increase crossing over and gene conversion frequencies in diploid strains of S. cerevisiae. Thus, DPDS presents a behavior similar to that of an intercalating agent. Mutants defective in excision-resynthesis repair (rad3, rad1), in error-prone repair (rad6) and in recombinational repair (rad52) showed higher than WT-sensitivity to DPDS. It appears that this compound is capable of inducing single and/or double strand breaks in DNA. An epistatic interaction was shown between rad3-e5 and rad52-1 mutant alleles, indicating that excision-resynthesis and strand-break repair may possess common steps in the repair of DNA damage induced by DPDS. DPDS was able to enhance the mutagenesis induced by oxidative mutagens in bacteria. N-acetylcysteine, a glutathione biosynthesis precursor, prevented mutagenesis induced by DPDS in yeast. We have shown that DPDS is a weak mutagen which probably generates DNA strand breaks through both its intercalating action and pro-oxidant effect.

Analysis of DNA interactions using single-molecule force spectroscopy.

PubMed

Ritzefeld, Markus; Walhorn, Volker; Anselmetti, Dario; Sewald, Norbert

2013-06-01

Protein-DNA interactions are involved in many biochemical pathways and determine the fate of the corresponding cell. Qualitative and quantitative investigations on these recognition and binding processes are of key importance for an improved understanding of biochemical processes and also for systems biology. This review article focusses on atomic force microscopy (AFM)-based single-molecule force spectroscopy and its application to the quantification of forces and binding mechanisms that lead to the formation of protein-DNA complexes. AFM and dynamic force spectroscopy are exciting tools that allow for quantitative analysis of biomolecular interactions. Besides an overview on the method and the most important immobilization approaches, the physical basics of the data evaluation is described. Recent applications of AFM-based force spectroscopy to investigate DNA intercalation, complexes involving DNA aptamers and peptide- and protein-DNA interactions are given.

Spectrophotometric analysis of flavonoid-DNA binding interactions at physiological conditions

NASA Astrophysics Data System (ADS)

Janjua, Naveed Kausar; Siddiqa, Asima; Yaqub, Azra; Sabahat, Sana; Qureshi, Rumana; Haque, Sayed ul

2009-12-01

Mode of interactions of three flavonoids [morin (M), quercetin (Q), and rutin (R)] with chicken blood ds.DNA (ck.DNA) has been investigated spectrophotometrically at different temperatures including body temperature (310 K) and at two physiological pH values, i.e. 7.4 (human blood pH) and 4.7 (stomach pH). The binding constants, Kf, evaluated using Benesi-Hildebrand equation showed that the flavonoids bind effectively through intercalation at both pH values and body temperature. Quercetin, somehow, showed greater binding capabilities with DNA. The free energies of flavonoid-DNA complexes indicated the spontaneity of their binding. The order of binding constants of three flavonoids at both pH values were found to be Kf(Q) > Kf(R) > Kf(M) and at 310 K.

Chemical Intercalation of Topological Insulator Grid Nanostructures for High-Performance Transparent Electrodes.

PubMed

Guo, Yunfan; Zhou, Jinyuan; Liu, Yujing; Zhou, Xu; Yao, Fengrui; Tan, Congwei; Wu, Jinxiong; Lin, Li; Liu, Kaihui; Liu, Zhongfan; Peng, Hailin

2017-11-01

2D layered nanomaterials with strong covalent bonding within layers and weak van der Waals' interactions between layers have attracted tremendous interest in recent years. Layered Bi 2 Se 3 is a representative topological insulator material in this family, which holds promise for exploration of the fundamental physics and practical applications such as transparent electrode. Here, a simultaneous enhancement of optical transmittancy and electrical conductivity in Bi 2 Se 3 grid electrodes by copper-atom intercalation is presented. These Cu-intercalated 2D Bi 2 Se 3 electrodes exhibit high uniformity over large area and excellent stabilities to environmental perturbations, such as UV light, thermal fluctuation, and mechanical distortion. Remarkably, by intercalating a high density of copper atoms, the electrical and optical performance of Bi 2 Se 3 grid electrodes is greatly improved from 900 Ω sq -1 , 68% to 300 Ω sq -1 , 82% in the visible range; with better performance of 300 Ω sq -1 , 91% achieved in the near-infrared region. These unique properties of Cu-intercalated topological insulator grid nanostructures may boost their potential applications in high-performance optoelectronics, especially for infrared optoelectronic devices. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Use of anionic clays for photoprotection and sunscreen photostability: Hydrotalcites and phenylbenzimidazole sulfonic acid

NASA Astrophysics Data System (ADS)

Perioli, Luana; Ambrogi, Valeria; Rossi, Carlo; Latterini, Loredana; Nocchetti, Morena; Costantino, Umberto

2006-05-01

Layered double hydroxides of hydrotalcite (HTlc) type have many applications as matrices in pharmaceutical and cosmetic fields when intercalated with active species in anionic form. The aim of this work was to intercalate 2-phenyl-1H-benzimidazole-5-sulfonic acid (Eusolex 232) (EUS) as sunscreen molecule into hydrotalcites in order to obtain the sunscreen stabilization, the reduction of its photodegradation and the elimination of close contact between skin and filter. Hydrotalcites MgAl and ZnAl were used as hosts and the intercalation products obtained were characterized by TG, RX and DSC. They were also submitted to spectrophotometric assays in order to study the matrix influence on sunlight protection and on sunscreen photostability. These experiments showed that both MgAl and ZnAl HTlc intercalation products maintained the sunscreen properties and eusolex photodegradation was reduced. The in vitro EUS release from both formulations was almost negligible when compared with formulations containing free EUS. The EUS intercalation in HTlc and the respective formulations provided advantages in the maintenance of photoprotection efficacy, filter photostabilization and avoidance of a close contact between skin and filter, with consequent elimination of allergy problems and photocross reactions.

Correlation of intercalation potential with d-electron configurations for cathode compounds of lithium-ion batteries.

PubMed

Chen, Zhenlian; Zhang, Caixia; Zhang, Zhiyong; Li, Jun

2014-07-14

The d-electron localization is widely recognized as important to transport properties of transition metal compounds, but its role in the energy conversion of intercalation reactions of cathode compounds is still not fully explored. In this work, the correlation of intercalation potential with electron affinity, a key energy term controlling electron intercalation, then with d-electron configuration, is investigated. Firstly, we find that the change of the intercalation potential with respect to the transition metal cations within the same structure class is correlated in an approximately mirror relationship with the electron affinity, based on first-principles calculations on three typical categories of cathode compounds including layered oxides and polyoxyanions Then, by using a new model Hamiltonian based on the crystal-field theory, we reveal that the evolution is governed by the combination of the crystal-field splitting and the on-site d-d exchange interactions. Further, we show that the charge order in solid-solution composites and the compatibility of multi-electron redox steps could be inferred from the energy terms with the d-electron configuration alternations. These findings may be applied to rationally designing new chemistry for the lithium-ion batteries and other metal-ion batteries.

Influence of metal ions intercalation on the vibrational dynamics of water confined between MXene layers

DOE PAGES

Osti, Naresh C.; Naguib, Michael; Ganeshan, Karthik; ...

2017-11-21

Two-dimensional carbides and nitrides of early transition metals (MXenes) combine high conductivity with hydrophilic surfaces, which make them promising for energy storage, electrocatalysis, and water desalination. Effects of intercalated metal ions on the vibrational states of water confined in Ti 3C 2T x MXenes have been explored using inelastic neutron scattering (INS) and molecular dynamics simulations to better understand the mechanisms that control MXenes’ behavior in aqueous electrolytes, water purification and other important applications. Here, we observe INS signal from water in all samples, pristine and with lithium, sodium or potassium ions intercalated between the 2D Ti 3C 2T xmore » layers. However, only a small amount of water is found to reside in Ti 3C 2T x intercalated with metal ions. Water in pristine Ti 3C 2T x is more disordered, with bulk-like characteristics, in contrast to intercalated Ti 3C 2T x, where water is more ordered, irrespective of the metal ions used for intercalation. The ordering of the confined water increases with the ion size. Lastly, this finding is further confirmed from molecular dynamics simulation which showed an increase in interference of water molecules with increasing ion size resulting in a concomitant decrease in water mobility, therefore, providing a guidance to tailor MXene properties for energy and environmental applications.« less

Decreasing the electronic confinement in layered perovskites through intercalation.

PubMed

Smith, Matthew D; Pedesseau, Laurent; Kepenekian, Mikaël; Smith, Ian C; Katan, Claudine; Even, Jacky; Karunadasa, Hemamala I

2017-03-01

We show that post-synthetic small-molecule intercalation can significantly reduce the electronic confinement of 2D hybrid perovskites. Using a combined experimental and theoretical approach, we explain structural, optical, and electronic effects of intercalating highly polarizable molecules in layered perovskites designed to stabilize the intercalants. Polarizable molecules in the organic layers substantially alter the optical and electronic properties of the inorganic layers. By calculating the spatially resolved dielectric profiles of the organic and inorganic layers within the hybrid structure, we show that the intercalants afford organic layers that are more polarizable than the inorganic layers. This strategy reduces the confinement of excitons generated in the inorganic layers and affords the lowest exciton binding energy for an n = 1 perovskite of which we are aware. We also demonstrate a method for computationally evaluating the exciton's binding energy by solving the Bethe-Salpeter equation for the exciton, which includes an ab initio determination of the material's dielectric profile across organic and inorganic layers. This new semi-empirical method goes beyond the imprecise phenomenological approximation of abrupt dielectric-constant changes at the organic-inorganic interfaces. This work shows that incorporation of polarizable molecules in the organic layers, through intercalation or covalent attachment, is a viable strategy for tuning 2D perovskites towards mimicking the reduced electronic confinement and isotropic light absorption of 3D perovskites while maintaining the greater synthetic tunability of the layered architecture.

Influence of metal ions intercalation on the vibrational dynamics of water confined between MXene layers

DOE Office of Scientific and Technical Information (OSTI.GOV)

Osti, Naresh C.; Naguib, Michael; Ganeshan, Karthik

Two-dimensional carbides and nitrides of early transition metals (MXenes) combine high conductivity with hydrophilic surfaces, which make them promising for energy storage, electrocatalysis, and water desalination. Effects of intercalated metal ions on the vibrational states of water confined in Ti 3C 2T x MXenes have been explored using inelastic neutron scattering (INS) and molecular dynamics simulations to better understand the mechanisms that control MXenes’ behavior in aqueous electrolytes, water purification and other important applications. Here, we observe INS signal from water in all samples, pristine and with lithium, sodium or potassium ions intercalated between the 2D Ti 3C 2T xmore » layers. However, only a small amount of water is found to reside in Ti 3C 2T x intercalated with metal ions. Water in pristine Ti 3C 2T x is more disordered, with bulk-like characteristics, in contrast to intercalated Ti 3C 2T x, where water is more ordered, irrespective of the metal ions used for intercalation. The ordering of the confined water increases with the ion size. Lastly, this finding is further confirmed from molecular dynamics simulation which showed an increase in interference of water molecules with increasing ion size resulting in a concomitant decrease in water mobility, therefore, providing a guidance to tailor MXene properties for energy and environmental applications.« less

Release behavior and toxicity profiles towards A549 cell lines of ciprofloxacin from its layered zinc hydroxide intercalation compound

PubMed Central

2013-01-01

Background Layered hydroxides salts (LHS), a layered inorganic compound is gaining attention in a wide range of applications, particularly due to its unique anion exchange properties. In this work, layered zinc hydroxide nitrate (LZH), a family member of LHS was intercalated with anionic ciprofloxacin (CFX), a broad spectrum antibiotic via ion exchange in a mixture solution of water:ethanol. Results Powder x-ray diffraction (XRD), Fourier transform infrared (FTIR) and thermogravimetric analysis (TGA) confirmed the drug anions were successfully intercalated in the interlayer space of LZH. Specific surface area of the obtained compound was increased compared to that of the host due to the different pore textures between the two materials. CFX anions were slowly released over 80 hours in phosphate-buffered saline (PBS) solution due to strong interactions that occurred between the intercalated anions and the host lattices. The intercalation compound demonstrated enhanced antiproliferative effects towards A549 cancer cells compared to the toxicity of CFX alone. Conclusions Strong host-guest interactions between the LZH lattice and the CFX anion give rise to a new intercalation compound that demonstrates sustained release mode and enhanced toxicity effects towards A549 cell lines. These findings should serve as foundations towards further developments of the brucite-like host material in drug delivery systems. PMID:23849189

Study of DNA-emodin interaction by FTIR and UV-vis spectroscopy.

PubMed

Saito, Samuel T; Silva, Givaldo; Pungartnik, Cristina; Brendel, Martin

2012-06-04

Emodin, a plant- and fungus-derived anthraquinone, exerts genotoxic and antioxidative effects and shows promise in antitumor and antibacterial therapies. The aim of this study was to examine the molecular interactions of emodin with DNA in aqueous solution at physiological pH using spectroscopic methods. Fourier Transform Infrared (FTIR) Spectroscopy and UV absorption spectra were used to determine the structural features, the binding mode and the association constants. Our UV-spectroscopic results indicate that emodin interacts with DNA by intercalation and by external binding. FTIR results suggest that emodin interaction occurs preferably via adenine and thymine base pairs and also weakly with the phosphate backbone of the DNA double helix. The binding constant for emodin-DNA complex formation is estimated to be K=5.59×10(3)M(-1). No significant changes of DNA conformation were observed upon emodin-DNA complexation. Copyright © 2012 Elsevier B.V. All rights reserved.

The nature of the force-induced conformation transition of dsDNA studied by using single molecule force spectroscopy.

PubMed

Liu, Ningning; Bu, Tianjia; Song, Yu; Zhang, Wei; Li, Jinjing; Zhang, Wenke; Shen, Jiacong; Li, Hongbin

2010-06-15

Single-stranded DNA binding proteins (SSB) interact with single-stranded DNA (ssDNA) specifically. Taking advantage of this character, we have employed Bacillus subtilis SSB protein to investigate the nature of force-induced conformation transition of double-stranded DNA (dsDNA) by using AFM-based single molecule force spectroscopy (SMFS) technique. Our results show that, when a dsDNA is stretched beyond its contour length, the dsDNA is partially melted, producing some ssDNA segments which can be captured by SSB proteins. We have also systematically investigated the effects of stretching length, waiting time, and salt concentration on the conformation transition of dsDNA and SSB-ssDNA interactions, respectively. Furthermore, the effect of proflavine, a DNA intercalator, on the SSB-DNA interactions has been investigated, and the results indicate that the proflavine-saturated dsDNA can be stabilized to the extent that the dsDNA will no longer melt into ssDNA under the mechanical force even up to 150 pN, and no SSB-DNA interactions are detectable.

Mechanism Responsible for Intercalation of Dimethyl Sulfoxide in Kaolinite: Molecular Dynamics Simulations.

PubMed

Zhang, Shuai; Liu, Qinfu; Cheng, Hongfei; Gao, Feng; Liu, Cun; Teppen, Brian J

2018-01-01

Intercalation is the promising strategy to expand the interlayer region of kaolinite for their further applications. Herein, the adaptive biasing force (ABF) accelerated molecular dynamics simulations were performed to calculate the free energies involved in the kaolinite intercalation by dimethyl sulfoxide (DMSO). Additionally, the classical all atom molecular dynamics simulations were carried out to calculate the interfacial interactions between kaolinite interlayer surfaces and DMSO with the aim at exploring the underlying force that drives the DMSO to enter the interlayer space. The results showed that the favorable interaction of DMSO with both kaolinite interlayer octahedral surface and tetrahedral surface can help in introducing DMSO enter kaolinite interlayer. The hydroxyl groups on octahedral surface functioned as H-donors attracting the S=O groups of DMSO through hydrogen bonding interaction. The tetrahedral surface featuring hydrophobic property attracted the methyl groups of DMSO through hydrophobic interaction. The results provided a detailed picture of the energetics and interlayer structure of kaolinite-DMSO intercalate.

Exfoliation and van der Waals heterostructure assembly of intercalated ferromagnet Cr1/3TaS2

NASA Astrophysics Data System (ADS)

Yamasaki, Yuji; Moriya, Rai; Arai, Miho; Masubuchi, Satoru; Pyon, Sunseng; Tamegai, Tsuyoshi; Ueno, Keiji; Machida, Tomoki

2017-12-01

Ferromagnetic van der Waals (vdW) materials are in demand for spintronic devices with all-two-dimensional-materials heterostructures. Here, we demonstrate mechanical exfoliation of magnetic-atom-intercalated transition metal dichalcogenide Cr1/3TaS2 from its bulk crystal; previously such intercalated materials were thought difficult to exfoliate. Magnetotransport in exfoliated tens-of-nanometres-thick flakes revealed ferromagnetic ordering below its Curie temperature T C ~ 110 K as well as strong in-plane magnetic anisotropy; these are identical to its bulk properties. Further, van der Waals heterostructure assembly of Cr1/3TaS2 with another intercalated ferromagnet Fe1/4TaS2 is demonstrated using a dry-transfer method. The fabricated heterojunction composed of Cr1/3TaS2 and Fe1/4TaS2 with a native Ta2O5 oxide tunnel barrier in between exhibits tunnel magnetoresistance (TMR), revealing possible spin injection and detection with these exfoliatable ferromagnetic materials through the vdW junction.

Superconductivity and hybrid soft modes in Ti Se 2

DOE PAGES

Maschek, M.; Rosenkranz, S.; Hott, R.; ...

2016-12-12

The interplay between superconductivity and charge-density-wave (CDW) order plays a central role in the layered transition-metal dichalcogenides. 1 T-TiSe 2 forms a prime example, featuring superconducting domes on intercalation as well as under applied pressure. Here, we present high energy-resolution inelastic x-ray scattering measurements of the CDW soft phonon mode in intercalated Cu xTiSe 2 and pressurized 1 T-TiSe 2 along with detailed ab-initio calculations for the lattice dynamical properties and phonon-mediated superconductivity. We find that the intercalation-induced superconductivity can be explained by a solely phonon-mediated pairing mechanism, while this is not possible for the superconducting phase under pressure. Wemore » argue that a hybridization of phonon and exciton modes in the pairing mechanism is necessary to explain the full observed temperature-pressure-intercalation phase diagram. Finally, these results indicate that 1 T-TiSe 2 under pressure is close to the elusive state of the excitonic insulator.« less

Tunable thermal expansion in framework materials through redox intercalation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Chen, Jun; Gao, Qilong; Sanson, Andrea

Thermal expansion properties of solids are of fundamental interest and control of thermal expansion is important for practical applications but can be difficult to achieve. Many framework type materials show negative thermal expansion when internal cages are empty but positive thermal expansion when additional atoms or molecules fill internal voids present, offering a potential route for control. Here we show that redox intercalation offers an effective method to control thermal expansion from positive to zero to negative by insertion of Li ions into the simple negative thermal expansion framework material ScF 3, doped with 10% Fe to enable reduction. Themore » small concentration of intercalated Li ions has a strong influence through steric hindrance of transverse fluoride ion vibrations, which directly controls the thermal expansion. As a result, redox intercalation of guest ions is thus likely to be a general and effective method for controlling thermal expansion in the many known framework materials with phonon-driven negative thermal expansion.« less

Tunable thermal expansion in framework materials through redox intercalation

DOE PAGES

Chen, Jun; Gao, Qilong; Sanson, Andrea; ...

2017-02-09

Thermal expansion properties of solids are of fundamental interest and control of thermal expansion is important for practical applications but can be difficult to achieve. Many framework type materials show negative thermal expansion when internal cages are empty but positive thermal expansion when additional atoms or molecules fill internal voids present, offering a potential route for control. Here we show that redox intercalation offers an effective method to control thermal expansion from positive to zero to negative by insertion of Li ions into the simple negative thermal expansion framework material ScF 3, doped with 10% Fe to enable reduction. Themore » small concentration of intercalated Li ions has a strong influence through steric hindrance of transverse fluoride ion vibrations, which directly controls the thermal expansion. As a result, redox intercalation of guest ions is thus likely to be a general and effective method for controlling thermal expansion in the many known framework materials with phonon-driven negative thermal expansion.« less

Room temperature deintercalation of alkali metal atoms from epitaxial graphene by formation of charge-transfer complexes

NASA Astrophysics Data System (ADS)

Shin, H.-C.; Ahn, S. J.; Kim, H. W.; Moon, Y.; Rai, K. B.; Woo, S. H.; Ahn, J. R.

2016-08-01

Atom (or molecule) intercalations and deintercalations have been used to control the electronic properties of graphene. In general, finite energies above room temperature (RT) thermal energy are required for the intercalations and deintercalations. Here, we demonstrate that alkali metal atoms can be deintercalated from epitaxial graphene on a SiC substrate at RT, resulting in the reduction in density of states at the Fermi level. The change in density of states at the Fermi level at RT can be applied to a highly sensitive graphene sensor operating at RT. Na atoms, which were intercalated at a temperature of 80 °C, were deintercalated at a high temperature above 1000 °C when only a thermal treatment was used. In contrast to the thermal treatment, the intercalated Na atoms were deintercalated at RT when tetrafluorotetracyanoquinodimethane (F4-TCNQ) molecules were adsorbed on the surface. The RT deintercalation occurred via the formation of charge-transfer complexes between Na atoms and F4-TCNQ molecules.

Electrochemical DNA biosensors based on long-range electron transfer: investigating the efficiency of a fluidic channel microelectrode compared to an ultramicroelectrode in a two-electrode setup.

PubMed

Horny, M-C; Lazerges, M; Siaugue, J-M; Pallandre, A; Rose, D; Bedioui, F; Deslouis, C; Haghiri-Gosnet, A-M; Gamby, J

2016-11-01

Here, we describe the transposition of an ultramicroelectrode (UME) setup into a microfluidic chip configuration for DNA biosensors. The hydrodynamic properties of the fluidic channel microelectrode were screened with an [Fe(iii)(CN) 6 ] 3- /[Fe(ii)(CN) 6 ] 4- redox couple by cyclic voltammetry to provide a basis for further biological processes. A 23-base DNA probe was self-assembled into a monolayer on gold microelectrodes both in classical configuration and integrated in a microfluidic setup. Special interest was focused on the DNA target mimicking the liver-specific micro-ribonucleic acid 122 (miRNA122). Long-range electron transfer was chosen for transducing the hybridization. This direct transduction was indeed significantly enhanced after hybridization due to DNA-duplex π-stacking and the use of redox methylene blue as a DNA intercalator. Quantification of the target was deduced from the resulting electrical signal characterized by cyclic voltammetry. The limit of detection for DNA hybridization was 0.1 fM in stopped flow experiments, where it can reach 1 aM over a 0.5 μL s -1 flow rate, a value 10 4 -fold lower than the one measured with a conventional UME dipped into an electrolyte droplet under the same analytical conditions. An explanation was that forced convection drives more biomolecules to the area of detection even if a balance between the speed of collection and the number of biomolecules collected has been found. The latter point is discussed here along with an attempt to explain why the sensor has reached such an unexpected value for the limit of detection.

Electronic characterization of silicon intercalated chevron graphene nanoribbons on Au(111)

DOE PAGES

Deniz, O.; Sánchez-Sánchez, C.; Jaafar, R.; ...

2018-01-08

Electronic and thermal properties of chevron-type graphene nanoribbons can be widely tuned, making them interesting candidates for electronic and thermoelectric applications. In this paper, we use post-growth silicon intercalation to unambiguously access nanoribbons’ energy position of their electronic frontier states. These are otherwise obscured by substrate effects when investigated directly on the growth substrate. Finally, in agreement with first-principles calculations we find a band gap of 2.4 eV.

Molecular Simulation Models of Carbon Dioxide Intercalation in Hydrated Sodium Montmorillonite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Myshakin, Evgeniy; Saidi, Wissam; Romanov, Vyacheslav

2016-11-22

In this study, classical molecular dynamics simulations and density functional theory (DFT)-based molecular dynamics are used to elucidate the process of CO 2 intercalation into hydrated Na-montmorillonite at P-T conditions relevant to geological formations suitable for CO 2 storage. Of particular interest are the structural and transport properties of interlayer species after CO 2 intercalation. The conducted simulations allowed the research team to quantify expansion/contraction of smectite as a function of CO 2 and H 2O compositions. The resulting swelling curves can be used to gauge the amount of stored CO 2, compare it to the experiment, and estimate changesmore » in geomechanical properties of the storage formation. The obtained results showed that the infrared signal of the asymmetric stretch vibration of CO 2 molecule is extremely sensitive to the solvent environment. The extent of the frequency shift relative to the gas-phase value can be used to probe hydration level in the interlayer with intercalated CO 2. Interaction of supercritical CO 2 with brine in deep geological formations promotes an increase of hydrophobicity of clay surfaces. As a result of wettability alteration, estimated diffusion constants of CO 2 and H 2O increase with the increased CO 2 load; this can contribute to faster migration of CO 2 throughout the formation.« less

Novel strategy combining SYBR Green I with carbon nanotubes for highly sensitive detection of Salmonella typhimurium DNA.

PubMed

Mao, Pingdao; Ning, Yi; Li, Wenkai; Peng, Zhihui; Chen, Yongzhe; Deng, Le

2014-01-10

A simple, selective, sensitive and label-free fluorescent method for detecting trpS-harboring Salmonella typhimurium was developed in this study. This assay used the non-covalent interaction of single-stranded DNA (ssDNA) probes with SWNTs, since SWNTs can quench fluorescence. Fluorescence recovery (78% with 1.8 nM target DNA) was detected in the presence of target DNA as ssDNA probes detached from SWNTs hybridized with target DNA, and the resulting double-stranded DNA (dsDNA) intercalated with SYBR Green I (SG) dyes. The increasing fluorescence intensity reached 4.54-fold. In contrast, mismatched oligonucleotides (1- or 3-nt difference to the target DNA) did not contribute to significant fluorescent recovery, which demonstrated the specificity of the assay. The increasing fluorescence intensity increased 3.15-fold when purified PCR products containing complementary sequences of trpS gene were detected. These results confirmed the ability to use this assay for detecting real samples. Copyright © 2013 Elsevier Inc. All rights reserved.

Visualization of drug-nucleic acid interactions at atomic resolution v. structure of two aminoacridine/dinucleoside monophosphate crystalline complexes, proflavine: 5-iodocytidylyl(3'-5') guanosine and acridine orange: 5-iodocytidylyl(3'-5') guanosine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Reddy, B.S.; Seshadri, T.P.; Sakore, T.D.

1979-01-01

Acridine orange and proflavine form complexes with the dinucleoside monophosphate, 5-iodocytidylyl(3'-5') guanosine (iodoCpG). The acridine orange-iodoCpG crystals are monoclinic, space group P2/sub 1/, with unit cell dimensions a = 14.36 A, b = 19.64 A, c = 20.67 A, ..beta.. = 102.5. The proflavine-iodoCpG crystals are monoclinic, space group C2, with unit cell dimensions a = 32.14 A, b = 22.23 A, c = 18.42 A, ..beta.. = 123.3. Both structures have been solved to atomic resolution by Patterson and Fourier methods, and refined by full matrix least squares. Acridine orange forms an intercalative structure with iodoCpG but the acridinemore » nucleus lies asymmetrically in the intercalation site. This asymmetric intercalation is accompanied by a sliding of base-pairs upon the acridine nucleus. Base-pairs above and below the drug are separated by about 6.8 A and are twisted about 10/sup 0/. Proflavine demonstrates symmetric intercalation with iodoCpG. Hydrogen bonds connect amino- groups on proflavine with phosphate oxygen atoms on the dinucleotide. Base-pairs above and below the intercalative proflavine molecule are twisted about 36/sup 0/. The altered magnitude of this angular twist reflects the sugar puckering pattern that is observed. We propose a proflavine-DNA and an acridine orange-DNA binding model. We will describe these models in detail in this paper.« less

Physicochemical properties of nanocomposite: Hydroxyapatite in reduced graphene oxide.

PubMed

Rajesh, A; Mangamma, G; Sairam, T N; Subramanian, S; Kalavathi, S; Kamruddin, M; Dash, S

2017-07-01

Graphene oxide (GO) based nanocomposites have gained considerable attention in the field of material science due to their excellent physicochemical and biological properties. Incorporation of nanomaterials into GO sheets prevents the formation of π-π stacking bond thereby giving rise to composites that show the improved properties compared to their individual counterparts. In this work, reduced graphene oxide (rGO) - hydroxyapatite (HAP) nanocomposites were synthesized by ultrasonic method. Increasing the c/a ratio of HAP in the diffraction pattern of rGO/HAP nanocomposites indicates the c-axis oriented grown HAP nanorods interacting with rGO layers. Shift in wavenumber (15cm -1 ) and increase of full width at half maximum (45cm -1 ) of G band in Raman spectra of the rGO/HAP nanocomposites are observed and attributed to the tensile strain induced due to the intercalated HAP nanorods between the rGO layers. Atomic force microscopy (AFM) and phase imaging studies revealed the intercalation of HAP nanorod with diameter 30nm and length 110-120nm in rGO sheets was clearly perceived along with improved elasticity compared to pristine HAP. 13 C-NMR results proved the synergistic interaction between both components in rGO/HAP nanocomposite. The novel properties observed and the microscopic mechanism responsible for this are a result of the structural modification in rGO layers brought about by the intercalation of HAP nanorods. Copyright © 2017. Published by Elsevier B.V.

Atomic intercalation to measure adhesion of graphene on graphite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wang, Jun; Sorescu, Dan C.; Jeon, Seokmin

The interest in mechanical properties of layered and 2D materials has reemerged in light of device concepts that take advantage of flexing, adhesion and friction in such systems. Here we provide an effective measurement of the nanoscale elastic adhesion of a graphene sheet atop highly ordered pyrolytic graphite (HOPG) based on the analysis of atomic intercalates in graphite. Atomic intercalation is carried out using conventional ion sputtering, creating blisters in the top-most layer of the HOPG surface. Scanning tunneling microscopy coupled with image analysis and density functional theory are used to reconstruct the atomic positions and the strain map withinmore » the deformed graphene sheet, as well as to demonstrate subsurface diffusion of the ions creating such blisters. To estimate the adhesion energy we invoke an analytical model originally devised for macroscopic deformations of graphene. This model yields a value of 0.221 ± 0.011 J/m -2 for the adhesion energy of graphite, which is in surprisingly good agreement with reported experimental and theoretical values. This implies that macroscopic mechanical properties of graphene scale down to at least a few nanometers length. The simplicity of our method, compared to the macroscale characterization, enables analysis of elastic mechanical properties in two-dimensional layered materials and provides a unique opportunity to investigate the local variability of mechanical properties on the nanoscale.« less

Atomic intercalation to measure adhesion of graphene on graphite

DOE PAGES

Wang, Jun; Sorescu, Dan C.; Jeon, Seokmin; ...

2016-10-31

The interest in mechanical properties of layered and 2D materials has reemerged in light of device concepts that take advantage of flexing, adhesion and friction in such systems. Here we provide an effective measurement of the nanoscale elastic adhesion of a graphene sheet atop highly ordered pyrolytic graphite (HOPG) based on the analysis of atomic intercalates in graphite. Atomic intercalation is carried out using conventional ion sputtering, creating blisters in the top-most layer of the HOPG surface. Scanning tunneling microscopy coupled with image analysis and density functional theory are used to reconstruct the atomic positions and the strain map withinmore » the deformed graphene sheet, as well as to demonstrate subsurface diffusion of the ions creating such blisters. To estimate the adhesion energy we invoke an analytical model originally devised for macroscopic deformations of graphene. This model yields a value of 0.221 ± 0.011 J/m -2 for the adhesion energy of graphite, which is in surprisingly good agreement with reported experimental and theoretical values. This implies that macroscopic mechanical properties of graphene scale down to at least a few nanometers length. The simplicity of our method, compared to the macroscale characterization, enables analysis of elastic mechanical properties in two-dimensional layered materials and provides a unique opportunity to investigate the local variability of mechanical properties on the nanoscale.« less

Atomic structures and electronic properties of 2H-NbSe2: The impact of Ti doping

NASA Astrophysics Data System (ADS)

Li, Hongping; Chen, Lin; Zhang, Kun; Liang, Jiaqing; Tang, Hua; Li, Changsheng; Liu, Xiaojuan; Meng, Jian; Wang, Zhongchang

2014-09-01

Layered transition metal dichalcogenides have aroused renewed interest as electronic materials, yet their electronic performances could be modified by chemical doping. Here, we perform a systematic first-principles calculation to investigate the effect of Ti doping on atomic structure and electronic properties of the 2H-NbSe2. We consider a total of three possible Ti-doping models and find that both the substitution and intercalated models are chemically preferred with the intercalation model being more favorable than the substitution one. Structural analyses reveal a slight lattice distortion triggered by Ti doping, but the original structure of 2H-NbSe2 is maintained. We also observe an expansion of c axis in the substituted model, which is attributed to the reduced van der Waals interaction arising from the increased Se-Se bond length. Our calculations also predict that the electron transport properties can be enhanced by the Ti doping, especially for the Ti-intercalated 2H-NbSe2, which should be beneficial for the realization of superconductivity. Furthermore, the covalence element is found in the Ti-Se bonds, which is ascribed to the hybridization of Ti 3d and Se 4p orbitals. The findings indicate that doping of transition metals can be regarded as a useful way to tailor electronic states so as to improve electron transport properties of 2H-NbSe2.

Resistance to Nucleotide Excision Repair of Bulky Guanine Adducts Opposite Abasic Sites in DNA Duplexes and Relationships between Structure and Function

PubMed Central

Liu, Zhi; Ding, Shuang; Kropachev, Konstantin; Lei, Jia; Amin, Shantu; Broyde, Suse; Geacintov, Nicholas E.

2015-01-01

The nucleotide excision repair of certain bulky DNA lesions is abrogated in some specific non-canonical DNA base sequence contexts, while the removal of the same lesions by the nucleotide excision repair mechanism is efficient in duplexes in which all base pairs are complementary. Here we show that the nucleotide excision repair activity in human cell extracts is moderate-to-high in the case of two stereoisomeric DNA lesions derived from the pro-carcinogen benzo[a]pyrene (cis- and trans-B[a]P-N 2-dG adducts) in a normal DNA duplex. By contrast, the nucleotide excision repair activity is completely abrogated when the canonical cytosine base opposite the B[a]P-dG adducts is replaced by an abasic site in duplex DNA. However, base excision repair of the abasic site persists. In order to understand the structural origins of these striking phenomena, we used NMR and molecular spectroscopy techniques to evaluate the conformational features of 11mer DNA duplexes containing these B[a]P-dG lesions opposite abasic sites. Our results show that in these duplexes containing the clustered lesions, both B[a]P-dG adducts adopt base-displaced intercalated conformations, with the B[a]P aromatic rings intercalated into the DNA helix. To explain the persistence of base excision repair in the face of the opposed bulky B[a]P ring system, molecular modeling results suggest how the APE1 base excision repair endonuclease, that excises abasic lesions, can bind productively even with the trans-B[a]P-dG positioned opposite the abasic site. We hypothesize that the nucleotide excision repair resistance is fostered by local B[a]P residue—DNA base stacking interactions at the abasic sites, that are facilitated by the absence of the cytosine partner base in the complementary strand. More broadly, this study sets the stage for elucidating the interplay between base excision and nucleotide excision repair in processing different types of clustered DNA lesions that are substrates of nucleotide excision repair or base excision repair mechanisms. PMID:26340000

DNA as a Target for Anticancer Phen-Imidazole Pd(II) Complexes.

PubMed

Heydari, Maryam; Moghadam, Mahboube Eslami; Tarlani, AliAkbar; Farhangian, Hossein

2017-05-01

Imidazole ring is a known structure in many natural or synthetic drug molecules and its metal complexes can interact with DNA and do the cleavage. Hence, to study the influence of the structure and size of the ligand on biological behavior of metal complexes, two water-soluble Pd(II) complexes of phen and FIP ligands (where phen is 1,10-phenanthroline and FIP is 2-(Furan-2-yl)-1H-Imidazo[4,5-f][1, 10]phenanthroline) with the formula of [Pd(phen)(FIP)](NO 3 ) 2 and [Pd(FIP) 2 ]Cl 2 , that were activated against chronic myelogenous leukemia cell line, K562, were selected. Also, the interaction of these anticancer Pd(II) complexes with highly polymerized calf thymus DNA was extensively studied by means of electronic absorption, fluorescence, and circular dichroism in Tris-buffer. The results showed that the binding was positive cooperation and [Pd(phen)(FIP)](NO 3 ) 2 (K f  = 127 M -1 G = 1.2) exhibited higher binding constant and number of binding sites than [Pd(FIP) 2 ]Cl 2 (K f  = 13 M -1 G = 1.03) upon binding to DNA. The fluorescence data indicates that quenching effect for [Pd(phen)(FIP)](NO 3 ) 2 (K SV  = 58 mM -1 ) was higher than [Pd(FIP) 2 ]Cl 2 (K SV  = 12 mM -1 ). Also, [Pd(FIP) 2 ]Cl 2 interacts with ethidium bromide-DNA, as non-competitive inhibition, and can bind to DNA via groove binding and [Pd(phen)(FIP)](NO 3 ) 2 can intercalate in DNA. These results were confirmed by circular dichroism spectra. Docking data revealed that longer complexes have higher interaction energy and bind to DNA via groove binding. Graphical Abstract Two anticancer Pd(II) complexes of imidazole derivative have been synthesized and interacted with calf thymus DNA. Modes of binding have been studied by electronic absorption, fluorescence, and CD measurements. [Pd(FIP) 2 ]Cl 2 can bind to DNA via groove binding while intercalation mode of binding is observed for [Pd(phen)(FIP)](NO 3 ) 2 .

Synthesis of kaolinite-filled EPDM rubber composites by solution intercalation: structural characterization and studies on mechanical properties

NASA Astrophysics Data System (ADS)

Ginil Mon, S.; Jaya Vinse Ruban, Y.; Vetha Roy, D.

2011-09-01

In the large field of nanotechnology, polymer matrix-based nanocomposites have become a prominent area of current research and development. Exfoliated clay-based nanocomposites have dominated the polymer world with excellent characteristics. EPDM rubber composites have been synthesized by solution-intercalation using the easily available kaolinite as filler. The composite structure has been elucidated by X-ray diffraction (XRD), Fourier transform IR, and scanning electron microscope studies. The molecular level dispersion of clay layers has been verified by the disappearance of basal XRD peak of kaolinite in the EPDM/kaolinite composites. The mechanical properties showed significant improvement of EPDM/kaolinite composites with respect to neat EPDM.

Tests of spool models for DNA packaging in phage lambda.

PubMed

Widom, J; Baldwin, R L

1983-12-25

Experiments are reported which bear on two spool models proposed for packaging the DNA of phage lambda. Both spool models fill an assumed spherical cavity with DNA wrapped in cylindrical or quasi-cylindrical layers composed of adjacent circular turns. In the curved-spool model, a single continuous segment of DNA, about 20% of the DNA length and probably located near the left end of the DNA, is in contact with the coat protein of the phage capsid. In the straight spool model, there are several DNA segments in contact with the capsid; they are concentrated in one half (probably the left half) of lambda DNA. We have identified the loci on the DNA which are in contact with the capsid by chemical crosslinking, induced by ultraviolet-irradiation of phage containing 5-bromodeoxyuridine in place of thymine. In an electron microscope experiment, phage are first lysed with EDTA, and then spread in a cytochrome c film by the formamide method. The disrupted capsid, which has the appearance of a phage ghost, serves as a marker showing where the DNA is crosslinked to the coat. The left end of the DNA is not distinguished from the right end, and so the map of DNA-capsid contacts is folded over on itself. Contacts are found nearly randomly over the entire map. In a second experiment, DNA from lysed, crosslinked phage is cut either with EcoRI or HindIII restriction endonucleases and the cut restriction fragments are labeled at their ends with 32P. Density centrifugation in a CsCl gradient separates free DNA from restriction fragments crosslinked to protein. After digestion with proteinase k, the DNA fragments previously crosslinked to protein are identified by size after agarose gel electrophoresis. DNA fragments from all parts of the genome are found. These two experiments show that, if the DNA of each phage is packaged identically, then the curved-spool model is ruled out and the straight spool model is unlikely. Alternatively, the manner of packaging the DNA may vary from one phage to the next. These results agree with other recent experiments on lambda DNA packaging by Hall & Schellman (1982a,b), and by Haas et al. (1982). A different experiment is also reported. The psoralen derivative aminomethyltrioxalen (AMT) is allowed to intercalate into lambda phage and then the DNA strands are crosslinked by ultraviolet-irradiation after the rapid phase of AMT intercalation is complete. The DNA is subsequently denatured by glyoxal modification and spread for electron microscopy in a cytochrome c film by the formamide method.(ABSTRACT TRUNCATED AT 400 WORDS)

Improved Efficiency and Robustness in qPCR and Multiplex End-Point PCR by Twisted Intercalating Nucleic Acid Modified Primers

PubMed Central

Schneider, Uffe Vest; Mikkelsen, Nikolaj Dam; Lindqvist, Anja; Okkels, Limei Meng; Jøhnk, Nina; Lisby, Gorm

2012-01-01

We introduce quantitative polymerase chain reaction (qPCR) primers and multiplex end-point PCR primers modified by the addition of a single ortho-Twisted Intercalating Nucleic Acid (o-TINA) molecule at the 5′-end. In qPCR, the 5′-o-TINA modified primers allow for a qPCR efficiency of 100% at significantly stressed reaction conditions, increasing the robustness of qPCR assays compared to unmodified primers. In samples spiked with genomic DNA, 5′-o-TINA modified primers improve the robustness by increased sensitivity and specificity compared to unmodified DNA primers. In unspiked samples, replacement of unmodified DNA primers with 5′-o-TINA modified primers permits an increased qPCR stringency. Compared to unmodified DNA primers, this allows for a qPCR efficiency of 100% at lowered primer concentrations and at increased annealing temperatures with unaltered cross-reactivity for primers with single nucleobase mismatches. In a previously published octaplex end-point PCR targeting diarrheagenic Escherichia coli, application of 5′-o-TINA modified primers allows for a further reduction (>45% or approximately one hour) in overall PCR program length, while sustaining the amplification and analytical sensitivity for all targets in crude bacterial lysates. For all crude bacterial lysates, 5′-o-TINA modified primers permit a substantial increase in PCR stringency in terms of lower primer concentrations and higher annealing temperatures for all eight targets. Additionally, crude bacterial lysates spiked with human genomic DNA show lesser formation of non-target amplicons implying increased robustness. Thus, 5′-o-TINA modified primers are advantageous in PCR assays, where one or more primer pairs are required to perform at stressed reaction conditions. PMID:22701644

Conformation of nanoconfined DNA as a function of ATP, AMP, CTP, Mg2+, and dye binding

NASA Astrophysics Data System (ADS)

Roushan, Maedeh; Riehn, Robert

2014-03-01

DNA molecules stretch in nanochannels with a channel cross-section of 100x100 nm2, thereby allowing analysis by observation of a fluorescent dye. The length and configuration of DNA can be directly observed, and the effect of different DNA-binding proteins on DNA configuration can be studied. Recently, we reported on the ability of T4 ligase to transiently manipulate DNA as a function of ATP and magnesium exposure. In this process we have extensively probed the interactions of dyes and enzyme co-factors with DNA under nanoconfinement. We find negligible effects if DNA is visualized using groove-binding dyes such as DAPI. However, if an intercalating dye (YOYO-1) is used, we find a significant shortening of the DNA in the presence of ATP that we attribute to an interaction of dye and ATP (as well as AMP and CTP). We did not record a noticeable effect due to Mg2+.

Complex Stoichiometry reordering of PTCDA on Ag(111) upon K Intercalation

NASA Astrophysics Data System (ADS)

Brivio, G. P.; Baby, A.; Zwick, C.; Gruenewald, M.; Forker, R.; Fritz, T.; Fratesi, G.; Hofmann, O. T.; Zojer, E.

Alkali metal atoms are a simple yet efficient n-type dopant of organic semiconductors. However, the molecular crystal structures need be controlled and well understood in order to optimize the electronic properties (charge carrier density and mobility) of the target material. Here, we report that potassium intercalation into PTCDA monolayer domains on a Ag(111) substrate induces distinct stoichiometry-dependent structural reordering processes, resulting in highly ordered and large KxPTCDA domains. The emerging structures are analyzed by low temperature scanning tunneling microscopy (STM), scanning tunneling hydrogen microscopy (STHM), and low-energy electron diffraction (LEED) as a function of the stoichiometry and by density functional theory (DFT) calculations. Large stable monolayer domains are found for x=2,4. The epitaxy types for all intercalated stages are determined as point-on-line. The K atoms adsorb in the vicinity of the oxygen atoms of the PTCDA molecules, and their positions are determined with sub-Angstrom precision. This is a crucial prerequisite for the prospective assessment of the electronic properties of such composite films, as they depend on the mutual alignment between donor atoms and acceptor molecules.

Calorimetric Determination of Thermodynamic Stability of MAX and MXene Phases

DOE PAGES

Sharma, Geetu; Naguib, Michael; Feng, Dawei; ...

2016-11-19

MXenes are layered two dimensional materials with exciting properties useful to a wide range of energy applications. They are derived from ceramics (MAX phases) by leaching and their properties reflect their resulting complex compositions which include intercalating cations and anions and water. Their thermodynamic stability is likely linked to these functional groups but has not yet been addressed by quantitative experimental measurements. We report enthalpies of formation from the elements at 25 °C measured using high temperature oxide melt solution calorimetry for a layered Ti-Al-C MAX phase, and the corresponding Ti-C based MXene. The thermodynamic stability of the Ti 3Cmore » 2T x MXene (Tx stands for anionic surface moieties, and intercalated cations) was assessed by calculating the enthalpy of reaction of the MAX phase (ideal composition Ti 3AlC 2) to form MXene, The very exothermic enthalpy of reaction confirms the stability of MXene in an aqueous environment. The surface terminations (O, OH and F) and cations (Li) chemisorbed on the surface and intercalated in the interlayers play a major role in the thermodynamic stabilization of MXene. These findings help to understand and potentially improve properties and performance by characterizing the energetics of species binding to MXene surfaces during synthesis and in energy storage, water desalination and other applications.« less

Electron Beam Irradiated Intercalated CNT Yarns For Aerospace Applications

NASA Technical Reports Server (NTRS)

Waters, Deborah L.; Gaier, James R.; Williams, Tiffany S.; Lopez Calero, Johnny E.; Ramirez, Christopher; Meador, Michael A.

2015-01-01

Multi-walled CNT yarns have been experimentally and commercially created to yield lightweight, high conductivity fibers with good tensile properties for application as electrical wiring and multifunctional tendons. Multifunctional tendons are needed as the cable structures in tensegrity robots for use in planetary exploration. These lightweight robust tendons can provide mechanical strength for movement of the robot in addition to power distribution and data transmission. In aerospace vehicles, such as Orion, electrical wiring and harnessing mass can approach half of the avionics mass. Use of CNT yarns as electrical power and data cables could reduce mass of the wiring by thirty to seventy percent. These fibers have been intercalated with mixed halogens to increase their specific electrical conductivity to that near copper. This conductivity, combined with the superior strength and fatigue resistance makes it an attractive alternative to copper for wiring and multifunctional tendon applications. Electron beam irradiation has been shown to increase mechanical strength in pristine CNT fibers through increased cross-linking. Both pristine and intercalated CNT yarns have been irradiated using a 5-megavolt electron beam for various durations and the conductivities and tensile properties will be discussed. Structural information obtained using a field emission scanning electron microscope, energy dispersive X-ray spectroscopy (EDS), and Raman spectroscopy will correlate microstructural details with bulk properties.

Biopolymer-modified graphite oxide nanocomposite films based on benzalkonium chloride-heparin intercalated in graphite oxide

NASA Astrophysics Data System (ADS)

Meng, Na; Zhang, Shuang-Quan; Zhou, Ning-Lin; Shen, Jian

2010-05-01

Heparin is a potent anticoagulant agent that interacts strongly with antithrombin III to prevent the formation of fibrin clots. In the present work, poly(dimethylsiloxane)(PDMS)/graphite oxide-benzalkonium chloride-heparin (PDMS/modified graphite oxide) nanocomposite films were obtained by the solution intercalation technique as a possible drug delivery system. The heparin-benzalkonium chloride (BAC-HEP) was intercalated into graphite oxide (GO) layers to form GO-BAC-HEP (modified graphite oxide). Nanocomposite films were characterized by XRD, SEM, TEM, ATR-FTIR and TGA. The modified graphite oxide was observed to be homogeneously dispersed throughout the PDMS matrix. The effect of modified graphite oxide on the mechanical properties of the nanocomposite film was investigated. When the modified graphite oxide content was lower than 0.2 wt%, the nanocomposites showed excellent mechanical properties. Furthermore, nanocomposite films become delivery systems that release heparin slowly to make the nanocomposite films blood compatible. The in vitro studies included hemocompatibility testing for effects on platelet adhesion, platelet activation, plasma recalcification profiles, and hemolysis. Results from these studies showed that the anticoagulation properties of PDMS/GO-BCA-HEP nanocomposite films were greatly superior to those for no treated PDMS. Cell culture assay indicated that PDMS/GO-BCA-HEP nanocomposite films showed enhanced cell adhesion.

Effects of preparation methods on the structure and mechanical properties of wet conditioned starch/montmorillonite nanocomposite films.

PubMed

Müller, Péter; Kapin, Éva; Fekete, Erika

2014-11-26

TPS/Na-montmorillonite nanocomposite films were prepared by solution and melt blending. Clay content changed between 0 and 25 wt% based on the amount of dry starch. Structure, tensile properties, and water content of wet conditioned films were determined as a function of clay content. Intercalated structure and VH-type crystallinity of starch were found for all the nanocomposites independently of clay and plasticizer content or preparation method, but at larger than 10 wt% clay content nanocomposites prepared by melt intercalation contained aggregated particles as well. In spite of the incomplete exfoliation clay reinforces TPS considerably. Preparation method has a strong influence on mechanical properties of wet conditioned films. Mechanical properties of the conditioned samples prepared by solution homogenization are much better than those of nanocomposites prepared by melt blending. Water, which was either adsorbed or bonded in the composites in conditioning or solution mixing process, respectively, has different effect on mechanical properties. Copyright © 2014 Elsevier Ltd. All rights reserved.

The structural basis of actinomycin D–binding induces nucleotide flipping out, a sharp bend and a left-handed twist in CGG triplet repeats

PubMed Central

Lo, Yu-Sheng; Tseng, Wen-Hsuan; Chuang, Chien-Ying; Hou, Ming-Hon

2013-01-01

The potent anticancer drug actinomycin D (ActD) functions by intercalating into DNA at GpC sites, thereby interrupting essential biological processes including replication and transcription. Certain neurological diseases are correlated with the expansion of (CGG)n trinucleotide sequences, which contain many contiguous GpC sites separated by a single G:G mispair. To characterize the binding of ActD to CGG triplet repeat sequences, the structural basis for the strong binding of ActD to neighbouring GpC sites flanking a G:G mismatch has been determined based on the crystal structure of ActD bound to ATGCGGCAT, which contains a CGG triplet sequence. The binding of ActD molecules to GCGGC causes many unexpected conformational changes including nucleotide flipping out, a sharp bend and a left-handed twist in the DNA helix via a two site-binding model. Heat denaturation, circular dichroism and surface plasmon resonance analyses showed that adjacent GpC sequences flanking a G:G mismatch are preferred ActD-binding sites. In addition, ActD was shown to bind the hairpin conformation of (CGG)16 in a pairwise combination and with greater stability than that of other DNA intercalators. Our results provide evidence of a possible biological consequence of ActD binding to CGG triplet repeat sequences. PMID:23408860

In vitro anticancer activities of Schiff base and its lanthanum complex

NASA Astrophysics Data System (ADS)

Neelima; Poonia, Kavita; Siddiqui, Sahabjada; Arshad, Md; Kumar, Dinesh

2016-02-01

Schiff base metal complexes are well-known to intercalate DNA. The La(III) complexes have been synthesized such that they hinder with the role of the topoisomerases, which control the topology of DNA during the cell-division cycle. Although several promising chemotherapeutics have been developed, on the basis of Schiff base metal complex DNA intercalating system they did not proceed past clinical trials due to their dose-limiting toxicity. Herein, we discuss an alternative compound, the La(III) complex, [La(L1)2Cl3]·7H2O based on a Schiff base ligand 2,3-dihydro-1H-indolo-[2,3-b]-phenazin-4(5H)-ylidene)benzothiazole-2-amine (L1), and report in vitro cell studies. Results of antitumor activity using cell viability assay, reactive oxygen species (ROS) generation and nuclear condensation in PC-3 (Human, prostate carcinoma) cells show that the metal complex is more potent than ligand. La(III) complexes have been synthesized by reaction of lanthanum(III) salt in 1:2 M ratio with ligands L1 and 3-(ethoxymethylene)-2,3-dihydro-1H-indolo[2,3-b]-phenazin-4(5H)-ylidene)benzathiazole-2-amine (L2) in methanol. The ligands and their La(III) complexes were characterized by molar conductance, magnetic susceptibility, elemental analyses, FT-IR, UV-Vis, 1H/13C NMR, thermogravimetric, XRD, and SEM analysis.

DNA biosensing with 3D printing technology.

PubMed

Loo, Adeline Huiling; Chua, Chun Kiang; Pumera, Martin

2017-01-16

3D printing, an upcoming technology, has vast potential to transform conventional fabrication processes due to the numerous improvements it can offer to the current methods. To date, the employment of 3D printing technology has been examined for applications in the fields of engineering, manufacturing and biological sciences. In this study, we examined the potential of adopting 3D printing technology for a novel application, electrochemical DNA biosensing. Metal 3D printing was utilized to construct helical-shaped stainless steel electrodes which functioned as a transducing platform for the detection of DNA hybridization. The ability of electroactive methylene blue to intercalate into the double helix structure of double-stranded DNA was then exploited to monitor the DNA hybridization process, with its inherent reduction peak serving as an analytical signal. The designed biosensing approach was found to demonstrate superior selectivity against a non-complementary DNA target, with a detection range of 1-1000 nM.

Interaction of Sulforaphane with DNA and RNA

PubMed Central

Abassi Joozdani, Farzaneh; Yari, Faramarz; Abassi Joozdani, Parvaneh; Nafisi, Shohreh

2015-01-01

Sulforaphane (SFN) is an isothiocyanate found in cruciferous vegetables with anti-inflammatory, anti-oxidant and anti-cancer activities. However, the antioxidant and anticancer mechanism of sulforaphane is not well understood. In the present research, we reported binding modes, binding constants and stability of SFN–DNA and -RNA complexes by Fourier transform infrared (FTIR) and UV–Visible spectroscopic methods. Spectroscopic evidence showed DNA intercalation with some degree of groove binding. SFN binds minor and major grooves of DNA and backbone phosphate (PO2), while RNA binding is through G, U, A bases with some degree of SFN–phosphate (PO2) interaction. Overall binding constants were estimated to be K(SFN–DNA)=3.01 (± 0.035)×104 M-1 and K(SFN–RNA)= 6.63 (±0.042)×103 M-1. At high SFN concentration (SFN/RNA = 1/1), DNA conformation changed from B to A occurred, while RNA remained in A-family structure. PMID:26030290

Conductive Composites Made Less Expensively

NASA Technical Reports Server (NTRS)

Gaier, James R.

2005-01-01

The use of electrically conductive composite structures for electrostatic dissipation, electromagnetic interference shielding, and ground return planes could save between 30 and 90 percent of the mass of the structure, in comparison to aluminum. One strategy that has been shown to make conducting composites effectively uses intercalated graphite fiber as the reinforcement. Intercalation--the insertion of guest atoms or molecules between the graphene planes--can lower the electrical resistivity of graphite fibers by as much as a factor of 10, without sacrificing mechanical or thermal properties.

Three-Dimensional Intercalated Porous Graphene on Si(111)

NASA Astrophysics Data System (ADS)

Pham, Trung T.; Sporken, Robert

2018-02-01

Three-dimensional intercalated porous graphene has been formed on Si(111) by electron beam evaporation under appropriate conditions and its structural and electronic properties investigated in detail by reflection high-energy electron diffraction, x-ray photoemission spectroscopy, Raman spectroscopy, high-resolution scanning electron microscopy, atomic force microscopy, and scanning tunneling microscopy. The results show that the crystalline quality of the porous graphene depended not only on the substrate temperature but also on the SiC layer thickness during carbon atom deposition.

Chemically Tunable Full Spectrum Optical Properties of 2D Silicon Telluride Nanoplates.

PubMed

Wang, Mengjing; Lahti, Gabriella; Williams, David; Koski, Kristie J

2018-06-07

Silicon telluride (Si 2 Te 3 ) is a two-dimensional, layered, p-type semiconductor that shows broad near-infrared photoluminescence. We show how, through various means of chemical modification, Si 2 Te 3 can have its optoelectronic properties modified in several independent ways without fundamentally altering the host crystalline lattice. Substitutional doping with Ge strongly redshifts the photoluminescence while substantially lowering the direct and indirect band gaps and altering the optical phonon modes. Intercalation with Ge introduces a sharp 4.3 eV ultraviolet resonance and shifts the bulk plasmon even while leaving the infrared response and band gaps virtually unchanged. Intercalation with copper strengthens the photoluminescence without altering its spectral shape. Thus silicon telluride is shown to be a chemically tunable platform of full spectrum optical properties promising for opto-electronic applications.

Molecular mechanisms of DNA repair inhibition by caffeine

DOE Office of Scientific and Technical Information (OSTI.GOV)

Selby, C.P.; Sancar, A.

1990-05-01

Caffeine potentiates the mutagenic and lethal effects of genotoxic agents. It is thought that this is due, at least in some organisms, to inhibition of DNA repair. However, direct evidence for inhibition of repair enzymes has been lacking. Using purified Escherichia coli DNA photolyase and (A)BC excinuclease, we show that the drug inhibits photoreactivation and nucleotide excision repair by two different mechanisms. Caffeine inhibits photoreactivation by interfering with the specific binding of photolyase to damaged DNA, and it inhibits nucleotide excision repair by promoting nonspecific binding of the damage-recognition subunit, UvrA, of (A)BC excinuclease. A number of other intercalators, includingmore » acriflavin and ethidium bromide, appear to inhibit the excinuclease by a similar mechanism--that is, by trapping the UvrA subunit in nonproductive complexes on undamaged DNA.« less

Radiation Protection of New Lightweight Electromagnetic Interference Shielding Materials Determined

NASA Technical Reports Server (NTRS)

1996-01-01

Weight savings as high as 80 percent could be achieved by simply switching from aluminum electromagnetic interference (EMI) shielding covers for spacecraft power systems to EMI covers made from intercalated graphite fiber composites. Because EMI covers typically make up about one-fifth of the power system mass, this change would decrease the mass of a spacecraft power system by more than 15 percent. Intercalated graphite fibers are made by diffusing guest atoms or molecules, such as bromine, between the carbon planes of the graphite fibers. The resulting bromine-intercalated fibers have mechanical and thermal properties nearly identical to pristine graphite fibers, but their resistivity is lower by a factor of 5, giving them better electrical conductivity than stainless steel and making these composites suitable for EMI shielding.

Ion-driven photoluminescence modulation of quasi-two-dimensional MoS2 nanoflakes for applications in biological systems.

PubMed

Ou, Jian Zhen; Chrimes, Adam F; Wang, Yichao; Tang, Shi-yang; Strano, Michael S; Kalantar-zadeh, Kourosh

2014-02-12

Quasi-two-dimensional (quasi-2D) molybdenum disulfide (MoS2) is a photoluminescence (PL) material with unique properties. The recent demonstration of its PL, controlled by the intercalation of positive ions, can lead to many opportunities for employing this quasi-2D material in ion-related biological applications. Here, we present two representative models of biological systems that incorporate the ion-controlled PL of quasi-2D MoS2 nanoflakes. The ion exchange behaviors of these two models are investigated to reveal enzymatic activities and cell viabilities. While the ion intercalation of MoS2 in enzymatic activities is enabled via an external applied voltage, the intercalation of ions in cell viability investigations occurs in the presence of the intrinsic cell membrane potential.

Synthesis, characterization, DNA/protein interaction and cytotoxicity studies of Cu(II) and Co(II) complexes derived from dipyridyl triazole ligands.

PubMed

Zhang, Wei; Yao, Di; Wei, Yi; Tang, Jie; Bian, He-Dong; Huang, Fu-Ping; Liang, Hong

2016-06-15

Four different transition metal complexes containing dipyridyl triazole ligands, namely [Cu(abpt)2Cl2]·2H2O (1), [Cu(abpt)2(ClO4)2] (2), [Co2(abpt)2(H2O)2Cl2]·Cl2·4H2O (3) and [Co2(Hbpt)2(CH3OH)2(NO3)2] (4) have been designed, synthesized and further structurally characterized by X-ray crystallography, ESI-MS, elemental analysis, IR and Raman spectroscopy. In these complexes, the both ligands act as bidentate ligands with N, N donors. DNA binding interactions with calf thymus DNA (ct-DNA) of the ligand and its complexes 1~4 were investigated via electronic absorption, fluorescence quenching, circular dichroism and viscosity measurements as well as confocal Laser Raman spectroscopy. The results show these complexes are able to bind to DNA via the non-covalent mode i.e. intercalation and groove binding or electrostatic interactions. The interactions with bovine serum albumin (BSA) were also studied using UV-Vis and fluorescence spectroscopic methods which indicated that fluorescence quenching of BSA by these compounds was the presence of both static and dynamic quenching. Moreover, the in vitro cytotoxic effects of the complexes against four cell lines SK-OV-3, HL-7702, BEL7404 and NCI-H460 showed the necessity of the coordination action on the biological properties on the respective complex and that all four complexes exhibited substantial cytotoxic activity. Copyright © 2016. Published by Elsevier B.V.

Multiplexed mRNA Sensing and Combinatorial-Targeted Drug Delivery Using DNA-Gold Nanoparticle Dimers.

PubMed

Kyriazi, Maria-Eleni; Giust, Davide; El-Sagheer, Afaf H; Lackie, Peter M; Muskens, Otto L; Brown, Tom; Kanaras, Antonios G

2018-04-24

The design of nanoparticulate systems which can perform multiple synergistic functions in cells with high specificity and selectivity is of great importance in applications. Here we combine recent advances in DNA-gold nanoparticle self-assembly and sensing to develop gold nanoparticle dimers that are able to perform multiplexed synergistic functions within a cellular environment. These dimers can sense two mRNA targets and simultaneously or independently deliver one or two DNA-intercalating anticancer drugs (doxorubicin and mitoxantrone) in live cells. Our study focuses on the design of sophisticated nanoparticle assemblies with multiple and synergistic functions that have the potential to advance sensing and drug delivery in cells.

First-Principles evaluation of the Chevrel phase intercalated with Be, Mg, Ca, Sr, and Ba

NASA Astrophysics Data System (ADS)

Juran, Taylor; Smeu, Manuel

Li ion batteries are extremely useful when an item requires portability and compactness, such as laptops and cell phones; due to the lightweight/compact nature of Li ion batteries. The lightweight and compact nature of Li ion batteries comes at a high cost. It is sensible to consider Li ion battery alternatives, which are more cost effective and useable when portability is not a priority. An option for a less expensive battery source is the Ca ion battery. The Ca ion battery is interesting as many researchers overlook the potential battery source due to the perplexity of finding suitable anode materials and electrolytes. In order for this technology to work, cathodes that allow for the reversible intercalation of Ca2+ ions and also provide a preferred voltage must be identified. We investigate the Chevrel phase compounds of Mo6X8 (X = S, Se, Te) which can intercalate various ions. The concentration of the ion intercalated with the Chevrel cathode is studied. We consider doped versions of the Chevrel phase, using various dopants to substitute Mo. We use density functional theory to calculate the voltage of several intercalation ions with the Chevrel material. The resulting electronic properties of the aforementioned materials will be investigated.

Exfoliation of Hexagonal Boron Nitride via Ferric Chloride Intercalation

NASA Technical Reports Server (NTRS)

Hung, Ching-cheh; Hurst, Janet; Santiago, Diana; Rogers, Richard B.

2014-01-01

Sodium fluoride (NaF) was used as an activation agent to successfully intercalate ferric chloride (FeCl3) into hexagonal boron nitride (hBN). This reaction caused the hBN mass to increase by approx.100 percent, the lattice parameter c to decrease from 6.6585 to between 6.6565 and 6.6569 ?, the x-ray diffraction (XRD) (002) peak to widen from 0.01deg to 0.05deg of the full width half maximum value, the Fourier transform infrared (FTIR) spectrum's broad band (1277/cm peak) to change shape, and new FTIR bands to emerge at 3700 to 2700 and 1600/cm. This indicates hBN's structural and chemical properties are significantly changed. The intercalated product was hygroscopic and interacted with moisture in the air to cause further structural and chemical changes (from XRD and FTIR). During a 24-h hold at room temperature in air with 100 percent relative humidity, the mass increased another 141 percent. The intercalated product, hydrated or not, can be heated to 750 C in air to cause exfoliation. Exfoliation becomes significant after two intercalation-air heating cycles, when 20-nm nanosheets are commonly found. Structural and chemical changes indicated by XRD and FTIR data were nearly reversed after the product was placed in hydrochloric acid (HCl), resulting in purified, exfoliated, thin hBN products.

DNA-Binding Interaction Studies of Microwave Assisted Synthesized Sulfonamide Substituted 8-Hydroxyquinoline Derivatives.

PubMed

Dixit, Ritu B; Patel, Tarosh S; Vanparia, Satish F; Kunjadiya, Anju P; Keharia, Harish R; Dixit, Bharat C

2011-01-01

Sulfonamide substituted 8-hydroxyquinoline derivatives were prepared using a microwave synthesizer. The interaction of sulfonamide substituted 8-hydroxyquinoline derivatives and their transition metal complexes with Plasmid (pUC 19) DNA and Calf Thymus DNA were investigated by UV spectroscopic studies and gel electrophoresis measurements. The interaction between ligand/metal complexes and DNA was carried out by increasing the concentration of DNA from 0 to 12 μl in UV spectroscopic study, while the concentration of DNA in gel electrophoresis remained constant at 10 μl. These studies supported the fact that, the complex binds to DNA by intercalation via ligand into the base pairs of DNA. The relative binding efficacy of the complexes to DNA was much higher than the binding efficacy of ligands, especially the complex of Cu-AHQMBSH had the highest binding ability to DNA. The mobility of the bands decreased as the concentration of the complex was increased, indicating that there was increase in the interaction between the metal ion and DNA. Complexes of AHQMBSH were excellent for DNA binding as compared to HQMABS.

Electrochemical and spectroscopic study on the interaction between isoprenaline and DNA using multivariate curve resolution-alternating least squares.

PubMed

Ni, Yongnian; Wei, Min; Kokot, Serge

2011-11-01

Interaction of isoprenaline (ISO) with calf-thymus DNA was studied by spectroscopic and electrochemical methods. The behavior of ISO was investigated at a glassy carbon electrode (GCE) by cyclic voltammetry (CV) and differential pulse stripping voltammetry (DPSV); ISO was oxidized and an irreversible oxidation peak was observed. The binding constant K and the stoichiometric coefficient m of ISO with DNA were evaluated. Also, with the addition of DNA, hyperchromicity of the UV-vis absorption spectra of ISO was noted, while the fluorescence intensity decreased significantly. Multivariate curve resolution-alternating least squares (MCR-ALS) chemometrics method was applied to resolve the combined spectroscopic data matrix, which was obtained by the UV-vis and fluorescence methods. Pure spectra of ISO, DNA and ISO-DNA complex, and their concentration profiles were then successfully obtained. The results indicated that the ISO molecule intercalated into the base-pairs of DNA, and the complex of ISO-DNA was formed. Copyright © 2011 Elsevier B.V. All rights reserved.

Genotoxicity of Tri- and Hexavalent Chromium Compounds In Vivo and Their Modes of Action on DNA Damage In Vitro

PubMed Central

Fang, Zhijia; Zhao, Min; Zhen, Hong; Chen, Lifeng; Shi, Ping; Huang, Zhiwei

2014-01-01

Chromium occurs mostly in tri- and hexavalent states in the environment. Hexavalent chromium [Cr(VI)] compounds are extensively used in diverse industries, and trivalent chromium [Cr(III)] salts are used as micronutrients and dietary supplements. In the present work, we report that they both induce genetic mutations in yeast cells. They both also cause DNA damage in both yeast and Jurkat cells and the effect of Cr(III) is greater than that of Cr(VI). We further show that Cr(III) and Cr(VI) cause DNA damage through different mechanisms. Cr(VI) intercalates DNA and Cr(III) interferes base pair stacking. Based on our results, we conclude that Cr(III) can directly cause genotoxicity in vivo. PMID:25111056

Effect of hydrotalcite-like compounds on the aqueous solubility of some poorly water-soluble drugs.

PubMed

Ambrogi, Valeria; Fardella, Giuseppe; Grandolini, Giuliano; Nocchetti, Morena; Perioli, Luana

2003-07-01

A new approach of improving drug dissolution properties is described. This method exploits the property of a carrier owing to the hydrotalcite-type anionic clays (HTlc). HTlc is an inorganic layered solid that lodges anionic compounds among its layers. As HTlc dissolves at acidic pH values (pH < 4), the anions intercalated among the layers are promptly released in the medium. In this article some nonsteroidal antiinflammatory drugs were chosen as models of poorly water-soluble drugs. They were intercalated in HTlc and solubility measurements in acidic medium were performed. A remarkable improvement of drug solubility was observed especially in the case of indomethacin. Copyright 2003 Wiley-Liss, Inc. and the American Pharmacists Association

Electrochemical Characterization of Vanadium Pentoxide (V 2O5) And Activated Carbon (AC) Electrodes in Multivalent Aluminum Nitrate (Al(NO3)3) Electrolyte for Battery-Type Hybrid Supercapacitor Applications

NASA Astrophysics Data System (ADS)

Solanki, Ketan Subhash

Hybrid supercapacitors (HSC) have been extensively investigated for enhanced charge storage capacity (Yoo, et al. 2014). Although Li-ion batteries are known for high energy density, but their limited power density has driven the research toward developing hybrid supercapacitors (Jayalakshmi and Balasubramanian 2008). They combine non-faradic properties of electric double layer capacitors (EDLC) and faradic properties of pseudocapacitors to provide high energy density without compromising high Power density (Yoo, et al. 2014) (Lukatskaya, Dunn and Gogotsi 2016). In HSC, one electrode will store energy by double layer mechanism whereas the other stores through redox intercalation or surface redox reactions (Lukatskaya, Dunn and Gogotsi 2016) (Karthikeyan, et al. 2010). In this study, we have examined the electrochemical characteristics of vanadium pentoxide (V2O5) and activated carbon (AC) in an aqueous multivalent aluminum nitrate (nonhydrate, Al(NO3)3) electrolyte for viable electrode applications in battery-type hybrid supercapacitors, also known as supercapattery. A Specific capacitance of 340 Fg -1 was obtained at a scanning rate of 10 mV/s. Although this configuration showed promising storage and cyclability capability but the voltage for intercalation of Al3+ ions occurred below zero voltage. Hence, right selection of electrodes for such configurations may help in obtaining intercalation and de-intercalation voltages above zero volt and thereby result in a viable practical application with better performance.

Monolayer atomic crystal molecular superlattices.

PubMed

Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A; Huang, Yu; Duan, Xiangfeng

2018-03-07

Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 10 7 , along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.

Monolayer atomic crystal molecular superlattices

NASA Astrophysics Data System (ADS)

Wang, Chen; He, Qiyuan; Halim, Udayabagya; Liu, Yuanyue; Zhu, Enbo; Lin, Zhaoyang; Xiao, Hai; Duan, Xidong; Feng, Ziying; Cheng, Rui; Weiss, Nathan O.; Ye, Guojun; Huang, Yun-Chiao; Wu, Hao; Cheng, Hung-Chieh; Shakir, Imran; Liao, Lei; Chen, Xianhui; Goddard, William A., III; Huang, Yu; Duan, Xiangfeng

2018-03-01

Artificial superlattices, based on van der Waals heterostructures of two-dimensional atomic crystals such as graphene or molybdenum disulfide, offer technological opportunities beyond the reach of existing materials. Typical strategies for creating such artificial superlattices rely on arduous layer-by-layer exfoliation and restacking, with limited yield and reproducibility. The bottom-up approach of using chemical-vapour deposition produces high-quality heterostructures but becomes increasingly difficult for high-order superlattices. The intercalation of selected two-dimensional atomic crystals with alkali metal ions offers an alternative way to superlattice structures, but these usually have poor stability and seriously altered electronic properties. Here we report an electrochemical molecular intercalation approach to a new class of stable superlattices in which monolayer atomic crystals alternate with molecular layers. Using black phosphorus as a model system, we show that intercalation with cetyl-trimethylammonium bromide produces monolayer phosphorene molecular superlattices in which the interlayer distance is more than double that in black phosphorus, effectively isolating the phosphorene monolayers. Electrical transport studies of transistors fabricated from the monolayer phosphorene molecular superlattice show an on/off current ratio exceeding 107, along with excellent mobility and superior stability. We further show that several different two-dimensional atomic crystals, such as molybdenum disulfide and tungsten diselenide, can be intercalated with quaternary ammonium molecules of varying sizes and symmetries to produce a broad class of superlattices with tailored molecular structures, interlayer distances, phase compositions, electronic and optical properties. These studies define a versatile material platform for fundamental studies and potential technological applications.

Single nucleotide polymorphism discrimination with and without an ethidium bromide intercalator.

PubMed

Fenati, Renzo A; Connolly, Ashley R; Ellis, Amanda V

2017-02-15

Single nucleotide polymorphism (SNP) genotyping is an important aspect in understanding genetic variations. Here, we discriminate SNPs using toe-hold mediated displacement reactions. The biological target is an 80 nucleotide long double-stranded-DNA from the mtDNA HV1 region, associated with maternal ancestry. This target has been specially designed with a pendant toehold and a cationic fluorophore, ATTO 647N, as a reporter, produced in a polymerase chain reaction. Rates of reaction for the toehold-polymerase chain reaction products (TPPs) with their corresponding complementary displacing sequences, labelled with a Black Hole Quencher 1, followed the order TPP-Cytosine > TPP-Thymine > TPP-Adenine ≥ TPP-Guanine. Non-complementary rates were the slowest with mismatches involving cytosine. These reactions, operating in a static/or contact mode, gave averaged readouts between SNPs within 15 min (with 80-90% quenching), compared to 25-30 min in previous studies involving fluorescence resonance energy transfer. Addition of an intercalating agent, ethidium bromide, retarded the rate of reaction in which cytosine was involved, presumably through stabilization of the base pairing, which resulted in markedly improved discrimination of cytosine containing SNPs. Copyright © 2016 Elsevier B.V. All rights reserved.

Room temperature deintercalation of alkali metal atoms from epitaxial graphene by formation of charge-transfer complexes

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shin, H.-C.; Ahn, S. J.; Kim, H. W.

2016-08-22

Atom (or molecule) intercalations and deintercalations have been used to control the electronic properties of graphene. In general, finite energies above room temperature (RT) thermal energy are required for the intercalations and deintercalations. Here, we demonstrate that alkali metal atoms can be deintercalated from epitaxial graphene on a SiC substrate at RT, resulting in the reduction in density of states at the Fermi level. The change in density of states at the Fermi level at RT can be applied to a highly sensitive graphene sensor operating at RT. Na atoms, which were intercalated at a temperature of 80 °C, were deintercalatedmore » at a high temperature above 1000 °C when only a thermal treatment was used. In contrast to the thermal treatment, the intercalated Na atoms were deintercalated at RT when tetrafluorotetracyanoquinodimethane (F4-TCNQ) molecules were adsorbed on the surface. The RT deintercalation occurred via the formation of charge-transfer complexes between Na atoms and F4-TCNQ molecules.« less

Multistage Mechanism of Lithium Intercalation into Graphite Anodes in the Presence of the Solid Electrolyte Interface.

PubMed

Dinkelacker, Franz; Marzak, Philipp; Yun, Jeongsik; Liang, Yunchang; Bandarenka, Aliaksandr S

2018-04-25

A so-called solid electrolyte interface (SEI) in a lithium-ion battery largely determines the performance of the whole system. However, it is one of the least understood objects in these types of batteries. SEIs are formed during the initial charge-discharge cycles, prevent the organic electrolytes from further decomposition, and at the same time govern lithium intercalation into the graphite anodes. In this work, we use electrochemical impedance spectroscopy and atomic force microscopy to investigate the properties of a SEI film and an electrified "graphite/SEI/electrolyte interface". We reveal a multistage mechanism of lithium intercalation and de-intercalation in the case of graphite anodes covered by SEI. On the basis of this mechanism, we propose a relatively simple model, which perfectly explains the impedance response of the "graphite/SEI/electrolyte" interface at different temperatures and states of charge. From the whole data obtained in this work, it is suggested that not only Li + but also negatively charged species, such as anions from the electrolyte or functional groups of the SEI, likely interact with the surface of the graphite anode.

Reversible Intercalation of Fluoride-Anion Receptor Complexes in Graphite

NASA Technical Reports Server (NTRS)

West, William C.; Whitacre, Jay F.; Leifer, Nicole; Greenbaum, Steve; Smart, Marshall; Bugga, Ratnakumar; Blanco, Mario; Narayanan, S. R.

2007-01-01

We have demonstrated a route to reversibly intercalate fluoride-anion receptor complexes in graphite via a nonaqueous electrochemical process. This approach may find application for a rechargeable lithium-fluoride dual-ion intercalating battery with high specific energy. The cell chemistry presented here uses graphite cathodes with LiF dissolved in a nonaqueous solvent through the aid of anion receptors. Cells have been demonstrated with reversible cathode specific capacity of approximately 80 mAh/g at discharge plateaus of upward of 4.8 V, with graphite staging of the intercalant observed via in situ synchrotron X-ray diffraction during charging. Electrochemical impedance spectroscopy and B-11 nuclear magnetic resonance studies suggest that cointercalation of the anion receptor with the fluoride occurs during charging, which likely limits the cathode specific capacity. The anion receptor type dictates the extent of graphite fluorination, and must be further optimized to realize high theoretical fluorination levels. To find these optimal anion receptors, we have designed an ab initio calculations-based scheme aimed at identifying receptors with favorable fluoride binding and release properties.

Change of the binding mode of the DNA/proflavine system induced by ethanol.

PubMed

García, Begoña; Leal, José M; Ruiz, Rebeca; Biver, Tarita; Secco, Fernando; Venturini, M

2010-07-01

The equilibria and kinetics of the binding of proflavine to poly(dG-dC).poly(dG-dC) and poly(dA-dT).poly(dA-dT) were investigated in ethanol/water mixtures using spectrophotometric, circular dichroism, viscometric, and T-jump methods. All methods concur in showing that two modes of interaction are operative: intercalation and surface binding. The latter mode is favored by increasing ethanol and/or the proflavine content. Both static and kinetic experiments show that, concerning the poly(dG-dC).poly(dG-dC)/proflavine system, intercalation largely prevails up to 20% EtOH. For higher EtOH levels surface binding becomes dominant. Concerning the poly(dA-dT).poly(dA-dT)/proflavine system, melting experiments show that addition of proflavine stabilizes the double stranded structure, but the effect is reduced in the presence of EtOH. The DeltaH degrees and DeltaS degrees values of the melting process, measured at different concentrations of added proflavine, are linearly correlated, revealing the presence of the enthalpy-entropy compensation phenomenon (EEC). The nonmonotonicity of the "entropic term" of the EEC reveals the transition between the two binding modes. T-jump experiments show two relaxation effects, but at the highest levels of EtOH (>25%) the kinetic curves become monophasic, confirming the prevalence of the surface complex. A branched mechanism is proposed where diffusion controlled formation of a precursor complex occurs in the early stage of the binding process. This evolves toward the surface and/or the intercalated complex according to two rate-determining parallel steps. CD spectra suggest that, in the surface complex, proflavine is bound to DNA in the form of an aggregate.

DNA binding studies of a new dicationic porphyrin. Insights into interligand interactions.

PubMed

Shelton, Alexander H; Rodger, Alison; McMillin, David R

2007-08-07

Cationic porphyrins have an affinity for DNA and potential for applications in the fields of photodynamic therapy and cellular imaging. This report describes a new dicationic porphyrin, 5,15-dimethyl-10,20-di(N-methylpyridinium-4-yl)porphyrin, abbreviated H2tMe2D4. Although tetrasubstituted, H2tMe2D4 presents modest steric requirements and forms in reasonable yield by a "2+2" synthetic method. Accordingly, studies of the zinc(II)- and copper(II)-containing derivatives, Zn(tMe2D4) and Cu(tMe2D4), have also been possible. Methods used to characterize DNA-binding motifs include absorption, emission, linear, and circular dichroism spectroscopies, as well as viscometry. An unusually detailed picture of porphyrin uptake emerges. As the ratio of DNA to porphyrin increases during a typical titration, H2tMe2D4 or Cu(tMe2D4) initially aggregates on the host and then shifts to intercalative binding at close quarters before finally dispersing into non-interacting intercalation sites of the host. Emission studies of the copper(II) porphyrin have been very valuable. The existence of a measurable signal is diagnostic of intercalative binding, and the saturation behavior establishes that internalization typically monopolizes approximately three base pairs. In the moderate loading regime, emission data are most telling because dipole-dipole interactions between near-neighbor porphyrins tend to confuse other spectroscopic assays. The third ligand, Zn(tMe2D4), behaves differently in that the uptake is a strictly cooperative process. The mode of binding also varies with the base content of the DNA host. When the DNA is rich in A=T base pairs, the porphyrin remains five-coordinate and binds externally; however, Zn(tMe2D4) loses its axial ligand and binds by intercalation if the host contains only G[triple bond]C base pairs.

Polymer Layered Silicate Nanocomposites: A Review

PubMed Central

Mittal, Vikas

2009-01-01

This review aims to present recent advances in the synthesis and structure characterization as well as the properties of polymer layered silicate nanocomposites. The advent of polymer layered silicate nanocomposites has revolutionized research into polymer composite materials. Nanocomposites are organic-inorganic hybrid materials in which at least one dimension of the filler is less than 100 nm. A number of synthesis routes have been developed in the recent years to prepare these materials, which include intercalation of polymers or pre-polymers from solution, in-situ polymerization, melt intercalation etc. The nanocomposites where the filler platelets can be dispersed in the polymer at the nanometer scale owing to the specific filler surface modifications, exhibit significant improvement in the composite properties, which include enhanced mechanical strength, gas barrier, thermal stability, flame retardancy etc. Only a small amount of filler is generally required for the enhancement in the properties, which helps the composite materials retain transparency and low density.

Rocking-Chair Configuration in Ultrathin Lithium Vanadate-Graphene Hybrid Nanosheets for Electrical Modulation

PubMed Central

Zhu, Haiou; Qin, Xinming; Sun, Xu; Yan, Wensheng; Yang, Jinlong; Xie, Yi

2013-01-01

The ability to control electronic property of a material by externally applied voltage is greatly anticipated in modern electronics, and graphene provide potential application foreground for this issue on account of its exotic ambipolar transport property. In this study, we proposed that inorganic-graphene intercalated nanosheet is an effective solution to optimize the transport property of graphene. As an example, lithium vanadate-graphene (LiVO-graphene) alternately intercalated nanosheets were designed and successfully synthesized. Theoretical calculation implied that its rocking chair configuration may provide a new pathway to switch the carrier in graphene layer between p-type and n-type while the position of embedded Li ions is controlled by an external field. Thus, a demo transistor was fabricated with layer-by-layer overlapping of LiVO-graphene nanosheets which proved that this inorganic-graphene structure could be used for electrical modulation in electronic devices. PMID:23409237

Preparation and properties of poly HTBN-based urethane-urea/organo reactive montmorillonite nanocomposites

NASA Astrophysics Data System (ADS)

Li, Zai-Feng; Wu, Yuan; Zhang, Fu-Tao; Cao, Yu-Yang; Wu, Shou-Peng; Wang, Ting

2012-12-01

With ultrasonic assistant mixing way, an intercalated mixture of polyol/organo reactive montmorillonite (ORMMT) was pretreated. The prepolymer composed MMT clay was prepared by reaction of polyol/ORMMT mixture with toluene diisocyanate (TDI). The resultant prepolymer reacted with extender (DMTDA) and then the polyurethane-urea/organo reactive montmorillonite (PUU/ORMMT) nanocomposites were obtained. The structure, morphology and properties of PUU/ORMMT nanocomposites were characterized by FT-IR, TEM, AFM, strain-stress machine, TGA, and dynamic mechanical analysis (DMA). The results showed that when the OMMT content is 3%, the PUU/ORMMT nanocomposities performed super mechanical properties. Because of the presence of ORMMT, both T g of the soft segment and tan δ of the PUU increased, and the decomposition temperature for the first step and the second step increased respectively. TEM images showed that the organophilic MMT particles in the PUU composite exhibit a high degree of intercalation and exfoliation.

New copper(I) complexes bearing lomefloxacin motif: Spectroscopic properties, in vitro cytotoxicity and interactions with DNA and human serum albumin.

PubMed

Komarnicka, Urszula K; Starosta, Radosław; Kyzioł, Agnieszka; Płotek, Michał; Puchalska, Małgorzata; Jeżowska-Bojczuk, Małgorzata

2016-12-01

In this paper we present lomefloxacin's (HLm, 2nd generation fluoroquinolone antibiotic agent) organic and inorganic derivatives: aminomethyl(diphenyl)phosphine (PLm), its oxide as well as new copper(I) iodide or copper(I) thiocyanate complexes with PLm and 2,9-dimethyl-1,10-phenanthroline (dmp) or 2,2'-biquinoline (bq) as the auxiliary ligands. The synthesized compounds were fully characterised by NMR, UV-Vis and luminescence spectroscopies. Selected structures were analysed by theoretical DFT (density functional theory) methods. High stability of the complexes in aqueous solutions in the presence of atmosferic oxygen was proven. Cytotoxic activity of all compounds was tested towards three cancer cell lines (CT26 - mouse colon carcinoma, A549 - human lung adenocarcinoma, and MCF7 - human breast adenocarcinoma). All complexes are characterised by cytotoxic activity higher than the activity of the parent drug and its organic derivatives as well as cisplatin. Studied derivatives as well as parent drug do not intercalate to DNA, except Cu(I) complexes with bq ligand. All studied complexes caused single-stranded cleavage of the sugar-phosphate backbone of plasmid DNA. The addition of H 2 O 2 caused distinct changes in the plasmid structure and led to single- and/or double-strain plasmid cleavage. Studied compounds interact with human serum albumin without affecting its secondary structure. Copyright © 2016 Elsevier Inc. All rights reserved.

Photoactive platinum(II) complexes of nonsteroidal anti-inflammatory drug naproxen: Interaction with biological targets, antioxidant activity and cytotoxicity.

PubMed

Srivastava, Payal; Singh, Khushbu; Verma, Madhu; Sivakumar, Sri; Patra, Ashis K

2018-01-20

The effect on the therapeutic efficacy of Pt(II) complexes on combining non-steroidal anti-inflammatory drugs (NSAIDs) is an attractive strategy to circumvent chronic inflammation mediated by cancer and metastasis. Two square-planar platinum(II) complexes: [Pt(dach)(nap)Cl] (1) and [Pt(dach)(nap) 2 ] (2), where dach = (1R,2R)-dichloro(cyclohexane-1,2-diamine) and NSAID drug naproxen (nap), have been designed for studying their biological activity. The naproxen bound to the Pt(II) centre get released upon photoirradiation with low-power UV-A light as confirmed by the significant enhancement in emission intensities of the complexes. The compounds were evaluated for their photophysical properties, photostability, reactivity with 5'-guanosine monophophosphate (5'-GMP), interactions with CT-DNA and BSA, antioxidant activity and reactive oxygen species mediated photo-induced DNA damage properties. ESI-MS studies demonstrated the formation of bis-adduct with 5'-GMP and the formation of Pt II -DNA crosslinks by gel electrophoretic mobility shift assay and ITC studies. The interaction of the complexes 1 and 2 with the CT-DNA exhibits potential binding affinity (K b  ∼ 10 4  M -1 , K app ∼ 10 5  M -1 ), implying intercalation to CT-DNA through planar naphthyl ring of the complexes. Both the complexes also exhibit strong binding affinity towards BSA (K BSA ∼ 10 5  M -1 ). The complexes exhibit efficient DNA damage activity on irradiation at 365 nm via formation of singlet oxygen ( 1 O 2 ) and hydroxyl radical ( • OH) under physiological conditions. Both the complexes were cytotoxic in dark and exhibit significant enhancement of cytotoxicity upon photo-exposure against HeLa and HepG2 cancer cells giving IC 50 values ranging from 8 to 12 μM for 1 and 2. The cellular internalization data showed cytosolic and nuclear localization of the complexes in the HeLa cells. Copyright © 2017 Elsevier Masson SAS. All rights reserved.

Electronic structure and partial charge distribution of doxorubicin under different molecular environments

NASA Astrophysics Data System (ADS)

Poudel, Lokendra

Doxorubicin (trade name Adriamycin, abbreviated DOX) is a well-known an- thracyclic chemotherapeutic used in treating a variety of cancers including acute leukemia, lymphoma, multiple myeloma, and a range of stomach, lung, bladder, bone, breast, and ovarian cancers. The purpose of the present work is to study electronic structure, partial charge distribution and interaction energy of DOX under different environments. It provides a framework for better understanding of bioactivity of DOX with DNA. While in this work, we focus on DOX -- DNA interactions; the obtained knowledge could be translated to other drug -- target interactions or biomolecular interactions. The electronic structure and partial charge distribution of DOX in three dierent molecular environments: isolated, solvated, and intercalated into a DNA complex,were studied by rst principles density functional methods. It is shown that the addition of solvating water molecules to DOX and the proximity and interaction with DNA has a signicant impact on the electronic structure as well as the partial charge distribution. The calculated total partial charges for DOX in the three models are 0.0, +0.123 and -0.06 electrons for the isolated, solvated, and intercalated state, respectively. Furthermore, by using the more accurate ab initio partial charge values on every atom in the models, signicant improvement in estimating the DOX-DNA interaction energy is obtained in conjunction with the NAnoscale Molecular Dynamics (NAMD) code. The electronic structure of the DOX-DNA is further elucidated by resolving the total density of states (TDOS) into dierent functional groups of DOX, DNA, water, co-crystallized Spermine molecule, and Na ions. The surface partial charge distribution in the DOX-DNA is calculated and displayed graphically. We conclude that the presence of the solvent as well as the details of the interaction geometry matter greatly in the determination of the stability of the DOX complexion. Ab initio calculations on realistic models are an important step towards a more accurate description of biomolecular interaction and in the eventual understanding of long-range interactions in biomolecular systems.

Systematic and reliable multiscale modelling of lithium batteries

NASA Astrophysics Data System (ADS)

Atalay, Selcuk; Schmuck, Markus

2017-11-01

Motivated by the increasing interest in lithium batteries as energy storage devices (e.g. cars/bycicles/public transport, social robot companions, mobile phones, and tablets), we investigate three basic cells: (i) a single intercalation host; (ii) a periodic arrangement of intercalation hosts; and (iii) a rigorously upscaled formulation of (ii) as initiated in. By systematically accounting for Li transport and interfacial reactions in (i)-(iii), we compute the associated chracteristic current-voltage curves and power densities. Finally, we discuss the influence of how the intercalation particles are arranged. Our findings are expected to improve the understanding of how microscopic properties affect the battery behaviour observed on the macroscale and at the same time, the upscaled formulation (iii) serves as an efficient computational tool. This work has been supported by EPSRC, UK, through the Grant No. EP/P011713/1.

Electrochemical behavior of LiV3O8 positive electrode in hybrid Li,Na-ion batteries

NASA Astrophysics Data System (ADS)

Maletti, S.; Sarapulova, A.; Tsirlin, A. A.; Oswald, S.; Fauth, F.; Giebeler, L.; Bramnik, N. N.; Ehrenberg, H.; Mikhailova, D.

2018-01-01

Vanadium(V)-containing oxides show superior intercalation properties for alkaline ions, although the performance of the material strongly depends on its surface morphology. In this work, intercalation activity of LiV3O8, prepared by a conventional solid state synthesis, is demonstrated for the first time in non-aqueous Li,Na-ion hybrid batteries with Na as negative electrode, and different Na/Li ratios in the electrolyte. In the pure Na-ion cell, one Na per formula unit of LiV3O8 can be reversibly inserted at room temperature via a two-step process, while further intercalation leads to gradual amorphisation of the material, with a specific capacity of 190 mAhg-1 after 10 cycles in the potential window of 0.8-3.4 V. Hybrid Li,Na-ion batteries feature simultaneous intercalation of Li+ and Na+ cations into LiV3O8, resulting in the formation of a second phase. Depending on the electrolyte composition, this second phase bears structural similarities either to Li0.7Na0.7V3O8 in Na-rich electrolytes, or to Li4V3O8 in Li-rich electrolytes. The chemical diffusion coefficients of Na+ and Li+ in crystalline LiV3O8 are very close, hence explaining the co-intercalation of these cations. As DFT calculations show, once formed, the Li0.7Na0.7V3O8-type structure favors intercalation of Na+, whereas the LiV3O8-type prefers to accommodate Li+ cations.

Structural and Kinetic Properties of Graphite Intercalation Compounds

DTIC Science & Technology

1982-08-21

the case of FeCI3 , and Dowel2 for Br2, HNO3 and PdC 2 have investigated rates of intercalation to determine diffusion coefficients. Bardhan et al.18...Chim. 21, 1312 (1954). 17. T. Sasa, Y. Takahashi and T. Mukaibo, Carbon 9, 407 (1971). 18. K. K. Bardhan and D. D. L. Chung, Carbon 18, 313 (1980). 19...S. H. Anderson and D. D. L. Chung, Ext. Abst. Program -- Bienn. Conf. Carbon 15, 361 (1981). 20. K. K. Bardhan and D. D. L. Chung, Carbon 18, 303

Electronic and structural properties of B i2S e3:Cu

NASA Astrophysics Data System (ADS)

Sobczak, Kamil; Strak, Pawel; Kempisty, Pawel; Wolos, Agnieszka; Hruban, Andrzej; Materna, Andrzej; Borysiuk, Jolanta

2018-04-01

Electronic and structural properties of B i2S e3 and its extension to copper doped B i2S e3:Cu were studied using combined ab initio simulations and transmission electron microscopy based techniques, including electron energy loss spectroscopy, energy filtered transmission electron microscopy, and energy dispersive x-ray spectroscopy. The stability of the mixed phases was investigated for substitutional and intercalation changes of basic B i2S e3 structure. Four systems were compared: B i2S e3 , structures obtaining by Cu intercalation of the van der Waals gap, by substitution of Bi by Cu in quintuple layers, and C u2Se . The structures were identified and their electronic properties were obtained. Transmission electron microscopy measurements of B i2S e3 and the B i2S e3:Cu system identified the first structure as uniform and the second as composite, consisting of a nonuniform lower-Cu-content matrix and randomly distributed high-Cu-concentration precipitates. Critical comparison of the ab initio and experimental data identified the matrix as having a B i2S e3 dominant part with randomly distributed Cu-intercalated regions having 1Cu-B i2S e3 structure. The precipitates were determined to have 3Cu-B i2S e3 structure.

Multi-Anion Intercalated Layered Double Hydroxide Nanosheet-Assembled Hollow Nanoprisms with Improved Pseudocapacitive and Electrocatalytic Properties.

PubMed

Li, Zhengping; Han, Fangchun; Li, Cheng; Jiao, Xiuling; Chen, Dairong

2018-05-04

Electrochemically active hollow nanostructured materials hold great promise in diverse energy conversion and storage applications, however, intricate synthesis steps and poor control over compositions and morphologies have limited the realization of delicate hollow structures with advanced functional properties. In this study, we demonstrate a one-step wet-chemical strategy for co-engineering the hollow nanostructure and anion intercalation of nickel cobalt layered double hydroxide (NiCo-LDH) to attain highly electrochemical active energy conversion and storage functionalities. Self-templated pseudomorphic transformation of cobalt acetate hydroxide solid nanoprisms using nickel nitrate leads to the construction of well-defined NiCo-LDH hollow nanoprisms (HNPs) with multi-anion intercalation. The unique hierarchical nanosheet-assembled hollow structure and efficiently expanded interlayer spacing offer an increased surface area and exposure of active sites, reduced mass and charge transfer resistance, and enhanced stability of the materials. This leads to a significant improvement in the pseudocapacitive and electrocatalytic properties of NiCo-LDH HNP with respect to specific capacitance, rate and cycling performance, and OER overpotential, outperforming most of the recently reported NiCo-based materials. This work establishes the potential of manipulating sacrificial template transformation for the design and fabrication of novel classes of functional materials with well-defined nanostructures for electrochemical applications and beyond. © 2018 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Synthesis of PDLLA/PLLA-bentonite nanocomposite through sonication

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sitompul, Johnner, E-mail: sitompul@che.itb.ac.id; Setyawan, Daru, E-mail: daru.setyawan@gmail.com; Kim, Daniel Young Joon, E-mail: daniel.kim12321@gmail.com

2016-04-19

This paper concerns the synthesis of poly(D,L-lactic acid)/poly(L-lactic acid) bentonite nanocomposites. Poly (D,L-lactic acid) (PDLLA) was synthesized using lactic acid through the ZnO-catalyzed direct polycondensation method at vacuum pressure and poly(L-lactic acid) (PLLA) was synthesized with L-lactide by ring-opening polymerization method. The PDLLA/PLLA-bentonite nanocomposite films were synthesized using the solvent casting method. The nanoclay, bentonite, was prepared using the solution-intercalation method by dissolving the nanoparticles into chloroform before sonication. In this study, PDLLA/PLLA-bentonite nanocomposite films were produced using variable amounts of nanoclay and sonication times during the mixing of PDLLA/PLLA and bentonite. The properties of the PDLLA/PLLA nanocomposites were thenmore » characterized using the X-ray Diffraction (XRD), Universal Testing Machine (UTM), Water Vapor Permeability (WVP) tests, and the enzymatic biodegradability test. The XRD test was used to measure the intercalation of nanoclay layers in the PDLLA/PLLA matrix and the PDLLA/PLLA-bentonite intercalated nanocomposite films. It was found through these various tests that adding bentonite to the PDLLA/PLLA increases tensile strength to 56.76 MP. Furthermore, the biodegradability increases as well as the barrier properties of the polymers The different sonication time used during the mixing of the polymer solution with bentonite also affected the properties of the PDLLA/PLLA-bentonite nanocomposite films.« less

Graphene/MoS2 heterostructures as templates for growing two-dimensional metals: Predictions from ab initio calculations

NASA Astrophysics Data System (ADS)

Šljivančanin, Željko; Belić, Milivoj

2017-09-01

Preparation of single-atom-thick layers of ordinary metals has been a challenging task since their closely packed atoms lack layered structure with highly anisotropic bonding. Using computational modeling based on density functional theory we showed that graphene/MoS2 heterostructures can be used as suitable templates to grow stable two-dimensional (2D) clusters, as well as extended monoatomic layers of metals with nonlayered structure in the bulk. Considering gold and lithium as two metals with markedly different properties, we found that Li intercalants strengthen coupling between graphene (G) and MoS2, mainly due to electrostatic attraction of 2D materials with positively charged Li atoms. However, intercalation with large Au atoms gives rise to a significant increase in the distance between G and MoS2 and thus, weakens their interaction. In addition to strong preference for 2D growth, we demonstrated that Au intercalants weakly interact with both G and MoS2, and hence G /MoS2 vertical heterostructures could be a promising framework to prepare gold 2D structures with electronic properties closely resembling those of the hypothetical free-standing hexagonal gold monolayer.

Tuning electronic properties by oxidation-reduction reactions at graphene-ruthenium interface

DOE PAGES

Kandyba, Viktor; Al-Mahboob, Abdullah; Giampietri, Alessio; ...

2018-06-06

Mass production of graphene is associated with the growth on catalysts used also in other chemical reactions. In this study, we exploit the oxidation-reduction to tailor the properties of single layer graphene domains with incorporated bi-layer patches on ruthenium. Using photoelectron spectromicroscopy techniques, we find that oxygen, intercalating under single layer and making it p-doped by the formation of Ru-O x, does not intercalate under the bilayer patches with n-doped upper layer, but decorates them under single layer surrounding creating lateral p-n junctions with chemical potential difference of 1.2 eV. O-reduction by thermal treatment in vacuum results in C-vacancy defectsmore » enhancing electronic coupling of remained graphene to Ru, whereas in H 2, vacancy formation is suppressed. Also, for the domains below 15–25 μm size, after O-reduction in H 2, graphene/Ru coupling is restored, while wrinkle pattern produced by O-intercalation is irreversible and can trap reaction products between the wrinkles and Ru surface step edges. In fact, in certain regions of bigger domains, the products, containing H 2O and/or its fragments, remain at the interface, making graphene decoupled and undoped.« less

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sukri, Shahratul Ain Mohd; Heng, Lee Yook; Karim, Nurul Huda Abd

A platinum (II) salphen complex was synthesised by condensation reaction of 2,4-dihydroxylbenzaldehyde and o-phenylenediamine with potassium tetrachloroplatinate to obtain N,N′-Bis-4-(hydroxysalicylidene)-phenylenediamine-platinum (II). The structure of the complex was confirmed by {sup 1}H and {sup 13}C NMR spectroscopy, FTIR spectroscopy, CHN elemental analyses and ESI-MS spectrometry. The platinum (II) salphen complex with four donor atoms N{sub 2}O{sub 2} from its salphen ligand coordinated to platinum (II) metal centre were determined. The binding mode and interaction of this complex with calf thymus DNA was determined by UV/Vis DNA titration and emission titration. The intercalation between the DNA bases by π-π stacking due tomore » its square planar geometry and aromatic rings structures was proposed.« less

Highly Efficient Iodine Capture by Layered Double Hydroxides Intercalated with Polysulfides

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ma, Shulan; Islam, Saiful M.; Shim, Yurina

2014-12-23

We demonstrate strong iodine (I-2) vapor adsorption using Mg/Al layered double hydroxide (MgAl-LDH) nanocomposites intercalated with polysulfide (S-x(2-)) groups (S-x-LDH, x = 2, 4, 6). The as-prepared LDH/polysulfide hybrid materials display highly efficient iodine capture resulting from the reducing property of the intercalated polysulfides. During adsorption, the I-2 molecules are reduced to I-3(-) anions by the intercalated [S-x](2-) groups that simultaneously are oxidized to form S8. In addition to the chemical adsorption, additional molecular I-2 is physically captured by the LDH composites. As a result of these parallel processes, and despite their very low BET surface areas, the iodine capturemore » capacities of S-2-LDH, S-4-LDH, and S-6-LDH are similar to 1.32, 1.52, and 1.43 g/g, respectively, with a maximum adsorption of 152% (wt %). Thermogravimetric and differential thermal analysis (TG-DTA), energy dispersive X-ray spectroscopy (EDS), and temperature-variable powder X-ray diffraction (XRD) measurements show the resulting I-3(-) ions that intercalated into the LDH gallery have high thermal stability (>= 350 degrees C). The excellent iodine adsorption performance combined with the facile preparation points to the S-x-LDH systems as potential superior materials for adsorption of radioactive iodine, a waste product of the nuclear power industry.« less

Study on the interaction of triadimenol with calf thymus DNA by multispectroscopic methods and molecular modeling

NASA Astrophysics Data System (ADS)

Zhang, Yepeng; Zhang, Guowen; Fu, Peng; Ma, Yadi; Zhou, Jia

2012-10-01

The binding mechanism of triadimenol (NOL) to calf thymus DNA (ctDNA) in physiological buffer (pH 7.4) was investigated by multispectroscopic methods including UV-vis absorption, fluorescence, circular dichroism (CD), Fourier transform infrared (FT-IR), and nuclear magnetic resonance (1H NMR) spectroscopy, coupled with viscosity measurements and atomic force microscopy (AFM) technique. The results suggested that NOL interacted with ctDNA by intercalation mode. CD and AFM assays showed that NOL can damage the base stacking of ctDNA and result in regional cleavage of the two DNA strands. FT-IR and 1H NMR spectra coupled with molecular docking revealed that a specific binding mainly exists between NOL and G-C base pairs of the ctDNA where two hydrogen bonds form. Moreover, the association constants of NOL with DNA at three different temperatures were determined to be in the 103 L mol-1 range. The calculated thermodynamic parameters suggested that the binding of NOL to ctDNA was driven mainly by hydrogen bond and van der Waals.

Screen for mitochondrial DNA copy number maintenance genes reveals essential role for ATP synthase

PubMed Central

Fukuoh, Atsushi; Cannino, Giuseppe; Gerards, Mike; Buckley, Suzanne; Kazancioglu, Selena; Scialo, Filippo; Lihavainen, Eero; Ribeiro, Andre; Dufour, Eric; Jacobs, Howard T

2014-01-01

The machinery of mitochondrial DNA (mtDNA) maintenance is only partially characterized and is of wide interest due to its involvement in disease. To identify novel components of this machinery, plus other cellular pathways required for mtDNA viability, we implemented a genome-wide RNAi screen in Drosophila S2 cells, assaying for loss of fluorescence of mtDNA nucleoids stained with the DNA-intercalating agent PicoGreen. In addition to previously characterized components of the mtDNA replication and transcription machineries, positives included many proteins of the cytosolic proteasome and ribosome (but not the mitoribosome), three proteins involved in vesicle transport, some other factors involved in mitochondrial biogenesis or nuclear gene expression, > 30 mainly uncharacterized proteins and most subunits of ATP synthase (but no other OXPHOS complex). ATP synthase knockdown precipitated a burst of mitochondrial ROS production, followed by copy number depletion involving increased mitochondrial turnover, not dependent on the canonical autophagy machinery. Our findings will inform future studies of the apparatus and regulation of mtDNA maintenance, and the role of mitochondrial bioenergetics and signaling in modulating mtDNA copy number. PMID:24952591

Astragalin from Cassia alata Induces DNA Adducts in Vitro and Repairable DNA Damage in the Yeast Saccharomyces cerevisiae

PubMed Central

Saito, Samuel; Silva, Givaldo; Santos, Regineide Xavier; Gosmann, Grace; Pungartnik, Cristina; Brendel, Martin

2012-01-01

Reverse phase-solid phase extraction from Cassia alata leaves (CaRP) was used to obtain a refined extract. Higher than wild-type sensitivity to CaRP was exhibited by 16 haploid Saccharomyces cerevisiae mutants with defects in DNA repair and membrane transport. CaRP had a strong DPPH free radical scavenging activity with an IC50 value of 2.27 μg mL−1 and showed no pro-oxidant activity in yeast. CaRP compounds were separated by HPLC and the three major components were shown to bind to DNA in vitro. The major HPLC peak was identified as kampferol-3-O-β-d-glucoside (astragalin), which showed high affinity to DNA as seen by HPLC-UV measurement after using centrifugal ultrafiltration of astragalin-DNA mixtures. Astragalin-DNA interaction was further studied by spectroscopic methods and its interaction with DNA was evaluated using solid-state FTIR. These and computational (in silico) docking studies revealed that astragalin-DNA binding occurs through interaction with G-C base pairs, possibly by intercalation stabilized by H-bond formation. PMID:22489129

Astragalin from Cassia alata induces DNA adducts in vitro and repairable DNA damage in the yeast Saccharomyces cerevisiae.

PubMed

Saito, Samuel; Silva, Givaldo; Santos, Regineide Xavier; Gosmann, Grace; Pungartnik, Cristina; Brendel, Martin

2012-01-01

Reverse phase-solid phase extraction from Cassia alata leaves (CaRP) was used to obtain a refined extract. Higher than wild-type sensitivity to CaRP was exhibited by 16 haploid Saccharomyces cerevisiae mutants with defects in DNA repair and membrane transport. CaRP had a strong DPPH free radical scavenging activity with an IC(50) value of 2.27 μg mL(-1) and showed no pro-oxidant activity in yeast. CaRP compounds were separated by HPLC and the three major components were shown to bind to DNA in vitro. The major HPLC peak was identified as kampferol-3-O-β-d-glucoside (astragalin), which showed high affinity to DNA as seen by HPLC-UV measurement after using centrifugal ultrafiltration of astragalin-DNA mixtures. Astragalin-DNA interaction was further studied by spectroscopic methods and its interaction with DNA was evaluated using solid-state FTIR. These and computational (in silico) docking studies revealed that astragalin-DNA binding occurs through interaction with G-C base pairs, possibly by intercalation stabilized by H-bond formation.

Retention of contaminants Cd and Hg adsorbed and intercalated in aluminosilicate clays: A first principles study

NASA Astrophysics Data System (ADS)

Crasto de Lima, F. D.; Miwa, R. H.; Miranda, Caetano R.

2017-11-01

Layered clay materials have been used to incorporate transition metal (TM) contaminants. Based on first-principles calculations, we have examined the energetic stability and the electronic properties due to the incorporation of Cd and Hg in layered clay materials, kaolinite (KAO) and pyrophyllite (PYR). The TM can be (i) adsorbed on the clay surface as well as (ii) intercalated between the clay layers. For the intercalated case, the contaminant incorporation rate can be optimized by controlling the interlayer spacing of the clay, namely, pillared clays. Our total energy results reveal that the incorporation of the TMs can be maximized through a suitable tuning of vertical distance between the clay layers. Based on the calculated TM/clay binding energies and the Langmuir absorption model, we estimate the concentrations of the TMs. Further kinetic properties have been examined by calculating the activation energies, where we found energy barriers of ˜20 and ˜130 meV for adsorbed and intercalated cases, respectively. The adsorption and intercalation of ionized TM adatoms were also considered within the deprotonated KAO surface. This also leads to an optimal interlayer distance which maximizes the TM incorporation rate. By mapping the total charge transfers at the TM/clay interface, we identify a net electronic charge transfer from the TM adatoms to the topmost clay surface layer. The effect of such a charge transfer on the electronic structure of the clay (host) has been examined through a set of X-ray absorption near edge structure (XANES) simulations, characterizing the changes of the XANES spectra upon the presence of the contaminants. Finally, for the pillared clays, we quantify the Cd and Hg K-edge energy shifts of the TMs as a function of the interlayer distance between the clay layers and the Al K-edge spectra for the pristine and pillared clays.

Photoinduced electron transfer from nucleotides to DNA intercalating viologens. A study by laser-flash photolysis and spectroelectrochemistry.

PubMed

Knapp, C; Lecomte, J P; Mesmaeker, A K; Orellana, G

1996-10-01

Fluorescent DNA-binding N,N'-dialkyl 6-(2-pyridinium)phenanthridinium dications (where dialkyl stands for -(CH2)2-or-(CH2)3-, abbreviated dq2pyp and dq3pyp, respectively) associate with GMP (guanosine-5'-monophosphate) in 0.1-mol l-1, pH 3.5-5.5, phosphate buffer solution to yield 1:1 and 1:2 non-emissive complexes, the formation constants of which range from 197-63 and 19-11 l mol-1, respectively. In addition to the strong static quenching, dynamic deactivation of their excited state occurs at diffusion-controlled rate ki = 5.2 x 10(9) l mol-1 s-1). Illumination of the GMP-containing solutions of the dyes with a 355 nm laser pulse produces a transient, with strong absorbance at 510 and 720 nm for dq2pyp, and 420 and 560 nm for dq3pyp. An identical transient is produced in the presence of ascorbic acid instead of the mononucleotide. By comparison to the electrochemically generated absorption spectra of the monoreduced dyes, the photogenerated transients have been assigned unequivocally to their corresponding radical-cations, formed by electron transfer to the anglet excited state. The back redox reaction between the oxidized quencher and dq2pyp+ proceeds at a rate of 1-2 x 10(9) l mol-1 s-1. The same transient has been observed also for the DNA intercalated viologens; this result, together with the little ability of these dyes to sensitize the formation of singlet dioxygen or to produce superoxide anion, demonstrate that their DNA photocleavaging activity is initiated by an efficient light-induced electron transfer from the nucleobases.

Positive and negative ion mode ESI-MS and MS/MS for studying drug-DNA complexes

NASA Astrophysics Data System (ADS)

Rosu, Frédéric; Pirotte, Sophie; Pauw, Edwin De; Gabelica, Valérie

2006-07-01

We report systematic investigation of duplex DNA complexes with minor groove binders (Hoechsts 33258 and 33342, netropsin and DAPI) and intercalators (daunomycin, doxorubicin, actinomycin D, ethidium, cryptolepine, neocryptolepine, m-Amsacrine, proflavine, ellipticine and mitoxantrone) by ESI-MS and ESI-MS/MS in the negative ion mode and in the positive ion mode. The apparent solution phase equilibrium binding constants can be determined by measuring relative intensities in the ESI-MS spectrum. While negative ion mode gives reliable results, positive ion mode gives a systematic underestimation of the binding constants and even a complete suppression of the complexes for intercalators lacking functional groups capable of interacting in the grooves. In the second part of the paper we systematically compare MS/MS fragmentation channels and breakdown curves in the positive and the negative modes, and discuss the possible uses and caveats of MS/MS in drug-DNA complexes. In the negative mode, the drugs can be separated in three groups: (1) those that leave the complex with no net charge; (2) those that leave the complex with a negative charge; and (3) those that remain attached on the strands upon dissociation of the duplex due to their positive charge. In the positive ion mode, all complexes fragment via the loss of protonated drug. Information on the stabilization of the complex by drug-DNA noncovalent interactions can be obtained straightforwardly only in the case of neutral drug loss. In all other cases, proton affinity (in the positive ion mode), gas-phase basicity (in the negative ion mode) and coulombic repulsion are the major factors influencing the fragmentation channel and the dissociation kinetics.

Probing Atomic, Electronic, and Optical Structures of Nanoparticle Photocatalysts Using Fast Electrons

NASA Astrophysics Data System (ADS)

Liu, Qianlang

Graphene has attracted great interest in many fields due to its outstanding electronic and chemical properties. Among them, its surface inertness and high thermal stability makes graphene a promising candidate as a protective material for transition metal surfaces. Recent studies show, however, that small molecules, such as O2, CO and H2O, intercalate between a graphene film and a metal substrate at particular temperatures. The intercalation of O2 between graphene and Ru(0001) is studied with 3 keV helium ion scattering and low energy electron diffraction. It is shown that O2 intercalates between the graphene and the Ru(0001) substrate at a temperature of 650 K and does not adsorb onto the graphene surface. Nevertheless, the graphene layer efficiently avoids both intercalation and adsorption of oxygen at room temperature. It is also found that the intercalated oxygen thermally desorbs from the surface after it is heated to 800 K. Such a desorption is not, however, observed for oxygen dissociatively adsorbed on a bare Ru(0001) surface until 1200 K. It is thus inferred that the oxygen intercalated between graphene and Ru(0001) is in a molecular form. In addition, part of the graphene overlayer is etched by a chemical reaction during the thermal desorption of oxygen. The role of the defects on the graphene layer is also studied. Defects are introduced by 50 eV Ar+ sputtering, which creates single vacancies with a quick sputtering or larger open areas of substrate following a prolonged sputtering. It is found that oxygen molecularly adsorbs at single carbon vacancies even at room temperature, which does not occur on a complete graphene layer. Following post-annealing to 600 K, it is observed that such adsorbed oxygen diffuses to become intercalated between graphene and Ru(0001). Oxygen dissociatively adsorbs in the large open areas of exposed substrate by forming strong oxygen-metal bonds. It is also found that the presence of defects facilitates the intercalation of oxygen and improves the etching efficiency of the graphene during the desorption of oxygen.

Photosensitization of DNA damage by a new cationic pyropheophorbide derivative: sequence-specific formation of a frank scission.

PubMed

Kanony, Claire; Fabiano-Tixier, Anne-Sylvie; Ravanat, Jean-Luc; Vicendo, Patricia; Paillous, Nicole

2003-06-01

Pyropheophorbides are red-absorbing porphyrin-like photosensitizers that may interact with DNA either by intercalation or by external binding with self-stacking according to the value of the nucleotide to chromophore molar ratio (N/C). This article reports on the nature and sequence selectivity of the DNA damage photoinduced by a water-soluble chlorhydrate of aminopyropheophorbide. First, this pyropheophorbide is shown to induce on irradiation the cleavage of phiX174 DNA by both Type-I and -II mechanisms, suggested by scavengers and D2O effects. These conclusions are then improved by sequencing experiments performed on a 20-mer oligodeoxynucleotide (ODN) irradiated at wavelengths >345 nm in the presence of the dye, N/C varying from 2.5 to 0.5. Oxidation of all guanine residues to the same extent is observed after piperidine treatment on both single- and double-stranded ODN. Moreover, unexpectedly, a remarkable sequence-selective cleavage occurring at a 5'-CG-3' site is detected before alkali treatment. This frank break is clearly predominant for a low nucleotide to chromophore molar ratio, corresponding to a self-stacking of the dye along the DNA helix. The electrophoretic properties of the band suggest that this lesion results from a sugar oxidation, which leads via a base release to a ribonolactone residue. The proposal is supported by high-performance liquid chromatography-matrix-assisted laser desorption-ionization mass spectrometry experiments that also reveal other sequence-selective frank scissions of lower intensity at 5'-GC-3' or other 5'-CG-3' sites. This sequence selectivity is discussed with regard to the binding selectivity of cationic porphyrins.

Preparation and properties of recycled HDPE/clay hybrids

Treesearch

Yong Lei; Qinglin Wu; Craig M. Clemons

2007-01-01

Hybrids based on recycled high density polyethylene (RHDPE) and organic clay were made by melt compounding. The influence of blending method, compatibilizers, and clay content on clay intercalation and exfoliation, RHDPE crystallization behavior, and the mechanical properties of RHDPE/clay hybrids were investigated. Both maleated polyethylene (MAPE) and titanate could...

Spectroscopic investigation on the interaction of copper porphyrazines and phthalocyanine with human telomeric G-quadruplex DNA.

PubMed

Hassani, Leila; Hakimian, Fatemeh; Safaei, Elham

2014-01-01

The G-quadruplex DNA is a novel target for anticancer drug discovery and many scientific groups are investigating interaction of small molecules with G-quadruplex DNA to discover therapeutic agents for cancer. Here, interaction of a phthalocyanine (Cu(PcTs)) and two tetrapyridinoporphyrazines ([Cu(2,3-tmtppa)](4+) and [Cu(3,4-tmtppa)](4+)) with Na(+) and K(+) forms of human telomeric G-quadruplex DNA has been investigated by spectroscopic techniques. The results indicated that interaction of the cationic porphyrazines is remarkably stronger than the anionic phthalocyanine and they presumably bind to the G-quadruplex DNA through end-stacking. Fluorescent intercalator displacement assay implied the displacement ability of the complexes with thiazole orange. In addition, circular dichroism spectra of both quadruplex forms converge to the Na(+) isoform after binding to the porphyrazines. In conclusion, the porphyrazines as the complexes that bind to the G-quadruplex DNA, could be suitable candidates for further investigations about inhibition of telomerase enzyme. Copyright © 2013 Elsevier B.V. All rights reserved.

Three-dimensional metal-intercalated covalent organic frameworks for near-ambient energy storage

PubMed Central

Gao, Fei; Ding, Zijing; Meng, Sheng

2013-01-01

A new form of nanoporous material, metal intercalated covalent organic framework (MCOF) is proposed and its energy storage property revealed. Employing density functional and thermodynamical analysis, we find that stable, chemically active, porous materials could form by stacking covalent organic framework (COF) layers with metals as a gluing agent. Metal acts as active sites, while its aggregation is suppressed by a binding energy significantly larger than the corresponding cohesive energy of bulk metals. Two important parameters, metal binding and metal-metal separation, are tuned by selecting suitable building blocks and linkers when constructing COF layers. Systematic searches among a variety of elements and organic molecules identify Ca-intercalated COF with diphenylethyne units as optimal material for H2 storage, reaching a striking gravimetric density ~ 5 wt% at near-ambient conditions (300 K, 20 bar), in comparison to < 0.1 wt% for bare COF-1 under the same condition. PMID:23698018

Controlling the photoconductivity: Graphene oxide and polyaniline self assembled intercalation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Vempati, Sesha, E-mail: svempati01@qub.ac.uk; Ozcan, Sefika; Department of Polymer Science and Technology, Middle East Technical University, Ankara 06800

2015-02-02

We report on controlling the optoelectronic properties of self-assembled intercalating compound of graphene oxide (GO) and HCl doped polyaniline (PANI). Optical emission and X-ray diffraction studies revealed a secondary doping phenomenon of PANI with –OH and –COOH groups of GO, which essentially arbitrate the intercalation. A control on the polarity and the magnitude of the photoresponse (PR) is harnessed by manipulating the weight ratios of PANI to GO (viz., 1:1.5 and 1:2.2 are abbreviated as PG1.5 and PG2.2, respectively), where ±PR = 100(R{sub Dark} – R{sub UV-Vis})/R{sub Dark} and R corresponds to the resistance of the device in dark or UV-Vis illumination.more » To be precise, the PR from GO, PANI, PG1.5, and PG2.2 are +34%, −111%, −51%, and +58%, respectively.« less

Strong-coupling superconductivity induced by calcium intercalation in bilayer transition-metal dichalcogenides

NASA Astrophysics Data System (ADS)

Szczȩśniak, R.; Durajski, A. P.; Jarosik, M. W.

2018-04-01

We theoretically investigate the possibility of achieving a superconducting state in transition-metal dichalcogenide bilayers through intercalation, a process previously and widely used to achieve metallization and superconducting states in novel superconductors. For the Ca-intercalated bilayers MoS2 and WS2, we find that the superconducting state is characterized by an electron-phonon coupling constant larger than 1.0 and a superconducting critical temperature of 13.3 and 9.3 K, respectively. These results are superior to other predicted or experimentally observed two-dimensional conventional superconductors and suggest that the investigated materials may be good candidates for nanoscale superconductors. More interestingly, we proved that the obtained thermodynamic properties go beyond the predictions of the mean-field Bardeen-Cooper-Schrieffer approximation and that the calculations conducted within the framework of the strong-coupling Eliashberg theory should be treated as those that yield quantitative results.

Effect of type and content of modified montmorillonite on the structure and properties of bio-nanocomposite films based on soy protein isolate and montmorillonite.

PubMed

Kumar, P; Sandeep, K P; Alavi, S; Truong, V D; Gorga, R E

2010-06-01

The nonbiodegradable and nonrenewable nature of plastic packaging has led to a renewed interest in packaging materials based on bio-nanocomposites (biopolymer matrix reinforced with nanoparticles such as layered silicates). Bio-nanocomposite films based on soy protein isolate (SPI) and modified montmorillonite (MMT) were prepared using melt extrusion. The effect of different type (Cloisite 20A and Cloisite 30B) and content (0% to 15%) of modified MMT on the structure (degree of intercalation and exfoliation) and properties (color, mechanical, dynamic mechanical, thermal stability, and water vapor permeability) of SPI-MMT bio-nanocomposite films were investigated. Extrusion of SPI and modified MMTs resulted in bio-nanocomposites with exfoliated structures at lower MMT content (5%). At higher MMT content (15%), the structure of bio-nanocomposites ranged from intercalated for Cloisite 20A to disordered intercalated for Cloisite 30B. At an MMT content of 5%, bio-nanocomposite films based on modified MMTs (Cloisite 20A and Cloisite 30B) had better mechanical (tensile strength and percent elongation at break), dynamic mechanical (glass transition temperature and storage modulus), and water barrier properties as compared to those based on natural MMT (Cloisite Na(+)). Bio-nanocomposite films based on 10% Cloisite 30B had mechanical properties comparable to those of some of the plastics that are currently used in food packaging applications. However, much higher WVP values of these films as compared to those of existing plastics might limit the application of these films to packaging of high moisture foods such as fresh fruits and vegetables.

Dynamic and Progressive Control of DNA Origami Conformation by Modulating DNA Helicity with Chemical Adducts.

PubMed

Chen, Haorong; Zhang, Hanyu; Pan, Jing; Cha, Tae-Gon; Li, Shiming; Andréasson, Joakim; Choi, Jong Hyun

2016-05-24

DNA origami has received enormous attention for its ability to program complex nanostructures with a few nanometer precision. Dynamic origami structures that change conformation in response to environmental cues or external signals hold great promises in sensing and actuation at the nanoscale. The reconfiguration mechanism of existing dynamic origami structures is mostly limited to single-stranded hinges and relies almost exclusively on DNA hybridization or strand displacement. Here, we show an alternative approach by demonstrating on-demand conformation changes with DNA-binding molecules, which intercalate between base pairs and unwind DNA double helices. The unwinding effect modulates the helicity mismatch in DNA origami, which significantly influences the internal stress and the global conformation of the origami structure. We demonstrate the switching of a polymerized origami nanoribbon between different twisting states and a well-constrained torsional deformation in a monomeric origami shaft. The structural transformation is shown to be reversible, and binding isotherms confirm the reconfiguration mechanism. This approach provides a rapid and reversible means to change DNA origami conformation, which can be used for dynamic and progressive control at the nanoscale.

Differentiating RNA from DNA by a molecular fluorescent probe based on the "door-bolt" mechanism biomaterials.

PubMed

Yao, Qichao; Li, Haidong; Xian, Liman; Xu, Feng; Xia, Jing; Fan, Jiangli; Du, Jianjun; Wang, Jingyun; Peng, Xiaojun

2018-09-01

Although excellent florescent probes have been developed for DNA, good probes for RNA remain lacking. The shortage of reported and commercial RNA probes is attributable to their severe interference from DNA. As DNA and RNA have similar structures but different functions, it has been an imperative challenge to develop RNA probes that differentiate from DNA. In this study, an NIR fluorescent probe, NBE, is described, which contains a bulky julolidine group that can fit in a spacious RNA pocket and emit intense fluorescence. However, NBE has no response to DNA, as it cannot intercalate into the double strands or even in the DNA minor groove. The sensing mechanism is similar to the effect of a door-bolt. NBE shows excellent performance in RNA sensing (outstanding photostability, high selectivity and fast response), whether in aqueous buffers, fixed cells or living cells. These findings might provide not only a potential imaging tool but also a new design strategy for the recognition of RNA while avoiding interference from DNA. Copyright © 2018 Elsevier Ltd. All rights reserved.

Elaboration et caracterisation de nanocomposites polyethylene/montmorillonite

NASA Astrophysics Data System (ADS)

Stoeffler, Karen

This research project consists in preparing polyethylene/montmorillonite nanocomposites for film packaging applications. Montmorillonite is a natural clay with an exceptional aspect ratio. In recent years, its incorporation in polymer matrices has attracted great interest. The pioneer work from Toyota on polyamide-6/montmorillonite composites has shown that it was possible to disperse the clay at a nanometric scale. Such a structure, so-called exfoliated, leads to a significant increase in mechanical, barrier and fire retardant properties, even at low volumetric fractions of clay. This allows a valorization of the polymeric material at moderate cost. Due to its high polarity, montmorilloite exfoliation in polymeric matrices is problematic. In the particular case of polyolefin matrices, the platelets dispersion remains limited: most frequently, the composites obtained exhibit conventional structures (microcomposites) or intercalated structures. To solve this problem, two techniques are commonly employed: the surface treatment of the clay, which allows the expansion of the interfoliar gallery while increasing the affinity between the clay and the polymer, and the use of a polar compatibilizing agent (grafted polyolefin). The first part of this thesis deals with the preparation and the characterization of highly thermally stable organophilic montmorillonites. Commercial organophilic montmorillonites are treated with quaternary ammonium intercalating agents. However, those intercalating agents present a poor thermal stability and are susceptible to decompose upon processing, thus affecting the clay dispersion and the final properties of the nanocomposites. In this work, it was proposed to modify the clay with alkyl pyridinium, alkyl imidazolium and alkyl phosphonium intercalating agents, which are more stable than ammonium based cations. Organophilic montmorillonites with enhanced thermal stabilites compared to commercial organoclays (+20°C to +70°C) were prepared. The effect of the chemical structure of the intercalating agent on the capacity of the organoclay to be dispersed in polyethylene matrices was analyzed. In addition, the influence of the dispersion on the thermal stability of the nanocomposites prepared is discussed. In a second part, the effect of the compatibilizing agent characteristics on the quality of the clay dispersion in polyethylene/montmorillonite nanocomposites was analyzed. The mechanical properties and the oxygen permeability of the nanocomposites were evaluated and related to the level of clay delamination and to the strength of the polymer/clay interface, which was evaluated through surface tension measurements.

A Sequence-Dependent DNA Condensation Induced by Prion Protein

PubMed Central

2018-01-01

Different studies indicated that the prion protein induces hybridization of complementary DNA strands. Cell culture studies showed that the scrapie isoform of prion protein remained bound with the chromosome. In present work, we used an oxazole dye, YOYO, as a reporter to quantitative characterization of the DNA condensation by prion protein. We observe that the prion protein induces greater fluorescence quenching of YOYO intercalated in DNA containing only GC bases compared to the DNA containing four bases whereas the effect of dye bound to DNA containing only AT bases is marginal. DNA-condensing biological polyamines are less effective than prion protein in quenching of DNA-bound YOYO fluorescence. The prion protein induces marginal quenching of fluorescence of the dye bound to oligonucleotides, which are resistant to condensation. The ultrastructural studies with electron microscope also validate the biophysical data. The GC bases of the target DNA are probably responsible for increased condensation in the presence of prion protein. To our knowledge, this is the first report of a human cellular protein inducing a sequence-dependent DNA condensation. The increased condensation of GC-rich DNA by prion protein may suggest a biological function of the prion protein and a role in its pathogenesis. PMID:29657864

A Sequence-Dependent DNA Condensation Induced by Prion Protein.

PubMed

Bera, Alakesh; Biring, Sajal

2018-01-01

Different studies indicated that the prion protein induces hybridization of complementary DNA strands. Cell culture studies showed that the scrapie isoform of prion protein remained bound with the chromosome. In present work, we used an oxazole dye, YOYO, as a reporter to quantitative characterization of the DNA condensation by prion protein. We observe that the prion protein induces greater fluorescence quenching of YOYO intercalated in DNA containing only GC bases compared to the DNA containing four bases whereas the effect of dye bound to DNA containing only AT bases is marginal. DNA-condensing biological polyamines are less effective than prion protein in quenching of DNA-bound YOYO fluorescence. The prion protein induces marginal quenching of fluorescence of the dye bound to oligonucleotides, which are resistant to condensation. The ultrastructural studies with electron microscope also validate the biophysical data. The GC bases of the target DNA are probably responsible for increased condensation in the presence of prion protein. To our knowledge, this is the first report of a human cellular protein inducing a sequence-dependent DNA condensation. The increased condensation of GC-rich DNA by prion protein may suggest a biological function of the prion protein and a role in its pathogenesis.

Standardization of Spore Inactivation Method for PMA-PhyloChip Analysis

NASA Technical Reports Server (NTRS)

Schrader, Michael

2011-01-01

In compliance with the Committee on Space Research (COSPAR) planetary protection policy, National Aeronautics and Space Administration (NASA) monitors the total microbial burden of spacecraft as a means for minimizing the inadvertent transfer of viable contaminant microorganisms to extraterrestrial environments (forward contamination). NASA standard assay-based counts are used both as a proxy for relative surface cleanliness and to estimate overall microbial burden as well as to assess whether forward planetary protection risk criteria are met for a given mission, which vary by the planetary body to be explored and whether or not life detection missions are present. Despite efforts to reduce presence of microorganisms from spacecraft prior to launch, microbes have been isolated from spacecraft and associated surfaces within the extreme conditions of clean room facilities using state of the art molecular technologies. Development of a more sensitive method that will better enumerate all viable microorganisms from spacecraft and associated surfaces could support future life detection missions. Current culture-based (NASA standard spore assay) and nucleic-acid-based polymerase chain reaction (PCR) methods have significant shortcomings in this type of analysis. The overall goal of this project is to evaluate and validate a new molecular method based on the use of a deoxyribonucleic acid (DNA) intercalating agent propidium monoazide (PMA). This is used in combination with DNA microarray (PhyloChip) which has been shown to identify very low levels of organisms on spacecraft associated surfaces. PMA can only penetrate the membrane of dead cells. Once penetrated, it intercalates the DNA and, upon photolysis using visible light it produces stable DNA monoadducts. This allows DNA to be unavailable for further PCR analysis. The specific aim of this study is to standardize the spore inactivation method for PMA-PhyloChip analysis. We have used the bacterial spores Bacillus subtilis 168 (standard laboratory isolate) as a test organism.

Azapsoralens: new potential photochemotherapeutic agents for psoriasis.

PubMed

Vedaldi, D; Caffieri, S; Miolo, G; Dall'Acqua, F; Baccichetti, F; Guiotto, A; Benetollo, F; Bombieri, G; Recchia, G; Cristofolini, M

1991-12-01

New bioisoters of psoralen, obtained by replacing carbon 8 of the central benzene ring with a nitrogen, were studied from the photochemical, photobiological and phototherapeutic points of view. In particular, 4,4'-, 4',5'-dimetyl, 4,4',5'-trimethyl and 3,4,4',5'-tetramethylazapsoralen were studied. The crystal and molecular structure of 4,4',5'-trimethylazapsoralen, obtained by X ray diffraction, was also reported. Like psoralen, these compounds form a molecular complex with DNA, undergoing intercalation inside the double helix of the macromolecule. When irridiated with long ultraviolet light (365 nm), the intercalated drug photoconjugates covalently to the macromolecule, forming mono- and diadducts. The photobinding rate show the following order of magnitude: 4,4',5'-trimetylazapsoralen (4,4',5'-TMAP) = 3,4,4',5'-tetramethylazapsoralen (3,4,4',5'-TMAP) greater than 4',5'-dimethylazapsoralen (4',5'-DMAP) = 4,4'-dimethylazapsoralen (4,4'-DMAP). The DNA photobinding rate of 8-methoxypsoralen (8-MOP), taken as reference compound, is similar to that of the two dimetylazapsoralens but lower than tri- and tetramethyl derivatives. The ability of azapsoralens to form cross-links in DNA is lower than that of 8-MOP. However, capacity to induce cross-links does not parallel the DNA photobinding rate; it is higher for trimethyl derivate and lower for tetramethylazapsoralen. Azapsoralens show evident antiproliferative activity. The trimethyl derivative is the most active, followed by tetrametyl, both these compounds showing activity slightly higher than that of 8-MOP. The two dimethylderivatives are less active. The mautagenic activity of azapsoralens on E. coli WP2 TM6 is lower than that of 8-MOP in the same conditions. The new compounds do not show any skin phototoxicity on guinea pig skin. On the basis of its DNA photobinding, antiproliferative activity, mutagenicity and lack of skin phototoxicity, 4,4',5'-TMAP was chosen for clinical evaluation. Clinical results obtained by topical treatment of psoriatic plaques reveal evident therapeutic effectiveness and clearing is between good and moderate, although 8-MOP, used as reference compound, is more effective.

Absence of Mutagenic Activity of Hycanthone in Serratia marcescens,

DTIC Science & Technology

1986-05-29

repair system but is enhanced by the plasmid pKMl01, which mediates the inducible error-prone repair system. Hycanthone, like proflavin , .1...enhanced by the plasmid pKM10, which mediates the inducible error-prone repair system. Hycanthone, like proflavin , intercalates between the stacked bases...Roth (1974) lave suggested that proflavin , which has a planar triple ring structure similar to hycanthone, interacts with DNA, which upon replication

Application of Diffusion Monte Carlo to Materials Dominated by van der Waals Interactions

DOE PAGES

Benali, Anouar; Shulenburger, Luke; Romero, Nichols A.; ...

2014-06-12

Van der Waals forces are notoriously difficult to account for from first principles. We perform extensive calculation to assess the usefulness and validity of diffusion quantum Monte Carlo when applied to van der Waals forces. We present results for noble gas solids and clusters - archetypical van der Waals dominated assemblies, as well as a relevant pi-pi stacking supramolecular complex: DNA + intercalating anti-cancer drug Ellipticine.

Reduction in the size of layered double hydroxide nanoparticles enhances the efficiency of siRNA delivery.

PubMed

Chen, Min; Cooper, Helen M; Zhou, Ji Zhi; Bartlett, Perry F; Xu, Zhi Ping

2013-01-15

Small interfering RNAs (siRNAs) are a potentially powerful new class of pharmaceutical drugs for many disease. However, the delivery of unprotected siRNAs is ineffective due to their susceptibility to degradation by ubiquitous nucleases under physiological conditions. Layered double hydroxide nanoparticles (LDHs) have been found to be efficient carriers of anionic drugs and nucleic acids. Our previous research has shown that LDHs (with the Z-average particle size of approximately 110 nm) can mediate siRNA delivery in mammalian cells, resulting in gene silencing. However, short double-stranded nucleic acids are mostly adsorbed onto the external surface and not well protected by LDHs. In order to enhance the intercalation of siRNA into the LDH interlayer and the efficiency of subsequent siRNA delivery, we prepared smaller LDHs (with the Z-average particle size of approximately 45 nm) with an engineered non-aqueous method. We demonstrate here that dsDNA/siRNA is more effectively intercalated into these small LDH nanoparticles, more dsDNA/siRNA is transfected into HEK 293T cells, and more efficient silencing of the target gene is achieved using smaller LDHs. Thus, smaller LDH particles have greater potential as a delivery system for the application of RNA interference. Copyright © 2012 Elsevier Inc. All rights reserved.

Digital DNA detection based on a compact optofluidic laser with ultra-low sample consumption.

PubMed

Lee, Wonsuk; Chen, Qiushu; Fan, Xudong; Yoon, Dong Ki

2016-11-29

DNA lasers self-amplify optical signals from a DNA analyte as well as thermodynamic differences between sequences, allowing quasi-digital DNA detection. However, these systems have drawbacks, such as relatively large sample consumption and complicated dye labelling. Moreover, although the lasing signal can detect the target DNA, it is superimposed on an unintended fluorescence background, which persists for non-target DNA samples as well. From an optical point of view, it is thus not truly digital detection and requires spectral analysis to identify the target. In this work, we propose and demonstrate an optofluidic laser that has a single layer of DNA molecules as the gain material. A target DNA produces intensive laser emission comparable to existing DNA lasers, while any unnecessary fluorescence background is successfully suppressed. As a result, the target DNA can be detected with a single laser pulse, in a truly digital manner. Since the DNA molecules cover only a single layer on the surface of the laser microcavity, the DNA sample consumption is a few orders of magnitude lower than that of existing DNA lasers. Furthermore, the DNA molecules are stained by simply immersing the microcavity in the intercalating dye solution, and thus the proposed DNA laser is free of any complex dye-labelling process prior to analysis.

Lactose-modified DNA tile nanostructures as drug carriers.

PubMed

Akkus Sut, Pinar; Tunc, Cansu Umran; Culha, Mustafa

2016-09-01

DNA hybridization allows the preparation of nanoscale DNA structures with desired shape and size. DNA structures using simple base pairing can be used for the delivery of drug molecules into the cells. Since DNA carries multiple negative charges, their cellular uptake efficiency is low. Thus, the modification of the DNA structures with molecules that may enhance the cellular internalization may be an option. The objective of this study is to construct DNA-based nanocarrier system and to investigate the cellular uptake of DNA tile with/without lactose modification. Doxorubicin was intercalated to DNA tile and cellular uptake of drug-loaded DNA-based carrier with/without lactose modification was investigated in vitro. HeLa, BT-474, and MDA-MB-231 cancer cells were used for cellular uptake studies and cytotoxicity assays. Using fluorescence spectroscopy, flow cytometry, and confocal microscopy, cellular uptake behavior of DNA tile was investigated. The cytotoxicity of DNA tile structures was determined with WST-1 assay. The results show that modification with lactose effectively increases the intracellular uptake of doxorubicin loaded DNA tile structure by cancer cells compared with the unmodified DNA tile. The findings of this study suggest that DNA-based nanostructures modified with carbohydrates can be used as suitable multifunctional nanocarriers with simple chemical modifications.

Thermodynamic investigation of the binding of dissymmetric pyrenyl-gemini surfactants to DNA.

PubMed

Wettig, Shawn D; Deubry, Rubena; Akbar, Javed; Kaur, Tranum; Wang, Haitang; Sheinin, Tatiana; Joseph, Jamie W; Slavcev, Roderick A

2010-05-14

Gemini surfactants have demonstrated significant potential for use in constructing non-viral transfection vectors for the delivery of genes into cells to induce protein expression. Previously, two asymmetric gemini surfactants containing pyrenyl groups in one of the alkyl tails of the surfactants were synthesized as fluorescence probes for use in mechanistic studies of the transfection process. Here we present the results of a thermodynamic investigation of the binding interaction(s) between the pyrenyl-modified surfactants and DNA. The thermodynamics of the interactions have been examined using isothermal titration calorimetry, light scattering, zeta potential, and circular dichroism measurements. Distinct differences are observed between the interaction of 12-s-12 vs. the pyrene modified py-s-12 surfactants with DNA; an intercalated binding is found for the py-s-12 surfactants that disrupts the typical interactions observed between DNA and gemini surfactants.

Flexible DNA bending in HU–DNA cocrystal structures

PubMed Central

Swinger, Kerren K.; Lemberg, Kathryn M.; Zhang, Ying; Rice, Phoebe A.

2003-01-01

HU and IHF are members of a family of prokaryotic proteins that interact with the DNA minor groove in a sequence-specific (IHF) or non-specific (HU) manner to induce and/or stabilize DNA bending. HU plays architectural roles in replication initiation, transcription regulation and site-specific recombination, and is associated with bacterial nucleoids. Cocrystal structures of Anabaena HU bound to DNA (1P71, 1P78, 1P51) reveal that while underlying proline intercalation and asymmetric charge neutralization mechanisms of DNA bending are similar for IHF and HU, HU stabilizes different DNA bend angles (∼105–140°). The two bend angles within a single HU complex are not coplanar, and the resulting dihedral angle is consistent with negative supercoiling. Comparison of HU–DNA and IHF–DNA structures suggests that sharper bending is correlated with longer DNA binding sites and smaller dihedral angles. An HU-induced bend may be better modeled as a hinge, not a rigid bend. The ability to induce or stabilize varying bend angles is consistent with HU’s role as an architectural cofactor in many different systems that may require differing geometries. PMID:12853489

DNA Electrochemistry with Tethered Methylene Blue

PubMed Central

Pheeney, Catrina G.

2012-01-01

Methylene blue (MB′), covalently attached to DNA through a flexible C12 alkyl linker, provides a sensitive redox reporter in DNA electrochemistry measurements. Tethered, intercalated MB′ is reduced through DNA-mediated charge transport; the incorporation of a single base mismatch at position 3, 10, or 14 of a 17-mer causes an attenuation of the signal to 62 ± 3% of the well-matched DNA, irrespective of position in the duplex. The redox signal intensity for MB′–DNA is found to be least 3-fold larger than that of Nile blue (NB)–DNA, indicating that MB′ is even more strongly coupled to the π-stack. The signal attenuation due to an intervening mismatch does, however, depend on DNA film density and the backfilling agent used to passivate the surface. These results highlight two mechanisms for reduction of MB′ on the DNA-modified electrode: reduction mediated by the DNA base pair stack and direct surface reduction of MB′ at the electrode. These two mechanisms are distinguished by their rates of electron transfer that differ by 20-fold. The extent of direct reduction at the surface can be controlled by assembly and buffer conditions. PMID:22512327

Atomic-scale recognition of surface structure and intercalation mechanism of Ti3C2X.

PubMed

Wang, Xuefeng; Shen, Xi; Gao, Yurui; Wang, Zhaoxiang; Yu, Richeng; Chen, Liquan

2015-02-25

MXenes represent a large family of functionalized two-dimensional (2D) transition-metal carbides and carbonitrides. However, most of the understanding on their unique structures and applications stops at the theoretical suggestion and lack of experimental support. Herein, the surface structure and intercalation chemistry of Ti3C2X are clarified at the atomic scale by aberration-corrected scanning transmission electron microscope (STEM) and density functional theory (DFT) calculations. The STEM studies show that the functional groups (e.g., OH(-), F(-), O(-)) and the intercalated sodium (Na) ions prefer to stay on the top sites of the centro-Ti atoms and the C atoms of the Ti3C2 monolayer, respectively. Double Na-atomic layers are found within the Ti3C2X interlayer upon extensive Na intercalation via two-phase transition and solid-solution reactions. In addition, aluminum (Al)-ion intercalation leads to horizontal sliding of the Ti3C2X monolayer. On the basis of these observations, the previous monolayer surface model of Ti3C2X is modified. DFT calculations using the new modeling help to understand more about their physical and chemical properties. These findings enrich the understanding of the MXenes and shed light on future material design and applications. Moreover, the Ti3C2X exhibits prominent rate performance and long-term cycling stability as an anode material for Na-ion batteries.

Superconductivity in Li{sub 3}Ca{sub 2}C{sub 6} intercalated graphite

DOE Office of Scientific and Technical Information (OSTI.GOV)

Emery, Nicolas; Herold, Claire; Mareche, Jean-Francois

2006-04-15

In this paper, we report the discovery of superconductivity in Li{sub 3}Ca{sub 2}C{sub 6}. Several graphite intercalation compounds (GICs) with electron donors, are well known as superconductors [T. Enoki, S. Masatsugu, E. Morinobu, Graphite Intercalation Compounds and Applications, Oxford University Press, Oxford, 2003]. It is probably not astonishing, since it is generally admitted that low dimensionality promotes high superconducting transition temperatures. Superconductivity is lacking in pristine graphite, but after charging the graphene planes by intercalation, its electronic properties change considerably and superconducting behaviour can appear. Li{sub 3}Ca{sub 2}C{sub 6} is a ternary GIC [S. Pruvost, C. Herold, A. Herold, P.more » Lagrange, Eur. J. Inorg. Chem. 8 (2004) 1661-1667], for which the intercalated sheets are very thick and poly layered (five lithium layers and two calcium ones). It contains a great amount of metal (five metallic atoms for six carbon ones). Its critical temperature of 11.15 K is very close to that of CaC{sub 6} GIC [T.E. Weller, M. Ellerby, S.S. Saxena, R.P. Smith, N.T. Skipper, Nat. Phys. 1 (2005) 39-41; N. Emery, C. Herold, M. d'Astuto, V. Garcia, Ch. Bellin, J.F. Mareche, P. Lagrange, G. Loupias, Phys. Rev. Lett. 95 (2005) 087003] (11.5 K). Both CaC{sub 6} and Li{sub 3}Ca{sub 2}C{sub 6} GICs possess currently the highest transition temperatures among all the GICs.« less

First-principles investigation of aluminum intercalation and diffusion in TiO2 materials: Anatase versus rutile

NASA Astrophysics Data System (ADS)

Tang, Weiqiang; Xuan, Jin; Wang, Huizhi; Zhao, Shuangliang; Liu, Honglai

2018-04-01

Aluminum-ion batteries, emerging as a promising post-lithium battery solution, have been a subject of increasing research interest. Yet, most existing aluminum-ion research has focused on electrode materials development and synthesis. There has been a lack of fundamental understanding of the electrode processes and thus theoretical guidelines for electrode materials selection and design. In this study, by using density functional theory, we for the first time report a first-principles investigation on the thermodynamic and kinetic properties of aluminum intercalation into two common TiO2 polymorphs, i.e., anatase and rutile. After examining the aluminum intercalation sites, intercalation voltages, storage capacities and aluminum diffusion paths in both cases, we demonstrate that the stable aluminum intercalation site locates at the center of the O6 octahedral for TiO2 rutile and off center for TiO2 anatase. The maximum achievable Al/Ti ratios for rutile and anatase are 0.34375 and 0.36111, respectively. Although rutile is found to have an aluminum storage capacity slightly higher than anatase, the theoretical specific energy of rutile can reach 20.90 Wh kg-1, nearly twice as high as anatase (9.84 Wh kg-1). Moreover, the diffusion coefficient of aluminum ions in rutile is 10-9 cm2 s-1, significantly higher than that in anatase (10-20 cm2 s-1). In this regard, TiO2 rutile appears to be a better candidate than anatase as an electrode material for aluminum-ion batteries.

New approach to elaborate exfoliated starch-based nanobiocomposites.

PubMed

Chivrac, Frédéric; Pollet, Eric; Schmutz, Marc; Avérous, Luc

2008-03-01

The present paper reports the successful elaboration of exfoliated plasticized starch-based nanobiocomposites. This was made possible by using cationic starch as a new clay organomodifier to better match the polarity of the matrix and thus to facilitate the clay exfoliation process. To demonstrate the efficiency of this new approach, either natural (MMT-Na) or organomodified (OMMT-CS) montmorillonite were incorporated into the starch nanobiocomposites by a melt blending process. The morphological analyses (SAXD and TEM) showed that MMT-Na leads to the formation of intercalated nanobiocomposites. On the contrary, OMMT-CS allowed the elaboration of well-exfoliated nanobiocomposites. Tensile tests performed on the obtained nanobiocomposites showed that exfoliated nanobiocomposites display enhanced mechanical properties compared to those of the intercalated nanobiocomposites and neat matrix. These results clearly highlight the great interest in using OMMT-CS to obtain starch-based nanobiocomposites with improved properties.

Multiphoton luminescent graphene quantum dots for in vivo tracking of human adipose-derived stem cells

NASA Astrophysics Data System (ADS)

Kim, Jin; Song, Sung Ho; Jin, Yoonhee; Park, Hyun-Ji; Yoon, Hyewon; Jeon, Seokwoo; Cho, Seung-Woo

2016-04-01

The applicability of graphene quantum dots (GQDs) for the in vitro and in vivo live imaging and tracking of different types of human stem cells is investigated. GQDs synthesized by the modified graphite intercalated compound method show efficient cellular uptake with improved biocompatibility and highly sensitive optical properties, indicating their feasibility as a bio-imaging probe for stem cell therapy.The applicability of graphene quantum dots (GQDs) for the in vitro and in vivo live imaging and tracking of different types of human stem cells is investigated. GQDs synthesized by the modified graphite intercalated compound method show efficient cellular uptake with improved biocompatibility and highly sensitive optical properties, indicating their feasibility as a bio-imaging probe for stem cell therapy. Electronic supplementary information (ESI) available: Additional results. See DOI: 10.1039/c6nr02143c

Pectins filled with LDH-antimicrobial molecules: preparation, characterization and physical properties.

PubMed

Gorrasi, Giuliana; Bugatti, Valeria; Vittoria, Vittoria

2012-06-05

Nanohybrids of layered double hydroxide (LDH) with intercalated active molecules: benzoate, 2,4-dichlorobenzoate, para-hydroxybenzoate and ortho-hydroxybenzoate, were incorporated into pectins from apples through high energy ball milling in the presence of water. Cast films were obtained and analysed. X-ray diffraction analysis showed a complete destructuration of all nanohybrids in the pectin matrix. Thermogravimetric analysis showed a better thermal resistance of pectin in the presence of fillers, especially para-hydroxybenzoate and ortho-hydroxybenzoate. Mechanical properties showed an improvement of elastic modulus in particular for LDH-para-hydroxybenzoate nanohybrid, due probably to a better interaction between pectin matrix and nanohybrid layers. Barrier properties (sorption and diffusion) to water vapour showed improvement in the dependence on the intercalated active molecule, the best improvement was achieved for composites containing para-hydroxybenzoate molecules, suggesting that the interaction between the filler phase and the polymer plays an important role in sorption and diffusion phenomena. Incorporation of these active molecules gave antimicrobial properties to the composite films giving opportunities in the field of active packaging. Copyright © 2012 Elsevier Ltd. All rights reserved.

A survey of the sequence-specific interaction of damaging agents with DNA: emphasis on antitumor agents.

PubMed

Murray, V

1999-01-01

This article reviews the literature concerning the sequence specificity of DNA-damaging agents. DNA-damaging agents are widely used in cancer chemotherapy. It is important to understand fully the determinants of DNA sequence specificity so that more effective DNA-damaging agents can be developed as antitumor drugs. There are five main methods of DNA sequence specificity analysis: cleavage of end-labeled fragments, linear amplification with Taq DNA polymerase, ligation-mediated polymerase chain reaction (PCR), single-strand ligation PCR, and footprinting. The DNA sequence specificity in purified DNA and in intact mammalian cells is reviewed for several classes of DNA-damaging agent. These include agents that form covalent adducts with DNA, free radical generators, topoisomerase inhibitors, intercalators and minor groove binders, enzymes, and electromagnetic radiation. The main sites of adduct formation are at the N-7 of guanine in the major groove of DNA and the N-3 of adenine in the minor groove, whereas free radical generators abstract hydrogen from the deoxyribose sugar and topoisomerase inhibitors cause enzyme-DNA cross-links to form. Several issues involved in the determination of the DNA sequence specificity are discussed. The future directions of the field, with respect to cancer chemotherapy, are also examined.

Nanocomposites of rice and banana flours blend with montmorillonite: partial characterization.

PubMed

Rodríguez-Marín, María L; Bello-Pérez, Luis A; Yee-Madeira, Hernani; Zhong, Qixin; González-Soto, Rosalía A

2013-10-01

Rice and banana flours are inexpensive starchy materials that can form films with more improved properties than those made with their starch because flour and starch present different hydrophobicity. Montmorillonite (MMT) can be used to further improve the properties of starch-based films, which has not received much research attention for starchy flours. The aim of this work was to evaluate the mechanical and barrier properties of nanocomposite films of banana and rice flours as matrix material with addition of MMT as a nanofiller. MMT was modified using citric acid to produce intercalated structures, as verified by the X-ray diffraction pattern. The intercalated MMT was blended with flour slurries, and films were prepared by casting. Nanocomposite films of banana and rice flours presented an increase in the tensile at break and elongation percentage, respectively, more than their respective control films without MMT. This study showed that banana and rice flours could be alternative raw materials to use in making nanocomposite films. Copyright © 2013 Elsevier B.V. All rights reserved.

Effect of Silver Doping on Transport Properties of Bi2Se3: AgxBi2Se3 and Bi2-xAgxSe3

NASA Astrophysics Data System (ADS)

Zhang, Min; Wei, Zhan-Tao

2018-05-01

Ag-doped Bi2Se3 with the formula AgxBi2Se3 and Bi2-xAgxSe3 were prepared and their electrical and magnetic transport properties have been investigated to study the influence of silver doping on transport properties of Bi2Se3 with different Ag-doped method. All samples exhibited metallic resistivity and the resistivity increased with increasing Ag concentration. The lattice parameter c of Ag-substituted and Ag-intercalated samples displays a contrary change as the Ag concentration increased. For the Ag-intercalated samples, both the resistance upturn were observed in the curves of temperature dependent of resistivity and temperature dependent of magnetoresistance, respectively, indicating that the enhanced surface effect was obtained in those samples. Monotonously, field-induced MR peaks around 200 K were also observed in those samples. Similar behaviors were not observed in the Ag-substituted samples.

Atomic intercalation to measure adhesion of graphene on graphite

PubMed Central

Wang, Jun; Sorescu, Dan C.; Jeon, Seokmin; Belianinov, Alexei; Kalinin, Sergei V.; Baddorf, Arthur P.; Maksymovych, Petro

2016-01-01

The interest in mechanical properties of two-dimensional materials has emerged in light of new device concepts taking advantage of flexing, adhesion and friction. Here we demonstrate an effective method to measure adhesion of graphene atop highly ordered pyrolytic graphite, utilizing atomic-scale ‘blisters' created in the top layer by neon atom intercalates. Detailed analysis of scanning tunnelling microscopy images is used to reconstruct atomic positions and the strain map within the deformed graphene layer, and demonstrate the tip-induced subsurface translation of neon atoms. We invoke an analytical model, originally devised for graphene macroscopic deformations, to determine the graphite adhesion energy of 0.221±0.011 J m−2. This value is in excellent agreement with reported macroscopic values and our atomistic simulations. This implies mechanical properties of graphene scale down to a few-nanometre length. The simplicity of our method provides a unique opportunity to investigate the local variability of nanomechanical properties in layered materials. PMID:27796294

Zn2+ selectively stabilizes FdU-substituted DNA through a unique major groove binding motif

PubMed Central

Ghosh, Supratim; Salsbury, Freddie R.; Horita, David A.; Gmeiner, William H.

2011-01-01

We report, based on semi-empirical calculations, that Zn2+ binds duplex DNA containing consecutive FdU–dA base pairs in the major groove with distorted trigonal bipyramidal geometry. In this previously uncharacterized binding motif, O4 and F5 on consecutive FdU are axial ligands while three water molecules complete the coordination sphere. NMR spectroscopy confirmed Zn2+ complexation occurred with maintenance of base pairing while a slight hypsochromic shift in circular dichroism (CD) spectra indicated moderate structural distortion relative to B-form DNA. Zn2+ complexation inhibited ethidium bromide (EtBr) intercalation and stabilized FdU-substituted duplex DNA (ΔTm > 15°C). Mg2+ neither inhibited EtBr complexation nor had as strong of a stabilizing effect. DNA sequences that did not contain consecutive FdU were not stabilized by Zn2+. A lipofectamine preparation of the Zn2+–DNA complex displayed enhanced cytotoxicity toward prostate cancer cells relative to the individual components prepared as lipofectamine complexes indicating the potential utility of Zn2+–DNA complexes for cancer treatment. PMID:21296761

Uncovering the self-assembly of DNA nanostructures by thermodynamics and kinetics.

PubMed

Wei, Xixi; Nangreave, Jeanette; Liu, Yan

2014-06-17

CONSPECTUS: DNA nanotechnology is one of the most flourishing interdisciplinary research fields. DNA nanostructures can be designed to self-assemble into a variety of periodic or aperiodic patterns of different shapes and length scales. They can be used as scaffolds for organizing other nanoparticles, proteins, and chemical groups, leveraging their functions for creating complex bioinspired materials that may serve as smart drug delivery systems, in vitro or in vivo biomolecular computing platforms, and diagnostic devices. Achieving optimal structural features, efficient assembly protocols, and precise functional group positioning and modification requires a thorough understanding of the thermodynamics and kinetics of the DNA nanostructure self-assembly process. The most common real-time measurement strategies include monitoring changes in UV absorbance based on the hyperchromic effect of DNA, and the emission signal changes of DNA intercalating dyes or covalently conjugated fluorescent dyes/pairs that accompany temperature dependent structural changes. Thermodynamic studies of a variety of DNA nanostructures have been performed, from simple double stranded DNA formation to more complex origami assembly. The key parameters that have been evaluated in terms of stability and cooperativity include the overall dimensions, the folding path of the scaffold, crossover and nick point arrangement, length and sequence of single strands, and salt and ion concentrations. DNA tile-tile interactions through sticky end hybridization have also been analyzed, and the steric inhibition and rigidity of tiles turn out to be important factors. Many kinetic studies have also been reported, and most are based on double stranded DNA formation. A two-state assumption and the hypothesis of several intermediate states have been applied to determine the rate constant and activation energy of the DNA hybridization process. A few simulated models were proposed to represent the structural, mechanical, and kinetic properties of DNA hybridization. The kinetics of strand displacement reactions has also been studied as a special case of DNA hybridization. The thermodynamic and kinetic characteristics of DNA nanostructures have been exploited to develop rapid and isothermal annealing protocols. It is conceivable that a more thorough understanding of the DNA assembly process could be used to guide the structural design process and optimize the conditions for assembly, manipulation, and functionalization, thus benefiting both upstream design and downstream applications.

New potential antitumoral fluorescent tetracyclic thieno[3,2- b]pyridine derivatives: interaction with DNA and nanosized liposomes

NASA Astrophysics Data System (ADS)

Castanheira, Elisabete Ms; Carvalho, Maria Solange D.; Rodrigues, Ana Rita O.; Calhelha, Ricardo C.; Queiroz, Maria-João Rp

2011-05-01

Fluorescence properties of two new potential antitumoral tetracyclic thieno[3,2- b]pyridine derivatives were studied in solution and in liposomes of DPPC (dipalmitoyl phosphatidylcholine), egg lecithin (phosphatidylcholine from egg yolk; Egg-PC) and DODAB (dioctadecyldimethylammonium bromide). Compound 1, pyrido[2',3':3,2]thieno[4,5- d]pyrido[1,2- a]pyrimidin-6-one, exhibits reasonably high fluorescence quantum yields in all solvents studied (0.20 ≤ ΦF ≤ 0.30), while for compound 2, 3-[( p-methoxyphenyl)ethynyl]pyrido[2',3':3,2]thieno[4,5- d]pyrido[1,2- a]pyrimidin-6-one, the values are much lower (0.01 ≤ ΦF ≤ 0.05). The interaction of these compounds with salmon sperm DNA was studied using spectroscopic methods, allowing the determination of intrinsic binding constants, K i = (8.7 ± 0.9) × 103 M-1 for compound 1 and K i = (5.9 ± 0.6) × 103 M-1 for 2, and binding site sizes of n = 11 ± 3 and n = 7 ± 2 base pairs, respectively. Compound 2 is the most intercalative compound in salmon sperm DNA (35%), while for compound 1 only 11% of the molecules are intercalated. Studies of incorporation of both compounds in liposomes of DPPC, Egg-PC and DODAB revealed that compound 2 is mainly located in the hydrophobic region of the lipid bilayer, while compound 1 prefers a hydrated and fluid environment.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Rubinson, Emily H.; Prakasha Gowda, A.S.; Spratt, Thomas E.

DNA glycosylases that remove alkylated and deaminated purine nucleobases are essential DNA repair enzymes that protect the genome, and at the same time confound cancer alkylation therapy, by excising cytotoxic N3-methyladenine bases formed by DNA-targeting anticancer compounds. The basis for glycosylase specificity towards N3- and N7-alkylpurines is believed to result from intrinsic instability of the modified bases and not from direct enzyme functional group chemistry. Here we present crystal structures of the recently discovered Bacillus cereus AlkD glycosylase in complex with DNAs containing alkylated, mismatched and abasic nucleotides. Unlike other glycosylases, AlkD captures the extrahelical lesion in a solvent-exposed orientation,more » providing an illustration for how hydrolysis of N3- and N7-alkylated bases may be facilitated by increased lifetime out of the DNA helix. The structures and supporting biochemical analysis of base flipping and catalysis reveal how the HEAT repeats of AlkD distort the DNA backbone to detect non-Watson-Crick base pairs without duplex intercalation.« less

Extension of nanoconfined DNA: Quantitative comparison between experiment and theory

NASA Astrophysics Data System (ADS)

Iarko, V.; Werner, E.; Nyberg, L. K.; Müller, V.; Fritzsche, J.; Ambjörnsson, T.; Beech, J. P.; Tegenfeldt, J. O.; Mehlig, K.; Westerlund, F.; Mehlig, B.

2015-12-01

The extension of DNA confined to nanochannels has been studied intensively and in detail. However, quantitative comparisons between experiments and model calculations are difficult because most theoretical predictions involve undetermined prefactors, and because the model parameters (contour length, Kuhn length, effective width) are difficult to compute reliably, leading to substantial uncertainties. Here we use a recent asymptotically exact theory for the DNA extension in the "extended de Gennes regime" that allows us to compare experimental results with theory. For this purpose, we performed experiments measuring the mean DNA extension and its standard deviation while varying the channel geometry, dye intercalation ratio, and ionic strength of the buffer. The experimental results agree very well with theory at high ionic strengths, indicating that the model parameters are reliable. At low ionic strengths, the agreement is less good. We discuss possible reasons. In principle, our approach allows us to measure the Kuhn length and the effective width of a single DNA molecule and more generally of semiflexible polymers in solution.

Spectroscopic analysis on the resveratrol-DNA binding interactions at physiological pH

NASA Astrophysics Data System (ADS)

Zhang, Shufang; Sun, Xuejun; Jing, Zhihong; Qu, Fengli

2011-11-01

The interaction of resveratrol with calf thymus deoxyribonucleic acid (ctDNA) under physiological conditions (Tris-HCl buffer solutions, pH 7.4) was studied by spectroscopy, fluorescence spectroscopy and viscosity measurement method, respectively. Results indicated that a complex of resveratrol with ctDNA was formed with a binding constant of K17 °C = 5.49 × 10 3 L mol -1 and K37 °C = 1.90 × 10 4 L mol -1. The fluorescence quenching mechanism of acridine orange (AO)-ctDNA by resveratrol was shown to be a static quenching type. The thermodynamic parameters of the complex were calculated by a double reciprocal method: ΔHms=4.64×10 J mol, ΔSms=231.8 J K mol and ΔGms=-2.54×10 J mol (37 °C). Spectroscopic techniques together with viscosity determination provided evidences of intercalation mode of binding for the interaction between resveratrol and ctDNA.

Spinel compounds as multivalent battery cathodes: A systematic evaluation based on ab initio calculations

DOE PAGES

Liu, Miao; Rong, Ziqin; Malik, Rahul; ...

2014-12-16

In this study, batteries that shuttle multivalent ions such as Mg 2+ and Ca 2+ ions are promising candidates for achieving higher energy density than available with current Li-ion technology. Finding electrode materials that reversibly store and release these multivalent cations is considered a major challenge for enabling such multivalent battery technology. In this paper, we use recent advances in high-throughput first-principles calculations to systematically evaluate the performance of compounds with the spinel structure as multivalent intercalation cathode materials, spanning a matrix of five different intercalating ions and seven transition metal redox active cations. We estimate the insertion voltage, capacity,more » thermodynamic stability of charged and discharged states, as well as the intercalating ion mobility and use these properties to evaluate promising directions. Our calculations indicate that the Mn 2O 4 spinel phase based on Mg and Ca are feasible cathode materials. In general, we find that multivalent cathodes exhibit lower voltages compared to Li cathodes; the voltages of Ca spinels are ~0.2 V higher than those of Mg compounds (versus their corresponding metals), and the voltages of Mg compounds are ~1.4 V higher than Zn compounds; consequently, Ca and Mg spinels exhibit the highest energy densities amongst all the multivalent cation species. The activation barrier for the Al³⁺ ion migration in the Mn₂O₄ spinel is very high (~1400 meV for Al 3+ in the dilute limit); thus, the use of an Al based Mn spinel intercalation cathode is unlikely. Amongst the choice of transition metals, Mn-based spinel structures rank highest when balancing all the considered properties.« less

Graphene-based materials via benzidine-assisted exfoliation and reduction of graphite oxide and their electrochemical properties

NASA Astrophysics Data System (ADS)

Vermisoglou, E. C.; Giannakopoulou, T.; Romanos, G.; Boukos, N.; Psycharis, V.; Lei, C.; Lekakou, C.; Petridis, D.; Trapalis, C.

2017-01-01

Benzidine, a compound bearing aromatic rings and terminal amino groups, was employed for the intercalation and simultaneous reduction of graphite oxide (GO). The aromatic diamine can be intercalated into GO as follows: (1) by grafting with the epoxy groups of GO, (2) by hydrogen bonding with the oxygen containing groups of GO. Stacking between benzidine aromatic rings and unoxidized domains of GO may occur through π-π interaction. The role of benzidine is influenced by pH conditions and the weight ratio GO/benzidine. Two weight ratios were tested i.e. 1:2 and 1:3. Under strong alkaline conditions through K2CO3 addition (pH ∼10.4-10.6) both intercalation and reduction of GO via amino groups occur, while under strong acidic conditions through HCl addition (pH ∼1.4-2.2) π-π stacking is preferred. When no base or acid is added (pH ∼5.2) and the weight ratio is 1:2, there are indications that reduction and π-π stacking occur, while at a GO/benzidine weight ratio 1:3 intercalation via amino groups and reduction seem to dominate. The aforementioned remarks render benzidine a multifunctional tool towards production of reduced graphene oxide. The effect of pH conditions and the GO/benzidine weight ratio on the quality and the electrochemical properties of the produced graphene-based materials were investigated. Cyclic voltammetry measurements using three-electrode cell and KCl aqueous solution as an electrolyte gave specific capacitance values up to ∼178 F/g. When electric double-layer capacitors (EDLC) were fabricated from these materials, the maximum capacitance in organic electrolyte i.e., tetraethyl ammonium tetrafluoroborate (TEABF4) in polycarbonate (PC) was ∼29 F/g.

Hydrophobic Modification of Layered Clays and Compatibility for Epoxy Nanocomposites

PubMed Central

Lin, Jiang-Jen; Chan, Ying-Nan; Lan, Yi-Fen

2010-01-01

Recent studies on the intercalation and exfoliation of layered clays with polymeric intercalating agents involving poly(oxypropylene)-amines and the particular uses for epoxy nanocomposites are reviewed. For intercalation, counter-ionic exchange reactions of clays including cationic layered silicates and anionic Al-Mg layered double hydroxide (LDH) with polymeric organic ions afforded organoclays led to spatial interlayer expansion from 12 to 92 Å (X-ray diffraction) as well as hydrophobic property. The inorganic clays of layered structure could be modified by the poly(oxypropylene)amine-salts as the intercalating agents with molecular weights ranging from 230 to 5,000 g/mol. Furthermore, natural montmorillonite (MMT) clay could be exfoliated into thin layer silicate platelets (ca. 1 nm thickness) in one step by using polymeric types of exfoliating agents. Different lateral dimensions of MMT, synthetic fluorinated Mica and LDH clays had been cured into epoxy nanocomposites. The hydrophobic amine-salt modification resulting in high spacing of layered or exfoliation of individual clay platelets is the most important factor for gaining significant improvements of properties. In particular, these modified clays were reported to gain significant improvements such as reduced coefficient of thermal expansion (CTE), enhanced thermal stability, and hardness. The utilization of these layered clays for initiating the epoxy self-polymerization was also reported to have a unique compatibility between clay and organic resin matrix. However, the matrix domain lacks of covalently bonded crosslink and leads to the isolation of powder material. It is generally concluded that the hydrophobic expansion of the clay inter-gallery spacing is the crucial step for enhancing the compatibility and the ultimate preparation of the advanced epoxy materials.

Anticancer Activity Expressed by a Library of 2,9-Diazaperopyrenium Dications

PubMed Central

2016-01-01

Polyaromatic compounds are well-known to intercalate DNA. Numerous anticancer chemotherapeutics have been developed upon the basis of this recognition motif. The compounds have been designed such that they interfere with the role of the topoisomerases, which control the topology of DNA during the cell-division cycle. Although many promising chemotherapeutics have been developed upon the basis of polyaromatic DNA intercalating systems, these candidates did not proceed past clinical trials on account of their dose-limiting toxicity. Herein, we discuss an alternative, water-soluble class of polyaromatic compounds, the 2,9-diazaperopyrenium dications, and report in vitro cell studies for a library of these dications. These investigations reveal that a number of 2,9-diazaperopyrenium dications show similar activities as doxorubicin toward a variety of cancer cell lines. Additionally, we report the solid-state structures of these dications, and we relate their tendency to aggregate in solution to their toxicity profiles. The addition of bulky substituents to these polyaromatic dications decreases their tendency to aggregate in solution. The derivative substituted with 2,6-diisopropylphenyl groups proved to be the most cytotoxic against the majority of the cell lines tested. In the solid state, the 2,6-diisopropylphenyl-functionalized derivative does not undergo π···π stacking, while in aqueous solution, dynamic light scattering reveals that this derivative forms very small (50–100 nm) aggregates, in contrast with the larger ones formed by dications with less bulky substituents. Alteration of the aromaticitiy in the terminal heterocycles of selected dications reveals a drastic change in the toxicity of these polyaromatic species toward specific cell lines. PMID:25555133

Low-density lipoprotein peptide-combined DNA nanocomplex as an efficient anticancer drug delivery vehicle.

PubMed

Zhang, Nan; Tao, Jun; Hua, Haiying; Sun, Pengchao; Zhao, Yongxing

2015-08-01

DNA is a type of potential biomaterials for drug delivery due to its nanoscale geometry, loading capacity of therapeutics, biocompatibility, and biodegradability. Unfortunately, DNA is easily degraded by DNases in the body circulation and has low intracellular uptake. In the present study, we selected three cationic polymers polyethylenimine (PEI), hexadecyl trimethyl ammonium bromide (CTAB), and low-density lipoprotein (LDL) receptor targeted peptide (RLT), to modify DNA and improve the issues. A potent anti-tumor anthracycline-doxorubicin (DOX) was intercalated into DNA non-covalently and the DOX/DNA was then combined with PEI, CTAB, and RLT, respectively. Compact nanocomplexes were formed by electrostatic interaction and could potentially protect DNA from DNases. More importantly, RLT had the potential to enhance intracellular uptake by LDL receptor mediated endocytosis. In a series of in vitro experiments, RLT complexed DNA enhanced intracellular delivery of DOX, increased tumor cell death and intracellular ROS production, and reduced intracellular elimination of DOX. All results suggested that the easily prepared and targeted RLT/DNA nanocomplexes had great potential to be developed into a formulation for doxorubicin with enhanced anti-tumor activity. Copyright © 2015 Elsevier B.V. All rights reserved.

Medicinal plants: a source of anti-parasitic secondary metabolites.

PubMed

Wink, Michael

2012-10-31

This review summarizes human infections caused by endoparasites, including protozoa, nematodes, trematodes, and cestodes, which affect more than 30% of the human population, and medicinal plants of potential use in their treatment. Because vaccinations do not work in most instances and the parasites have sometimes become resistant to the available synthetic therapeutics, it is important to search for alternative sources of anti-parasitic drugs. Plants produce a high diversity of secondary metabolites with interesting biological activities, such as cytotoxic, anti-parasitic and anti-microbial properties. These drugs often interfere with central targets in parasites, such as DNA (intercalation, alkylation), membrane integrity, microtubules and neuronal signal transduction. Plant extracts and isolated secondary metabolites which can inhibit protozoan parasites, such as Plasmodium, Trypanosoma, Leishmania, Trichomonas and intestinal worms are discussed. The identified plants and compounds offer a chance to develop new drugs against parasitic diseases. Most of them need to be tested in more detail, especially in animal models and if successful, in clinical trials.

New cobalt(II) and nickel(II) complexes of benzyl carbazate Schiff bases: Syntheses, crystal structures, in vitro DNA and HSA binding studies.

PubMed

Nithya, Palanivelu; Helena, Sannasi; Simpson, Jim; Ilanchelian, Malaichamy; Muthusankar, Aathi; Govindarajan, Subbiah

2016-12-01

In the present study, new Schiff base complexes with the composition [M(NCS) 2 (L1) 2 ]·nH 2 O, where M=Co (n=0) (1) and Ni (n=2) (2); [M(NCS) 2 (L2) 2 ], M=Co (3) and Ni (4) as well as [M(NCS) 2 (L3) 2 ], M=Co (5) and Ni (6); (L1=benzyl 2-(propan-2-ylidene)hydrazinecarboxylate, L2=benzyl 2-(butan-2-ylidene)hydrazinecarboxylate and L3=benzyl 2-(pentan-3-ylidene)hydrazinecarboxylate) have been synthesized by a template method. The complexes were characterised by analytical methods, spectroscopic studies, thermal and X-ray diffraction techniques. The structures of all the complexes explore that the metal(II) cation has a trans-planar coordination environment, the monomeric units containing a six-coordinated metal center in octahedral geometry with N-bound isothiocyanate anions coordinated as terminal ligands. Furthermore, the binding of the two Schiff base ligands to the metal centers involves the azomethine nitrogen and the carbonyl oxygen in mutually trans configuration. The binding interactions of all the complexes with Calf thymus-deoxyribonucleic acid (CT-DNA) and human serum albumin (HSA) have been investigated using absorption and emission spectral techniques. The CT-DNA binding properties of these complexes reveal that they bind to CT-DNA through a partial intercalation mode and the binding constant values were calculated using the absorption and emission spectral data. The binding constant values (~10×10 6 moldm -3 ) indicate strong binding of metal complexes with CT-DNA. HSA binding interaction studies showed that the cobalt and nickel complexes can quench the intrinsic fluorescence of HSA through static quenching process. Also, molecular docking studies were supported out to apprehend the binding interactions of these complexes with DNA and HSA which offer new understandings into the experimental model observations. Copyright © 2016 Elsevier B.V. All rights reserved.

Intercalation of IR absorber into layered double hydroxides: Preparation, thermal stability and selective IR absorption

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Haifeng; Tang, Pinggui; Feng, Yongjun, E-mail: yjfeng@mail.buct.edu.cn

2012-03-15

Highlights: Black-Right-Pointing-Pointer PMIDA anions were intercalated into Mg{sub 2}Al-NO{sub 3} LDH by anion-exchange method. Black-Right-Pointing-Pointer The prepared material has highly selective IR absorption property in 9-11 {mu}m. Black-Right-Pointing-Pointer The obtained material has practical applications as heat-retaining additive. -- Abstract: N-phosphonomethyl aminodiacetic acid (PMIDA) was intercalated into the interlayer spacing of layered double hydroxides (LDH) by an anion-exchange method. The intercalated LDHs were characterized by various techniques such as powder X-ray diffraction (XRD), FT-IR spectroscopy, elemental analysis and simultaneous thermogravimetric and mass spectrometry (TG-MS) in details. The results show the formation of Mg{sub 2}Al-PMIDA LDH based on the expansion of d-spacingmore » from 0.89 nm to 1.22 nm and the disappearance of the characteristic IR absorption band at 1384 cm{sup -1} for NO{sub 3}{sup -} anions. The incorporation of Mg{sub 2}Al-PMIDA LDH into the low density polyethylene (LDPE) as an additive enhances the selectivity of IR absorption in the main wavelength region 9-11 {mu}m for radiant heat loss at night. Mg{sub 2}Al-PMIDA LDH as a heat-retaining additive has practical application in agricultural plastic films.« less

Rapid mass production of two-dimensional metal oxides and hydroxides via the molten salts method

PubMed Central

Hu, Zhimi; Xiao, Xu; Jin, Huanyu; Li, Tianqi; Chen, Ming; Liang, Zhun; Guo, Zhengfeng; Li, Jia; Wan, Jun; Huang, Liang; Zhang, Yanrong; Feng, Guang; Zhou, Jun

2017-01-01

Because of their exotic electronic properties and abundant active sites, two-dimensional (2D) materials have potential in various fields. Pursuing a general synthesis methodology of 2D materials and advancing it from the laboratory to industry is of great importance. This type of method should be low cost, rapid and highly efficient. Here, we report the high-yield synthesis of 2D metal oxides and hydroxides via a molten salts method. We obtained a high-yield of 2D ion-intercalated metal oxides and hydroxides, such as cation-intercalated manganese oxides (Na0.55Mn2O4·1.5H2O and K0.27MnO2·0.54H2O), cation-intercalated tungsten oxides (Li2WO4 and Na2W4O13), and anion-intercalated metal hydroxides (Zn5(OH)8(NO3)2·2H2O and Cu2(OH)3NO3), with a large lateral size and nanometre thickness in a short time. Using 2D Na2W4O13 as an electrode, a high performance electrochemical supercapacitor is achieved. We anticipate that our method will enable new path to the high-yield synthesis of 2D materials for applications in energy-related fields and beyond. PMID:28555669

Inosine Can Increase DNA's Susceptibility to Photo-oxidation by a RuII Complex due to Structural Change in the Minor Groove.

PubMed

Keane, Páraic M; Hall, James P; Poynton, Fergus E; Poulsen, Bjørn C; Gurung, Sarah P; Clark, Ian P; Sazanovich, Igor V; Towrie, Michael; Gunnlaugsson, Thorfinnur; Quinn, Susan J; Cardin, Christine J; Kelly, John M

2017-08-01

Key to the development of DNA-targeting phototherapeutic drugs is determining the interplay between the photoactivity of the drug and its binding preference for a target sequence. For the photo-oxidising lambda-[Ru(TAP) 2 (dppz)] 2+ (Λ-1) (dppz=dipyridophenazine) complex bound to either d{T 1 C 2 G 3 G 4 C 5 G 6 C 7 C 8 G 9 A 10 } 2 (G9) or d{TCGGCGCCIA} 2 (I9), the X-ray crystal structures show the dppz intercalated at the terminal T 1 C 2 ;G 9 A 10 step or T 1 C 2 ;I 9 A 10 step. Thus substitution of the G 9 nucleobase by inosine does not affect intercalation in the solid state although with I9 the dppz is more deeply inserted. In solution it is found that the extent of guanine photo-oxidation, and the rate of back electron-transfer, as determined by pico- and nanosecond time-resolved infrared and transient visible absorption spectroscopy, is enhanced in I9, despite it containing the less oxidisable inosine. This is attributed to the nature of the binding in the minor groove due to the absence of an NH 2 group. Similar behaviour and the same binding site in the crystal are found for d{TTGGCGCCAA} 2 (A9). In solution, we propose that intercalation occurs at the C 2 G 3 ;C 8 I 9 or T 2 G 3 ;C 8 A 9 steps, respectively, with G 3 the likely target for photo-oxidation. This demonstrates how changes in the minor groove (in this case removal of an NH 2 group) can facilitate binding of Ru II dppz complexes and hence influence any sensitised reactions occurring at these sites. No similar enhancement of photooxidation on binding to I9 is found for the delta enantiomer. © 2017 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim.

Improving the electrochemical performance of the li4 ti5 o12 electrode in a rechargeable magnesium battery by lithium-magnesium co-intercalation.

PubMed

Wu, Na; Yang, Zhen-Zhong; Yao, Hu-Rong; Yin, Ya-Xia; Gu, Lin; Guo, Yu-Guo

2015-05-04

Rechargeable magnesium batteries have attracted recent research attention because of abundant raw materials and their relatively low-price and high-safety characteristics. However, the sluggish kinetics of the intercalated Mg(2+) ions in the electrode materials originates from the high polarizing ability of the Mg(2+) ion and hinders its electrochemical properties. Here we report a facile approach to improve the electrochemical energy storage capability of the Li4 Ti5 O12 electrode in a Mg battery system by the synergy between Mg(2+) and Li(+) ions. By tuning the hybrid electrolyte of Mg(2+) and Li(+) ions, both the reversible capacity and the kinetic properties of large Li4 Ti5 O12 nanoparticles attain remarkable improvement. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

The effect of interlayer anion on the reactivity of Mg-Al layered double hydroxides: improving and extending the customization capacity of anionic clays.

PubMed

Rojas, Ricardo; Bruna, Felipe; de Pauli, Carlos P; Ulibarri, M Ángeles; Giacomelli, Carla E

2011-07-01

Layered double hydroxides (LDHs) reactivity and interfacial behavior are closely interconnected and control particle properties relevant to the wide range of these solids' applications. Despite their importance, their relationship has been hardly described. In this work, chloride and dodecylsulfate (DDS(-)) intercalated LDHs are studied combining experimental data (electrophoretic mobility and contact angle measurements, hydroxyl and organic compounds uptake) and a simple mathematical model that includes anion-binding and acid-base reactions. This approach evidences the anion effect on LDHs interfacial behavior, reflected in the opposite particle charge and the different surface hydrophobic/hydrophilic character. LDHs reactivity are also determined by the interlayer composition, as demonstrated by the cation uptake capability of the DDS(-) intercalated sample. Consequently, the interlayer anion modifies the LDHs interfacial properties and reactivity, which in turn extends the customization capacity of these solids. Copyright © 2011 Elsevier Inc. All rights reserved.

Theoretical prediction of honeycomb carbon as Li-ion batteries anode material

NASA Astrophysics Data System (ADS)

Hu, Junping; Zhang, Xiaohang

2018-05-01

First principles calculations are performed to study the electronic properties and Li storage capability of honeycomb carbon. We find its right model consistent with the experimental result, the honeycomb carbon and its Li-intercalated configurations are all metallic which is beneficial to the electrode materials for lithium-ion batteries. The model 1 configuration shows fast Li diffusion and theoretical Li storage capacity of 319 mAh/g. Moreover, the average intercalation potentials for honeycomb carbon material is calculated to be low relatively. Our results suggest that the honeycomb carbon would be a new promising pure carbon anode material for Li-ion batteries.

A comparison of corrosion inhibition of magnesium aluminum and zinc aluminum vanadate intercalated layered double hydroxides on magnesium alloys

NASA Astrophysics Data System (ADS)

Guo, Lian; Zhang, Fen; Lu, Jun-Cai; Zeng, Rong-Chang; Li, Shuo-Qi; Song, Liang; Zeng, Jian-Min

2018-04-01

The magnesium aluminum and zinc aluminum layered double hydroxides intercalated with NO3 -(MgAl-NO3-LDH and ZnAl-NO3-LDH) were prepared by the coprecipitation method, and the magnesium aluminum and the zinc aluminum layered double hydroxides intercalated with VO x -(MgAl-VO x -LDH and ZnAl-VO x -LDH) were prepared by the anion-exchange method. Morphologies, microstructures and chemical compositions of LDHs were investigated by SEM, EDS, XRD, FTIR, Raman and TG analyses. The immersion tests were carried to determine the corrosion inhibition properties of MgAl-VO x -LDH and ZnAl-VO x -LDH on AZ31 Mg alloys. The results showed that ZnAl-VO x -LDH possesses the best anion-exchange and inhibition abilities. The influence of treatment parameters on microstructures of LDHs were discussed. Additionally, an inhibition mechanism for ZnAl-VO x -LDH on the AZ31 magnesium alloy was proposed and discussed.

Piezo-Electrochemical Energy Harvesting with Lithium-Intercalating Carbon Fibers.

PubMed

Jacques, Eric; Lindbergh, Göran; Zenkert, Dan; Leijonmarck, Simon; Kjell, Maria Hellqvist

2015-07-01

The mechanical and electrochemical properties are coupled through a piezo-electrochemical effect in Li-intercalated carbon fibers. It is demonstrated that this piezo-electrochemical effect makes it possible to harvest electrical energy from mechanical work. Continuous polyacrylonitrile-based carbon fibers that can work both as electrodes for Li-ion batteries and structural reinforcement for composites materials are used in this study. Applying a tensile force to carbon fiber bundles used as Li-intercalating electrodes results in a response of the electrode potential of a few millivolts which allows, at low current densities, lithiation at higher electrode potential than delithiation. More electrical energy is thereby released from the cell at discharge than provided at charge, harvesting energy from the mechanical work of the applied force. The measured harvested specific electrical power is in the order of 1 μW/g for current densities in the order of 1 mA/g, but this has a potential of being increased significantly.

Functional interface of polymer modified graphite anode

NASA Astrophysics Data System (ADS)

Komaba, S.; Ozeki, T.; Okushi, K.

Graphite electrodes were modified by polyacrylic acid (PAA), polymethacrylic acid (PMA), and polyvinyl alcohol (PVA). Their electrochemical properties were examined in 1 mol dm -3 LiClO 4 ethylene carbonate:dimethyl carbonate (EC:DMC) and propylene carbonate (PC) solutions as an anode of lithium ion batteries. Generally, lithium ions hardly intercalate into graphite in the PC electrolyte due to a decomposition of the PC electrolyte at ca. 0.8 V vs. Li/Li +, and it results in the exfoliation of the graphene layers. However, the modified graphite electrodes with PAA, PMA, and PVA demonstrated the stable charge-discharge performance due to the reversible lithium intercalation not only in the EC:DMC but also in the PC electrolytes since the electrolyte decomposition and co-intercalation of solvent were successfully suppressed by the polymer modification. It is thought that these improvements were attributed to the interfacial function of the polymer layer on the graphite which interacted with the solvated lithium ions at the electrode interface.

Reversible superconductor-insulator transition in LiTi2O4 induced by Li-ion electrochemical reaction

PubMed Central

Yoshimatsu, K.; Niwa, M.; Mashiko, H.; Oshima, T.; Ohtomo, A.

2015-01-01

Transition metal oxides display various electronic and magnetic phases such as high-temperature superconductivity. Controlling such exotic properties by applying an external field is one of the biggest continuous challenges in condensed matter physics. Here, we demonstrate clear superconductor-insulator transition of LiTi2O4 films induced by Li-ion electrochemical reaction. A compact electrochemical cell of pseudo-Li-ion battery structure is formed with a superconducting LiTi2O4 film as an anode. Li content in the film is controlled by applying a constant redox voltage. An insulating state is achieved by Li-ion intercalation to the superconducting film by applying reduction potential. In contrast, the superconducting state is reproduced by applying oxidation potential to the Li-ion intercalated film. Moreover, superconducting transition temperature is also recovered after a number of cycles of Li-ion electrochemical reactions. This complete reversible transition originates in difference in potentials required for deintercalation of initially contained and electrochemically intercalated Li+ ions. PMID:26541508

Reversible superconductor-insulator transition in LiTi2O4 induced by Li-ion electrochemical reaction.

PubMed

Yoshimatsu, K; Niwa, M; Mashiko, H; Oshima, T; Ohtomo, A

2015-11-06

Transition metal oxides display various electronic and magnetic phases such as high-temperature superconductivity. Controlling such exotic properties by applying an external field is one of the biggest continuous challenges in condensed matter physics. Here, we demonstrate clear superconductor-insulator transition of LiTi2O4 films induced by Li-ion electrochemical reaction. A compact electrochemical cell of pseudo-Li-ion battery structure is formed with a superconducting LiTi2O4 film as an anode. Li content in the film is controlled by applying a constant redox voltage. An insulating state is achieved by Li-ion intercalation to the superconducting film by applying reduction potential. In contrast, the superconducting state is reproduced by applying oxidation potential to the Li-ion intercalated film. Moreover, superconducting transition temperature is also recovered after a number of cycles of Li-ion electrochemical reactions. This complete reversible transition originates in difference in potentials required for deintercalation of initially contained and electrochemically intercalated Li(+) ions.

Differential water sorption studies on Kevlar 49 and As-polymerized poly(p-phenylene terephthalamide): determination of water transport properties.

PubMed

Mooney, Damian A; MacElroy, J M Don

2007-11-06

Water vapor sorption experiments have been conducted on Kevlar 49 at 30 degrees C over a range of water vapor pressures in 0-90% of saturation and on the as-polymerized form of the material at 30, 45, and 60 degrees C over a series of water vapor pressures of 0-60%, 0-25%, and 0-15%, respectively. For each of the differential steps in water vapor pressure, dynamic uptake curves were generated and analyzed according to a number of different mathematical models, including Fickian, Coaxial cylindrical, and intercalation models. The intercalation model was demonstrated to be the most successful model and considered two time-scales involved in the diffusion process, i.e., a penetrant-diffusive time-scale and a polymer-local-matrix-relaxation time-scale. The success of this model reinforces previously reported adsorption and desorption isotherms which suggested that water may penetrate into the surface layers of the polymer crystallite through a process known as intercalation.

New multifunctional materials obtained by the intercalation of anionic dyes into layered zinc hydroxide nitrate followed by dispersion into poly(vinyl alcohol) (PVA).

PubMed

Marangoni, Rafael; Ramos, Luiz Pereira; Wypych, Fernando

2009-02-15

Different anionic blue and orange dyes have been immobilized on a zinc hydroxide nitrate (Zn(5)(OH)(8)(NO(3))(2)nH(2)O--Zn-OH-NO(3)) by anion exchange with interlayer and/or outer surface nitrate ions of the layered matrix. Orange G (OG) was totally intercalated, orange II (OII) was partially intercalated, while Niagara blue 3B (NB) and Evans blue (EV) were only adsorbed at the outer surface. Several composite films of poly(vinyl alcohol)--PVA were prepared by casting through the dispersion of the hybrid material (Zn-OH-OG) into a PVA aqueous solution and evaporation of water in a vacuum oven. The obtained composite films were transparent, colored, and capable of absorbing UV radiation. Improved mechanical properties were also obtained in relation to the nonfilled PVA films. These results demonstrate the onset of a new range of potential applications for layered hydroxide salts in the preparation of polymer composite multifunctional materials.

Actinomycin D binding mode reveals the basis for its potent HIV-1 and cancer activity

NASA Astrophysics Data System (ADS)

Paramanathan, Thayaparan; Vladescu, Ioana D.; McCauley, Micah J.; Rouzina, Ioulia; Williams, Mark C.

2011-03-01

Actinomycin D (ActD) is one of the most studied antibiotics, which has been used as an anti-cancer agent and also shown to inhibit HIV reverse transcription. Initial studies with ActD established that it intercalates double stranded DNA (dsDNA). However, recent studies have shown that ActD binds with even higher affinity to single stranded DNA (ssDNA). In our studies we use optical tweezers to stretch and hold single dsDNA molecule at constant force in the presence of varying ActD concentrations until the binding reaches equilibrium. The change in dsDNA length upon ActD binding measured as a function of time yields the rate of binding in addition to the equilibrium lengthening of DNA. The results suggest extremely slow kinetics, on the order of several minutes and 0.52 +/- 0.06 μ M binding affinity. Holding DNA at constant force while stretching and relaxing suggests that ActD binds to two single strands that are close to each other rather than to pure dsDNA or ssDNA. This suggests that biological activity of ActD that contributes towards the inhibition of cellular replication is due to its ability to bind at DNA bubbles during RNA transcription, thereby stalling the transcription process.

Green synthesis, characterization and anticancer potential of platinum nanoparticles Bioplatin.

PubMed

Bendale, Yogesh; Bendale, Vineeta; Paul, Saili; Bhattacharyya, Soumya Sundar

2012-06-01

In the present study, the anticancer potential of platinum nanoparticles Bioplatin is explored and the mode of interactions of Bioplatin with calf thymus DNA and honey was analyzed. Bioplatin was synthesized with the help of green nanotechnology and characterized by particle size, zeta potential and surface morphology. The interaction of Bioplatin with DNA and honey was also checked with the help of circular dichroism spectroscopy and Fourier-transform infrared spectroscopy, respectively. The anticancer potential of Bioplatin was evaluated on peripheral blood mononuclear cells and A375 cells in vitro by analyzing results of MTT (3-(4,5)-dimethyl-thiahiazo-(-z-y1)-3,5-di-phenytetrazoliumromide), fluorescence microscopic studies and DNA fragmentation assay. Bioplatin exhibited a small particle size of 137.5 nm and a surface charge of -35.8 mV. Bioplatin interacted with DNA and brought in effective changes in structure and conformation of DNA, and formed a new complex that increased its stability of DNA intercalated with the base pair of DNA. In vitro studies demonstrated that Bioplatin arrested cell proliferation, and induced chromatin condensation and internucleosomal DNA fragmentation. Bioplatin induces apoptosis in cancer cells and may have some beneficial effect against human carcinoma. It interacts with DNA, brings stabilization to DNA, and thus prevents the replication of DNA.

Detection of DNA via the fluorescence quenching of Mn-doped ZnSe D-dots/doxorubicin/DNA ternary complexes system.

PubMed

Gao, Xue; Niu, Lu; Su, Xingguang

2012-01-01

This manuscript reports a method for the detection of double-stranded DNA, based on Mn:ZnSe d-dots and intercalating agent doxorubicin (DOX). DOX can quench the photoluminescence (PL) of Mn:ZnSe d-dots through photoinduced electron transfer process, after binding with Mn:ZnSe d-dots. The addition of DNA can result in the formation of the Mn:ZnSe d-dots-DOX-DNA ternary complexes, the fluorescence of the Mn:ZnSe d-dots-DOX complexes would be further quenched by the addition of DNA, thus allowing the detection of DNA. The formation mechanism of the Mn:ZnSe d-dots-DOX-DNA ternary complexes was studied in detail in this paper. Under optimal conditions, the quenched fluorescence intensity of Mn:ZnSe d-dots-DOX system are perfectly described by Stern-Volmer equation with the concentration of hsDNA ranging from 0.006 μg mL(-1) to 6.4 μg mL(-1). The detection limit (S/N = 3) for hsDNA is 0.5 ng mL(-1). The proposed method was successfully applied to the detection of DNA in synthetic samples and the results were satisfactory.

Construction and DNA condensation of cyclodextrin-coated gold nanoparticles with anthryl grafts.

PubMed

Zhao, Di; Chen, Yong; Liu, Yu

2014-07-01

The condensation of DNA in a controlled manner is one of the key steps in gene delivery and gene therapy. For this purpose, a water-soluble supramolecular nanostructure is constructed by coating 14 β-cyclodextrins onto the surface of a gold nanoparticle, followed by the noncovalent association of different amounts of anthryl-modified adamantanes with coated β-cyclodextrins. The strong binding of β-cyclodextrins with anthryl adamantanes (K(S) =8.61×10(4)  M(-1)) efficiently stabilizes the supramolecular nanostructure. Spectrophotometric fluorescence spectra and microscopic studies demonstrated that, with many anthryl grafts that can intercalate in the outer space of the DNA double helix, this supramolecular nanostructure showed good condensation abilities to calf thymus DNA. Significantly, the condensation efficiency of supramolecular nanostructure towards DNA could be conveniently controlled by adjusting the ratio between gold nanoparticles and anthryl adamantane grafts, leading to the formation of DNA condensates of a size that are suitable for the endocytosis of hepatoma cells, which will make it potentially applicable in many fields of medicinal science and biotechnology. © 2014 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Exploration of cellular DNA lesion, DNA-binding and biocidal ordeal of novel curcumin based Knoevenagel Schiff base complexes incorporating tryptophan: Synthesis and structural validation

NASA Astrophysics Data System (ADS)

Chandrasekar, Thiravidamani; Raman, Natarajan

2016-07-01

A few novel Schiff base transition metal complexes of general formula [MLCl] (where, L = Schiff base, obtained by the condensation reaction of Knoevenagel condensate of curcumin, L-tryptophan and M = Cu(II), Ni(II), Co(II), and Zn(II)), were prepared by stencil synthesis. They were typified using UV-vis, IR, EPR spectral techniques, micro analytical techniques, magnetic susceptibility and molar conductivity. Geometry of the metal complexes was examined and recognized as square planar. DNA binding and viscosity studies revealed that the metal(II) complexes powerfully bound via an intercalation mechanism with the calf thymus DNA. Gel-electrophoresis technique was used to investigate the DNA cleavage competence of the complexes and they establish to approve the cleavage of pBR322 DNA in presence of oxidant H2O2. This outcome inferred that the synthesized complexes showed better nuclease activity. Moreover, the complexes were monitored for antimicrobial activities. The results exposed that the synthesized compounds were forceful against all the microbes under exploration.

The DNA binding site specificity and antiproliferative property of ternary Pt(II) and Zn(II) complexes of phenanthroline and N,N'-ethylenediaminediacetic acid.

PubMed

Nakamura, Yusuke; Taruno, Yoko; Sugimoto, Masashi; Kitamura, Yusuke; Seng, Hoi Ling; Kong, Siew Ming; Ng, Chew Hee; Chikira, Makoto

2013-03-14

The binding site specificity of the ternary complexes, [M(II)(phen)(edda)] (M(II) = Pt(2+) and Zn(2+); phen = 1,10-phenanthroline; edda = N,N'-ethylenediaminediacetic acid), for the self-complementary oligonucleotides (ODNs), ds(C(1)G(2)C(3)G(4)A(5)A(6)T(7)T(8)C(9)G(10)C(11)G(12))(2) (ODN1) and ds(C(1)G(2)C(3)G(4)T(5)A(6)T(7)A(8)C(9)G(10)C(11)G(12))(2) (ODN2), was studied by NMR measurements. The results indicated that [Pt(ii)(phen)(edda)] was partially intercalated between C(3)/G(10) and G(4)/C(9) base pairs of ODN1 and ODN2 in the major grooves, whereas [Zn(II)(phen)(edda)] was bound specifically to the TATA region of ODN2 in the minor groove and to the terminal G(2)/C(11) base pair of ODN1 in the major groove. The preference for the TATA sequence over the AATT sequence in the binding of [Zn(phen)(edda)] was attributed to the wider minor groove width of the TATA sequence. The bindings of the complexes to ct-DNA were also studied by UV, CD, and fluorescence spectroscopy. Additionally, the antiproliferative property of [Pt(II)(phen)(edda)] towards MCF7 breast cancer cells and normal MCF10-A cells was compared with that of [Zn(II)(phen)(edda)].

Two high-mobility group box domains act together to underwind and kink DNA

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sánchez-Giraldo, R.; Acosta-Reyes, F. J.; Malarkey, C. S.

The crystal structure of HMGB1 box A bound to an unmodified AT-rich DNA fragment is reported at a resolution of 2 Å. A new mode of DNA recognition for HMG box proteins is found in which two box A domains bind in an unusual configuration generating a highly kinked DNA structure. High-mobility group protein 1 (HMGB1) is an essential and ubiquitous DNA architectural factor that influences a myriad of cellular processes. HMGB1 contains two DNA-binding domains, box A and box B, which have little sequence specificity but have remarkable abilities to underwind and bend DNA. Although HMGB1 box A ismore » thought to be responsible for the majority of HMGB1–DNA interactions with pre-bent or kinked DNA, little is known about how it recognizes unmodified DNA. Here, the crystal structure of HMGB1 box A bound to an AT-rich DNA fragment is reported at a resolution of 2 Å. Two box A domains of HMGB1 collaborate in an unusual configuration in which the Phe37 residues of both domains stack together and intercalate the same CG base pair, generating highly kinked DNA. This represents a novel mode of DNA recognition for HMGB proteins and reveals a mechanism by which structure-specific HMG boxes kink linear DNA.« less

Intercalation compounds and electrodes for batteries

DOEpatents

Chiang, Yet-Ming; Sadoway, Donald R.; Jang, Young-Il; Huang, Biyan

2004-09-07

This invention concerns intercalation compounds and in particular lithium intercalation compounds which have improved properties for use in batteries. Compositions of the invention include particulate metal oxide material having particles of multicomponent metal oxide, each including an oxide core of at least first and second metals in a first ratio, and each including a surface coating of metal oxide or hydroxide that does not include the first and second metals in the first ratio formed by segregation of at least one of the first and second metals from the core. The core may preferably comprise Li.sub.x M.sub.y N.sub.z O.sub.2 wherein M and N are metal atom or main group elements, x, y and z are numbers from about 0 to about 1 and y and z are such that a formal charge on M.sub.y N.sub.z portion of the compound is (4-x), and having a charging voltage of at least about 2.5V. The invention may also be characterized as a multicomponent oxide microstructure usable as a lithium intercalation material including a multiphase oxide core and a surface layer of one material, which is a component of the multiphase oxide core, that protects the underlying intercalation material from chemical dissolution or reaction. In a particular preferred example the multicomponent oxide may be an aluminum-doped lithium manganese oxide composition. Such aluminum-doped lithium manganese oxide compositions, having an orthorhombic structure, also form a part of the invention. In addition, the invention includes articles, particularly electrodes, for batteries formed from the compositions of the invention, and batteries including such electrodes. The invention further relates to a composite intercalation material comprising at least two compounds in which at least one compound has an orthorhombic structure Li.sub.x Al.sub.y Mn.sub.1-y O.sub.2, where y is nonzero, or a mixture of orthorhombic and monoclinic Li.sub.x Al.sub.y Mn.sub.1-y O.sub.2.

Electromagnetic and optical characteristics of Nb5+-doped double-crossover and salmon DNA thin films

NASA Astrophysics Data System (ADS)

Babu Mitta, Sekhar; Reddy Dugasani, Sreekantha; Jung, Soon-Gil; Vellampatti, Srivithya; Park, Tuson; Park, Sung Ha

2017-10-01

We report the fabrication and physical characteristics of niobium ion (Nb5+)-doped double-crossover DNA (DX-DNA) and salmon DNA (SDNA) thin films. Different concentrations of Nb5+ ([Nb5+]) are coordinated into the DNA molecules, and the thin films are fabricated via substrate-assisted growth (DX-DNA) and drop-casting (SDNA) on oxygen plasma treated substrates. We conducted atomic force microscopy to estimate the optimum concentration of Nb5+ ([Nb5+]O = 0.08 mM) in Nb5+-doped DX-DNA thin films, up to which the DX-DNA lattices maintain their structures without deformation. X-ray photoelectron spectroscopy (XPS) was performed to probe the chemical nature of the intercalated Nb5+ in the SDNA thin films. The change in peak intensities and the shift in binding energy were witnessed in XPS spectra to explicate the binding and charge transfer mechanisms between Nb5+ and SDNA molecules. UV-visible, Raman, and photoluminescence (PL) spectra were measured to determine the optical properties and thus investigate the binding modes, Nb5+ coordination sites in Nb5+-doped SDNA thin films, and energy transfer mechanisms, respectively. As [Nb5+] increases, the absorbance peak intensities monotonically increase until ˜[Nb5+]O and then decrease. However, from the Raman measurements, the peak intensities gradually decrease with an increase in [Nb5+] to reveal the binding mechanism and binding sites of metal ions in the SDNA molecules. From the PL, we observe the emission intensities to reduce them at up to ˜[Nb5+]O and then increase after that, expecting the energy transfer between the Nb5+ and SDNA molecules. The current-voltage measurement shows a significant increase in the current observed as [Nb5+] increases in the SDNA thin films when compared to that of pristine SDNA thin films. Finally, we investigate the temperature dependent magnetization in which the Nb5+-doped SDNA thin films reveal weak ferromagnetism due to the existence of tiny magnetic dipoles in the Nb5+-doped SDNA complex.

Variation, differential reproduction and oscillation: the evolution of nucleic acid hybridization.

PubMed

Suárez-Díaz, Edna

2013-01-01

This paper builds upon Hans-Jörg Rheinberger ideas on the oscillation and intercalation of epistemic things and technical objects in experimental systems, to give a fine-grained analysis of what here is called the problems of "adaptation" between our material and cognitive tools and the phenomena of the material world. To do so, it relies on the case-study of the evolution of nucleic acid hybridization and the stabilization of satellite DNA.

Graphite fiber intercalation: Dynamics of the bromine intercalation process

NASA Technical Reports Server (NTRS)

Jaworske, D. A.; Zinolabedini, R.

1985-01-01

The resistance of pitch-based graphite fibers was monitored, in situ, during a series of bromine intercalation experiments. The threshold pressure for the bromine intercalation of pitch-based fibers was estimated to be 102 torr. When the bromine atmosphere was removed from the reaction chamber, the resistivity of the intercalated graphite fibers increased consistently. This increase was attributed to loss of bromine from the perimeter of the fiber. The loss was confirmed by mapping the bromine concentration across the diameter of single intercalated fibers with either energy dispersive spectroscopy or scanning Auger microscopy. A statistical study comparing fibers intercalated in bromine vapor with fibers intercalated in bromine liquid showed that similar products were obtained with both methods of intercalation.

Molecular Technique to Reduce PCR Bias for Deeper Understanding of Microbial Diversity

NASA Technical Reports Server (NTRS)

Vaishampayan, Parag A.; Venkateswaran, Kasthuri J.

2012-01-01

Current planetary protection policies require that spacecraft targeted to sensitive solar system bodies be assembled and readied for launch in controlled cleanroom environments. A better understanding of the distribution and frequency at which high-risk contaminant microbes are encountered on spacecraft surfaces would significantly aid in assessing the threat of forward contamination. However, despite a growing understanding of the diverse microbial populations present in cleanrooms, less abundant microbial populations are probably not adequately taken into account due to technological limitations. This novel approach encompasses a wide spectrum of microbial species and will represent the true picture of spacecraft cleanroom-associated microbial diversity. All of the current microbial diversity assessment techniques are based on an initial PCR amplification step. However, a number of factors are known to bias PCR amplification and jeopardize the true representation of bacterial diversity. PCR amplification of a minor template appears to be suppressed by the amplification of a more abundant template. It is widely acknowledged among environmental molecular microbiologists that genetic biosignatures identified from an environment only represent the most dominant populations. The technological bottleneck overlooks the presence of the less abundant minority population and may underestimate their role in the ecosystem maintenance. DNA intercalating agents such as propidium monoazide (PMA) covalently bind with DNA molecules upon photolysis using visible light, and make it unavailable for DNA polymerase enzyme during polymerase chain reaction (PCR). Environmental DNA samples will be treated with suboptimum PMA concentration, enough to intercalate with 90 99% of the total DNA. The probability of PMA binding with DNA from abundant bacterial species will be much higher than binding with DNA from less abundant species. This will increase the relative DNA concentration of previously "shadowed" less abundant species available for PCR amplification. These PCR products obtained with and without PMA treatment will then be subjected to downstream diversity analyses such as sequencing and DNA microarray. It is expected that PMA-coupled PCR will amplify the "minority population" and help in understanding microbial diversity spectrum of an environmental sample at a much deeper level. This new protocol aims to overcome the major potential biases faced when analyzing microbial 16S rRNA gene diversity. This study will lead to a technological advancement and a commercial product that will aid microbial ecologists in understanding microbial diversity from various environmental niches. Implementation of this technique may lead to discoveries of novel microbes and their functions in sustenance of the ecosystem.

The dynamics of copper intercalated molybdenum ditelluride

NASA Astrophysics Data System (ADS)

Onofrio, Nicolas; Guzman, David; Strachan, Alejandro

2016-11-01

Layered transition metal dichalcogenides are emerging as key materials in nanoelectronics and energy applications. Predictive models to understand their growth, thermomechanical properties, and interaction with metals are needed in order to accelerate their incorporation into commercial products. Interatomic potentials enable large-scale atomistic simulations connecting first principle methods and devices. We present a ReaxFF reactive force field to describe molybdenum ditelluride and its interactions with copper. We optimized the force field parameters to describe the energetics, atomic charges, and mechanical properties of (i) layered MoTe2, Mo, and Cu in various phases, (ii) the intercalation of Cu atoms and small clusters within the van der Waals gap of MoTe2, and (iii) bond dissociation curves. The training set consists of an extensive set of first principles calculations computed using density functional theory (DFT). We validate the force field via the prediction of the adhesion of a single layer MoTe2 on a Cu(111) surface and find good agreement with DFT results not used in the training set. We characterized the mobility of the Cu ions intercalated into MoTe2 under the presence of an external electric field via finite temperature molecular dynamics simulations. The results show a significant increase in drift velocity for electric fields of approximately 0.4 V/Å and that mobility increases with Cu ion concentration.

End-specific strategies of attachment of long double stranded DNA onto gold-coated nanofiber arrays

NASA Astrophysics Data System (ADS)

Peckys, Diana B.; de Jonge, Niels; Simpson, Michael L.; McKnight, Timothy E.

2008-10-01

We report the effective and site-specific binding of long double stranded (ds)DNA to high aspect ratio carbon nanofiber arrays. The carbon nanofibers were first coated with a thin gold layer to provide anchorage for two controllable binding methods. One method was based on the direct binding of thiol end-labeled dsDNA. The second and enhanced method used amine end-labeled dsDNA bound with crosslinkers to a carboxyl-terminated self-assembled monolayer. The bound dsDNA was first visualized with a fluorescent, dsDNA-intercalating dye. The specific binding onto the carbon nanofiber was verified by a high resolution detection method using scanning electron microscopy in combination with the binding of neutravidin-coated fluorescent microspheres to the immobilized and biotinylated dsDNA. Functional activity of thiol end-labeled dsDNA on gold-coated nanofiber arrays was verified with a transcriptional assay, whereby Chinese hamster lung cells (V79) were impaled upon the DNA-modified nanofibers and scored for transgene expression of the tethered template. Thiol end-labeled dsDNA demonstrated significantly higher expression levels than nanofibers prepared with control dsDNA that lacked a gold-binding end-label. Employing these site-specific and robust techniques of immobilization of dsDNA onto nanodevices can be of advantage for the study of DNA/protein interactions and for gene delivery applications.

Nanoengineered Plasmonic Hybrid Systems for Bio-nanotechnology

NASA Astrophysics Data System (ADS)

Leong, Kirsty

Plasmonic hybrid systems are fabricated using a combination of lithography and layer-by-layer directed self-assembly approaches to serve as highly sensitive nanosensing devices. This layer-by-layer directed self-assembly approach is utilized as a hybrid methodology to control the organization of quantum dots (QDs), nanoparticles, and biomolecules onto inorganic nanostructures with site-specific attachment and functionality. Here, surface plasmon-enhanced nanoarrays are fabricated where the photoluminescence of quantum dots and conjugated polymer nanoarrays are studied. This study was performed by tuning the localized surface plasmon resonance and the distance between the emitter and the metal surface using genetically engineered polypeptides as binding agents and biotin-streptavidin binding as linker molecules. In addition, these nanoarrays were also chemically modified to support the immobilization and label-free detection of DNA using surface enhanced Raman scattering. The surface of the nanoarrays was chemically modified using an acridine containing molecule which can act as an intercalating agent for DNA. The self-assembled monolayer (SAM) showed the ability to immobilize and intercalate DNA onto the surface. This SAM system using surface enhanced Raman scattering (SERS) serves as a highly sensitive methodology for the immobilization and label-free detection of DNA applicable into a wide range of bio-diagnostic platforms. Other micropatterned arrays were also fabricated using a combination of soft lithography and surface engineering. Selective single cell patterning and adhesion was achieved through chemical modifications and surface engineering of poly(dimethylsiloxane) surface. The surface of each microwell was functionally engineered with a SAM which contained an aldehyde terminated fused-ring aromatic thiolated molecule. Cells were found to be attracted and adherent to the chemically modified microwells. By combining soft lithography and surface engineering, a simple methodology produced single cell arrays on biocompatible substrates. Thus the design of plasmonic devices relies heavily on the nature of the plasmonic interactions between nanoparticles in the devices which can potentially be fabricated into lab-on-a-chip devices for multiplex sensing capabilities.

Chemistry and Biology of Aflatoxin-DNA Adducts

DOE Office of Scientific and Technical Information (OSTI.GOV)

Stone, Michael P.; Banerjee, Surajit; Brown, Kyle L.

Aspergillus flavus is a fungal contaminant of stored rice, wheat, corn, and other grainstuffs, and peanuts. This is of concern to human health because it produces the mycotoxin aflatoxin B{sub 1} (AFB{sub 1}), which is genotoxic and is implicated in the etiology of liver cancer. AFB{sub 1} is oxidized in vivo by cytochrome P450 to form aflatoxin B{sub 1} epoxide, which forms an N7-dG adduct (AFB{sub 1}-N7-dG) in DNA. The latter rearranges to a formamidopyrimidine (AFB{sub 1}-FAPY) derivative that equilibrates between {alpha} and {beta} anomers of the deoxyribose. In DNA, both the AFB{sub 1}-N7-dG and AFB{sub 1}-{beta}-FAPY adducts intercalate abovemore » the 5'-face of the damaged guanine. Each produces G {yields} T transversions in Escherichia coli, but the AFB{sub 1}-{beta}-FAPY adduct is more mutagenic. The Sulfolobus solfataricus P2 DNA polymerase IV (Dpo4) provides a model for understanding error-prone bypass of the AFB{sub 1}-N7-dG and AFB{sub 1}-{beta}-FAPY adducts. It bypasses the AFB{sub 1}-N7-dG adduct, but it conducts error-prone replication past the AFB{sub 1}-FAPY adduct, including mis-insertion of dATP, consistent with the G {yields} T mutations characteristic of AFB{sub 1} mutagenesis in E. coli. Crystallographic analyses of a series of binary and ternary complexes with the Dpo4 polymerase revealed differing orientations of the N7-C8 bond of the AFB{sub 1}-N7-dG adduct as compared to the N{sup 5}-C8 bond in the AFB{sub 1}-{beta}-FAPY adduct, and differential accommodation of the intercalated AFB{sub 1} moieties within the active site. These may modulate AFB{sub 1} lesion bypass by this polymerase.« less

Direct measurement of torque and twist generated by a dye binding to DNA

NASA Astrophysics Data System (ADS)

Gore, Jeff; Bryant, Zev; Bustamante, Carlos

2004-03-01

Many biologically important chemicals and proteins change the twist of DNA upon binding. We have used magnetic tweezers to directly measure the torque and twist generated when ethidium bromide binds and unbinds to DNA. One end of the DNA is bound specifically to a glass coverslip and the opposite end is held away from the surface by a paramagnetic bead. Attached to the middle of the DNA is a second fluorescent bead whose position can be tracked with high angular and temporal resolution. On one side of the fluorescent bead binding site we have engineered a single strand nick that acts like a free swivel. Addition of ethidium bromide then powered rotation of the central fluorescent bead. After the ethidium bromide was bound we used magnesium to compete out the intercalated ethidium bromide, thus inducing a rotation in the opposite direction. We studied the torque generation, energetics, and kinetics associated with ethidium bromide binding and unbinding by tracking the rotation of the fluorescent bead. This system is a demonstration of a reversible chemically powered DNA-based rotary motor. We also expect that this technique will be useful in studying proteins that bind to or rotate DNA, including recA, polymerases, and topoisomerases.

Establishment of dsDNA/GNs/chit/GCE biosensor and electrochemical study on interaction between 6-mercaptopurine and DNA.

PubMed

Tang, Wenwei; Zhang, Min; Zeng, Xinping

2014-01-01

In this paper, the anti-cancer drug 6-mercaptopurine (6-MP) was taken as the detection object. The biosensor of dsDNA/GNs/chit/GCE was established using the grapheme (GNs) and chitosan (chit) as the compound modified material. The electrochemical behavior of 6-MP on the sensor was discussed, and the damage and its mechanism of 6-MP on DNA were studied. The experimental result showed that, after the modification of GNs-chit, the electrode activation area of GNs/chit/GCE increased remarkably, which was improved from 1.76cm2 to 8.64 cm2, and the responsive oxidation peak current of GNs/chit/GCE to K3[Fe(CN)6] also increased remarkably. At the meantime, it was demonstrated that DNA was effectively fixed on the GNs/chit/GCE electrode;6-MP caused obvious damage to dsDNA, and the damage degree on the adenine was bigger than that on the guanine; the interaction between 6-MP and dsDNA was preliminarily deduced as the intercalation, and its electrochemical oxidation process was an irreversible process controlled by the adsorption.

INTERACTION OF BENZO(A)PYRENE DIOL EPOXIDE WITH SVAO MINICHROMOSOMES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gamper, Howard B.; Yokota, Hisao A.; Bartholomew, James C.

SV40 minichromosomes were reacted with (+)7{beta},8{alpha}-dihydroxy-9{alpha},10{alpha}-epoxy- 7,8,9,10-tetrahydrobenzo[a]pyrene (BaP diol epoxide). Low levels of modification (< 5 DNA adducts/minichromosome) did not detectably alter the structure of the minichromosomes but high levels (> 200 DNA adducts/minichromosome) led to extensive fragmentation. Relative to naked SV40 DNA BaP diol epoxide induced alkylation and strand scission of minichromosomal DNA was reduced or enhanced by factors of 1.5 and 2.0, respectively. The reduction in covalent binding was attributed to the presence of histones, which competed with DNA for the hydrocarbon and reduced the probability of BaP diol epoxide intercalation by tightening the helix. The enhancement ofmore » strand scission was probably due to the catalytic effect of histones on the rate of S-elimination at apurinic sites, although an altered adduct profile or the presence of a repair endonuclease were not excluded. Staphylococcal nuclease digestion indicated that BaP dial epoxide randomly alkylated the minichromosomal DNA. This is in contrast to studies with cellular chromatin where internucleosomal DNA was preferentially modified. Differences in the minichromosomal protein complement were responsible for this altered susceptibility.« less

Effect of ionic strength and cationic DNA affinity binders on the DNA sequence selective alkylation of guanine N7-positions by nitrogen mustards

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hartley, J.A.; Forrow, S.M.; Souhami, R.L.

Large variations in alkylation intensities exist among guanines in a DNA sequence following treatment with chemotherapeutic alkylating agents such as nitrogen mustards, and the substituent attached to the reactive group can impose a distinct sequence preference for reaction. In order to understand further the structural and electrostatic factors which determine the sequence selectivity of alkylation reactions, the effect of increase ionic strength, the intercalator ethidium bromide, AT-specific minor groove binders distamycin A and netropsin, and the polyamine spermine on guanine N7-alkylation by L-phenylalanine mustard (L-Pam), uracil mustard (UM), and quinacrine mustard (QM) was investigated with a modification of the guanine-specificmore » chemical cleavage technique for DNA sequencing. The result differed with both the nitrogen mustard and the cationic agent used. The effect, which resulted in both enhancement and suppression of alkylation sites, was most striking in the case of netropsin and distamycin A, which differed from each other. DNA footprinting indicated that selective binding to AT sequences in the minor groove of DNA can have long-range effects on the alkylation pattern of DNA in the major groove.« less

Investigating the impacts of DNA binding mode and sequence on thermodynamic quantities and water exchange values for two small molecule drugs.

PubMed

Kenney, Rachael M; Buxton, Katherine E; Glazier, Samantha

2016-09-01

Doxorubicin and nogalamycin are antitumor antibiotics that interact with DNA via intercalation and threading mechanisms, respectively. Because the importance of water, particularly its impact on entropy changes, has been established in other biological processes, we investigated the role of water in these two drug-DNA binding events. We used the osmotic stress method to calculate the number of water molecules exchanged (Δnwater), and isothermal titration calorimetry to measure Kbinding, ΔH, and ΔS for two synthetic DNAs, poly(dA·dT) and poly(dG·dC), and calf thymus DNA (CT DNA). For nogalamycin, Δnwater<0 for CT DNA and poly(dG·dC). For doxorubicin, Δnwater>0 for CT DNA and Δnwater<0 for poly(dG·dC). For poly(dA·dT), Δnwater~0 with both drugs. Net enthalpy changes were always negative, but net entropy changes depended on the drug. The effect of water exchange on the overall sign of entropy change appears to be smaller than other contributions. Copyright © 2016 Elsevier B.V. All rights reserved.

Integrated nanoparticle-biomolecule systems for biosensing and bioelectronics.

PubMed

Willner, Itamar; Baron, Ronan; Willner, Bilha

2007-04-15

The similar dimensions of biomolecules such as enzymes, antibodies or DNA, and metallic or semiconductor nanoparticles (NPs) enable the synthesis of biomolecule-NP hybrid systems where the unique electronic, photonic and catalytic properties of NPs are combined with the specific recognition and biocatalytic properties of biomolecules. The unique functions of biomolecule-NP hybrid systems are discussed with several examples: (i) the electrical contacting of redox enzymes with electrodes is the basis for the development of enzymatic electrodes for amperometric biosensors or biofuel cell elements. The reconstitution of the apo-glucose oxidase or apo-glucose dehydrogenase on flavin adenine dinucleotide (FAD)-functionalized Au NPs (1.4 nm) associated with electrodes, or on pyrroloquinoline quinone (PQQ)-functionalized Au NPs (1.4 nm) associated with electrodes, respectively, yields electrically contacted enzyme electrodes. The aligned, reconstituted enzymes on the electrode surfaces reveal effective electrical contacting, and the glucose oxidase and glucose dehydrogenase reveal turnover rates of 5000 and 11,800 s(-1), respectively. (ii) The photoexcitation of semiconductor nanoparticles yields fluorescence with a wavelength controlled by the size of the NPs. The fluorescence functions of semiconductor NPs are used to develop a fluorescence resonance energy transfer (FRET) assay for nucleic acids, and specifically, for analyzing telomerase activity in cancer cells. CdSe-ZnS NPs are functionalized by a primer recognized by telomerase, and this is elongated by telomerase extracted from HeLa cancer cells in the presence of dNTPs and Texas-red-functionalized dUTP. The dye integrated into the telomers allows the FRET process that is intensified as telomerization proceeds. Also, the photoexcited electron-hole pair generated in semiconductor NPs is used to generate photocurrents in a CdS-DNA hybrid system associated with an electrode. A redox-active intercalator, methylene blue, was incorporated into a CdS-duplex DNA monolayer associated with a Au electrode, and this facilitated the electron transfer between the electrode and the CdS NPs. The direction of the photocurrent was controlled by the oxidation state of the intercalator. (iii) Biocatalysts grow metallic NPs, and the absorbance of the NPs provides a means to assay the biocatalytic transformations. This is exemplified with the glucose oxidase-induced growth of Au NPs and with the tyrosinase-stimulated growth of Au NPs, in the presence of glucose or tyrosine, respectively. The biocatalytic growth of the metallic NPs is used to grow nanowires on surfaces. Glucose oxidase or alkaline phosphatase functionalized with Au NPs (1.4 nm) acted as 'biocatalytic inks' for the synthesis of metallic nanowires. The deposition of the Au NP-modified glucose oxidase, or the Au NP-modified alkaline phosphatase on Si surfaces by dip-pen nanolithography led to biocatalytic templates, that after interaction with glucose/AuCl4- or p-aminophenolphosphate/Ag+, allowed the synthesis of Au nanowires or Ag nanowires, respectively.

c-MYC G-quadruplex binding by the RNA polymerase I inhibitor BMH-21 and analogues revealed by a combined NMR and biochemical Approach.

PubMed

Musso, Loana; Mazzini, Stefania; Rossini, Anna; Castagnoli, Lorenzo; Scaglioni, Leonardo; Artali, Roberto; Di Nicola, Massimo; Zunino, Franco; Dallavalle, Sabrina

2018-03-01

Pyridoquinazolinecarboxamides have been reported as RNA polymerase I inhibitors and represent a novel class of potential antitumor agents. BMH-21, was reported to intercalate with GC-rich rDNA, resulting in nucleolar stress as a primary mechanism of cytotoxicity. The interaction of BMH-21 and analogues with DNA G-quadruplex structures was studied by NMR and molecular modelling. The cellular response was investigated in a panel of human tumor cell lines and protein expression was examined by Western Blot analysis. We explored the ability of BMH-21 and its analogue 2 to bind to G-quadruplex present in the c-MYC promoter, by NMR and molecular modelling studies. We provide evidence that both compounds are not typical DNA intercalators but are effective binders of the tested G-quadruplex. The interaction with c-MYC G-quadruplex was reflected in down-regulation of c-Myc expression in human tumor cells. The inhibitory effect was almost complete in lymphoma cells SUDHL4 characterized by overexpression of c-Myc protein. This downregulation reflected an early and persistent modulation of cMyc mRNA. Given the relevance of c-MYC in regulation of ribosome biogenesis, it is conceivable that the inhibition of c-MYC contributes to the perturbation of nuclear functions and RNA polymerase I activity. Similar experiments with CX-5461, another RNA polymerase I transcription inhibitor, indicate the same behaviour in G-quadruplex stabilization. Our results support the hypothesis that BMH-21 and analogue compounds share the same mechanism, i.e. G-quadruplex binding as a primary event of a cascade leading to inhibition of RNA polymerase I and apoptosis. Copyright © 2017 Elsevier B.V. All rights reserved.

Single-Color Digital PCR Provides High-Performance Detection of Cancer Mutations from Circulating DNA.

PubMed

Wood-Bouwens, Christina; Lau, Billy T; Handy, Christine M; Lee, HoJoon; Ji, Hanlee P

2017-09-01

We describe a single-color digital PCR assay that detects and quantifies cancer mutations directly from circulating DNA collected from the plasma of cancer patients. This approach relies on a double-stranded DNA intercalator dye and paired allele-specific DNA primer sets to determine an absolute count of both the mutation and wild-type-bearing DNA molecules present in the sample. The cell-free DNA assay uses an input of 1 ng of nonamplified DNA, approximately 300 genome equivalents, and has a molecular limit of detection of three mutation DNA genome-equivalent molecules per assay reaction. When using more genome equivalents as input, we demonstrated a sensitivity of 0.10% for detecting the BRAF V600E and KRAS G12D mutations. We developed several mutation assays specific to the cancer driver mutations of patients' tumors and detected these same mutations directly from the nonamplified, circulating cell-free DNA. This rapid and high-performance digital PCR assay can be configured to detect specific cancer mutations unique to an individual cancer, making it a potentially valuable method for patient-specific longitudinal monitoring. Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology. Published by Elsevier Inc. All rights reserved.

Design, synthesis and biological evaluation of 5-fluorouracil-derived benzimidazoles as novel type of potential antimicrobial agents.

PubMed

Fang, Xue-Jie; Jeyakkumar, Ponmani; Avula, Srinivasa Rao; Zhou, Qian; Zhou, Cheng-He

2016-06-01

A series of 5-fluorouracil benzimidazoles as novel type of potential antimicrobial agents were designed and synthesized for the first time. Bioactive assay manifested that some of the prepared compounds exhibited good or even stronger antibacterial and antifungal activities against the tested strains in comparison with reference drugs norfloxacin, chloromycin and fluconazole. Noticeably, 3-fluorobenzyl benzimidazole derivative 5c gave remarkable antimicrobial activities against Saccharomyces cerevisiae, MRSA and Bacillus proteus with MIC values of 1, 2 and 4μg/mL, respectively. Experimental research revealed that compound 5c could effectively intercalate into calf thymus DNA to form compound 5c-DNA complex which might block DNA replication and thus exert antimicrobial activities. Molecular docking indicated that compound 5c should bind with DNA topoisomerase IA through three hydrogen bonds by the use of fluorine atom and oxygen atoms in 5-fluorouracil with the residue Lys 423. Copyright © 2016 Elsevier Ltd. All rights reserved.

DNA-Targeted 2-Nitroimidazoles: Studies of the Influence of the Phenanthridine-Linked Nitroimidazoles, 2-NLP-3 and 2-NLP-4, on DNA Damage Induced by Ionizing Radiation

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buchko, Garry W.; Weinfeld, Michael

The nitroimidazole-linked phenanthridines 2-NLP-3 (5-[3-(2-nitro-1-imidazoyl)-propyl]-phenanthridinium bromide) and 2-NLP-4 (5-[3-(2-nitro-1-imidazoyl)-butyl1]-phenanthridinium bromide) are composed of the radiosensitizer, 2-nitroimidazole, attached to the DNA intercalator phenanthridine via a 3- and 4-carbon linker, respectively. Previous in vitro assays show both compounds to be 10 - 100 times more efficient as hypoxic cell radiosensitizer, misonidazole[Cowan et al., Radiat. Res. 127, 81-89, 1991]. Here we have used a 32P postlabeling assay and 5'-end labeled oligonucleotide assay to compare the radiogenic DNA damage generated in the presence of 2-NLP-3, 2-NLP-4 compared to irradiation in the presence of misonidazole. This may account, at least in part, for the greatermore » cellular radiosensitization shown by the nitroimidazole-linked phenanthridines over misonidazole.« less

IDLN-MSP: Idiolocal normalization of real-time methylation-specific PCR for genetic imbalanced DNA specimens.

PubMed

Santourlidis, Simeon; Ghanjati, Foued; Beermann, Agnes; Hermanns, Thomas; Poyet, Cédric

2016-02-01

Sensitive, accurate, and reliable measurements of tumor cell-specific DNA methylation changes are of fundamental importance in cancer diagnosis, prognosis, and monitoring. Real-time methylation-specific PCR (MSP) using intercalating dyes is an established method of choice for this purpose. Here we present a simple but crucial adaptation of this widely applied method that overcomes a major obstacle: genetic abnormalities in the DNA samples, such as aneuploidy or copy number variations, that could result in inaccurate results due to improper normalization if the copy numbers of the target and reference sequences are not the same. In our idiolocal normalization (IDLN) method, the locus for the normalizing, methylation-independent reference amplification is chosen close to the locus of the methylation-dependent target amplification. This ensures that the copy numbers of both the target and reference sequences will be identical in most cases if they are close enough to each other, resulting in accurate normalization and reliable comparative measurements of DNA methylation in clinical samples when using real-time MSP.

Microwave-assisted synthesis and electrochemical evaluation of VO 2 (B) nanostructures

DOE PAGES

Ashton, Thomas E.; Borras, David Hevia; Iadecola, Antonella; ...

2015-12-01

Understanding how intercalation materials change during electrochemical operation is paramount to optimising their behaviour and function and in situ characterisation methods allow us to observe these changes without sample destruction. Here, we first report the improved intercalation properties of bronze phase vanadium dioxide VO2 (B) prepared by a microwave assisted route which exhibits a larger electrochemical capacity (232 mAh g -1) compared to VO 2 (B) prepared by a solvothermal route (197 mAh g -1). These electrochemical differences have also been followed using in situ X-ray absorption spectroscopy allowing us to follow oxidation state changes as they occur during batterymore » operation.« less

Bioinspired artificial photonic nanoarchitecture using the elytron of the beetle Trigonophorus rothschildi varians as a ‘blueprint’

PubMed Central

Biró, L. P.; Kertész, K.; Horváth, E.; Márk, G. I.; Molnár, G.; Vértesy, Z.; Tsai, J.-F.; Kun, A.; Bálint, Zs.; Vigneron, J. P.

2010-01-01

An unusual, intercalated photonic nanoarchitecture was discovered in the elytra of Taiwanese Trigonophorus rothschildi varians beetles. It consists of a multilayer structure intercalated with a random distribution of cylindrical holes normal to the plane of the multilayer. The nanoarchitectures were characterized structurally by scanning electron microscopy and optically by normal incidence, integrated and goniometric reflectance measurements. They exhibit an unsaturated specular and saturated non-specular component of the reflected light. Bioinspired, artificial nanoarchitectures of similar structure and with similar properties were realized by drilling holes of submicron size in a multilayer structure, showing that such photonic nanoarchitectures of biological origin may constitute valuable blueprints for artificial photonic materials. PMID:19933221

Density-functional studies of tungsten trioxide, tungsten bronzes, and related systems

NASA Astrophysics Data System (ADS)

Ingham, B.; Hendy, S. C.; Chong, S. V.; Tallon, J. L.

2005-08-01

Tungsten trioxide adopts a variety of structures which can be intercalated with charged species to alter the electronic properties, thus forming “tungsten bronzes.” Similar effects are observed upon removing oxygen from WO3 . We present a computational study of cubic and hexagonal alkali bronzes and examine the effects on cell size and band structure as the size of the intercalated ion is increased. With the exception of hydrogen (which is predicted to be unstable as an intercalate), the behavior of the bronzes are relatively consistent. NaWO3 is the most stable of the cubic systems, although in the hexagonal system the larger ions are more stable. The band structures are identical, with the intercalated atom donating its single electron to the tungsten 5d valence band. A study of fractional doping in the NaxWO3 system (0⩽x⩽1) showed a linear variation in cell parameter and a systematic shift in the Fermi level into the conduction band. In the oxygen-deficient WO3-x system the Fermi level undergoes a sudden jump into the conduction band at around x=0.2 . Lastly, three compounds of a layered WO4•α,ω -diaminoalkane hybrid series were studied and found to be insulating, with features in the band structure similar to those of the parent WO3 compound that relate well to experimental UV-visible spectroscopy results.

Layered gadolinium hydroxides for simultaneous drug delivery and imaging.

PubMed

Xu, Yadong; Goyanes, Alvaro; Wang, Yuwei; Weston, Andrew J; So, Po-Wah; Geraldes, Carlos F G C; Fogg, Andrew M; Basit, Abdul W; Williams, Gareth R

2018-02-27

The potential of the layered gadolinium hydroxide (LGdH) [Gd 2 (OH) 5 ]Cl·yH 2 O (LGdH-Cl) for simultaneous drug delivery and magnetic resonance imaging was explored in this work. Three non-steroidal anti-inflammatory drugs (diclofenac [dic], ibuprofen [ibu], and naproxen [nap]) were intercalated into LGdH-Cl for the first time, using three different routes (ion exchange intercalation, coprecipitation, and exfoliation-self-assembly). X-ray diffraction, elemental microanalysis and IR spectroscopy confirmed successful incorporation of the drug into the interlayer spaces of the LGdH in all cases. From a comparison of the guest anion sizes and interlayer spacings, the active ingredients are believed to adopt intertwined bilayer configurations between the LGdH layers. The materials prepared by coprecipitation in general have noticeably higher drug loadings than those produced by ion exchange or self-assembly, as a result of the incorporation of some neutral drug into the composites. The LGdH-drug intercalates are stable at neutral pH, but rapidly degrade in acidic conditions to free Gd 3+ into solution. While LGdH-nap releases its drug loading into solution very rapidly (within ca. 1.5 h) at pH 7.4, LGdH-dic shows sustained release over 4 h, and LGdH-ibu extends this to 24 h. The latter composites therefore can be incorporated into enteric-coated tablets to provide sustained release in the small intestine. The drug intercalates are highly biocompatible and retain the proton relaxivity properties of the parent LGdH-Cl, with the materials most promising for use as negative contrast agents in MRI. Overall, the LGdH-drug intercalation compounds appear to have great potential for use in theranostic applications.

Mechanisms of enhanced lithium intercalation into thin film V2O5 in ionic liquids investigated by X-ray photoelectron spectroscopy and time-of-flight secondary ion mass spectrometry

NASA Astrophysics Data System (ADS)

Santos, Luis; Światowska, Jolanta; Lair, Virginie; Zanna, Sandrine; Seyeux, Antoine; Melendez-Ceballos, Arturo; Tran-Van, Pierre; Cassir, Michel; Marcus, Philippe

2017-10-01

Room temperature ionic liquids (RTILs) attract much attention as a new type of environmentally benign electrolytes for Li-ion batteries due to their numerous interesting physicochemical properties. Here, in this paper, Li intercalation/deintercalation in presence of the N-butyl-N-methylpyrrolidinium bis(trifluoromethanesulfonyl) imide (PYR14TFSI) and N-methyl-N-propylpyrrolidinium bis(fluorosulfonyl)imide (PYR13FSI) containing 0.3 M LiTFSI, was evaluated in a thin 100 nm layer of V2O5 deposited on Al substrate by atomic layer deposition. Potentiodynamic tests performed in LiTFSI/Pyr14TFSI show a quasi-reversible Li intercalation during 10 cycles (between 2.4 and 5 V) with an average coulombic efficiency of 99%. The capacity, calculated from the 1st cycle, is found to be 182 mAh g-1, about 19% (±2%) higher than the theoretical capacity reported for V2O5 (147 mAh g-1). X-ray photoelectron spectroscopy analysis confirms that the intercalation of more than 1 mol of Li+ per V2O5 is achieved as also the possible presence of a solid permeable interface (SPI) layer on the V2O5 surface. Likewise, the Li+ in-depth distribution on the V2O5 layer after intercalation in RTILs measured by time-of-flight secondary ion mass spectrometry ion depth profiles, show small irreversible electrode modifications with the presence of lithium through the entire V2O5 layer with significant lithium trapping at the V2O5 layer/Al substrate interface.

Bis-anthracycline WP760 abrogates melanoma cell growth by transcription inhibition, p53 activation and IGF1R downregulation.

PubMed

Olbryt, Magdalena; Rusin, Aleksandra; Fokt, Izabela; Habryka, Anna; Tudrej, Patrycja; Student, Sebastian; Sochanik, Aleksander; Zieliński, Rafał; Priebe, Waldemar

2017-10-01

Anthracycline chemotherapeutics, e.g. doxorubicin and daunorubicin, are active against a broad spectrum of cancers. Their cytotoxicity is mainly attributed to DNA intercalation, interference with topoisomerase activity, and induction of double-stranded DNA breaks. Since modification of anthracyclines can profoundly affect their pharmacological properties we attempted to elucidate the mechanism of action, and identify possible molecular targets, of bis-anthracycline WP760 which previously demonstrated anti-melanoma activity at low nanomolar concentrations. We studied the effect of WP760 on several human melanoma cell lines derived from tumors in various development stages and having different genetic backgrounds. WP760 inhibited cell proliferation (IC 50  = 1-99 nM), impaired clonogenic cell survival (100 nM), and inhibited spheroid growth (≥300 nM). WP760 did not induce double-stranded DNA breaks but strongly inhibited global transcription. Moreover, WP760 caused nucleolar stress and led to activation of the p53 pathway. PCR array analysis showed that WP760 suppressed transcription of ten genes (ABCC1, MTOR, IGF1R, EGFR, GRB2, PRKCA, PRKCE, HDAC4, TXNRD1, AKT1) associated with, inter alia, cytoprotective mechanisms initiated in cancer cells during chemotherapy. Furthermore, WP760 downregulated IGF1R and upregulated PLK2 expression in most of the tested melanoma cell lines. These results suggest that WP760 exerts anti-melanoma activity by targeting global transcription and activation of the p53 pathway and could become suitable as an effective therapeutic agent.

Cytotoxicity, DNA binding and localisation of novel bis-naphthalimidopropyl polyamine derivatives.

PubMed

Pavlov, V; Kong Thoo Lin, P; Rodilla, V

2001-07-31

Bis-naphthalimidopropyl spermidine (BNIPSpd), spermine (BNIPSpm) and oxa-spermine (BNIPOSpm) showed high in vitro cytotoxicity against human breast cancer MCF-7 cells with IC(50) values of 1.38, 2.91 and 8.45 microM, respectively. These compounds were found to effectively displace the intercalating agent ethidium bromide bound to the calf thymus DNA using fluorimetric methods (C(50) 0.08-0.12 microM) and their apparent equilibrium binding constants (K(app)) were calculated to be in the range of 10.5-18 x 10(7) M(-1). Furthermore, strong stabilisation of calf thymus DNA duplex in the presence of bis-naphthalimidopropyl polyamine derivatives (BNIPSpd, BNIPSpm and BNIPOSpm) was observed by UV spectrophotometric analysis (T(m)=93.3-97 degrees C compared with 75 degrees C for calf thymus DNA without drug). Because of their inherent fluorescence, these compounds were localised preferentially inside the nucleus as evidenced by their direct observation under the fluorescence microscope. The results obtained suggest that the cytotoxic activity of the bis-naphthalimidopropyl polyamines may be in part, caused by their effects on DNA.

Human telomeric DNA: G-quadruplex, i-motif and Watson–Crick double helix

PubMed Central

Phan, Anh Tuân; Mergny, Jean-Louis

2002-01-01

Human telomeric DNA composed of (TTAGGG/CCCTAA)n repeats may form a classical Watson–Crick double helix. Each individual strand is also prone to quadruplex formation: the G-rich strand may adopt a G-quadruplex conformation involving G-quartets whereas the C-rich strand may fold into an i-motif based on intercalated C·C+ base pairs. Using an equimolar mixture of the telomeric oligonucleotides d[AGGG(TTAGGG)3] and d[(CCCTAA)3CCCT], we defined which structures existed and which would be the predominant species under a variety of experimental conditions. Under near-physiological conditions of pH, temperature and salt concentration, telomeric DNA was predominantly in a double-helix form. However, at lower pH values or higher temperatures, the G-quadruplex and/or the i-motif efficiently competed with the duplex. We also present kinetic and thermodynamic data for duplex association and for G-quadruplex/i-motif unfolding. PMID:12409451

Cationic pentaheteroaryls as selective G-quadruplex ligands by solvent-free microwave-assisted synthesis.

PubMed

Petenzi, Michele; Verga, Daniela; Largy, Eric; Hamon, Florian; Doria, Filippo; Teulade-Fichou, Marie-Paule; Guédin, Aurore; Mergny, Jean-Louis; Mella, Mariella; Freccero, Mauro

2012-11-05

We report herein a solvent-free and microwaved-assisted synthesis of several water soluble acyclic pentaheteroaryls containing 1,2,4-oxadiazole moieties (1-7). Their binding interactions with DNA quadruplex structures were thoroughly investigated by FRET melting, fluorescent intercalator displacement assay (G4-FID) and CD spectroscopy. Among the G-quadruplexes considered, attention was focused on telomeric repeats together with the proto-oncogenic c-kit sequences and the c-myc oncogene promoter. Compound 1, and to a lesser extent 2 and 5, preferentially stabilise an antiparallel structure of the telomeric DNA motif, and exhibit an opposite binding behaviour to structurally related polyoxazole (TOxaPy), and do not bind duplex DNA. The efficiency and selectivity of the binding process was remarkably controlled by the structure of the solubilising moieties. Copyright © 2012 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

DNA binding and biological studies of some novel water-soluble polymer-copper(II)-phenanthroline complexes.

PubMed

Kumar, Rajendran Senthil; Arunachalam, Sankaralingam; Periasamy, Vaiyapuri Subbarayan; Preethy, Christo Paul; Riyasdeen, Anvarbatcha; Akbarsha, Mohammad Abdulkader

2008-10-01

Some novel water-soluble polymer-copper(II)-phenanthroline complex samples, [Cu(phen)2(BPEI)]Cl(2).4H2O (phen=1,10-phenanthroline, BPEI=branched polyethyleneimine), with different degrees of copper complex content in the polymer chain have been prepared by ligand substitution method in water-ethanol medium and characterized by infrared, UV-visible, EPR spectral and elemental analysis methods. The binding of these complex samples with DNA has been investigated by electronic absorption spectroscopy, emission spectroscopy and gel retardation assay. Electrostatic interactions between DNA molecule and polymer-copper(II) complex molecule containing many high positive charges have been observed. Besides these ionic interactions, van der Waals interactions, hydrogen bonding and other partial intercalation binding modes may also exist in this system. The polymer-copper(II) complex with higher degree of copper complex content was screened for its antimicrobial activity and antitumor activity.

A natural anticancer agent thaspine targets human topoisomerase IB.

PubMed

Castelli, Silvia; Katkar, Prafulla; Vassallo, Oscar; Falconi, Mattia; Linder, Stig; Desideri, Alessandro

2013-02-01

The different steps of the topoisomerase I catalytic cycle have been analyzed in the presence of the plant alkaloid thaspine (1- (2-(Dimethylamino)ethyl)-3,8-dimethoxychromeno[5,4,3-cde]chromene-5,10-dione), known to induce apoptosis in colon carcinoma cells. The experiments indicate that thaspine inhibits both the cleavage and the religation steps of the enzyme reaction. The inhibition is reversible and the effect is enhanced upon pre-incubation. Molecular docking simulations of thaspine over topoisomerase I, in the presence or absence of the DNA substrate, show that thaspine, when interacting with the enzyme alone in the closed or in the open state, can bind in proximity of the active residues preventing the cleavage reaction, whilst when docked with the enzyme-DNA cleavable complex intercalates between the DNA bases in a way similar to that found for camptothecin, explaining its religation inhibition. These results unequivocally demonstrate that thaspine targets human topoisomerase I .

Interaction of Ionizing Radiation, Genetically Active Chemicals, and Radiofrequency Radiation in Human and Rodent Cells

DTIC Science & Technology

1990-12-01

proflavin , a drug known to intercalate with DNA. Again, when cells were exposed simultaneously to RFR SAR = 40.8- + 13.4 (SD) W/kg or 40 W/kg at power...densities of 87 or 65 mW/cm ), no effect of the RFR on the proflavin induced mutagenicity was observed (Meltz et al., 1990). SCE Induction Previously...Meltz ML, Eagan P, and Erwin DN (1990). Proflavin and Microwave Radiation: Absence of a Mutagenic Interaction. Bioelectromagnetics 11:149-157. Ciaravino

Further characterization of Bacillus subtilis antibiotic biosensors and their use for antibacterial mode-of-action studies.

PubMed

Mariner, Katherine R; Ooi, Nicola; Roebuck, Deborah; O'Neill, Alex J; Chopra, Ian

2011-04-01

We further examined the usefulness of previously reported Bacillus subtilis biosensors for antibacterial mode-of-action studies. The biosensors could not detect the tRNA synthetase inhibitors mupirocin, indolmycin, and borrelidin, some inhibitors of peptidoglycan synthesis, and most membrane-damaging agents. However, the biosensors confirmed the modes of action of several RNA polymerase inhibitors and DNA intercalators and provided new insights into the possible modes of action of ciprofloxacin, anhydrotetracycline, corralopyronin, 8-hydroxyquinoline, and juglone.

DNA octaplex formation with an I-motif of water-mediated A-quartets: reinterpretation of the crystal structure of d(GCGAAAGC).

PubMed

Sato, Yoshiteru; Mitomi, Kenta; Sunami, Tomoko; Kondo, Jiro; Takénaka, Akio

2006-12-01

The crystal structure of the tetragonal form of d(gcGAAAgc) has been revised and reasonably refined including the disordered residues. The two DNA strands form a base-intercalated duplex, and the four duplexes are assembled according to the crystallographic 222 symmetry to form an octaplex. In the central region, the eight strands are associated by I-motif of double A-quartets. Furthermore, eight hydrated-magnesium cations link the four duplexes to support the octaplex formation. Based on these structural features, a proposal that folding of d(GAAA)n, found in the non-coding region of genomes, into an octaplex can induce slippage during replication to facilitate length polymorphism is presented.

Bioelectrochemical sensing of promethazine with bamboo-type multiwalled carbon nanotubes dispersed in calf-thymus double stranded DNA.

PubMed

Primo, Emiliano N; Oviedo, M Belén; Sánchez, Cristián G; Rubianes, María D; Rivas, Gustavo A

2014-10-01

We report the quantification of promethazine (PMZ) using glassy carbon electrodes (GCE) modified with bamboo-like multi-walled carbon nanotubes (bCNT) dispersed in double stranded calf-thymus DNA (dsDNA) (GCE/bCNT-dsDNA). Cyclic voltammetry measurements demonstrated that PMZ presents a thin film-confined redox behavior at GCE/bCNT-dsDNA, opposite to the irreversibly-adsorbed behavior obtained at GCE modified with bCNT dispersed in ethanol (GCE/bCNT). Differential pulse voltammetry-adsorptive stripping with medium exchange experiments performed with GCE/bCNT-dsDNA and GCE modified with bCNTs dispersed in single-stranded calf-thymus DNA (ssDNA) confirmed that the interaction between PMZ and bCNT-dsDNA is mainly hydrophobic. These differences are due to the intercalation of PMZ within the dsDNA that supports the bCNTs, as evidenced from the bathochromic displacement of UV-Vis absorption spectra of PMZ and quantum dynamics calculations at DFTB level. The efficient accumulation of PMZ at GCE/bCNT-dsDNA made possible its sensitive quantification at nanomolar levels (sensitivity: (3.50±0.05)×10(8) μA·cm(-2)·M(-1) and detection limit: 23 nM). The biosensor was successfully used for the determination of PMZ in a pharmaceutical product with excellent correlation. Copyright © 2014 Elsevier B.V. All rights reserved.

Dynamics of graphite fiber intercalation: In situ resistivity measurements with a four point probe

NASA Technical Reports Server (NTRS)

Jaworske, D. A.

1984-01-01

The dynamics of ferric chloride intercalation of single graphite fibers were studied, in situ, using a four point dc bridge. Measurements before, during and after the intercalation showed that the intercalation occurred within minutes at 200 C. Changes in fiber resistivity after exposure to air suggested hydration of the graphite intercalation compound. Deintercalation of the ferric chloride was initiated at temperatures in excess of 400 C. cycling the intercalant into and out of the graphite fiber gave no improvements in fiber resistivity. The activation energy of the ferric chloride intercalation reaction was found to be 17 + or - 4 kcal/mol 1 consistent with the concept of a preliminary nucleation step in the intercalation reaction.

Exploiting hydrogen bonding interactions to probe smaller linear and cyclic diamines binding to G-quadruplexes: a DFT and molecular dynamics study.

PubMed

Kanti Si, Mrinal; Sen, Anik; Ganguly, Bishwajit

2017-05-10

G-quadruplexes are formed by the association of four guanine bases through Hoogsteen hydrogen bonding in guanine-rich sequences of DNA and exist in the telomere as well as in promoter regions of certain oncogenes. The sequences of G-quadruplex-DNA are targets for the design of molecules that can bind and can be developed as anti-cancer drugs. The linear and cyclic protonated diamines have been explored to bind to G-quadruplex-DNA through hydrogen bonding interactions. The quadruplex-DNA binders exploit π-stacking and hydrogen bonding interactions with the phosphate backbone of loops and grooves. In this study, linear and cyclic protonated diamines showed remarkable binding affinity for G-tetrads using hydrogen bonding interactions. The DFT M06-2X/6-31G(d)//B3LYP/6-31+G(d) level of theory showed that the cyclic ee-1,2-CHDA (equatorial-equatorial form of 1,2-disubstituted cyclohexadiamine di-cation) binds to the G-tetrads very strongly (∼70.0 kcal mol -1 ), with a much higher binding energy than the linear protonated diamines. The binding affinity of ligands for G-tetrads with counterions has also been examined. The binding preference of these small ligands for G-tetrads is higher than for DNA-duplex. The binding affinity of an intercalated acridine-based ligand (BRACO-19) for G-quadruplexes has been examined and the binding energy is relatively lower than that for the 1,2 disubstituted cyclohexadiamine di-cation with G-tetrads. The atoms-in-molecules (AIM) analysis reveals that the hydrogen bonding interactions between the organic systems with G-tetrads are primarily electrostatic in nature. The molecular dynamics simulations performed using a classical force field (GROMACS) also supported the phosphate backbone sites of G-quadruplex-DNA to bind to these diamines. To mimic the structural pattern of BRACO-19, the designed inhibitor N,2-bis-2(3,4-aminocyclohexyl) acetamide (9) examined possesses two 1,2-CHDA moieties linked through an acetamide group. The molecular dynamics results showed that the designed molecule 9 can efficiently bind to the base-pairs and the phosphate backbone of G quadruplex-DNA using H-bonding interactions. The binding affinity calculated for the intercalated acridine-based drug (BRACO-19) with G-quadruplexes is weaker compared to ee-1,2-CHDA. These ligands deliver a different binding motif (hydrogen bonding) compared to the reported G-quadruplex binders of π-delocalized systems and will kindle interest in examining such scaffolds to stabilize DNA.

Hydrogen bonded charge transfer molecular salt (4-chloro anilinium-3-nitrophthalate) for photophysical and pharmacological applications

NASA Astrophysics Data System (ADS)

Singaravelan, K.; Chandramohan, A.; Saravanabhavan, M.; Muthu Vijayan Enoch, I. V.; Suganthi, V. S.

2017-09-01

Radical scavenging activity against DPPH radical and binding properties of a hydrogen bonded charge transfer molecular salt 4-chloro anilinium-3-nitrophthalate(CANP) with calf thymus DNA has been studied by electronic absorption and emission spectroscopy. The molecular structure and crystallinity of the CANP salt have been established by carried out powder and single crystal X-ray diffraction analysis which indicated that cation and anion are linked through strong N+sbnd H…O- type of hydrogen bond. FTIR spectroscopic study was carried out to know the various functional groups present in the crystal. 1H and 13C NMR spectra were recorded to further confirm the molecular structure of the salt crystal. The thermal stability of the title salt was established by TG/DTA analyses simultaneously on the powdered sample of the title crystal. Further, the CANP salt was examined against various bacteria and fungi strains which showed a remarkable antimicrobial activity compared to that of the standards Ciproflaxin and Clotrimazole. The results showed that the CANP salt could interact with CT-DNA through intercalation. Antioxidant studies of the substrates alone and synthesized CANP salt showed that the latter has been better radical scavenging activity than that of the former against DPPH radical. The third order nonlinear susceptibility of the CANP salt was established by the Z-scan study.

Physicochemical characterization, and relaxometry studies of micro-graphite oxide, graphene nanoplatelets, and nanoribbons.

PubMed

Paratala, Bhavna S; Jacobson, Barry D; Kanakia, Shruti; Francis, Leonard Deepak; Sitharaman, Balaji

2012-01-01

The chemistry of high-performance magnetic resonance imaging contrast agents remains an active area of research. In this work, we demonstrate that the potassium permanganate-based oxidative chemical procedures used to synthesize graphite oxide or graphene nanoparticles leads to the confinement (intercalation) of trace amounts of Mn(2+) ions between the graphene sheets, and that these manganese intercalated graphitic and graphene structures show disparate structural, chemical and magnetic properties, and high relaxivity (up to 2 order) and distinctly different nuclear magnetic resonance dispersion profiles compared to paramagnetic chelate compounds. The results taken together with other published reports on confinement of paramagnetic metal ions within single-walled carbon nanotubes (a rolled up graphene sheet) show that confinement (encapsulation or intercalation) of paramagnetic metal ions within graphene sheets, and not the size, shape or architecture of the graphitic carbon particles is the key determinant for increasing relaxivity, and thus, identifies nano confinement of paramagnetic ions as novel general strategy to develop paramagnetic metal-ion graphitic-carbon complexes as high relaxivity MRI contrast agents.

Physicochemical Characterization, and Relaxometry Studies of Micro-Graphite Oxide, Graphene Nanoplatelets, and Nanoribbons

PubMed Central

Paratala, Bhavna S.; Jacobson, Barry D.; Kanakia, Shruti; Francis, Leonard Deepak; Sitharaman, Balaji

2012-01-01

The chemistry of high-performance magnetic resonance imaging contrast agents remains an active area of research. In this work, we demonstrate that the potassium permanganate-based oxidative chemical procedures used to synthesize graphite oxide or graphene nanoparticles leads to the confinement (intercalation) of trace amounts of Mn2+ ions between the graphene sheets, and that these manganese intercalated graphitic and graphene structures show disparate structural, chemical and magnetic properties, and high relaxivity (up to 2 order) and distinctly different nuclear magnetic resonance dispersion profiles compared to paramagnetic chelate compounds. The results taken together with other published reports on confinement of paramagnetic metal ions within single-walled carbon nanotubes (a rolled up graphene sheet) show that confinement (encapsulation or intercalation) of paramagnetic metal ions within graphene sheets, and not the size, shape or architecture of the graphitic carbon particles is the key determinant for increasing relaxivity, and thus, identifies nano confinement of paramagnetic ions as novel general strategy to develop paramagnetic metal-ion graphitic-carbon complexes as high relaxivity MRI contrast agents. PMID:22685555