Sample records for nucleic acid isolation

  1. Nucleic acid isolation process

    DOEpatents

    Longmire, Jonathan L. (Los Alamos, NM); Lewis, Annette K. (La Jolla, CA); Hildebrand, Carl E. (Los Alamos, NM)

    1990-01-01

    A method is provided for isolating DNA from eukaryotic cell and flow sorted chromosomes. When DNA is removed from chromosome and cell structure, detergent and proteolytic digestion products remain with the DNA. These products can be removed with organic extraction, but the process steps associated with organic extraction reduce the size of DNA fragments available for experimental use. The present process removes the waste products by dialyzing a solution containing the DNA against a solution containing polyethylene glycol (PEG). The waste products dialyze into the PEG leaving isolated DNA. The remaining DNA has been prepared with fragments containing more than 160 kb. The isolated DNA has been used in conventional protocols without affect on the protocol.

  2. Method for nucleic acid isolation using supercritical fluids

    DOEpatents

    Nivens, David E. (11912 Kingsgate Rd., Knoxville, TN 37911); Applegate, Bruce M. (3700 Sutherland Ave. #Q2, Knoxville, TN 37911)

    1999-01-01

    A method for detecting the presence of a microorganism in an environmental sample involves contacting the sample with a supercritical fluid to isolate nucleic acid from the microorganism, then detecting the presence of a particular sequence within the isolated nucleic acid. The nucleic acid may optionally be subjected to further purification.

  3. Method for nucleic acid isolation using supercritical fluids

    DOEpatents

    Nivens, D.E.; Applegate, B.M.

    1999-07-13

    A method is disclosed for detecting the presence of a microorganism in an environmental sample involves contacting the sample with a supercritical fluid to isolate nucleic acid from the microorganism, then detecting the presence of a particular sequence within the isolated nucleic acid. The nucleic acid may optionally be subjected to further purification. 4 figs.

  4. Silicon Dioxide Thin Film Mediated Single Cell Nucleic Acid Isolation

    PubMed Central

    Bogdanov, Evgeny; Dominova, Irina; Shusharina, Natalia; Botman, Stepan; Kasymov, Vitaliy; Patrushev, Maksim

    2013-01-01

    A limited amount of DNA extracted from single cells, and the development of single cell diagnostics make it necessary to create a new highly effective method for the single cells nucleic acids isolation. In this paper, we propose the DNA isolation method from biomaterials with limited DNA quantity in sample, and from samples with degradable DNA based on the use of solid-phase adsorbent silicon dioxide nanofilm deposited on the inner surface of PCR tube. PMID:23874571

  5. Isolated nucleic acids encoding antipathogenic polypeptides and uses thereof

    DOEpatents

    Altier, Daniel J.; Crane, Virginia C.; Ellanskaya, Irina; Ellanskaya, Natalia; Gilliam, Jacob T.; Hunter-Cevera, Jennie; Presnail, James K.; Schepers, Eric J.; Simmons, Carl R.; Torok, Tamas; Yalpani, Nasser

    2010-04-20

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include amino acid sequences, and variants and fragments thereof, for antipathogenic polypeptides that were isolated from fungal fermentation broths. Nucleic acids that encode the antipathogenic polypeptides are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  6. Microfluidic devices for nucleic acid (NA) isolation, isothermal NA amplification, and real-time detection.

    PubMed

    Mauk, Michael G; Liu, Changchun; Sadik, Mohamed; Bau, Haim H

    2015-01-01

    Molecular (nucleic acid)-based diagnostics tests have many advantages over immunoassays, particularly with regard to sensitivity and specificity. Most on-site diagnostic tests, however, are immunoassay-based because conventional nucleic acid-based tests (NATs) require extensive sample processing, trained operators, and specialized equipment. To make NATs more convenient, especially for point-of-care diagnostics and on-site testing, a simple plastic microfluidic cassette ("chip") has been developed for nucleic acid-based testing of blood, other clinical specimens, food, water, and environmental samples. The chip combines nucleic acid isolation by solid-phase extraction; isothermal enzymatic amplification such as LAMP (Loop-mediated AMPlification), NASBA (Nucleic Acid Sequence Based Amplification), and RPA (Recombinase Polymerase Amplification); and real-time optical detection of DNA or RNA analytes. The microfluidic cassette incorporates an embedded nucleic acid binding membrane in the amplification reaction chamber. Target nucleic acids extracted from a lysate are captured on the membrane and amplified at a constant incubation temperature. The amplification product, labeled with a fluorophore reporter, is excited with a LED light source and monitored in situ in real time with a photodiode or a CCD detector (such as available in a smartphone). For blood analysis, a companion filtration device that separates plasma from whole blood to provide cell-free samples for virus and bacterial lysis and nucleic acid testing in the microfluidic chip has also been developed. For HIV virus detection in blood, the microfluidic NAT chip achieves a sensitivity and specificity that are nearly comparable to conventional benchtop protocols using spin columns and thermal cyclers. PMID:25626529

  7. Specific Features of Nucleic Acid Synthesis in Isolated Mitochondria of Elymus sibiricus from Different Natural Populations

    Microsoft Academic Search

    G. N. Lutsenko; V. V. Zykova; Yu. M. Konstantinov

    2003-01-01

    Conditions and kinetic characteristics of nucleic acid synthesis were studied in the isolated mitochondria of Elymus sibiricus from different natural populations. The results showed the reciprocal dependence of RNA and DNA synthesis rates in the mitochondrial genetic system of E. sibiricus seedlings of different genotypes.

  8. Improved method for simultaneous isolation of proteins and nucleic acids

    Microsoft Academic Search

    Soroth Chey; Claudia Claus; Uwe Gerd Liebert

    2011-01-01

    Guanidinium thiocyanate–phenol–chloroform extraction (GTPC extraction) is widely used in molecular biology for isolating DNA, RNA, and proteins. Protein isolation by commercially available GTPC solutions is time consuming and the resulting pellets are only incompletely soluble. In this study ethanol–bromochloropropane–water was used for precipitation of proteins from the phenol–ethanol phase after GTPC extraction of RNA and DNA. The precipitated proteins can

  9. Nucleic acid detection assays

    DOEpatents

    Prudent, James R.; Hall, Jeff G.; Lyamichev, Victor I.; Brow, Mary Ann; Dahlberg, James E.

    2005-04-05

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  10. Cleavage of nucleic acids

    DOEpatents

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Waunakee, WI); Lyamichev, Victor I. (Madison, WI); Brow; Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2010-11-09

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  11. Nucleic acid detection compositions

    SciTech Connect

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Brow, Mary Ann (Madison, WI); Dahlberg, James L. (Madison, WI)

    2008-08-05

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  12. Cleavage of nucleic acids

    DOEpatents

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor L. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2007-12-11

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  13. Cleavage of nucleic acids

    DOEpatents

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2000-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  14. Nucleic acid detection kits

    DOEpatents

    Hall, Jeff G.; Lyamichev, Victor I.; Mast, Andrea L.; Brow, Mary Ann; Kwiatkowski, Robert W.; Vavra, Stephanie H.

    2005-03-29

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of nucleic acid from various viruses in a sample.

  15. Detection and isolation of nucleic acid sequences using competitive hybridization probes

    DOEpatents

    Lucas, J.N.; Straume, T.; Bogen, K.T.

    1997-04-01

    A method for detecting a target nucleic acid sequence in a sample is provided using hybridization probes which competitively hybridize to a target nucleic acid. According to the method, a target nucleic acid sequence is hybridized to first and second hybridization probes which are complementary to overlapping portions of the target nucleic acid sequence, the first hybridization probe including a first complexing agent capable of forming a binding pair with a second complexing agent and the second hybridization probe including a detectable marker. The first complexing agent attached to the first hybridization probe is contacted with a second complexing agent, the second complexing agent being attached to a solid support such that when the first and second complexing agents are attached, target nucleic acid sequences hybridized to the first hybridization probe become immobilized on to the solid support. The immobilized target nucleic acids are then separated and detected by detecting the detectable marker attached to the second hybridization probe. A kit for performing the method is also provided. 7 figs.

  16. Composition for nucleic acid sequencing

    Microsoft Academic Search

    Jonas Korlach; Watt W. Webb; Michael Levene; Stephen Turner; Harold G. Craighead; Mathieu Foquet

    2008-01-01

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is

  17. Portable nucleic acid thermocyclers.

    PubMed

    Almassian, David R; Cockrell, Lisa M; Nelson, William M

    2013-11-21

    A nucleic acid thermal cycler is considered to be portable if it is under ten pounds, easily carried by one individual, and battery powered. Nucleic acid amplification includes both polymerase chain reaction (e.g. PCR, RT-PCR) and isothermal amplification (e.g. RPA, HDA, LAMP, NASBA, RCA, ICAN, SMART, SDA). There are valuable applications for portable nucleic acid thermocyclers in fields that include clinical diagnostics, biothreat detection, and veterinary testing. A system that is portable allows for the distributed detection of targets at the point of care and a reduction of the time from sample to answer. The designer of a portable nucleic acid thermocycler must carefully consider both thermal control and the detection of amplification. In addition to thermal control and detection, the designer may consider the integration of a sample preparation subsystem with the nucleic acid thermocycler. There are a variety of technologies that can achieve accurate thermal control and the detection of nucleic acid amplification. Important evaluation criteria for each technology include maturity, power requirements, cost, sensitivity, speed, and manufacturability. Ultimately the needs of a particular market will lead to user requirements that drive the decision between available technologies. PMID:24030680

  18. Nucleic Acids Molecular Biology Tools

    E-print Network

    Qiu, Weigang

    Nucleic Acids Proteins Molecular Biology Tools Molecular Biology and Genomics Weigang Qiu Weigang Qiu Molecular Biology and Genomics #12;Nucleic Acids Proteins Molecular Biology Tools Outline 1 Nucleic Acids 2 Proteins 3 Molecular Biology Tools Weigang Qiu Molecular Biology and Genomics #12;Nucleic

  19. Rotary-based platform with disposable fluidic modules for automated isolation of nucleic acids.

    PubMed

    Mamaev, Dmitry; Shaskolskiy, Boris; Dementieva, Ekaterina; Khodakov, Dmitry; Yurasov, Dmitry; Yurasov, Roman; Zimenkov, Danila; Mikhailovich, Vladimir; Zasedatelev, Alexander; Gryadunov, Dmitry

    2015-02-01

    We describe the development and evaluation of a rotary-based platform with multiple disposable fluidic modules for simultaneous automatic nucleic acid (NA) isolation from up to 24 biological samples. The procedure is performed inside insulated individual disposable modules, which minimizes both the risk of infection of personnel and laboratory cross-contamination. Each module is a segment of a circular cylinder containing a leak-proof inlet port for sample input, reservoirs with lyophilized chemicals and solvents, fluidic channels, stoppers, valves, a waste reservoir and an outlet port equipped with the standard micro test tube for NA collection. The entire platform, apart from the rotor that accommodates 24 modules, consists of functional elements that provide spinning of the rotor, reagent mixing, pressure delivery, and heating of reaction mixtures. The transfer of the reaction mixtures inside the modules is performed either with rotation of the rotor or with excessive air pressure applied to the module's reservoirs. The entire process takes less than 40 min, starting from the sample loading to the recovery of the purified NA, and it allows NA isolation both from bacterial cells and viral particles. The feasibility and reproducibility of the developed platform was demonstrated by the NA isolation from suspensions of Bacillus thuringiensis and Mycobacterium tuberculosis cells within a concentration range of 10(8) to 10(2) cells/ml. Isolation of NAs from blood plasma samples with varying concentration of hepatitis B and C viruses from 10(7) to 10(2) particles/ml were also successful. The purity and integrity of the extracted NAs were both reliable for performing quantitative PCR. PMID:25653066

  20. Invasive cleavage of nucleic acids

    DOEpatents

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  1. Invasive cleavage of nucleic acids

    DOEpatents

    Prudent, James R. (Madison, WI); Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

    2002-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof.

  2. Nucleic Acid Detection Methods

    Microsoft Academic Search

    Cassandra L. Smith; Ron Yaar; Przemyslaw Szafranski; Charles R. Cantor

    1998-01-01

    The invention relates to methods for rapidly determining the sequence and\\/or length a target sequence. The target sequence may be a series of known or unknown repeat sequences which are hybridized to an array of probes. The hybridized array is digested with a single-strand nuclease and free 3'-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be

  3. Nucleic acid detection methods

    Microsoft Academic Search

    C. L. Smith; R. Yaar; P. Szafranski; C. R. Cantor

    1998-01-01

    The invention relates to methods for rapidly determining the sequence and\\/or length a target sequence. The target sequence may be a series of known or unknown repeat sequences which are hybridized to an array of probes. The hybridized array is digested with a single-strand nuclease and free 3â²-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be

  4. Chip-based sequencing nucleic acids

    SciTech Connect

    Beer, Neil Reginald

    2014-08-26

    A system for fast DNA sequencing by amplification of genetic material within microreactors, denaturing, demulsifying, and then sequencing the material, while retaining it in a PCR/sequencing zone by a magnetic field. One embodiment includes sequencing nucleic acids on a microchip that includes a microchannel flow channel in the microchip. The nucleic acids are isolated and hybridized to magnetic nanoparticles or to magnetic polystyrene-coated beads. Microreactor droplets are formed in the microchannel flow channel. The microreactor droplets containing the nucleic acids and the magnetic nanoparticles are retained in a magnetic trap in the microchannel flow channel and sequenced.

  5. Functional nucleic acid probes and uses thereof

    DOEpatents

    Nilsen-Hamilton, Marit

    2006-10-03

    The present invention provides functional nucleic acid probes, and methods of using functional nucleic acid probes, for binding a target to carry out a desired function. The probes have at least one functional nucleic acid, at least one regulating nucleic acid, and at least one attenuator. The functional nucleic acid is maintained in an inactive state by the attenuator and activated by the regulating nucleic acid only in the presence of a regulating nucleic acid target. In its activated state the functional nucleic acid can bind to its target to carry out a desired function, such as generating a signal, cleaving a nucleic acid, or catalyzing a reaction.

  6. Nucleic Acid Chaperone Activity of HIV1

    E-print Network

    Levin, Judith G.

    Nucleic Acid Chaperone Activity of HIV1 Nucleocapsid Protein: Critical Role in Reverse ............................................................................ 218 II. Structure and Nucleic Acid Binding Properties of HIV1 NC ........................................................................... 219 A. Specific and Nonspecific Nucleic Acid Binding .............................. 220 B. Structural

  7. Nucleic acid arrays and methods of synthesis

    SciTech Connect

    Sabanayagam, Chandran R. (Allston, MA); Sano, Takeshi (Needham, MA); Misasi, John (Syracuse, NY); Hatch, Anson (Seattle, WA); Cantor, Charles (Del Mar, CA)

    2001-01-01

    The present invention generally relates to high density nucleic acid arrays and methods of synthesizing nucleic acid sequences on a solid surface. Specifically, the present invention contemplates the use of stabilized nucleic acid primer sequences immobilized on solid surfaces, and circular nucleic acid sequence templates combined with the use of isothermal rolling circle amplification to thereby increase nucleic acid sequence concentrations in a sample or on an array of nucleic acid sequences.

  8. Direct isolation of high-quality low molecular weight RNA of pear peel from the extraction mixture containing nucleic acid.

    PubMed

    Wang, Xin-wei; Xiong, Ai-sheng; Yao, Quan-hong; Zhang, Zhen; Qiao, Yu-shan

    2010-01-01

    Low molecular weight RNA (LMW RNA) is generally obtained either from the total RNA or from total nucleic acids solution. Many steps and chemical reagents are involved in traditional methods for LMW RNA isolation where degradation of LMW RNA often occurs, especially for plant materials with high levels of secondary catabolites. In this study, an efficient method was developed to directly isolate pure LMW RNA from pear peel, a material rich in polyphenolics that is covered with a layer of wax. The method was based on polyethylene glycol (PEG) precipitation combining CTAB buffer which is often used to isolate RNA from polysaccharide-rich and polyphenolics-rich materials. The entire procedure could be completed within 6 h and many samples could be processed at the same time. Few and common chemicals are used with this method. Hence, it could be used as an ordinary method in the laboratory. The developed method was further tested by isolating LMW RNA from Arabidopsis. Using the isolated LMW RNA samples, microRNAs were successfully detected and characterized. PMID:19669950

  9. A Simpler Nucleic Acid

    NASA Technical Reports Server (NTRS)

    Orgel, Leslie

    2000-01-01

    It has been supposed that for a nucleic acid analog to pair with RNA it must, like RNA, have a backbone with at least a sixatom repeat; a shorter backbone presumably would not stretch far enough to bind RNA properly. The Eschenmoser group has shown, however, that this first impression is incorrect.As they report in their new paper, Eschenmoser and co-workers ( I ) have now synthesized a substantial number of these polymers, which are called (L)-a-threofuranosyl oligonucleotides or TNAs. They are composed of bases linked to a threose sugar-phosphate backbone, with phosphodiester bonds connecting the nucleotides. The investigators discovered that pairs of complementary TNAs do indeed form stable Watson-Crick double helices and, perhaps more importantly, that TNAs form stable double helices with complementary RNAs and DNAs.

  10. Direct Isolation of Purines and Pyrimidines from Nucleic Acids Using Sublimation

    NASA Technical Reports Server (NTRS)

    Glavin, Daniel P.; Schubert, Michael; Bada, Jeffrey L.

    2003-01-01

    A sublimation technique was developed to isolate purines and pyrimidines directly from lambda-deoxyribonucleic acid (lambda-DNA) and Escherichia coli cells. The sublimation of adenine, cytosine, guanine, and thymine from lambda-DNA was tested under reduced pressure (approx. 0.5 Torr) at temperatures of >150 C. With the exception of guanine, approximately 60 -75% of each base was sublimed directly from the lambda-DNA and recovered on a coldfinger of the sublimation apparatus after heating to 450 C. Several nucleobases including adenine, cytosine, thymine, and uracil were also recovered from E. coli bacteria after heating the cells to the same temperature, although some thermal decomposition of the bases also occurred. These results demonstrate the feasibility of using sublimation to isolate purines and pyrimidines from native E. coli DNA and RNA without any chemical treatment of the cells.

  11. Identifying a base in a nucleic acid

    SciTech Connect

    Fodor, Stephen P. A.; Lipshutz, Robert J.; Huang, Xiaohua

    2005-02-08

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  12. Amyloid-Associated Nucleic Acid Hybridisation

    Microsoft Academic Search

    Sebastian Braun; Christine Humphreys; Elizabeth Fraser; Andrea Brancale; Matthias Bochtler; Trevor C. Dale

    2011-01-01

    Nucleic acids promote amyloid formation in diseases including Alzheimer's and Creutzfeldt-Jakob disease. However, it remains unclear whether the close interactions between amyloid and nucleic acid allow nucleic acid secondary structure to play a role in modulating amyloid structure and function. Here we have used a simplified system of short basic peptides with alternating hydrophobic and hydrophilic amino acid residues to

  13. The Nucleic Acid Database (NDB)

    NSDL National Science Digital Library

    Designed by John Westbrook, and housed at Rutgers University, the goal of the NDB is to assemble and distribute structural information about nucleic acids. The database contains the coordinates of nucleic acid-containing crystal structures, including a searchable atlas of structures, Protein Finder, a search-engine for locating protein structures in the PDB database, a macromolecular crystallographic information file, and archived reports about the structures contained in the database. This site provides information of general interest to researchers in the field, and develops and distributes standard geometry information for use in refinement and molecular modeling programs. Users can also subscribe to the NDB electronic newsletter.

  14. Replica amplification of nucleic acid arrays

    DOEpatents

    Church, George M. (Brookline, MA)

    2002-01-01

    A method of producing a plurality of a nucleic acid array, comprising, in order, the steps of amplifying in situ nucleic acid molecules of a first randomly-patterned, immobilized nucleic acid array comprising a heterogeneous pool of nucleic acid molecules affixed to a support, transferring at least a subset of the nucleic acid molecules produced by such amplifying to a second support, and affixing the subset so transferred to the second support to form a second randomly-patterned, immobilized nucleic acid array, wherein the nucleic acid molecules of the second array occupy positions that correspond to those of the nucleic acid molecules from which they were amplified on the first array, so that the first array serves as a template to produce a plurality, is disclosed.

  15. Methods for detecting nucleic acid sequences

    SciTech Connect

    Duck, P.; Bender, R.

    1991-04-30

    This patent describes a method for detecting a single-stranded target nucleic acid. It comprises: obtaining the single-stranded target nucleic acid; forming a reaction mixture which includes the target nucleic acid and a complementary single-stranded nucleic acid probe under conditions which allow the target nucleic acid and the probe to hybridize to each other and form a double-stranded, target-probe complex, the probe being present in molar excess relative to the target; treating the double-stranded, target-probe complex so as to cleave the probe within a predetermined sequence of the scissile nucleic acid linkage and thereby form at least one intact DNA-containing oligonucleotide fragment from the probe, such fragment being, or being treated so as to be, no longer capable of remaining hybridized to the target nucleic acid; detecting the intact DNA-containing fragments so formed and thereby detecting the single-stranded target nucleic acid.

  16. Volume 11 Number 7 1983 Nucleic Acids Research Statistical characterizationof nucleic acid sequence functional domains

    E-print Network

    Waterman, Michael S.

    Volume 11 Number 7 1983 Nucleic Acids Research Statistical characterizationof nucleic acid sequence among these domains but suggest others. The ability of these simple statistics of nucleic acid sequences body of nucleic acid sequence data. In this study we review the statistical characteristics

  17. Origin of the photostabilityOrigin of the photostability of nucleic acid basesof nucleic acid bases

    E-print Network

    Wang, Wei Hua

    Origin of the photostabilityOrigin of the photostability of nucleic acid basesof nucleic acid basesSuperfluid helium dropletshelium droplets #12;Stability of Nucleic Acid BasesStability of Nucleic Acid Bases BackgroundBackground Experimental resultsExperimental results IIsolated speciessolated

  18. Optimizing the specificity of nucleic acid hybridization

    E-print Network

    Zhang, David Yu

    Optimizing the specificity of nucleic acid hybridization David Yu Zhang1,2 *, Sherry Xi Chen3, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature to 37 88888C, from 1 mM Mg21 to 47 mM Mg21 , and with nucleic acid concentrations from 1 nM to 5 m

  19. Rapid hybridization of nucleic acids using isotachophoresis

    E-print Network

    Santiago, Juan G.

    Rapid hybridization of nucleic acids using isotachophoresis Moran Bercovicia,b,1,2 , Crystal M of nucleic acid hybridization reactions in free solution. We present a new physical model, validation are generally applicable to acceleration of reactions invol- ving nucleic acids, and may be applicable to a wide

  20. Characterization of Nucleic Acids by Nanopore Analysis

    E-print Network

    Characterization of Nucleic Acids by Nanopore Analysis DAVID W. DEAMER* Department of Chemistry-molecule analysis of nucleic acids. In the 1970s, it became apparent that biological membranes of cells incorporate in a bilayer, it seemed possible that linear ionic polymers as large as a nucleic acid might be driven through

  1. Gold Nanoparticles for Nucleic Acid Delivery

    PubMed Central

    Ding, Ya; Jiang, Ziwen; Saha, Krishnendu; Kim, Chang Soo; Kim, Sung Tae; Landis, Ryan F; Rotello, Vincent M

    2014-01-01

    Gold nanoparticles provide an attractive and applicable scaffold for delivery of nucleic acids. In this review, we focus on the use of covalent and noncovalent gold nanoparticle conjugates for applications in gene delivery and RNA-interference technologies. We also discuss challenges in nucleic acid delivery, including endosomal entrapment/escape and active delivery/presentation of nucleic acids in the cell. PMID:24599278

  2. Molecular Dynamics Simulation of Nucleic Acids

    Microsoft Academic Search

    Thomas E. Cheatham III; Peter A. Kollman

    2000-01-01

    We review molecular dynamics simulations of nucleic acids, including those completed from 1995 to 2000, with a focus on the applications and results rather than the methods. After the introduction, which discusses recent advances in the simulation of nucleic acids in solution, we describe force fields for nucleic acids and then provide a detailed summary of the published literature. We

  3. Applications of peptide nucleic acids

    Microsoft Academic Search

    Peter E Nielsen

    1999-01-01

    Several exciting new developments in the applications of the DNA mimic peptide nucleic acid (PNA) have been published recently. A possible breakthrough may have come in efforts to develop PNA into gene therapeutic drugs. In eukaryotic systems, antisense activity of PNAs (as peptide conjugates) has been reported in nerve cells and even in rats upon injection into the brain, and

  4. Nucleic acid delivery with microbubbles and ultrasound

    PubMed Central

    Rychak, Joshua J.; Klibanov, Alexander L.

    2014-01-01

    Nucleic acid-based therapy is a growing field of drug delivery research. Although ultrasound has been suggested to enhance transfection decades ago, it took a combination of ultrasound with nucleic acid carrier systems (microbubbles, liposomes, polyplexes, viral carriers) to achieve reasonable nucleic acid delivery efficacy. Microbubbles serve as foci for local deposition of ultrasound energy near the target cell, and greatly enhance sonoporation. Major advantage of this approach is in the minimal transfection in the non-insonated non-target tissues. Microbubbles can be simply co-administered with the nucleic acid carrier or can be modified to carry nucleic acid themselves. Liposomes with embedded gas or gas precursor particles can also be used to carry nucleic acid, release and deliver it by the ultrasound trigger. Successful testing in a wide variety of animal models (myocardium, solid tumors, skeletal muscle, pancreas) proves the potential usefulness of this technique for nucleic acid drug delivery. PMID:24486388

  5. Isolation and identification of products from alkylation of nucleic acids: ethyl- and isopropyl-purines.

    PubMed Central

    Lawley, P D; Orr, D J; Jarman, M

    1975-01-01

    Ethylation and isopropylation of guanine in alkaline solution, or of adenine in formic acid, by alkyl methanesulphonates gave the following products: 1-, N2-, 3-, O6-, 7- and 9-alkylguanines; 1-, 3-, 7- and 9-alkyladenines. The products were identified from their characteristic u.v-absorption spectra, by comparison with either known ethyladenines or with the corresponding known methyladenines, and were also characterized by mass spectrometry. Their chromatographic properties on paper, t.l.c. and various columns were determined. DNA was alkylated in neutral solution with 14C-labelled alkyl methanesulphonates and the ratios of the alkylpurines formed were obtained, and compared for alkylation by methyl, ethyl and isopropyl methanesulphonates and by N-methyl-N-nitrosourea. The extents of alkylation at O-6 of guanine relative to those at N-7 of guanine varied with the reactivity of the methylating agents according to the predictions of Swain & Scott (1953) relating nucleophilicity of the groups alkylated with the substrate constants of the alkylating agents. The relative extents of alkylation at N-3 of adenine did not follow this correlation. PMID:172066

  6. Thermoplastic Microfluidic Device for On-Chip Purification of Nucleic Acids for Disposable

    E-print Network

    Thermoplastic Microfluidic Device for On-Chip Purification of Nucleic Acids for Disposable)-based isolation of nucleic acids is demonstrated. The plastic chip can function as a disposable sample preparation by this method allowed for successful extraction and elution of nucleic acids in the polymeric microchip

  7. Nucleic acids, compositions and uses thereof

    DOEpatents

    Preston, III, James F. (Micanopy, FL); Chow, Virginia (Gainesville, FL); Nong, Guang (Gainesville, FL); Rice, John D. (Gainesville, FL); St. John, Franz J. (Baltimore, MD)

    2012-02-21

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  8. Nucleic acid compositions and the encoding proteins

    DOEpatents

    Preston, III, James F.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

    2014-09-02

    The subject invention provides at least one nucleic acid sequence encoding an aldouronate-utilization regulon isolated from Paenibacillus sp. strain JDR-2, a bacterium which efficiently utilizes xylan and metabolizes aldouronates (methylglucuronoxylosaccharides). The subject invention also provides a means for providing a coordinately regulated process in which xylan depolymerization and product assimilation are coupled in Paenibacillus sp. strain JDR-2 to provide a favorable system for the conversion of lignocellulosic biomass to biobased products. Additionally, the nucleic acid sequences encoding the aldouronate-utilization regulon can be used to transform other bacteria to form organisms capable of producing a desired product (e.g., ethanol, 1-butanol, acetoin, 2,3-butanediol, 1,3-propanediol, succinate, lactate, acetate, malate or alanine) from lignocellulosic biomass.

  9. Nucleic acid based logical systems.

    PubMed

    Han, Da; Kang, Huaizhi; Zhang, Tao; Wu, Cuichen; Zhou, Cuisong; You, Mingxu; Chen, Zhuo; Zhang, Xiaobing; Tan, Weihong

    2014-05-12

    Researchers increasingly visualize a significant role for artificial biochemical logical systems in biological engineering, much like digital logic circuits in electrical engineering. Those logical systems could be utilized as a type of servomechanism to control nanodevices in vitro, monitor chemical reactions in situ, or regulate gene expression in vivo. Nucleic acids (NA), as carriers of genetic information with well-regulated and predictable structures, are promising materials for the design and engineering of biochemical circuits. A number of logical devices based on nucleic acids (NA) have been designed to handle various processes for technological or biotechnological purposes. This article focuses on the most recent and important developments in NA-based logical devices and their evolution from in vitro, through cellular, even towards in vivo biological applications. PMID:24692306

  10. Nucleic Acid Detection using MNAzymes

    PubMed Central

    Gerasimova, Yulia V.; Kolpashchikov, Dmitry M.

    2010-01-01

    Deoxyribozymes are promising biotechnological tools. In a recent JACS article Mokany et al. reported on the design of multi-component deoxyribozyme (MNAzyme) sensors based on 10–23 and 8–17 DNA enzymes. The sensors can detect down to 5 pM of a specific nucleic acid. The versatility of MNAzyme platform allows the design of catalytic cascades for signal amplification. This work is a step forward to PCR-free molecular diagnostics. PMID:20189100

  11. Nucleic acid detection using MNAzymes.

    PubMed

    Gerasimova, Yulia V; Kolpashchikov, Dmitry M

    2010-02-26

    Deoxyribozymes are promising biotechnological tools. In a recent JACS article, Mokany et al. reported on the design of multi-component deoxyribozyme (MNAzyme) sensors based on 10-23 and 8-17 DNA enzymes. The sensors can detect down to 5 pM of a specific nucleic acid. The versatility of MNAzyme platform allows the design of catalytic cascades for signal amplification. This work is a step forward to PCR-free molecular diagnostics. PMID:20189100

  12. Metal-nucleic acid cages

    Microsoft Academic Search

    Hua Yang; Christopher K. McLaughlin; Faisal A. Aldaye; Graham D. Hamblin; Andrzej Z. Rys; Isabelle Rouiller; Hanadi F. Sleiman

    2009-01-01

    Metal-nucleic acid cages are a promising new class of materials. Like metallo-supramolecular cages, these systems can use their metals for redox, photochemical, magnetic and catalytic control over encapsulated cargo. However, using DNA provides the potential to program pore size, geometry, chemistry and addressability, and the ability to symmetrically and asymmetrically position transition metals within the three-dimensional framework. Here we report

  13. Metal–nucleic acid cages

    Microsoft Academic Search

    Hua Yang; Christopher K. McLaughlin; Faisal A. Aldaye; Graham D. Hamblin; Andrzej Z. Rys; Isabelle Rouiller; Hanadi F. Sleiman

    2009-01-01

    Metal–nucleic acid cages are a promising new class of materials. Like metallo-supramolecular cages, these systems can use their metals for redox, photochemical, magnetic and catalytic control over encapsulated cargo. However, using DNA provides the potential to program pore size, geometry, chemistry and addressability, and the ability to symmetrically and asymmetrically position transition metals within the three-dimensional framework. Here we report

  14. CHTN :: Nucleic Acid Isolation

    Cancer.gov

    Skip to Main Content CHTN Home | Admin Login Connect with the CHTN About Us What is the CHTN? Why use the CHTN? CHTN Divisions History of the CHTN Biospecimens We Provide Biospecimen Collection & Type Biospecimen Processing, Preservation & Shipping Quality

  15. Self-assembling multimeric nucleic acid constructs

    DOEpatents

    Cantor, C.R.; Niemeyer, C.M.; Smith, C.L.; Sano, Takeshi; Hnatowich, D.J.; Rusckowski, M.

    1996-10-01

    The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products. 5 figs.

  16. Self-assembling multimeric nucleic acid constructs

    DOEpatents

    Cantor, Charles R. (Boston, MA); Niemeyer, Christof M. (Bremen, DE); Smith, Cassandra L. (Boston, MA); Sano, Takeshi (Boston, MA); Hnatowich, Donald J. (Brookline, MA); Rusckowski, Mary (Southborough, MA)

    1999-10-12

    The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products.

  17. Self-assembling multimeric nucleic acid constructs

    DOEpatents

    Cantor, Charles R. (Boston, MA); Niemeyer, Christof M. (Bremen, DE); Smith, Cassandra L. (Boston, MA); Sano, Takeshi (Boston, MA); Hnatowich, Donald J. (Brookline, MA); Rusckowski, Mary (Southborough, MA)

    1996-01-01

    The invention is directed to constructs and compositions containing multimeric forms of nucleic acid. Multimeric nucleic acids comprise single-stranded nucleic acids attached via biotin to streptavidin and bound with a functional group. These constructs can be utilized in vivo to treat or identify diseased tissue or cells. Repeated administrations of multimeric nucleic acid compositions produce a rapid and specific amplification of nucleic acid constructs and their attached functional groups. For treatment purposes, functional groups may be toxins, radioisotopes, genes or enzymes. Diagnostically, labeled multimeric constructs may be used to identify specific targets in vivo or in vitro. Multimeric nucleic acids may also be used in nanotechnology and to create self-assembling polymeric aggregates such as membranes of defined porosity, microcircuits and many other products.

  18. Amyloid-Associated Nucleic Acid Hybridisation

    PubMed Central

    Braun, Sebastian; Humphreys, Christine; Fraser, Elizabeth; Brancale, Andrea; Bochtler, Matthias; Dale, Trevor C.

    2011-01-01

    Nucleic acids promote amyloid formation in diseases including Alzheimer's and Creutzfeldt-Jakob disease. However, it remains unclear whether the close interactions between amyloid and nucleic acid allow nucleic acid secondary structure to play a role in modulating amyloid structure and function. Here we have used a simplified system of short basic peptides with alternating hydrophobic and hydrophilic amino acid residues to study nucleic acid - amyloid interactions. Employing biophysical techniques including X-ray fibre diffraction, circular dichroism spectroscopy and electron microscopy we show that the polymerized charges of nucleic acids concentrate and enhance the formation of amyloid from short basic peptides, many of which would not otherwise form fibres. In turn, the amyloid component binds nucleic acids and promotes their hybridisation at concentrations below their solution Kd, as shown by time-resolved FRET studies. The self-reinforcing interactions between peptides and nucleic acids lead to the formation of amyloid nucleic acid (ANA) fibres whose properties are distinct from their component polymers. In addition to their importance in disease and potential in engineering, ANA fibres formed from prebiotically-produced peptides and nucleic acids may have played a role in early evolution, constituting the first entities subject to Darwinian evolution. PMID:21625537

  19. Double stranded nucleic acid biochips

    DOEpatents

    Chernov, Boris; Golova, Julia

    2006-05-23

    This invention describes a new method of constructing double-stranded DNA (dsDNA) microarrays based on the use of pre-synthesized or natural DNA duplexes without a stem-loop structure. The complementary oligonucleotide chains are bonded together by a novel connector that includes a linker for immobilization on a matrix. A non-enzymatic method for synthesizing double-stranded nucleic acids with this novel connector enables the construction of inexpensive and robust dsDNA/dsRNA microarrays. DNA-DNA and DNA-protein interactions are investigated using the microarrays.

  20. Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences

    E-print Network

    Nowak, Martin A.

    Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences of life, the biological information of nucleic acid polymers must have increased to encode functional work suggests that prebiotically plausible chemical mechanisms of nucleic acid polymerization

  1. Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications

    E-print Network

    Condon, Anne

    Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications Baharak of pseudoknotted nucleic acid secondary structure is an impor- tant computational challenge. Prediction algorithms Nucleic acids - that is, DNA and RNA molecules - play fundamental roles in the cell: in translation

  2. Identification of random nucleic acid sequence aberrations using dual capture probes which hybridize to different chromosome regions

    DOEpatents

    Lucas, Joe N. (San Ramon, CA); Straume, Tore (Tracy, CA); Bogen, Kenneth T. (Walnut Creek, CA)

    1998-01-01

    A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration.

  3. Adaptive Recognition by Nucleic Acid Aptamers

    Microsoft Academic Search

    Thomas Hermann; Dinshaw J. Patel

    2000-01-01

    Nucleic acid molecules play crucial roles in diverse biological processes including the storage, transport, processing, and expression of the genetic information. Nucleic acid aptamers are selected in vitro from libraries containing random sequences of up to a few hundred nucleotides. Selection is based on the ability to bind ligand molecules with high affinity and specificity. Three-dimensional structures have been determined

  4. Inhibition and Facilitation of Nucleic Acid Amplification

    Microsoft Academic Search

    IAN G. WILSON

    1997-01-01

    Factors that inhibit the amplification of nucleic acids by PCR are present with target DNAs from many sources. The inhib- itors generally act at one or more of three essential points in the reaction in the following ways: they interfere with the cell lysis necessary for extraction of DNA, they interfere by nucleic acid degradation or capture, and they inhibit

  5. Optimizing the specificity of nucleic acid hybridization

    Microsoft Academic Search

    Sherry Xi Chen; David Yu Zhang; Peng Yin

    2012-01-01

    The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable near-optimal single-base discrimination and perform robustly across diverse

  6. An Introduction to Peptide Nucleic Acid

    Microsoft Academic Search

    Peter E. Nielsen; Michael Egholm

    1999-01-01

    Peptide Nucleic Acid (PNA) is a powerful new biomolecular tool with a wide range of important applications. PNA mimics the behaviour of DNA and binds complementary nucleic acid strands. The unique chemical, physical and biological properties of PNA have been exploited to produce powerful biomolecular tools, antisense and antigene agents, molecular probes and biosensors.

  7. Antisense properties of peptide nucleic acid

    Microsoft Academic Search

    H. Jakob Larsen; Thomas Bentin; Peter E Nielsen

    1999-01-01

    Peptide nucleic acid (PNA) is a nucleic acid mimic in which the deoxyribose phosphate backbone has been replaced by a pseudo-peptide polymer to which the nucleobases are linked. PNA-oligomers can be synthesized in relatively large amounts, are highly stable in biological environments, and bind complementary DNA and RNA targets with remarkably high affinity and specificity. Thus PNA possesses many of

  8. Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same

    SciTech Connect

    Brown, Kimberly; Harris, Paul; Zaretsky, Elizabeth; Re, Edward; Vlasenko, Elena; McFarland, Keith; Lopez de Leon, Alfredo

    2010-06-22

    The present invention relates to isolated polypeptides having cellulolytic enhancing activity and isolated polynucleotides encoding the polypeptides. The invention also relates to nucleic acid constructs, vectors, and host cells comprising the polynucleotides as well as methods for producing and using the polypeptides.

  9. Sequence Comparison and Phylogeny of Nucleotide Sequence of Coat Protein and Nucleic Acid Binding Protein of a Distinct Isolate of Shallot virus X from India.

    PubMed

    Majumder, S; Baranwal, V K

    2011-06-01

    Shallot virus X (ShVX), a type species in the genus Allexivirus of the family Alfaflexiviridae has been associated with shallot plants in India and other shallot growing countries like Russia, Germany, Netherland, and New Zealand. Coat protein (CP) and nucleic acid binding protein (NB) region of the virus was obtained by reverse transcriptase polymerase chain reaction from scales leaves of shallot bulbs. The partial cDNA contained two open reading frames encoding proteins of molecular weights of 28.66 and 14.18 kDa belonging to Flexi_CP super-family and viral NB super-family, respectively. The percent identity and phylogenetic analysis of amino acid sequences of CP and NB region of the virus associated with shallot indicated that it was a distinct isolate of ShVX. PMID:23637504

  10. Universal nucleic acids sample preparation method for cells, spores and their mixture

    DOEpatents

    Bavykin, Sergei (Darien, IL)

    2011-01-18

    The present invention relates to a method for extracting nucleic acids from biological samples. More specifically the invention relates to a universal method for extracting nucleic acids from unidentified biological samples. An advantage of the presently invented method is its ability to effectively and efficiently extract nucleic acids from a variety of different cell types including but not limited to prokaryotic or eukaryotic cells and/or recalcitrant organisms (i.e. spores). Unlike prior art methods which are focused on extracting nucleic acids from vegetative cell or spores, the present invention effectively extracts nucleic acids from spores, multiple cell types or mixtures thereof using a single method. Important that the invented method has demonstrated an ability to extract nucleic acids from spores and vegetative bacterial cells with similar levels effectiveness. The invented method employs a multi-step protocol which erodes the cell structure of the biological sample, isolates, labels, fragments nucleic acids and purifies labeled samples from the excess of dye.

  11. The search for scrapie agent nucleic acid.

    PubMed Central

    Aiken, J M; Marsh, R F

    1990-01-01

    Despite decades of research, the identity of the scrapie agent has remained elusive. Recent studies have discovered much about the influence of the host genome upon scrapie infection, yet relatively little is known about the causative agent itself. The predominant hypothesis in the scrapie field (the prion hypothesis) argues that the disease is the result of an infectious protein and that nucleic acid is not required for infection. Biological studies of the scrapie agent, however, suggest that a nucleic acid may be involved in the disease. Sensitive molecular biology techniques have yet to identify this putative nucleic acid. PMID:2120561

  12. Nucleic acid analysis using terminal-phosphate-labeled nucleotides

    Microsoft Academic Search

    Jonas Korlach; Watt W. Webb; Michael Levene; Stephen Turner; Harold G. Craighead; Mathieu Foquet

    2008-01-01

    The present invention is directed to a method of sequencing a target nucleic acid molecule having a plurality of bases. In its principle, the temporal order of base additions during the polymerization reaction is measured on a molecule of nucleic acid, i.e. the activity of a nucleic acid polymerizing enzyme on the template nucleic acid molecule to be sequenced is

  13. Probing Interactions Between Plant Virus Movement Proteins and Nucleic Acids

    E-print Network

    Citovsky, Vitaly

    and Nucleic Acids Tzvi Tzfira and Vitaly Citovsky Abstract Most plant viruses move between plant cells is almost invariably binding to nucleic acids. Presumably, the MP­nucleic acid interaction is directly or not it binds nucleic acids, and to characterize the hallmark parameters of such binding, i.e., prefer- ence

  14. Biochemistry 766: Nucleic Acids http://carmen.osu.edu

    E-print Network

    Foster, Mark P.

    Biochemistry 766: Nucleic Acids http://carmen.osu.edu Winter Quarter 2011, 3 cr., Course No. 6738, or by appointment Primary Text: Nucleic Acids in Chemistry and Biology. Blackburn, Gait, Loakes and Williams, eds Nucleic acids biochemistry; history and context Nucleic acid nomenclature; tautomerism; ionization

  15. In vitro selection from combinatorial nucleic acid libraries has provided new RNA and DNA molecules that have catalytic

    E-print Network

    Weiblen, George D

    257 In vitro selection from combinatorial nucleic acid libraries has provided new RNA and DNA of nucleic acid molecules. The future application of in vitro selected RNA and DNA catalysts in bioorganic-state analog Introduction Combinatorial nucleic-acid libraries have found increasing use for the isolation

  16. NMR studies of nucleic acid dynamics

    PubMed Central

    Al-Hashimi, Hashim M.

    2014-01-01

    Nucleic acid structures have to satisfy two diametrically opposite requirements; on one hand they have to adopt well-defined 3D structures that can be specifically recognized by proteins; on the other hand, their structures must be sufficiently flexible to undergo very large conformational changes that are required during key biochemical processes, including replication, transcription, and translation. How do nucleic acids introduce flexibility into their 3D structure without losing biological specificity? Here, I describe the development and application of NMR spectroscopic techniques in my laboratory for characterizing the dynamic properties of nucleic acids that tightly integrate a broad set of NMR measurements, including residual dipolar couplings, spin relaxation, and relaxation dispersion with sample engineering and computational approaches. This approach allowed us to obtain fundamental new insights into directional flexibility in nucleic acids that enable their structures to change in a very specific functional manner. PMID:24149218

  17. Replica amplification of nucleic acid arrays

    DOEpatents

    Church, George M. (Brookline, MA); Mitra, Robi D. (Chestnut Hill, MA)

    2010-08-31

    Disclosed are improved methods of making and using immobilized arrays of nucleic acids, particularly methods for producing replicas of such arrays. Included are methods for producing high density arrays of nucleic acids and replicas of such arrays, as well as methods for preserving the resolution of arrays through rounds of replication. Also included are methods which take advantage of the availability of replicas of arrays for increased sensitivity in detection of sequences on arrays. Improved methods of sequencing nucleic acids immobilized on arrays utilizing single copies of arrays and methods taking further advantage of the availability of replicas of arrays are disclosed. The improvements lead to higher fidelity and longer read lengths of sequences immobilized on arrays. Methods are also disclosed which improve the efficiency of multiplex PCR using arrays of immobilized nucleic acids.

  18. Covalent binding of modified nucleic acids to proteins as a method for investigation of specific protein–nucleic acid interactions

    Microsoft Academic Search

    Timofei S Zatsepin; N G Dolinnaya; Elena A Kubareva; Marina G Ivanovskaya; V G Metelev; Tat'yana S Oretskaya

    2005-01-01

    Methods for specific covalent binding of modified nucleic acids to proteins and enzymes with conservation of their native structures are discussed. Possible applications of synthetic nucleic acids containing reactive (nucleophilic and electrophilic) groups and groups that can be photoactivated for testing protein–nucleic acid contacts and studying protein functioning are considered. The structures of protein–nucleic acid conjugates formed in the enzymatic

  19. Covalent binding of modified nucleic acids to proteins as a method for investigation of specific protein-nucleic acid interactions

    Microsoft Academic Search

    Timofei S. Zatsepin; N. G. Dolinnaya; Elena A. Kubareva; Marina G. Ivanovskaya; V. G. Metelev; Tat'yana S. Oretskaya

    2005-01-01

    Methods for specific covalent binding of modified nucleic acids to proteins and enzymes with conservation of their native structures are discussed. Possible applications of synthetic nucleic acids containing reactive (nucleophilic and electrophilic) groups and groups that can be photoactivated for testing protein-nucleic acid contacts and studying protein functioning are considered. The structures of protein-nucleic acid conjugates formed in the enzymatic

  20. Structure and Conformation of Nucleic Acids and Protein-Nucleic Acid Interactions

    E-print Network

    Church, George M.

    Structure and Conformation of Nucleic Acids and Protein-Nucleic Acid Interactions Edited by M by the protein, and the · er case, in which the base-paired double strand itself is recognized . The model posed acid sidechains on the inside of antiparalle1 "~-ribbon." MODEL BUILDING Space filling (CPK) models

  1. Hybridization and sequencing of nucleic acids using base pair mismatches

    SciTech Connect

    Fodor, Stephen P. A. (Palo Alto, CA); Lipshutz, Robert J. (Palo Alto, CA); Huang, Xiaohua (Mt. View, CA)

    2001-01-01

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  2. Method of Identifying a Base in a Nucleic Acid

    DOEpatents

    Fodor, Stephen P. A. (Palo Alto, CA); Lipshutz, Robert J. (Palo Alto, CA); Huang, Xiaohua (Mt. View, CA)

    1999-01-01

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  3. Probe kit for identifying a base in a nucleic acid

    DOEpatents

    Fodor, Stephen P. A. (Palo Alto, CA); Lipshutz, Robert J. (Palo Alto, CA); Huang, Xiaohua (Mt. View, CA)

    2001-01-01

    Devices and techniques for hybridization of nucleic acids and for determining the sequence of nucleic acids. Arrays of nucleic acids are formed by techniques, preferably high resolution, light-directed techniques. Positions of hybridization of a target nucleic acid are determined by, e.g., epifluorescence microscopy. Devices and techniques are proposed to determine the sequence of a target nucleic acid more efficiently and more quickly through such synthesis and detection techniques.

  4. Amplification of trace amounts of nucleic acids

    DOEpatents

    Church, George M. (Brookline, MA); Zhang, Kun (Brighton, MA)

    2008-06-17

    Methods of reducing background during amplification of small amounts of nucleic acids employ careful analysis of sources of low level contamination. Ultraviolet light can be used to reduce nucleic acid contaminants in reagents and equipment. "Primer-dimer" background can be reduced by judicious design of primers. We have shown clean signal-to-noise with as little as starting material as one single human cell (.about.6 picogram), E. coli cell (.about.5 femtogram) or Prochlorococcus cell (.about.3 femtogram).

  5. In vitro evolution of nucleic acids

    NASA Technical Reports Server (NTRS)

    Joyce, G. F.; Miller, S. L. (Principal Investigator)

    1994-01-01

    The author reviews recent published reports of in vitro selection and evolution of nucleic acids. These nucleic acids will bind to a target ligand or catalyze a specific chemical reaction. The terms aptamers and systematic evolution of ligands by exponential enrichment (SELEX) are explained. The review focuses on protein binders, small molecule binders, and ribozymes obtained by directed evolution. The reference list identifies articles of special or outstanding interest.

  6. Evaluation of peptide nucleic acid-mediated multiplex real-time PCR kits for rapid detection of carbapenemase genes in gram-negative clinical isolates.

    PubMed

    Jeong, Seri; Kim, Jung Ok; Jeong, Seok Hoon; Bae, Il Kwon; Song, Wonkeun

    2015-06-01

    The emergence of clinical isolates of carbapenemase-producing microbes confers multidrug-resistance to these bacteria and renders them difficult to treat. This study was performed to evaluate peptide nucleic acid (PNA) probe-based multiplex real-time PCR kits used to detect carbapenemase genes. In total, 324 carbapenemase genes, collected from 318 gram-negative clinical isolates in 36 different hospital laboratories, were assayed to evaluate multiplex real-time PCR kits (PANAGENE; Daejeon, Korea). The nine most prevalent carbapenemase genes (KPC, OXA-48, GES, IMP, VIM, NDM, ISAba1-OXA-51, OXA-23, and OXA-58) were included in this study. The sensitivity and specificity of the multiplex real-time PCR assay to all of the carbapenemase genes were above 99.0%, except for ISAba1-OXA-51. The detection limit of the assay was 100 target copies per 25?L of reaction volume for all of the nine genetic types of carbapenemases, and the genes were all detected in a single three-hour PCR. The assay also showed considerable efficiency (above 80.0%), stable reproducibility (coefficient of variation, below 5.0%) and a long shelf-life (more than eight months) with no cross reactivity. The developed PNA-mediated multiplex real-time PCR assay was useful for the rapid, accurate and simultaneous identification of nine carbapenemase genes in gram-negative clinical isolates, suggesting its potential to help choose the appropriate antibiotics and aid the control of carbapenemase genes. PMID:25819308

  7. Understanding Nucleic Acid–Ion Interactions

    PubMed Central

    Lipfert, Jan; Doniach, Sebastian; Das, Rhiju; Herschlag, Daniel

    2015-01-01

    Ions surround nucleic acids in what is referred to as an ion atmosphere. As a result, the folding and dynamics of RNA and DNA and their complexes with proteins and with each other cannot be understood without a reasonably sophisticated appreciation of these ions’ electrostatic interactions. However, the underlying behavior of the ion atmosphere follows physical rules that are distinct from the rules of site binding that biochemists are most familiar and comfortable with. The main goal of this review is to familiarize nucleic acid experimentalists with the physical concepts that underlie nucleic acid–ion interactions. Throughout, we provide practical strategies for interpreting and analyzing nucleic acid experiments that avoid pitfalls from oversimplified or incorrect models. We briefly review the status of theories that predict or simulate nucleic acid–ion interactions and experiments that test these theories. Finally, we describe opportunities for going beyond phenomenological fits to a next-generation, truly predictive understanding of nucleic acid–ion interactions. PMID:24606136

  8. Nucleic Acid Aptamers for Living Cell Analysis

    NASA Astrophysics Data System (ADS)

    Xiong, Xiangling; Lv, Yifan; Chen, Tao; Zhang, Xiaobing; Wang, Kemin; Tan, Weihong

    2014-06-01

    Cells as the building blocks of life determine the basic functions and properties of a living organism. Understanding the structure and components of a cell aids in the elucidation of its biological functions. Moreover, knowledge of the similarities and differences between diseased and healthy cells is essential to understanding pathological mechanisms, identifying diagnostic markers, and designing therapeutic molecules. However, monitoring the structures and activities of a living cell remains a challenging task in bioanalytical and life science research. To meet the requirements of this task, aptamers, as “chemical antibodies,” have become increasingly powerful tools for cellular analysis. This article reviews recent advances in the development of nucleic acid aptamers in the areas of cell membrane analysis, cell detection and isolation, real-time monitoring of cell secretion, and intracellular delivery and analysis with living cell models. Limitations of aptamers and possible solutions are also discussed.

  9. Nucleic acids, proteins, and chirality

    NASA Technical Reports Server (NTRS)

    Usher, D. A.; Profy, A. T.; Walstrum, S. A.; Needels, M. C.; Bulack, S. C.; Lo, K. M.

    1984-01-01

    The present investigation is concerned with experimental results related, in one case, to the chirality of nucleotides, and, in another case, to the possibility of a link between the chirality of nucleic acids, and that of peptides. It has been found that aminoacylation of the 'internal' hydroxyl group of a dinucleoside monophosphate can occur stereoselectively. However, this reaction has not yet been made a part of a working peptide synthesis scheme. The formation and cleavage of oligonucleotides is considered. In the event of the formation of a helical complex between the oligonucleotide and the polymer, 1-prime,5-prime-bonds in the oligomer are found to become more resistant towards cleavage. The conditions required for peptide bond formation are examined, taking into account the known structures of RNA and possible mechanisms for prebiotic peptide bond formation. The possibility is considered that the 2-prime,5-prime-internucleotide linkage could have played an important part in the early days of biological peptide synthesis.

  10. Nucleic acid crystallography: a view from the nucleic acid database.

    PubMed

    Berman, H M; Gelbin, A; Westbrook, J

    1996-01-01

    What are the future directions of the field of nucleic acid crystallography? Although there have been many duplex structures determined, the sample is still relatively small. This is especially true if one wants to derive enough information about the relationships between sequence and structure. Indeed, there are data for all the possible 10 dimer steps, but for some steps it is very limited. If the structural code resides in trimers or tetrad steps then there is simply not enough data to do meaningful statistical analyses. So the first direction that needs to be explored is the determination of more structures with more varied sequences. The other noticeable thing about the data is the shortness of the strands. While it is probably true that attempts to crystallize very long sequences will not meet with success, the idea of crystallizing sequences engineered to fit together via sticky ends such as has been done for the CAP-DNA complex (Schultz et al., 1990) should give data about the behavior of much longer stretches of DNA. The question of the effects of environment on the structure of DNA continues to be a very important one to address since DNA is rarely alone. The preliminary data we have analysed from the current sample shows that the conformation of some steps are very sensitive to packing type. Numerous studies of the hydration around DNA shows that there is a real synergy between the hydration structure and the base conformation. More data will allow further quantitation of these observations. RNA structure is the next very exciting frontier. The emerging structures of duplexes with internal loops, the two hammerhead ribozyme structures and the group I intron ribozyme have given us a glimpse of the complexity and elegance of this class of molecules. With the technology now in place to allow the determination of the structures of these molecules, the expectation is that now we will see a large increase in the number of these structures in the NDB. PMID:9284453

  11. Detection of nucleic acid sequences by invader-directed cleavage

    DOEpatents

    Brow, Mary Ann D. (Madison, WI); Hall, Jeff Steven Grotelueschen (Madison, WI); Lyamichev, Victor (Madison, WI); Olive, David Michael (Madison, WI); Prudent, James Robert (Madison, WI)

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The 5' nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based by charge.

  12. Fmoc mediated synthesis of Peptide Nucleic Acids

    Microsoft Academic Search

    Stephen A. Thomson; John A. Josey; Rodolfo Cadilla; Micheal D. Gaul; C. Fred Hassman; Michael J. Luzzio; Adrian J. Pipe; Kathryn L. Reed; Daniel J. Ricca; Robert W. Wiethe; Stewart A. Noble

    1995-01-01

    The syntheses of the Fmoc-protected Peptide Nucleic Acid (PNA) monomer pentafluorophenyl esters of adenine (26), cytosine (23), guanine (29) and thymine (20), and their oligomerization are described. The Fmoc PNA backbone 1 is prepared as a stable hydrochloride salt. The base acetic acids of adenine (4) and cytosine (3) were prepared by Cbz protection of the exocyclic amino groups followed

  13. New Real-Time PCR Assay Using Locked Nucleic Acid Probes To Assess Prevalence of ParC Mutations in Fluoroquinolone-Susceptible Streptococcus pneumoniae Isolates from France

    PubMed Central

    Decousser, Jean-Winoc; Methlouthi, Imen; Pina, Patrick; Collignon, Anne; Allouch, Pierre

    2006-01-01

    A real-time PCR assay with locked nucleic acid probes was developed to screen mutations at codons 79 and 83 of the Streptococcus pneumoniae parC gene. Only silent mutations were detected among 236 French invasive fluoroquinolone-susceptible strains. This test could be useful for some high-risk patients or in national surveys. PMID:16569894

  14. Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences

    E-print Network

    Stadler, Peter F.

    Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences Roman R. Stocsits 1 , Ivo L sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however

  15. Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences

    E-print Network

    Stadler, Peter F.

    Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences Roman R. Stocsits1 , Ivo L data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared use of the amino acid sequence when aligning coding nucleic acid sequences. In many cases, however

  16. 7-9/99 Neuman Chapter 23 Nucleic Acids

    E-print Network

    Reed, Christopher A.

    7-9/99 Neuman Chapter 23 0 Chapter 23 Nucleic Acids from Organic Chemistry by Robert C. Neuman, Jr. Peptides, Proteins, and -Amino Acids 23. Nucleic Acids ************************************************************************************** *Note: Chapters marked with an (*) are not yet posted. #12;7-9/99 Neuman Chapter 23 1 23: Nucleic Acids

  17. Adaptive Recognition by Nucleic Acid Aptamers

    NSDL National Science Digital Library

    Thomas Hermann (Memorial Sloan-Kettering Cancer Center; Cellular Biochemistry and Biophysics Program)

    2000-02-04

    Nucleic acid molecules play crucial roles in diverse biological processes including the storage, transport, processing, and expression of the genetic information. Nucleic acid aptamers are selected in vitro from libraries containing random sequences of up to a few hundred nucleotides. Selection is based on the ability to bind ligand molecules with high affinity and specificity. Three-dimensional structures have been determined at high resolution for a number of aptamers in complex with their cognate ligands. Structures of aptamer complexes reveal the key molecular interactions conferring specificity to the aptamer-ligand association, including the precise stacking of flat moieties, specific hydrogen bonding, and molecular shape complementarity. These basic principles of discriminatory molecular interactions in aptamer complexes parallel recognition events central to many cellular processes involving nucleic acids.

  18. Limitations in the Use of Fluorescein Diacetate/Propidium Iodide (FDA/PI) and Cell Permeable Nucleic Acid Stains for Viability Measurements of Isolated Islets of Langerhans

    PubMed Central

    Boyd, Vinc; Cholewa, Olivia Maria; Papas, Klearchos K.

    2010-01-01

    Background A review of current literature shows that the combined use of the cell permeable esterase-substrate fluorescein diacetate (FDA) and the cell impermeant nucleic acid stain propidium iodide (PI) to be one of the most common fluorescence-based methods to assess the viability of isolated islets of Langerhans, and it is currently used for islet product release prior to transplantation in humans. However, results from this assay do not correlate with islet viability and function or islet transplantation success in animals or humans (Eckhard et al. 2004; Ricordi et al. 2001). This may be in part attributed to considerable differences as well as discrepancies in the use of these reagents on islets. We critically surveyed the literature and evaluated the impact of a number of variables associated with the use of FDA/PI to determine their reliability in assessing islet cell viability. In addition, we evaluated other fluorescent stains, such as SYTO®13, SYTO®24 and SYBR®14 as possible alternatives to FDA. Results We found that the stability of stains in storage and stock solutions, the number of islets stained, concentration of stains, staining incubation time, the buffer/media used, and the method of examining islets were significant in the final scoring of viability. For archival file photos, the exposure time and camera/software settings can also impact interpretation of viability. Although our results show that FDA does detect intracellular esterase activity and staining with PI does assess cell membrane integrity, the results obtained from using these stains did not correlate directly with expected islet function and viability per transplantation into diabetic athymic nude mice (Papas et al. 2007). In addition, the use of two nucleic acid stains, such as SYTO®13 and PI, for live/dead scoring exhibited staining anomalies which limit their accuracy in assessing islet viability. Conclusions From a review of the literature and from our observations on the impact of reagent handling and various staining and imaging parameters used to visually evaluate islets, consistent interpretation of islet cell membrane integrity and viability is dependent upon a number of factors. We discuss the utility and limitations of these reagents in evaluating islet cell membrane integrity and viability. PMID:20814586

  19. Advances in nucleic acid-based detection methods.

    PubMed Central

    Wolcott, M J

    1992-01-01

    Laboratory techniques based on nucleic acid methods have increased in popularity over the last decade with clinical microbiologists and other laboratory scientists who are concerned with the diagnosis of infectious agents. This increase in popularity is a result primarily of advances made in nucleic acid amplification and detection techniques. Polymerase chain reaction, the original nucleic acid amplification technique, changed the way many people viewed and used nucleic acid techniques in clinical settings. After the potential of polymerase chain reaction became apparent, other methods of nucleic acid amplification and detection were developed. These alternative nucleic acid amplification methods may become serious contenders for application to routine laboratory analyses. This review presents some background information on nucleic acid analyses that might be used in clinical and anatomical laboratories and describes some recent advances in the amplification and detection of nucleic acids. PMID:1423216

  20. MACROMOLECULES, Part 1* Carbohydrates, Lipids, and Nucleic Acids

    E-print Network

    Prestwich, Ken

    MACROMOLECULES, Part 1* Carbohydrates, Lipids, and Nucleic Acids Introduction: Living organisms are unique in being composed of long, massive molecules called macromolecules. Biochemistry, the study of macromolecules: carbohydrates, lipids, proteins and nucleic acids. All macromolecules are polymers (chains

  1. Complexes of Nucleic Acids with Group I and II Cations

    E-print Network

    Williams, Loren

    CHAPTER 1 Complexes of Nucleic Acids with Group I and II Cations CHIAOLONG HSIAO,a EMMANUEL experiments, show cations in diverse and sometimes unexpected environments. The interactions of nucleic acids is the coordination of Na1 , K1 , Ca21 and Mg21 by phosphates and nucleic acids. We describe coordination chemistry

  2. Purification of Nucleic Acids from Whole Blood Using Isotachophoresis

    E-print Network

    Santiago, Juan G.

    PAGE S1 Purification of Nucleic Acids from Whole Blood Using Isotachophoresis Supplementary the principle of ITP (Figure S-1); the method for on-chip nucleic acid quantitation (Figure S-3); a figure showing two methods for localizing extracted nucleic acids during ITP (Figure S-2); and the experimental

  3. Interaction of Nucleic Acids with the Glycocalyx Michael J. Palte

    E-print Network

    Raines, Ronald T.

    Interaction of Nucleic Acids with the Glycocalyx Michael J. Palte and Ronald T. Raines*, Medical Supporting Information ABSTRACT: Mammalian cells resist the uptake of nucleic acids. The lipid bilayer. To create a sensitive probe for nucleic acid-cell interactions, we synthesized fluorescent conjugates

  4. Electrostatics of Nucleic Acid Folding under Conformational Peter C. Anthony,

    E-print Network

    Herschlag, Dan

    Electrostatics of Nucleic Acid Folding under Conformational Constraint Peter C. Anthony, Adelene Y: RNA folding is enabled by interactions between the nucleic acid and its ion atmosphere, the mobile quantitative and predictive understanding of nucleic acid folding. INTRODUCTION RNA molecules carry genetic

  5. Paradigms for Computational Nucleic Acid Design Robert M. Dirks

    E-print Network

    Winfree, Erik

    Paradigms for Computational Nucleic Acid Design Robert M. Dirks , Milo Lin¶ , Erik Winfree 91125 Nucleic Acids Research, in press ABSTRACT The design of DNA and RNA sequences is critical for many of a unified approach to nucleic acid design as parameter sets are further refined. Finally, we observe

  6. Volume 14 Number 1 1986 Nucleic Acids Research Sequence landscapes

    E-print Network

    McConnell, Ross

    Volume 14 Number 1 1986 Nucleic Acids Research Sequence landscapes B.Clift, D.Haussler, R the structure of ropeating sequences In nucleic-acids, proteins and other texts. A portion of the sequence. INTRODUCTION It is often useful to examine nucleic-acid sequences for subsequences that are either unusually

  7. Synthesis of Neomycin-DNA/ Peptide Nucleic Acid

    E-print Network

    Stuart, Steven J.

    Synthesis of Neomycin-DNA/ Peptide Nucleic Acid Conjugates I. Charles and Dev P. Arya Laboratory conjugates of DNA and peptide nucleic acid (PNA) is reported. The DNA and PNA conjugates were prepared-coupled nucleic acid biopolymers is described. Keywords Neomycin, PNA, DNA, Neomycin isothiocyanate INTRODUCTION

  8. AminoglycosideNucleic Acid Interactions: The Case for Neomycin

    E-print Network

    Stuart, Steven J.

    Aminoglycoside­Nucleic Acid Interactions: The Case for Neomycin Dev P.Arya ( ) 461 Hunter Aminoglycosides and Nucleic Acids: The Attraction for RNA? . . . . . . . . . 152 2.1 The Need for New Approaches: DNA vs RNA Recognition . . . . . . . . . . . 152 3 The Nucleic Acid Triplex: Role of Aminoglycosides

  9. Advances in magnetofection—magnetically guided nucleic acid delivery

    NASA Astrophysics Data System (ADS)

    Schillinger, Ulrike; Brill, Thomas; Rudolph, Carsten; Huth, Stephanie; Gersting, Sören; Krötz, Florian; Hirschberger, Johannes; Bergemann, Christian; Plank, Christian

    2005-05-01

    Magnetofection is nucleic acid delivery to cells supported and site-specifically guided by the attractive forces of magnetic fields acting on nucleic acid shuttles (vectors) which are associated with magnetic nanoparticles. Recent progress with the method confirms its general applicability with small and large nucleic acids and viruses. The method's therapeutic application as well as mechanistic studies will be discussed.

  10. Miniaturized isothermal nucleic acid amplification, a review.

    PubMed

    Asiello, Peter J; Baeumner, Antje J

    2011-04-21

    Micro-Total Analysis Systems (µTAS) for use in on-site rapid detection of DNA or RNA are increasingly being developed. Here, amplification of the target sequence is key to increasing sensitivity, enabling single-cell and few-copy nucleic acid detection. The several advantages to miniaturizing amplification reactions and coupling them with sample preparation and detection on the same chip are well known and include fewer manual steps, preventing contamination, and significantly reducing the volume of expensive reagents. To-date, the majority of miniaturized systems for nucleic acid analysis have used the polymerase chain reaction (PCR) for amplification and those systems are covered in previous reviews. This review provides a thorough overview of miniaturized analysis systems using alternatives to PCR, specifically isothermal amplification reactions. With no need for thermal cycling, isothermal microsystems can be designed to be simple and low-energy consuming and therefore may outperform PCR in portable, battery-operated detection systems in the future. The main isothermal methods as miniaturized systems reviewed here include nucleic acid sequence-based amplification (NASBA), loop-mediated isothermal amplification (LAMP), helicase-dependent amplification (HDA), rolling circle amplification (RCA), and strand displacement amplification (SDA). Also, important design criteria for the miniaturized devices are discussed. Finally, the potential of miniaturization of some new isothermal methods such as the exponential amplification reaction (EXPAR), isothermal and chimeric primer-initiated amplification of nucleic acids (ICANs), signal-mediated amplification of RNA technology (SMART) and others is presented. PMID:21387067

  11. Thermodynamic Analysis of Nylon Nucleic Acids

    PubMed Central

    Liu, Yu; Wang, Risheng; Ding, Liang; Sha, Ruojie; Lukeman, Philip S.

    2010-01-01

    The stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides containing nylon nucleic acids (1 to 5 amide linkages) revealed that the amide linkage enhanced significantly the binding affinity of nylon nucleic acids towards both complementary DNA (up to 26°C increase in the thermal transition temperature (Tm) for 5 linkages) and RNA (around 15°C increase in Tm for 5 linkages) when compared with non-amide linked precursor strands. For both DNA and RNA complements, increasing derivatization decreased the melting temperatures of uncoupled molecules relative to unmodified strands; by contrast, increasing lengths of coupled copolymer raised Tm from less to slightly greater than Tm of unmodified strands. Thermodynamic data extracted from melting curves and CD spectra of nylon nucleic acid duplexes were consistent with loss of stability due to incorporation of pendent groups on the 2? position of ribose, and recovery of stability upon linkage of the side chains. PMID:18543259

  12. Thermodynamic Analysis of Interacting Nucleic Acid Strands

    Microsoft Academic Search

    Robert M. Dirks; Justin S. Bois; Joseph M. Schaeffer; Erik Winfree

    2007-01-01

    Motivated by the analysis of natural and engineered DNA and RNA systems, we present the first algorithm for calculating the partition function of an unpseudoknotted complex of multiple interacting nucleic acid strands. This dynamic program is based on a rigorous extension of secondary structure models to the multistranded case, addressing representa- tion and distinguishability issues that do not arise for

  13. Cellular delivery of peptide nucleic acid (PNA)

    Microsoft Academic Search

    Uffe Koppelhus; Peter E. Nielsen

    2003-01-01

    Peptide nucleic acid (PNA) is a DNA mimic having a pseudopeptide backbone that makes it extremely stable in biological fluids. PNA binds complementary RNA and DNA with high affinity and specificity. These qualities make PNA a leading agent among ‘third generation’ antisense and antigene agents. Unfortunately, fast progress in the exploration of PNA as an experimental and therapeutical regulator of

  14. Phospholipid membrane permeability of peptide nucleic acid

    Microsoft Academic Search

    Pernilla Wittung; Johan Kajanus; Katarina Edwards; Peter Nielsen; Bengt Nordén; Bo G. Malmström

    1995-01-01

    Phospholipid vesicles (liposomes) as membrane models have been used to study the penetration properties of peptide nucleic acid (PNA), a new DNA analog in which the nucleobases are attached to a pseudo-peptide backbone. The liposomes were characterised by carboxyfluorescein efflux, light-scattering and cryogenic transmission electron microscopy. The liposome structure was found not to be affected by the incorporation of PNA

  15. Human jagged polypeptide, encoding nucleic acids and methods of use

    DOEpatents

    Li, Linheng (Seattle, WA); Hood, Leroy (Seattle, WA)

    2000-01-01

    The present invention provides an isolated polypeptide exhibiting substantially the same amino acid sequence as JAGGED, or an active fragment thereof, provided that the polypeptide does not have the amino acid sequence of SEQ ID NO:5 or SEQ ID NO:6. The invention further provides an isolated nucleic acid molecule containing a nucleotide sequence encoding substantially the same amino acid sequence as JAGGED, or an active fragment thereof, provided that the nucleotide sequence does not encode the amino acid sequence of SEQ ID NO:5 or SEQ ID NO:6. Also provided herein is a method of inhibiting differentiation of hematopoietic progenitor cells by contacting the progenitor cells with an isolated JAGGED polypeptide, or active fragment thereof. The invention additionally provides a method of diagnosing Alagille Syndrome in an individual. The method consists of detecting an Alagille Syndrome disease-associated mutation linked to a JAGGED locus.

  16. Fluorescent Complexes of Nucleic Acids\\/8Hydroxyquinoline\\/Lanthanum(III) and the Fluorometry of Nucleic Acids

    Microsoft Academic Search

    Cheng Zhi Huang; Ke An Li; Shen Yang Tong

    1996-01-01

    The ternary fluorescent complexes of nucleic acids\\/8-hydroxyquinoline\\/ lanthanum (III) were studied. Nucleic acids in the study involve natured and thermally denatured calf thymus DNA, fish sperm DNA and yeast RNA. In the range of pH 8.0–8.4 (controlled by NH3-NH4Cl buffer) ternary fluorescent complexes are formed which emit at 485.0 nm for calf thymus DNA and at 480.0 nm for yeast

  17. Flexible identification of structural objects in nucleic acid sequences: palindromes, mirror repeats, pseudoknots and

    E-print Network

    Sagot, Marie-France

    Flexible identification of structural objects in nucleic acid sequences: palindromes, mirror algorithms for flexibly identifying structural objects in nucleic acid se­ quences. These objects, and | # | is the size of the alphabet of nucleotides. keywords : nucleic acid sequence, nucleic structural object

  18. In vitro selection of functional nucleic acids

    NASA Technical Reports Server (NTRS)

    Wilson, D. S.; Szostak, J. W.

    1999-01-01

    In vitro selection allows rare functional RNA or DNA molecules to be isolated from pools of over 10(15) different sequences. This approach has been used to identify RNA and DNA ligands for numerous small molecules, and recent three-dimensional structure solutions have revealed the basis for ligand recognition in several cases. By selecting high-affinity and -specificity nucleic acid ligands for proteins, promising new therapeutic and diagnostic reagents have been identified. Selection experiments have also been carried out to identify ribozymes that catalyze a variety of chemical transformations, including RNA cleavage, ligation, and synthesis, as well as alkylation and acyl-transfer reactions and N-glycosidic and peptide bond formation. The existence of such RNA enzymes supports the notion that ribozymes could have directed a primitive metabolism before the evolution of protein synthesis. New in vitro protein selection techniques should allow for a direct comparison of the frequency of ligand binding and catalytic structures in pools of random sequence polynucleotides versus polypeptides.

  19. Antitumor Activity and Nucleic Acid Binding Properties of Dercitin, a New Acridine Alkaloid Isolated from a Marine Detritus Species Sponge

    Microsoft Academic Search

    Neal S. Burres; Sharareh Sazesh; Geewananda P. Gunawardana; Jacob J. Clement

    A new cytotoxic acridine alkaloid that exhibited antitumor activity in vivo was isolated from a marine Dercitus species sponge collected at a depth of 160 m in the Bahamas. This violet alkaloid, designated dercitin, inhibited the proliferation of cultured murine and human leukemia, lung, and colon tumor cells at MM concentrations (K.� values of 63-150 MM ) and prolonged the

  20. Nucleic acids encoding antifungal polypeptides and uses thereof

    DOEpatents

    Altier, Daniel J. (Granger, IA); Ellanskaya, I. A. (Kyiv, UA); Gilliam, Jacob T. (Norwalk, IA); Hunter-Cevera, Jennie (Elliott City, MD); Presnail, James K (Avondale, PA); Schepers, Eric (Port Deposit, MD); Simmons, Carl R. (Des Moines, IA); Torok, Tamas (Richmond, CA); Yalpani, Nasser (Johnston, IA)

    2010-11-02

    Compositions and methods for protecting a plant from a pathogen, particularly a fungal pathogen, are provided. Compositions include an amino acid sequence, and variants and fragments thereof, for an antipathogenic polypeptide that was isolated from a fungal fermentation broth. Nucleic acid molecules that encode the antipathogenic polypeptides of the invention, and antipathogenic domains thereof, are also provided. A method for inducing pathogen resistance in a plant using the nucleotide sequences disclosed herein is further provided. The method comprises introducing into a plant an expression cassette comprising a promoter operably linked to a nucleotide sequence that encodes an antipathogenic polypeptide of the invention. Compositions comprising an antipathogenic polypeptide or a transformed microorganism comprising a nucleic acid of the invention in combination with a carrier and methods of using these compositions to protect a plant from a pathogen are further provided. Transformed plants, plant cells, seeds, and microorganisms comprising a nucleotide sequence that encodes an antipathogenic polypeptide of the invention are also disclosed.

  1. Development of a rapid total nucleic acid extraction method for the isolation of hepatitis A virus from fresh produce.

    PubMed

    Hida, Kaoru; Kulka, Michael; Papafragkou, Efstathia

    2013-02-15

    Recently, there have been increasing reports of foodborne illnesses associated with the consumption of fresh produce. Among these, hepatitis A virus (HAV) remains epidemiologically important and has been continually implicated in several outbreaks. We describe a rapid method (<8h) for the isolation and subsequent detection with real-time quantitative PCR (RT-qPCR) of the HAV HM-175 cytopathic strain seeded onto baby spinach and sliced tomatoes using a total RNA extraction method, utilizing a high concentration (4M) guanidine thiocyanate buffer. Consistent detection of HAV genome from both produce items was achieved at an inoculation level of 3×10³ PFU/25 g of food, with less consistent detection achieved at 3×10² PFU/25g. Initial studies revealed that a final precipitation of recovered RNA with potassium acetate to reduce carryover of polysaccharides and the addition of polyvinylpyrrolidone to remove polyphenolics in spinach were essential. For tomatoes, virus isolation was achieved with the incorporation of either an elution step with a high pH Tris-glycine-beef extract (TGBE) buffer or with an enzymatic digestion with pectinase. We also describe the development of a protocol for the detection of HAV from tomatoes utilizing a Luminex® microbead-based suspension array. The results correlated well with the RT-qPCR assay suggesting the feasibility of the Bioplex® as a detection platform for viruses isolated from foods. PMID:23334093

  2. Detection of nucleic acids by multiple sequential invasive cleavages 02

    DOEpatents

    Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Mast, Andrea L. (Madison, WI); Brow, Mary Ann D. (Madison, WI)

    2002-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  3. Detection of nucleic acids by multiple sequential invasive cleavages

    DOEpatents

    Hall, Jeff G. (Madison, WI); Lyamichev, Victor I. (Madison, WI); Mast, Andrea L. (Madison, WI); Brow, Mary Ann D. (Madison, WI)

    1999-01-01

    The present invention relates to means for the detection and characterization of nucleic acid sequences, as well as variations in nucleic acid sequences. The present invention also relates to methods for forming a nucleic acid cleavage structure on a target sequence and cleaving the nucleic acid cleavage structure in a site-specific manner. The structure-specific nuclease activity of a variety of enzymes is used to cleave the target-dependent cleavage structure, thereby indicating the presence of specific nucleic acid sequences or specific variations thereof. The present invention further relates to methods and devices for the separation of nucleic acid molecules based on charge. The present invention also provides methods for the detection of non-target cleavage products via the formation of a complete and activated protein binding region. The invention further provides sensitive and specific methods for the detection of human cytomegalovirus nucleic acid in a sample.

  4. Technical Notes Purification of Nucleic Acids from Whole Blood

    E-print Network

    Santiago, Juan G.

    Technical Notes Purification of Nucleic Acids from Whole Blood Using Isotachophoresis Alexandre for the purification of nucleic acids from biological samples using isotachophoresis (ITP). We demonstrate a simple used prepurified, ideal samples as analyte. One important application is the purification of nucleic

  5. Diagnostic Applications of Nucleic Acid Circuits

    PubMed Central

    2015-01-01

    Conspectus While the field of DNA computing and molecular programming was engendered in large measure as a curiosity-driven exercise, it has taken on increasing importance for analytical applications. This is in large measure because of the modularity of DNA circuitry, which can serve as a programmable intermediate between inputs and outputs. These qualities may make nucleic acid circuits useful for making decisions relevant to diagnostic applications. This is especially true given that nucleic acid circuits can potentially directly interact with and be triggered by diagnostic nucleic acids and other analytes. Chemists are, by and large, unaware of many of these advances, and this Account provides a means of touching on what might seem to be an arcane field. We begin by explaining nucleic acid amplification reactions that can lead to signal amplification, such as catalytic hairpin assembly (CHA) and the hybridization chain reaction (HCR). In these circuits, a single-stranded input acts on kinetically trapped substrates via exposed toeholds and strand exchange reactions, refolding the substrates and allowing them to interact with one another. As multiple duplexes (CHA) or concatemers of increasing length (HCR) are generated, there are opportunities to couple these outputs to different analytical modalities, including transduction to fluorescent, electrochemical, and colorimetric signals. Because both amplification and transduction are at their root dependent on the programmability of Waston–Crick base pairing, nucleic acid circuits can be much more readily tuned and adapted to new applications than can many other biomolecular amplifiers. As an example, robust methods for real-time monitoring of isothermal amplification reactions have been developed recently. Beyond amplification, nucleic acid circuits can include logic gates and thresholding components that allow them to be used for analysis and decision making. Scalable and complex DNA circuits (seesaw gates) capable of carrying out operations such as taking square roots or implementing neural networks capable of learning have now been constructed. Into the future, we can expect that molecular circuitry will be designed to make decisions on the fly that reconfigure diagnostic devices or lead to new treatment options. PMID:24828239

  6. Diagnostic applications of nucleic acid circuits.

    PubMed

    Jung, Cheulhee; Ellington, Andrew D

    2014-06-17

    CONSPECTUS: While the field of DNA computing and molecular programming was engendered in large measure as a curiosity-driven exercise, it has taken on increasing importance for analytical applications. This is in large measure because of the modularity of DNA circuitry, which can serve as a programmable intermediate between inputs and outputs. These qualities may make nucleic acid circuits useful for making decisions relevant to diagnostic applications. This is especially true given that nucleic acid circuits can potentially directly interact with and be triggered by diagnostic nucleic acids and other analytes. Chemists are, by and large, unaware of many of these advances, and this Account provides a means of touching on what might seem to be an arcane field. We begin by explaining nucleic acid amplification reactions that can lead to signal amplification, such as catalytic hairpin assembly (CHA) and the hybridization chain reaction (HCR). In these circuits, a single-stranded input acts on kinetically trapped substrates via exposed toeholds and strand exchange reactions, refolding the substrates and allowing them to interact with one another. As multiple duplexes (CHA) or concatemers of increasing length (HCR) are generated, there are opportunities to couple these outputs to different analytical modalities, including transduction to fluorescent, electrochemical, and colorimetric signals. Because both amplification and transduction are at their root dependent on the programmability of Waston-Crick base pairing, nucleic acid circuits can be much more readily tuned and adapted to new applications than can many other biomolecular amplifiers. As an example, robust methods for real-time monitoring of isothermal amplification reactions have been developed recently. Beyond amplification, nucleic acid circuits can include logic gates and thresholding components that allow them to be used for analysis and decision making. Scalable and complex DNA circuits (seesaw gates) capable of carrying out operations such as taking square roots or implementing neural networks capable of learning have now been constructed. Into the future, we can expect that molecular circuitry will be designed to make decisions on the fly that reconfigure diagnostic devices or lead to new treatment options. PMID:24828239

  7. Method for analyzing nucleic acids by means of a substrate having a microchannel structure containing immobilized nucleic acid probes

    DOEpatents

    Ramsey, J. Michael; Foote, Robert S.

    2003-12-09

    A method and apparatus for analyzing nucleic acids includes immobilizing nucleic probes at specific sites within a microchannel structure and moving target nucleic acids into proximity to the probes in order to allow hybridization and fluorescence detection of specific target sequences.

  8. Rapid hybridization of nucleic acids using isotachophoresis

    PubMed Central

    Bercovici, Moran; Han, Crystal M.; Liao, Joseph C.; Santiago, Juan G.

    2012-01-01

    We use isotachophoresis (ITP) to control and increase the rate of nucleic acid hybridization reactions in free solution. We present a new physical model, validation experiments, and demonstrations of this assay. We studied the coupled physicochemical processes of preconcentration, mixing, and chemical reaction kinetics under ITP. Our experimentally validated model enables a closed form solution for ITP-aided reaction kinetics, and reveals a new characteristic time scale which correctly predicts order 10,000-fold speed-up of chemical reaction rate for order 100 pM reactants, and greater enhancement at lower concentrations. At 500 pM concentration, we measured a reaction time which is 14,000-fold lower than that predicted for standard second-order hybridization. The model and method are generally applicable to acceleration of reactions involving nucleic acids, and may be applicable to a wide range of reactions involving ionic reactants. PMID:22733732

  9. Peptide nucleic acid delivery to human mitochondria

    Microsoft Academic Search

    P F Chinnery; R W Taylor; K Diekert; R Lill; D M Turnbull; R N Lightowlers

    1999-01-01

    Peptide nucleic acids (PNAs) are synthetic polynucleobase molecules, which bind to DNA and RNA with high affinity and specificity. Although PNAs have enormous potential as anti-sense agents, the success of PNA-mediated gene therapy will require efficient cellular uptake and sub-cellular trafficking. At present these mechanisms are poorly understood. To address this, we have studied the uptake of biotinylated PNAs into

  10. Carbohydrate Polymers for Nonviral Nucleic Acid Delivery

    PubMed Central

    Sizovs, Antons; McLendon, Patrick M.; Srinivasachari, Sathya

    2014-01-01

    Carbohydrates have been investigated and developed as delivery vehicles for shuttling nucleic acids into cells. In this review, we present the state of the art in carbohydrate-based polymeric vehicles for nucleic acid delivery, with the focus on the recent successes in preclinical models, both in vitro and in vivo. Polymeric scaffolds based on the natural polysaccharides chitosan, hyaluronan, pullulan, dextran, and schizophyllan each have unique properties and potential for modification, and these results are discussed with the focus on facile synthetic routes and favorable performance in biological systems. Many of these carbohydrates have been used to develop alternative types of biomaterials for nucleic acid delivery to typical polyplexes, and these novel materials are discussed. Also presented are polymeric vehicles that incorporate copolymerized carbohydrates into polymer backbones based on polyethylenimine and polylysine and their effect on transfection and biocompatibility. Unique scaffolds, such as clusters and polymers based on cyclodextrin (CD), are also discussed, with the focus on recent successes in vivo and in the clinic. These results are presented with the emphasis on the role of carbohydrate and charge on transfection. Use of carbohydrates as molecular recognition ligands for cell-type specific delivery is also briefly reviewed. We contend that carbohydrates have contributed significantly to progress in the field of non-viral DNA delivery, and these new discoveries are impactful for developing new vehicles and materials for treatment of human disease. PMID:21504102

  11. Radiochemical Reactions of Nucleic Acids and Nucleic Acid Components; STRAHLENCHEMISCHE REAKTIONEN VON NUCLEINSAURE UND NUCLEINSAUREKOMPONENTEN

    Microsoft Academic Search

    Weinblum

    1961-01-01

    The effects of ultraviolet radiation on nucleic acids were investigated. ; The problem, results, research on bacteria, stereoisomerism, sensitization, and ; the water addition reaction are discussed. X irradiation of pyrimidines was also ; studied using bacteria. Methionine was investigated as a radiation protection ; agent. The structure of adenine-1Noxide in bacteria desoxyribonucleic acid was ; determined. (M.C.G);

  12. Nucleic Acid Database: a Repository of Three-Dimensional Information about Nucleic Acids

    DOE Data Explorer

    Berman, H. M.; Olson, W. K.; Beveridge, D. L.; Westbrook, J.; Gelbin, A.; Demeny, T.; Hsieh, S. H.; Srinivasan, A. R.; Schneider, B.

    The Nucleic Acid Database (NDB) provides 3-D structural information about nucleic acids.  It is a relational database designed to facilitate the easy search for nucleic acid structures using any of the stored primary or derived structural features. Reports can then be created describing any properties of the selected structures and structures may be viewed in several different formats, including the mmCIF format, the NDB Atlas format, the NDB coordinate format, or the PDB coordinate format. Browsing structure images created directly from coordinates in the repository can also be done. More than 7000 structures have been released as of May 2014. This website also includes a number of specialized tools and interfaces. The NDB Project is funded by the National Institutes of Health and has been funded by the National Science Foundation and the Department of Energy in the past.

  13. Determination of Three-Bond 1 P Couplings in Nucleic Acids

    E-print Network

    Clore, G. Marius

    Determination of Three-Bond 1 H3 ­31 P Couplings in Nucleic Acids and Protein­Nucleic Acid- periment is described for measuring 3 JH3 ­P couplings in nucleic acids and protein­nucleic acid complexes the constant-time evolution period. For protein­nucleic acid complexes where the protein is 13 C

  14. Fluorimetric determination of nucleic acids with terbium and lutetium

    Microsoft Academic Search

    Cunguo Lin; Guiling Zhang; Jinghe Yang

    2002-01-01

    In this paper, fluorescence-enhancement of Tb–nucleic acids [fish sperm DNA (fsDNA) and yeast RNA (yRNA)] by Lu3+ is studied in detail and is applied to determine nucleic acids. The experiments indicated that under the optimum conditions, a linear relationship was obtained between the fluorescence intensity (If) and the concentration of nucleic acids. The linear range is 1.2×10?8–1.0×10?4 g\\/ml for DNA

  15. Lipid-based Nanoparticles for Nucleic Acid Delivery

    Microsoft Academic Search

    Weijun Li; Francis C. Szoka Jr

    2007-01-01

    Abstract  Lipid-based colloidal particles have been extensively studied as systemic gene delivery carriers. The topic that we would\\u000a like to emphasize is the formulation\\/assembly of lipid-based nanoparticles (NP) with diameter under 100 nm for delivering\\u000a nucleic acid in vivo. NP are different from cationic lipid–nucleic acid complexes (lipoplexes) and are vesicles composed of lipids and encapsulated\\u000a nucleic acids with a diameter less

  16. CRC handbook of chromatography: Nucleic acids and related compounds

    SciTech Connect

    Krstulovic, A.M.

    1987-01-01

    This book's contents include: Structure Elucidation of Nucleic Acid Components; Fundamentals of HPLC; Analysis of Nucleic Acids and Oligonucleotides; Extraction of Nucleic Acids from Tissues; Gel Filtration Chromatography of RNAs and DNS Fragments; Separation of tRNAs and Oligonucleotides by Mixed Mode Chromatography; Anion-Exchange and Reversed-Phase HPLC of Synthetic Oligonucleotides; Nucleic Acid Components in Biological Fluids; RPLC Separation of RNA and DNA Hydrolysates; Nucleotides in Tissue Extracts; and Determination of Adenine Nucleotides and Creatine Phosphate in Various Mammalian Tissues.

  17. EGVII endoglucanase and nucleic acids encoding the same

    DOEpatents

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2008-11-11

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  18. EGVII endoglucanase and nucleic acids encoding the same

    DOEpatents

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-05-16

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl7, and the corresponding EGVII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVII, recombinant EGVII proteins and methods for producing the same.

  19. EGVIII endoglucanase and nucleic acids encoding the same

    DOEpatents

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-05-23

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl8, and the corresponding EGVIII amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVIII, recombinant EGVIII proteins and methods for producing the same.

  20. EGVI endoglucanase and nucleic acids encoding the same

    DOEpatents

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2008-04-01

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  1. EGVI endoglucanase and nucleic acids encoding the same

    DOEpatents

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-06-06

    The present invention provides a novel endoglucanase nucleic acid sequence, designated egl6, and the corresponding EGVI amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding EGVI, recombinant EGVI proteins and methods for producing the same.

  2. Difference in conformational diversity between nucleic acids with a six-membered 'sugar' unit and natural 'furanose' nucleic acids

    Microsoft Academic Search

    Eveline Lescrinier; Matheus Froeyen; Piet Herdewijn

    2003-01-01

    Natural nucleic acids duplexes formed by Watson-Crick base pairing fold into right-handed helices that are classified in two families of second- ary structures, i.e. the A- and B-form. For a long time, these A and B allomorphic nucleic acids have been considered as the 'non plus ultra' of double- stranded nucleic acids geometries with the only exception of Z-DNA, a

  3. The Sensitive Determination of Nucleic Acids Using Fluorescence Enhancement of Eu 3+ -BenzoylacetoneCetyltrimethylammonium Bromide-Nucleic Acid System

    Microsoft Academic Search

    Xia Wu; Changying Guo; Jinghe Yang; Minqin Wang; Yanjing Chen; Jian Liu

    2005-01-01

    A new quantitative method for micro amounts of nucleic acids in aqueous solution is proposed using Eu3+-benzoylacetone (BA) complex as fluorescent probe in the presence of cetyltrimethyl-ammonium bromide (CTMAB). Under the optimum\\u000a condition, the ratio of the fluorescence intensities with and without nucleic acids is proportional to the concentration of\\u000a nucleic acid in the range of 1.0 × 10-9 to

  4. Selenium modification of nucleic acids: preparation of phosphoroselenoate derivatives for crystallographic phasing of nucleic acid structures

    Microsoft Academic Search

    Pradeep S Pallan; Martin Egli

    2007-01-01

    This protocol describes a simplified means of introducing an anomalously scattering atom into oligonucleotides by conventional solid-phase synthesis. Replacement of a nonbridging phosphate oxygen in the backbone with selenium is practically suitable for any nucleic acid. The resulting oligonucleotide P-diastereomers can be separated using anion exchange HPLC to yield diastereomerically pure phosphoroselenoates (PSes). The total time for the synthesis and

  5. Nucleic Acids Research doi:10.1093/nar/gki514

    E-print Network

    Paris-Sud XI, Université de

    Nucleic Acids Research doi:10.1093/nar/gki514 33:2192-2203, 2005.Nucleic Acids Res. Mailliet, JeanPoint slide. Journal information http://nar.oxfordjournals.org Additional information about Nucleic Acids

  6. Nucleic Acids Research doi:10.1093/nar/gki1012

    E-print Network

    Paris-Sud XI, Université de

    Nucleic Acids Research doi:10.1093/nar/gki1012 33:7138-7150, 2005.Nucleic Acids Res. Carine Barreau://nar.oxfordjournals.org Additional information about Nucleic Acids Research, including how to subscribe can be found at Published

  7. Nucleic Acids Research doi:10.1093/nar/gkf586

    E-print Network

    Paris-Sud XI, Université de

    Nucleic Acids Research doi:10.1093/nar/gkf586 30:4667-4674, 2002.Nucleic Acids Res. Sylvie Bonnet information about Nucleic Acids Research, including how to subscribe can be found at Published on behalf

  8. Simultaneous Purification and Fractionation of Nucleic Acids and Proteins from Complex Samples Using Bidirectional

    E-print Network

    Santiago, Juan G.

    Simultaneous Purification and Fractionation of Nucleic Acids and Proteins from Complex Samples and fractionate nucleic acids and proteins from complex samples using isotachophoresis (ITP). We have developed binding of proteins and DNA. Accessing correlated information between nucleic acids and proteins

  9. 21 CFR 866.3980 - Respiratory viral panel multiplex nucleic acid assay.

    Code of Federal Regulations, 2011 CFR

    2011-04-01

    ...Respiratory viral panel multiplex nucleic acid assay. 866.3980 Section 866.3980...Respiratory viral panel multiplex nucleic acid assay. (a) Identification . A respiratory viral panel multiplex nucleic acid assay is a qualitative in vitro...

  10. 21 CFR 866.3980 - Respiratory viral panel multiplex nucleic acid assay.

    Code of Federal Regulations, 2010 CFR

    2010-04-01

    ...Respiratory viral panel multiplex nucleic acid assay. 866.3980 Section 866.3980...Respiratory viral panel multiplex nucleic acid assay. (a) Identification . A respiratory viral panel multiplex nucleic acid assay is a qualitative in vitro...

  11. Charge Transfer through Single-Stranded Peptide Nucleic Acid Composed of Thymine Nucleotides

    E-print Network

    Borguet, Eric

    Charge Transfer through Single-Stranded Peptide Nucleic Acid Composed of Thymine Nucleotides Amit; In Final Form: February 18, 2008 Self-assembled monolayers (SAMs) of single-stranded peptide nucleic acids. Peptide nucleic acid (PNA) is an analo

  12. Nucleic acid interactions with pyrite surfaces

    NASA Astrophysics Data System (ADS)

    Mateo-Martí, E.; Briones, C.; Rogero, C.; Gomez-Navarro, C.; Methivier, Ch.; Pradier, C. M.; Martín-Gago, J. A.

    2008-09-01

    The study of the interaction of nucleic acid molecules with mineral surfaces is a field of growing interest in organic chemistry, origin of life, material science and biotechnology. We have characterized the adsorption of single-stranded peptide nucleic acid (ssPNA) on a natural pyrite surface, as well as the further adsorption of ssDNA on a PNA-modified pyrite surface. The characterization has been performed by means of reflection absorption infrared spectroscopy (RAIRS), atomic force microscopy (AFM) and X-ray photoemission spectroscopy (XPS) techniques. The N(1s) and S(2p) XPS core level peaks of PNA and PNA + DNA have been decomposed in curve-components that we have assigned to different chemical species. RAIRS spectra recorded for different concentrations show the presence of positive and negative adsorption bands, related to the semiconducting nature of the surface. The combination of the information gathered by these techniques confirms that PNA adsorbs on pyrite surface, interacting through nitrogen-containing groups of the nucleobases and the iron atoms of the surface, instead of the thiol group of the molecule. The strong PNA/pyrite interaction inhibits further hybridization of PNA with complementary ssDNA, contrary to the behavior reported on gold surfaces.

  13. The Effect of Nucleic Acid Geometry on Counterion Association

    Microsoft Academic Search

    Martha C. Olmsted

    1996-01-01

    The very high axial charge density of nucleic acids is a physical characteristic that substantially influences the thermodynamics of virtually all processes in which they are involved. This arises from long range electrostatic interacts between nucleic acids and the counter- and co- ions in solution so that salt concentration dramatically effects the activities of both reactants and products. A significant

  14. Nucleic Acids in Prion Preparations: Unspecific Background or Essential Component?

    Microsoft Academic Search

    K. Kellings; S. B. Prusiner; D. Riesner

    1994-01-01

    As recently published (Kellings et al. J. gen Vir. 73, 1025-1029 (1992)), the analysis of purified scrapie prions by return refocusing gel electrophoresis revealed remaining nucleic acids in the size range up to 1100 nucleotides. The results defined the possible characteristics of a hypothetical scrapie-specific nucleic acid. If homogeneous in size, such a molecule would be less than 80 nucleotides

  15. Nucleic acids encoding metal uptake transporters and their uses

    DOEpatents

    Schroeder, Julian I. (La Jolla, CA); Antosiewicz, Danuta M. (Warsaw, PL); Schachtman, Daniel P. (Tranmere, AU); Clemens, Stephan (San Diego, CA)

    1999-01-01

    The invention provides LCT1 nucleic acids which encode metal ion uptake transporters. The invention also provides methods of modulating heavy metal and alkali metal uptake in plants. The methods involve producing transgenic plants comprising a recombinant expression cassette containing an LCT1 nucleic acid linked to a plant promoter.

  16. Nucleic Acid Amplification Testing in Suspected Child Sexual Abuse

    ERIC Educational Resources Information Center

    Esernio-Jenssen, Debra; Barnes, Marilyn

    2011-01-01

    The American Academy of Pediatrics recommends that site-specific cultures be obtained, when indicated, for sexually victimized children. Nucleic acid amplification testing is a highly sensitive and specific methodology for identifying sexually transmitted infections. Nucleic acid amplification tests are also less invasive than culture, and this…

  17. Nucleic Acid Amplification Testing in Suspected Child Sexual Abuse

    Microsoft Academic Search

    Debra Esernio-Jenssen; Marilyn Barnes

    2011-01-01

    The American Academy of Pediatrics recommends that site-specific cultures be obtained, when indicated, for sexually victimized children. Nucleic acid amplification testing is a highly sensitive and specific methodology for identifying sexually transmitted infections. Nucleic acid amplification tests are also less invasive than culture, and this may provide an efficacious alternative for children suspected of being sexually abused.

  18. Enhancing nucleic acid delivery with ultrasound and microbubbles.

    PubMed

    Cool, Steven K; Geers, Bart; Lentacker, Ine; De Smedt, Stefaan C; Sanders, Niek N

    2013-01-01

    For gene therapy to work in vivo, nucleic acids need to reach the target cells without causing major side effects to the patient. In many cases the gene only has to reach a subset of cells in the body. Therefore, targeted delivery of genes to the desired tissue is a major issue in gene delivery. Many different possibilities of targeted gene delivery have been studied. A relatively novel approach to target nucleic acids and other drugs to specific regions in the body is the use of ultrasound and microbubbles. Microbubbles are gas-filled spheres with a stabilizing lipid, protein, or polymer shell. When these microbubbles enter an ultrasonic field, they start to oscillate. The bubble expansion and compression are inversely related to the pressure phases in the ultrasonic field. When microbubbles are exposed to high-intensity ultrasound they will eventually implode and fragment. This generates shockwaves and microjets which can temporarily permeate cell membranes and blood vessels. Nucleic acids or (non)-viral vectors can extravasate through these pores to gain access to the cell's cytoplasm or the surrounding tissue. The nucleic acids can either be mixed with the microbubbles or loaded on the microbubbles. Nucleic acid-loaded microbubbles can be obtained by coupling nucleic acid-containing particles (i.e., lipoplexes) to the microbubbles. Upon ultrasound-mediated implosion of the microbubbles, the nucleic acid-containing particles will be released and will deliver their nucleic acids in the ultrasound-targeted region. PMID:23070772

  19. Peptide Nucleic Acid-Assisted Topological Labeling of Duplex DNA

    Microsoft Academic Search

    Vadim V. Demidov; Heiko Kuhn; Irina V. Lavrentieva-Smolina; Maxim D. Frank-Kamenetskii

    2001-01-01

    Peptide nucleic acids (PNAs) are a family of synthetic polyamide mimics of nucleic acids that offer a variety of applications. Pyrimidine bis-PNAs can be used for rational design of novel interlocked DNA nanostructures, earring labels, representing locked pseudorotaxanes or locked catenanes. These structures are created through DNA ligase-mediated catenation of duplex DNA with a circularized oligonucleotide tag at a designated

  20. Structural and biological properties of peptide nucleic acid (PNA)

    Microsoft Academic Search

    Peter E. Nielsen

    1998-01-01

    The chemical, physical and biological properties of PNA (peptide nucleic acid) is briefly reviewed. In particular, recent X-ray crystallography and NMR structural data on PNA complexes are discussed. Furthermore, effects of backbone or nucleobase modifications on the PNA nucleic acid hybridization properties are discussed.

  1. Simultaneous purification and fractionation of nucleic acids and proteins from complex

    E-print Network

    Santiago, Juan G.

    Simultaneous purification and fractionation of nucleic acids and proteins from complex samples purification and fractionation of nucleic acids and proteins from complex biological samples: · Figure S-1

  2. Light-Up Probes: Thiazole Orange-Conjugated Peptide Nucleic Acid for Detection of Target Nucleic Acid in Homogeneous Solution

    Microsoft Academic Search

    Nicke Svanvik; Gunnar Westman; Dongyuan Wang; Mikael Kubista

    2000-01-01

    We have constructed light-up probes for nucleic acid detection. The light-up probe is a peptide nucleic acid (PNA) oligonucleotide to which the asymmetric cyanine dye thiazole orange (TO) is tethered. It combines the excellent hybridization properties of PNA and the large fluorescence enhancement of TO upon binding to DNA. When the PNA hybridizes to target DNA, the dye binds and

  3. Macromolecular Structure Description: This course covers the principles of protein and nucleic acid structure, stability

    E-print Network

    Sherrill, David

    and nucleic acid structure, stability and dynamics. Topics will include interactions, conformations, forces of Biopolymers Amino Acids The Peptide Bond Protein Rotamers: Ramachandran plots The Nucleic Acid Bases The Nucleic Acid Backbone Nucleic Acid Rotamers Introduction to PYMOL: visualization software Introduction

  4. Poisson-Boltzmann calculations for nucleic acids and nucleic acids complexes

    Microsoft Academic Search

    Krystyna Zakrzewska; Andrea Madami; Richard Lavery

    1996-01-01

    Numerical solution of Poisson-Boltzmann equation with the finite difference DelPhi program is applied to calculations of the electrostatic energy of nucleic acids and their complexes with ligands. It is shown that this approach improves on the results obtained with a simple distance dielectric function. In the case of DNA-drug complexation, the correct preference for binding mode is observed and complexation

  5. Mechanism of helicase translocation along nucleic acid

    E-print Network

    Zhang, Yunxin

    2012-01-01

    In cells, helicase translocation along nucleic acid is essential for many biological processes. However, so far, the mechanism of this translocation is not fully understood. Recent studies show that helicase might translocate through two processes, active process and passive process, with different translocation rate. In this study, a model including such two processes is presented. In which, each of these two processes consists of two sub-processes, chemical sub-process in which needed translocation factors are attached, and mechanochemical sub-process in which helicase makes a forward translocation step. Helicase can switch stochastically between these two processes with external force dependent rates. By this model, ribosome translocation along message RNA is detailed discussed. We found that, with the increase of external force, the mean translocation rate of ribosome increases from one lower limit to one upper limit, and both of these two limits increase with concentrations of the translocation factors. ...

  6. Gamma Peptide Nucleic Acids: As Orthogonal Nucleic Acid Recognition Codes for Organizing Molecular Self-Assembly.

    PubMed

    Sacui, Iulia; Hsieh, Wei-Che; Manna, Arunava; Sahu, Bichismita; Ly, Danith H

    2015-07-01

    Nucleic acids are an attractive platform for organizing molecular self-assembly because of their specific nucleobase interactions and defined length scale. Routinely employed in the organization and assembly of materials in vitro, however, they have rarely been exploited in vivo, due to the concerns for enzymatic degradation and cross-hybridization with the host's genetic materials. Herein we report the development of a tight-binding, orthogonal, synthetically versatile, and informationally interfaced nucleic acid platform for programming molecular interactions, with implications for in vivo molecular assembly and computing. The system consists of three molecular entities: the right-handed and left-handed conformers and a nonhelical domain. The first two are orthogonal to each other in recognition, while the third is capable of binding to both, providing a means for interfacing the two conformers as well as the natural nucleic acid biopolymers (i.e., DNA and RNA). The three molecular entities are prepared from the same monomeric chemical scaffold, with the exception of the stereochemistry or lack thereof at the ?-backbone that determines if the corresponding oligo adopts a right-handed or left-handed helix, or a nonhelical motif. These conformers hybridize to each other with exquisite affinity, sequence selectivity, and level of orthogonality. Recognition modules as short as five nucleotides in length are capable of organizing molecular assembly. PMID:26079820

  7. Practical application of nucleic acid techniques to avian disease problems.

    PubMed

    Purchase, H G

    1989-01-01

    A workshop in which 17 practicing scientists participated was intended to address primarily people who use or could use biotechnology in their work and was confined to five techniques. Endonuclease fingerprinting and mapping involved cleaving nucleic acid with a specific restriction enzyme and separating the nucleic acid fragments by electrophoresis. Field and vaccine isolates of Pasteurella multocida could be distinguished; Salmonella enteritidis could be divided into three groups; chlamydia could be grouped into seven groups; and vaccinia, quail pox, and fowl pox could be clearly distinguished. Preparation of nucleic acid probes involved producing large amounts of labeled oligonucleotides, usually of unknown sequence. Successful probes had been made for infectious bursal disease virus, avian influenza virus, Newcastle disease virus, and infectious bronchitis virus. In Southern, Northern, and dot blotting, either DNA or RNA fragments were placed on or transferred to a solid substrate and probed. The procedure was able to detect infectious bursal disease virus, infectious bronchitis virus, Mycoplasma gallisepticum, and Marek's disease virus. In situ hybridization involved applying a labeled probe to frozen or fixed sections or to intact cells. In Polymerase chain reaction, two primers, some distance apart, were annealed to a denatured target DNA. Repeated cycles of DNA synthesis with a thermostable polymerase, denaturing, and reannealing resulted in great amplification of a rare sequence. After 30 cycles, a rare gene sequence could be amplified more than 10(6) times. It was used successfully to detect minute quantities of influenza virus and infectious bursal disease virus, and the process was used to facilitate DNA sequencing of coccidiosis gene segments. PMID:2559697

  8. Nucleic acid-binding polymers as anti-inflammatory agents

    PubMed Central

    Lee, Jaewoo; Sohn, Jang Wook; Zhang, Ying; Leong, Kam W.; Pisetsky, David; Sullenger, Bruce A.

    2011-01-01

    Dead and dying cells release nucleic acids. These extracellular RNAs and DNAs can be taken up by inflammatory cells and activate multiple nucleic acid-sensing toll-like receptors (TLR3, 7, 8, and 9). The inappropriate activation of these TLRs can engender a variety of inflammatory and autoimmune diseases. The redundancy of the TLR family encouraged us to seek materials that can neutralize the proinflammatory effects of any nucleic acid regardless of its sequence, structure or chemistry. Herein we demonstrate that certain nucleic acid-binding polymers can inhibit activation of all nucleic acid-sensing TLRs irrespective of whether they recognize ssRNA, dsRNA or hypomethylated DNA. Furthermore, systemic administration of such polymers can prevent fatal liver injury engendered by proinflammatory nucleic acids in an acute toxic shock model in mice. Therefore these polymers represent a novel class of anti-inflammatory agent that can act as molecular scavengers to neutralize the proinflammatory effects of various nucleic acids. PMID:21844380

  9. On the statistical significance of nucleic acid similarities

    Microsoft Academic Search

    David J. Lipman; W. John Wilbur; Temple F. Smith; Michael S. Waterman

    1984-01-01

    Abstract: When evaluating sequence similarities among nucleic acids bythe usual methods, statistical significance is often found whenthe biological significance of the similarity is dubious. Wedemonstrate that the known statistical properties of nucleic acidsequences strongly affect the statistical distribution ofsimilarity values when calculated by standard procedures. Wepropose a series of models which account for some of these knownstatistical properties. The utility

  10. Nucleic Acids Research doi:10.1093/nar/gkn315

    E-print Network

    Minnesota, University of

    Nucleic Acids Research doi:10.1093/nar/gkn315 First published online 4 Jun 2008;Nucleic Acids Res://nar.oxfordjournals.org Additional information about Nucleic Acids Research, including how to subscribe can be found at Published -- Bio-Medical Library on 20 June 2008http://nar.oxfordjournals.orgDownloaded from #12;Nucleic Acids

  11. Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins

    E-print Network

    Levin, Judith G.

    Nucleic acid binding and chaperone properties of HIV-1 Gag and nucleocapsid proteins Margareta and NCp7) with nucleic acids using solution and single molecule experi- ments. The NC cleavage products as a nucleic acid binding and packaging protein and the primary function of the NC proteins as nucleic acid

  12. Nucleic Acid Conformational Changes Essential for HIV-1 Nucleocapsid Protein-mediated Inhibition of

    E-print Network

    Levin, Judith G.

    Nucleic Acid Conformational Changes Essential for HIV-1 Nucleocapsid Protein-mediated Inhibition) is a nucleic acid chaperone protein that has been shown to greatly facilitate the nucleic acid rearrangements and a TAR-containing acceptor RNA molecule, we find that when both nucleic acids are present, NC facilitates

  13. Biochemistry 766: Nucleic Acids http://www.biosci.ohio-state.edu/~mfoster/biochem766/

    E-print Network

    Gopalan, Venkat

    Biochemistry 766: Nucleic Acids http://www.biosci.ohio-state.edu/~mfoster/biochem766/ http Riffe Primary Text: Nucleic Acids in Chemistry and Biology. Blackburn, Gait, Loakes and Williams, eds Nucleic acids biochemistry; history and context Nucleic acid nomenclature; tautomerism; ionization

  14. Nucleic Acids Research doi:10.1093/nar/gkn295

    E-print Network

    Paris-Sud XI, Université de

    Nucleic Acids Research doi:10.1093/nar/gkn295 First published online 20 Jun 2008;Nucleic Acids Res://nar.oxfordjournals.org Additional information about Nucleic Acids Research, including how to subscribe can be found at Published-Médiathèque scientifique on 27 June 2008http://nar.oxfordjournals.orgDownloaded from #12;Nucleic Acids Research, 2008, 1

  15. Thermodynamics of Nucleic Acid "Shape Readout" by an Hongjuan Xi, Erik Davis, Nihar Ranjan, Liang Xue,

    E-print Network

    Stuart, Steven J.

    Thermodynamics of Nucleic Acid "Shape Readout" by an Aminosugar Hongjuan Xi, Erik Davis, Nihar ABSTRACT: Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid- protein interactions. In addition to the direct readout mechanisms

  16. NUCLEIC ACID DETECTION USING BIOLUMINESCENCE REGENERATIVE CYCLE AND STATISTICAL SIGNAL PROCESSING

    E-print Network

    Hassibi, Arjang

    NUCLEIC ACID DETECTION USING BIOLUMINESCENCE REGENERATIVE CYCLE AND STATISTICAL SIGNAL PROCESSING H- velopment of signal processing techniques for rapid real- time nucleic acid detection [1]. In this paper, we experimental results. 1. ON NUCLEIC ACID DETECTION The identification and quantification of nucleic acid

  17. Efficient and Sequence-Specific DNA-Templated Polymerization of Peptide Nucleic Acid Aldehydes

    E-print Network

    Liu, David R.

    Efficient and Sequence-Specific DNA-Templated Polymerization of Peptide Nucleic Acid Aldehydes. Peptide nucleic acids (PNAs) are attractive candidates for synthetic polymer evolution because and sequence-specific nucleic acid-templated polymerization of proteins and nucleic acids is a fundamental

  18. Nucleic acid duplexes incorporating a dissociable covalent base pair

    NASA Technical Reports Server (NTRS)

    Gao, K.; Orgel, L. E.; Bada, J. L. (Principal Investigator)

    1999-01-01

    We have used molecular modeling techniques to design a dissociable covalently bonded base pair that can replace a Watson-Crick base pair in a nucleic acid with minimal distortion of the structure of the double helix. We introduced this base pair into a potential precursor of a nucleic acid double helix by chemical synthesis and have demonstrated efficient nonenzymatic template-directed ligation of the free hydroxyl groups of the base pair with appropriate short oligonucleotides. The nonenzymatic ligation reactions, which are characteristic of base paired nucleic acid structures, are abolished when the covalent base pair is reduced and becomes noncoplanar. This suggests that the covalent base pair linking the two strands in the duplex is compatible with a minimally distorted nucleic acid double-helical structure.

  19. Optimization of Encoded Hydrogel Particles for Nucleic Acid Quantification

    E-print Network

    Pregibon, Daniel C.

    The accurate quantification of nucleic acids is of utmost importance for clinical diagnostics, drug discovery, and basic science research. These applications require the concurrent measurement of multiple targets while ...

  20. Geometric properties of nucleic acids with potential for autobuilding

    SciTech Connect

    Gruene, Tim; Sheldrick, George M. [Department of Structural Chemistry, Georg-August-University Göttingen, Tammanstrasse 4, D-37077 Göttingen (Germany)

    2011-01-01

    Algorithms and geometrical properties are described for the automated building of nucleic acids in experimental electron density. Medium- to high-resolution X-ray structures of DNA and RNA molecules were investigated to find geometric properties useful for automated model building in crystallographic electron-density maps. We describe a simple method, starting from a list of electron-density ‘blobs’, for identifying backbone phosphates and nucleic acid bases based on properties of the local electron-density distribution. This knowledge should be useful for the automated building of nucleic acid models into electron-density maps. We show that the distances and angles involving C1? and the P atoms, using the pseudo-torsion angles ?' and ?' that describe the …P—C1?—P—C1?… chain, provide a promising basis for building the nucleic acid polymer. These quantities show reasonably narrow distributions with asymmetry that should allow the direction of the phosphate backbone to be established.

  1. Molecular assembly for high-performance bivalent nucleic acid inhibitor

    E-print Network

    Tan, Weihong

    of a biological entity, such as small molecules, oligosaccharides, proteins, nucleic acids (NAs), lipids of galactose- terminated oligosaccharides to C-type mammalian hepatic lec- tins (2). In addition to increased

  2. Lanthanide Chelates as a Tool in Nucleic Acid Chemistry

    PubMed Central

    Mukkala, Veli-Matti; Takalo, Harri; Liitti, Päivi; Kankare, Jouko; Kuusela, Satu

    1994-01-01

    The potentiality of lanthanide chelates as photoluminescent markers and cleaving agents of nucleic acids is discussed, the main emphasis being on the chelates derived from aromatic nitrogen bases. PMID:18476232

  3. Molecular Modeling of Nucleic Acid Structure: Setup and Analysis

    PubMed Central

    Galindo-Murillo, Rodrigo; Bergonzo, Christina; Cheatham, Thomas E.

    2014-01-01

    The last in a set of units by these authors, this unit addresses some important remaining questions about molecular modeling of nucleic acids. It describes how to choose an appropriate molecular mechanics force field; how to set up and equilibrate the system for accurate simulation of a nucleic acid in an explicit solvent by molecular dynamics or Monte Carlo simulation; and provides some information about how to analyze molecular dynamics trajectories. PMID:18428869

  4. Changes of nucleic acids of wheat seedlings under spaceflight conditions

    NASA Technical Reports Server (NTRS)

    Sytnyk, K. M.; Musatenko, L. I.

    1983-01-01

    The effects of space flight on the growth of wheat seedlings and their nucleic acid content were studied. It was shown that both space and ground seedlings have almost the same appearance, dry weight and nucleic acid content in the root, coleoptile and leaves. The only difference found is in the RNA and DNA content, which is twice as much in the ground seedling apices as in the space-grown seedlings.

  5. Nucleic Acid Transport in Plant-Pathogen Interactions

    Microsoft Academic Search

    Robert Lartey; Vitaly Citovsky

    \\u000a Transport of nucleic acid molecules is central to many plant-pathogen interactions. Nucleic acids are transported between\\u000a cells when plant viruses move their genomes from the infected into adjacent uninfected cells through plant intercellular connections,\\u000a the plasmodesmata. DNA and RNA molecules are also transported from the host cell cytoplasm into the nucleus during many viral\\u000a infections. In addition, nuclear import of

  6. [Specific features of nucleic acid synthesis in mitochondria of Elymus sibiricus from different natural populations].

    PubMed

    Lutsenko, G N; Zykova, V V; Konstantinov, Iu M

    2003-01-01

    Conditions and kinetic characteristics of nucleic acid synthesis were studied in the isolated mitochondria of Elymus sibiricus from different natural populations. The results showed the reciprocal dependence of RNA and DNA synthesis rates in the mitochondrial genetic system of E. sibiricus seedlings of different genotypes. PMID:12816062

  7. Targeted Delivery of DNA to the Mitochondrial Compartment via Import Sequence-Conjugated Peptide Nucleic Acid

    Microsoft Academic Search

    A. Flierl; C. Jackson; B. Cottrell; D. Murdock; P. Seibel; D. C. Wallace

    2003-01-01

    We report that oligonucleotides can be introduced into the mitochondria of living mammalian cells by annealing them to peptide nucleic acids coupled to mitochondrial targeting peptides. These complexes are imported into the mitochondrial matrix through the outer and inner membrane import channels of isolated mitochondria. They are also imported into the mitochondria of cultured cells, provided that the cytosolic uptake

  8. Towards Accurate Prediction of Protonation Equilibrium of Nucleic Acids.

    PubMed

    Goh, Garrett B; Knight, Jennifer L; Brooks, Charles L

    2013-03-01

    The role of protonated nucleotides in modulating the pH-dependent properties of nucleic acids is one of the emerging frontiers in the field of nucleic acid biology. The recent development of a constant pH molecular dynamics simulation (CPHMD(MS?D)) framework for simulating nucleic acids has provided a tool for realistic simulations of pH-dependent dynamics. We enhanced the CPHMD(MS?D) framework with pH-based replica exchange (pH-REX), which significantly improves the sampling of both titration and spatial coordinates. The results from our pKa calculations for the GAAA tetraloop, which was predicted with lower accuracy previously due to sampling challenges, demonstrates that pH-REX reduces the average unsigned error (AUE) to 0.7 pKa units, and the error of the most poorly predicted residue A17 was drastically reduced from 2.9 to 1.2 pKa unit. Lastly, we show that pH-REX CPHMD(MS?D) simulations can be used to identify the dominant conformation of nucleic acid structures in alternate pH environments. This work suggests that pH-REX CPHMD(MS?D) simulations provide a practical tool for predicting nucleic acid protonation equilibrium from first-principles, and offering structural and mechanistic insight into the study of pH-dependent properties of nucleic acids. PMID:23526474

  9. Dioxaphosphorinane-Constrained Nucleic Acid Dinucleotides as Tools for Structural Tuning of Nucleic Acids

    PubMed Central

    Catana, Dan-Andrei; Renard, Brice-Loïc; Maturano, Marie; Payrastre, Corinne; Tarrat, Nathalie; Escudier, Jean-Marc

    2012-01-01

    We describe a rational approach devoted to modulate the sugar-phosphate backbone geometry of nucleic acids. Constraints were generated by connecting one oxygen of the phosphate group to a carbon of the sugar moiety. The so-called dioxaphosphorinane rings were introduced at key positions along the sugar-phosphate backbone allowing the control of the six-torsion angles ? to ? defining the polymer structure. The syntheses of all the members of the D-CNA family are described, and we emphasize the effect on secondary structure stabilization of a couple of diastereoisomers of ?,?-D-CNA exhibiting wether B-type canonical values or not. PMID:23150809

  10. Determination of Nucleic Acids Based on their Resonance Light Scattering Enhancement Effect on Metalloporphyrin Derivatives

    Microsoft Academic Search

    Zhanguang Chen; Weifeng Ding; Yizeng Liang; Fenglian Ren; Yali Han; Jinbin Liu

    2005-01-01

    A new method for the determination of nucleic acids at nanogram per mL level is proposed based on the enhanced resonance light scattering (RLS) signal resulting from the interaction of metalloporphyrins with nucleic acids. Under optimum conditions, the weak RLS signal of metalloporphyrin is enhanced by nucleic acids, and the enhanced RLS intensity is proportional to the concentration of nucleic

  11. Nucleic Acids Research doi:10.1093/nar/gkn325

    E-print Network

    Nucleic Acids Research doi:10.1093/nar/gkn325 36:377-384, 2008. First published 28 May 2008;Nucleic://nar.oxfordjournals.org Additional information about Nucleic Acids Research, including how to subscribe can be found at Published 2008 Nucleic Acids Research, 2008, Vol. 36, Web Server issue W377­W384 doi:10.1093/nar/gkn325 ENDEAVOUR

  12. Nucleic Acids Research doi:10.1093/nar/gkn305

    E-print Network

    Lin, Guohui

    Nucleic Acids Research doi:10.1093/nar/gkn305 36:496-502, 2008. First published 30 May 2008;Nucleic://nar.oxfordjournals.org Additional information about Nucleic Acids Research, including how to subscribe can be found at Published 2008http://nar.oxfordjournals.orgDownloaded from #12;W496­W502 Nucleic Acids Research, 2008, Vol. 36

  13. Chemical and structural biology of nucleic acids and protein-nucleic acid complexes for novel drug discovery

    Microsoft Academic Search

    JianHua Gan; Jia Sheng; Zhen Huang

    2011-01-01

    Since nucleic acids (DNA and RNA) play very important roles in cells, they are molecular targets of many clinically used drugs,\\u000a such as anticancer drugs and antibiotics. Because of clinical demands for treating various deadly cancers and drug-resistant\\u000a strains of pathogens, there are urgent needs to develop novel therapeutic agents. Targeting nucleic acids hasn’t been the\\u000a mainstream of drug discovery

  14. Fluorimetric determination of nucleic acid using the enhancement of terbium–gadolinium–nucleic acid–cetylpyridine bromide system

    Microsoft Academic Search

    Lei Li; Jinghe Yang; Xia Wu; Changxia Sun; Guangjun Zhou

    2003-01-01

    It is found that the fluorescence intensity of Tb–cetylpyridine bromide (CPB)–nucleic acid system can be enhanced by La3+, Gd3+, Lu3+, Sc3+ and Y3+, of which Gd3+ has the greatest enhancement. The experiments indicate that under the optimum condition, the fluorescence intensity of the system is in proportion to the concentration of nucleic acids in the range from 9×10?8 to 1×10?5

  15. Enhanced nucleic acid capture and flow cytometry detection with peptide nucleic acid probes and tunable-surface microparticles

    Microsoft Academic Search

    Darrell P. Chandler; Ann E. Jarrell

    2003-01-01

    New methods for automated, direct nucleic acid purification and detection are required for the next generation of unattended environmental monitoring devices. In this study we investigated whether tunable-surface bead chemistry and peptide nucleic acids (PNA) could enhance the recovery and detection of intact rRNA in both test tube and automated suspension array hybridization formats. Intact rRNA was easily captured and

  16. Study of the interaction of nucleic acids with acridine orange-CTMAB and determination of nucleic acids at nanogram levels based on the enhancement of resonance light scattering

    Microsoft Academic Search

    Rutao Liu; Jinghe Yang; Changxia Sun; Lei Li; Xia Wu; Zhengmin Li; Chuansong Qi

    2003-01-01

    The resonance light scattering (RLS) of acridine orange (AO) are greatly enhanced by both nucleic acid and cetyltrimethyl ammonium bromide (CTMAB). Based on this, nucleic acids can be sensitively determined. The interaction of AO with nucleic acid in the presence of CTMAB is studied by using RLS, absorption spectroscopy, zeta potential assay, transmission electron microscope (TEM) image and molecular molding.

  17. Rapid Kinetics of Protein–Nucleic Acid Interaction is a Major Component of HIV1 Nucleocapsid Protein’s Nucleic Acid Chaperone Function

    Microsoft Academic Search

    Margareta Cruceanu; Robert J. Gorelick; Karin Musier-Forsyth; Ioulia Rouzina; Mark C. Williams

    2006-01-01

    The nucleic acid chaperone activity of the human immunodeficiency virus type-1 (HIV-1) nucleocapsid protein (NC) plays an important role in the retroviral life cycle, in part, by facilitating numerous nucleic acid rearrangements throughout the reverse transcription process. Recent studies have identified duplex destabilization and nucleic acid aggregation as the two major components of NC's chaperone activity. In order to better

  18. Recent Progress in Nucleic Acid Aptamer-Based Biosensors and Bioassays

    PubMed Central

    Mok, Wendy; Li, Yingfu

    2008-01-01

    As the key constituents of the genetic code, the importance of nucleic acids to life has long been appreciated. Despite being composed of only four structurally similar nucleotides, single-stranded nucleic acids, as in single-stranded DNAs and RNAs, can fold into distinct three-dimensional shapes due to specific intramolecular interactions and carry out functions beyond serving as templates for protein synthesis. These functional nucleic acids (FNAs) can catalyze chemical reactions, regulate gene expression, and recognize target molecules. Aptamers, whose name is derived from the Latin word aptus meaning “to fit”, are oligonucleotides that can bind their target ligands with high affinity and specificity. Since aptamers exist in nature but can also be artificially isolated from pools of random nucleic acids through a process called in vitro selection, they can potentially bind a diverse array of compounds. In this review, we will discuss the research that is being done to develop aptamers against various biomolecules, the progress in engineering biosensors by coupling aptamers to signal transducers, and the prospect of employing these sensors for a range of chemical and biological applications. Advances in aptamer technology emphasizes that nucleic acids are not only the fundamental molecules of life, they can also serve as research tools to enhance our understanding of life. The possibility of using aptamer-based tools in drug discovery and the identification of infectious agents can ultimately augment our quality of life.

  19. [Method for automated extraction and purification of nucleic acids and its implementation in microfluidic system].

    PubMed

    Mamaev, D D; Khodakov, D A; Dement'eva, E I; Filatov, I V; Iurasov, D A; Cherepanov, A I; Vasiliskov, V A; Smoldovskaia, O V; Zimenkov, D V; Griadunov, D A; Mikha?lovich, V M; Zasedatelev, A S

    2011-01-01

    A method and a microfluidic device for automated extraction and purification of nucleic acids from biological samples have been developed. The method involves disruption of bacterial cells and/or viral particles by combining enzymatic and chemical lysis procedures followed by solid-phase sorbent extraction and purification of nucleic acids. The procedure is carried out in an automated mode in a microfluidic module isolated from the outside environment, which minimizes contact of the researcher with potentially infectious samples and, consequently, decreases the risk of laboratory-acquired infections. The module includes reservoirs with lyophilized components for lysis and washing buffers; a microcolumn with a solid-phase sorbent; reservoirs containing water, ethanol, and water-ethanol buffer solutions for dissolving freeze-dried buffer components, rinsing the microcolumn, and eluting of nucleic acids; and microchannels and valves needed for directing fluids inside the module. The microfluidic module is placed into the control unit that delivers pressure, heats, mixes reagents, and flows solutions within the microfluidic module. The microfluidic system performs extraction and purification of nucleic acids with high efficiency in 40 min, and nucleic acids extracted can be directly used in PCR reaction and microarray assays. PMID:22808749

  20. Study on the interaction between nucleic acid and Eu 3+–oxolinic acid and the determination of nucleic acid using the resonance light scattering technique

    Microsoft Academic Search

    Xia Wu; Shuna Sun; Jinghe Yang; Minqin Wang; Liyan Liu; Changying Guo

    At pH 9.75, the resonance light scattering (RLS) intensity of OA–Eu3+ system is greatly enhanced by nucleic acid. Based on this phenomenon, a new quantitative method for nucleic acid in aqueous solution has been developed. Under the optimum condition, the enhanced RLS is proportional to the concentration of nucleic acid in the range of 1.0×10?9 to 1.0×10?6g\\/ml for herring sperm

  1. Study on the interaction between nucleic acid and Eu 3+–oxolinic acid and the determination of nucleic acid using the resonance light scattering technique

    Microsoft Academic Search

    Xia Wu; Shuna Sun; Jinghe Yang; Minqin Wang; Liyan Liu; Changying Guo

    2005-01-01

    At pH 9.75, the resonance light scattering (RLS) intensity of OA–Eu3+ system is greatly enhanced by nucleic acid. Based on this phenomenon, a new quantitative method for nucleic acid in aqueous solution has been developed. Under the optimum condition, the enhanced RLS is proportional to the concentration of nucleic acid in the range of 1.0×10?9 to 1.0×10?6g\\/ml for herring sperm

  2. Optimization of influencing factors of nucleic acid adsorption onto silica-coated magnetic particles: application to viral nucleic acid extraction from serum.

    PubMed

    Sun, Ning; Deng, Congliang; Liu, Yi; Zhao, Xiaoli; Tang, Yan; Liu, Renxiao; Xia, Qiang; Yan, Wenlong; Ge, Guanglu

    2014-01-17

    We present a detailed study of nucleic acid adsorption onto silica-coated magnetic particles in the presence of guanidinium thiocyanate, and extraction of nucleic acid from two important transfusion-transmitted viruses using these particles. Silica-coated magnetic particles were prepared by encapsulating Fe3O4 nanoparticles with tetraethylorthosilicate (TEOS) hydrolysis. Scanning electron microscopy (SEM), transmission electron microscopy (TEM), dynamic light scattering (DLS) and vibrating sample magnetometer (VSM) were used for particle characterization. The results indicate that silica-coated magnetic particles are spheroid with a narrow hydrodynamic size distribution of about 500nm. VSM data indicates that these particles display paramagnetic behavior with saturation magnetization of about 30emu/g. The adsorption capacities were evaluated with DNA from salmon sperm and RNA of Escherichia coli strain JM109 in the presence of guanidinium thiocyanate. The maximum of adsorption is up to 10.6mg DNA or 7.7mg RNA per 1g of silica-coated magnetic particles with 4M guanidinium thiocyanate (GTC) at pH 5.5 without adding ethanol. The influencing factors were analyzed in term of the adsorption of nucleic acids onto silica-coated magnetic particles. The adsorption capacity in acidic condition is found to be larger than that in alkaline condition and increases with adding equivalent volume of ethanol. A simple method was therefore established to extract nucleic acids of two important transfusion-transmitted viruses from serum and compared with the commercial kits. The results indicate that the extraction method based on silica-coated magnetic particles can be adapted to rapidly and facilely isolate viral nucleic acid for diagnosis of viral infection from serum within 30min, irrespective of genome compositions of virus. PMID:24360257

  3. Pseudointrinsic probes for generating spectrally enhanced proteins and nucleic acids

    NASA Astrophysics Data System (ADS)

    Ross, J. B. Alexander; Hasselbacher, Carol A.; Rusinova, Elena; Senear, D. F.; Laws, William R.

    1995-04-01

    The convergence of methods and techniques in biological fluorescence spectroscopy and molecular biotechnology have resulted in improved strategies for labelling specific sites in proteins and nucleic acids. Extrinsic probes, such as dansyl or fluorescein, are commonly used for labelling of proteins and nucleic acids. Introduction of extrinsic probes by covalent modification, however, is always accompanied by the potential risk of altering structure and/or function of these macromolecules. As an alternative to the use of extrinsic probes, there has been a developing interest in the use of tryptophan or nucleic acid base analogs as pseudo intrinsic probes in proteins and nucleic acids. The objective is to generate spectrally enhanced proteins or nucleic acids that are labelled at specific sites and that retain most or all of the functional features of the non-enhanced parent macromolecule. Base analogs with desirable spectroscopic properties can be introduced by direct synthesis. Tryptophan analogs with desirable spectroscopic properties can be introduced into proteins by expression in vivo or in vitro, or by direct chemical synthesis.

  4. Synthesis and characterization of peptide nucleic acid platinum nanoclusters

    Microsoft Academic Search

    Xu Wang; Rajeev R. Pandey; Krishna V. Singh; G. T. Senthil Andavan; Chunglin Tsai; Roger Lake; Mihrimah Ozkan; Cengiz S. Ozkan

    2006-01-01

    Peptide nucleic acid (PNA) is an analogue of deoxyribonucleic acid (DNA) and possesses a neutral backbone that affords stronger hybridization, greater stability and higher specificity in base pairing. However, it has not been explored as much as DNA in self-assembling functional nanostructures or nanoelectronic devices. We report here for the first time the metallization of PNA with platinum (Pt) nanoparticles

  5. Nucleic acid compositions with scissile linkage useful for detecting nucleic acid sequences

    SciTech Connect

    Duck, P.; Bender, R.; Crosby, W.; Robertson, J.G.

    1989-10-24

    This patent describes a composition. It comprises the structure: S-L(NA{sub 1}-S-NA{sub 2}){sub n}M. NA{sub 1} and NA{sub 2} are nucleic acid sequences; -S- is a scissile linkage which is capable of being cleaved or disrupted without cleaving or disrupting the nuclei acid sequences of NA{sub 1} or NA{sub 2} or of a target nuclei acid sequence capable of hybridizing to the NA{sub 1} and NA{sub 2} sequences, or to the NA{sub 1} and NA{sub 2} sequences and the scissile linkage of the composition, wherein if the scissile linkage is a nuclei acid sequence it is RNA when both NA{sub 1} and NA{sub 2} are DNA sequences, or the scissile linkage is DNA when both NA{sub 1} and NA{sub 2} are RNA sequences; and n is an integer from 1 to 4. The solid lines represent chemical bonds; X is a solid support; L is a chemical entity which links NA{sub 1} to the solid support; and M is a marker.

  6. Interaction of resveratrol and genistein with nucleic acids.

    PubMed

    Usha, Subbiah; Johnson, Irudayam Maria; Malathi, Raghunathan

    2005-03-31

    Resveratrol (RES) and genistein (GEN) are the dietary natural products known to possess chemopreventive property and also the ability to repair DNA damage induced by mutagens/carcinogens. It is believed that the therapeutic activity of these compounds could be primarily due to their interaction with nucleic acids but detailed reports are not available. We here explore the interaction of these drugs with nucleic acids considering DNA and RNA as a potential therapeutic target. The interaction of RES and GEN has been analysed in buffered solution with DNA [saline sodium citrate (SSC)] and RNA [tris ethylene diammine tetra acetic acid (TE)] using UV-absorption and Fourier transform infrared (FTIR) spectroscopy. The UV analysis revealed lesser binding affinity with nucleic acids at lower concentration of RES (P/D = 5.00 and 10.00), while at higher drug concentration (P/D = 0.75, 1.00 and 2.50) hyperchromic effect with shift in the lambda(max) is noted for DNA and RNA. A major RES-nucleic acids complexes was observed through base pairs and phosphate backbone groups with K = 35.782 M(-1) and K = 34.25 M(-1) for DNARES and RNA-RES complexes respectively. At various concentrations of GEN (P/D = 0.25, 0.50, 0.75, 1.00 and 2.50) hyperchromicity with shift in the lambda(max) from 260-->263 nm and 260--> 270 nm is observed for DNA-GEN and RNA-GEN complexes respectively. The binding constant (from UV analysis) for GEN-nucleic acids complexes could not be obtained due to GEN absorbance overlap with that of nucleic acids at 260 nm. Nevertheless a detailed analysis with regard to the interaction of these drugs (RES/GEN) with DNA and RNA could feasibly be understood by FTIR. PMID:15826497

  7. Vibrational Raman optical activity of proteins, nucleic acids, and viruses.

    PubMed

    Blanch, Ewan W; Hecht, Lutz; Barron, Laurence D

    2003-02-01

    Due to its sensitivity to chirality, Raman optical activity (ROA), which may be measured as a small difference in vibrational Raman scattering from chiral molecules in right- and left-circularly polarized incident light, is a powerful probe of biomolecular structure in solution. Protein ROA spectra provide information on the secondary and tertiary structures of the polypeptide backbone, hydration, side-chain conformation, and structural elements present in denatured states. Nucleic acid ROA spectra yield information on the sugar ring conformation, the base stacking arrangement, and the mutual orientation of the sugar and base rings around the C-N glycosidic linkage. ROA is able to simultaneously probe the structures of both the protein and the nucleic acid components of intact viruses. This article gives a brief account of the theory and measurement of ROA and presents the ROA spectra of a selection of proteins, nucleic acids, and viruses which illustrate the applications of ROA spectroscopy in biomolecular research. PMID:12606225

  8. Nature and Magnitude of Aromatic Stacking of Nucleic Acid Bases

    SciTech Connect

    Sponer, Jiri; Riley, Kevin E.; Hobza, Pavel

    2008-04-07

    This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase basestacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for basestacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.

  9. Nucleic acids within urinary exosomes/microvesicles are potential biomarkers for renal disease

    PubMed Central

    Miranda, Kevin C.; Bond, Daniel T.; McKee, Mary; Skog, Johan; P?unescu, Teodor G.; Da Silva, Nicolas; Brown, Dennis; Russo, Leileata M.

    2015-01-01

    Urinary exosomes or microvesicles are being studied intensively to identify potential new biomarkers for renal disease. We sought to identify whether these microvesicles contain nucleic acids. We isolated microvesicles from human urine in the same density range as that previously described for urinary exosomes and found them to have an RNA integrity profile similar to that of kidney tissue, including 18S and 28S rRNA. This profile was better preserved in urinary microvesicles compared with whole cells isolated from urine, suggesting that microvesicles may protect RNA during urine passage. We were able to detect mRNA in the human urinary microvesicles encoding proteins from all regions of the nephron and the collecting duct. Further, to provide a proof of principle, we found that microvesicles isolated from the urine of the V-ATPase B1 subunit knockout mice lacked mRNA of this subunit while containing a normal amount of the B2 subunit and aquaporin 2. The microvesicles were found to be contaminated with extraneous DNA potentially on their surface; therefore, we developed a rapid and reliable means to isolate nucleic acids from within urine microvesicles devoid of this extraneous contamination. Our study provides an experimental strategy for the routine isolation and use of urinary microvesicles as a novel and non-invasive source of nucleic acids to further renal disease biomarker discovery. PMID:20428099

  10. Protein and nucleic acid methylating enzymes: mechanisms and regulation

    PubMed Central

    Le, Daniel D; Fujimori, Danica Galoni?

    2012-01-01

    Protein and nucleic acid methylating enzymes are implicated in myriad cellular processes. These enzymes utilize diverse chemical mechanisms ranging from nucleophilic substitution-displacement to a novel radical-based reaction found in bacterial iron–sulfur cluster proteins. Within the cell, methylation activity is governed by interactions with endogenous molecular machinery. Of particular interest are the observations that methylating enzyme activity can be allosterically controlled by regulatory binding partners. Recent advances and emerging trends in the study of methylating enzyme mechanisms and regulation highlight the importance of protein and nucleic acid methylation in cellular physiology and disease. PMID:23085277

  11. Nanopores and nucleic acids: prospects for ultrarapid sequencing

    NASA Technical Reports Server (NTRS)

    Deamer, D. W.; Akeson, M.

    2000-01-01

    DNA and RNA molecules can be detected as they are driven through a nanopore by an applied electric field at rates ranging from several hundred microseconds to a few milliseconds per molecule. The nanopore can rapidly discriminate between pyrimidine and purine segments along a single-stranded nucleic acid molecule. Nanopore detection and characterization of single molecules represents a new method for directly reading information encoded in linear polymers. If single-nucleotide resolution can be achieved, it is possible that nucleic acid sequences can be determined at rates exceeding a thousand bases per second.

  12. A titer plate-based polymer microfluidic platform for high throughput nucleic acid purification

    E-print Network

    Lee, Jeong-Bong

    A titer plate-based polymer microfluidic platform for high throughput nucleic acid purification D immobilization . UV-LIGA . Large area mold insert . Micro molding . Nucleic acid purification 1 Introduction

  13. Polymerase chain reaction system using magnetic beads for analyzing a sample that includes nucleic acid

    DOEpatents

    Nasarabadi, Shanavaz (Livermore, CA)

    2011-01-11

    A polymerase chain reaction system for analyzing a sample containing nucleic acid includes providing magnetic beads; providing a flow channel having a polymerase chain reaction chamber, a pre polymerase chain reaction magnet position adjacent the polymerase chain reaction chamber, and a post pre polymerase magnet position adjacent the polymerase chain reaction chamber. The nucleic acid is bound to the magnetic beads. The magnetic beads with the nucleic acid flow to the pre polymerase chain reaction magnet position in the flow channel. The magnetic beads and the nucleic acid are washed with ethanol. The nucleic acid in the polymerase chain reaction chamber is amplified. The magnetic beads and the nucleic acid are separated into a waste stream containing the magnetic beads and a post polymerase chain reaction mix containing the nucleic acid. The reaction mix containing the nucleic acid flows to an analysis unit in the channel for analysis.

  14. Multicenter Evaluation of the Verigene Clostridium difficile Nucleic Acid Assay

    PubMed Central

    Buchan, Blake W.; Tan, Sokha; Stamper, Paul D.; Riebe, Katherine M.; Pancholi, Preeti; Kelly, Cheryl; Rao, Arundhati; Fader, Robert; Cavagnolo, Robert; Watson, Wendy; Goering, Richard V.; Trevino, Ernest A.; Weissfeld, Alice S.; Ledeboer, Nathan A.

    2013-01-01

    The Verigene Clostridium difficile Nucleic Acid test (Verigene CDF test) (Nanosphere, Northbrook, IL) is a multiplex qualitative PCR assay that utilizes a nanoparticle-based array hybridization method to detect C. difficile tcdA and tcdB in fecal specimens. In addition, the assay detects binary toxin gene sequences and the single base pair deletion at nucleotide 117 (? 117) in tcdC to provide a presumptive identification of the epidemic strain 027/NAP1/BI (referred to here as ribotype 027). This study compared the Verigene CDF test with anaerobic direct and enriched toxigenic culture on stool specimens from symptomatic patients among five geographically diverse laboratories within the United States. The Verigene CDF test was performed according to the manufacturer's instructions, and the reference methods performed by a central laboratory included direct culture onto cycloserine cefoxitin fructose agar (CCFA) and enriched culture using cycloserine cefoxitin mannitol broth with taurocholate and lysozyme. Recovered isolates were identified as C. difficile using gas liquid chromatography and were tested for toxin using a cell culture cytotoxicity neutralization assay. Strains belonging to ribotype 027 were determined by PCR ribotyping and bidirectional sequencing for ? 117 in tcdC. A total of 1,875 specimens were evaluable. Of these, 275 specimens (14.7%) were culture positive by either direct or enriched culture methods. Compared to direct culture alone, the overall sensitivity, specificity, positive predictive value, and negative predictive value for the Verigene CDF test were 98.7%, 87.5%, 42%, and 99.9%, respectively. Compared to combined direct and enriched culture results, the sensitivity, specificity, positive predictive value, and negative predictive values of the Verigene CDF test were 90.9%, 92.5%, 67.6%, and 98.3%, respectively. Of the 250 concordantly culture-positive specimens, 59 (23.6%) were flagged as “hypervirulent”; 53 were confirmed as ribotype 027, and all 59 possessed ? 117 in tcdC. Time to results was approximately 2.5 h per specimen. The Verigene CDF test is a novel nucleic acid microarray that reliably detects both C. difficile toxins A and B in unformed stool specimens and appears to adequately identify ribotype 027 isolates. PMID:24088862

  15. 1998 Oxford University Press 439445Nucleic Acids Research, 1998, Vol. 26, No. 2 Molecular definition of heterogeneous nuclear

    E-print Network

    Dreyfuss, Gideon

    © 1998 Oxford University Press 439­445Nucleic Acids Research, 1998, Vol. 26, No. 2 Molecular definition of heterogeneous nuclear ribonucleoprotein R (hnRNP R) using autoimmune antibody: immunological.5 kb cDNA clone was isolated which encoded the complete sequence of a protein of 633 amino acids

  16. Improved Phosphoramidite Building Blocks for the Synthesis of the Simplified Nucleic Acid GNA

    E-print Network

    Meggers, Eric

    acid backbone. The propylene glycol nucleotide building blocks contain just three carbon atoms and one of glycol nucleic acids is reported using new phosphoramidite building blocks in which the exocyclic amino oligonucleotides. Glycol nucleic acid (GNA) constitutes a minimal solution for a phosphodiester-containing nucleic

  17. Nucleic Acids Research doi:10.1093/nar/gkj007

    E-print Network

    Benham, Craig J.

    Nucleic Acids Research doi:10.1093/nar/gkj007 34:373-378, 2006.Nucleic Acids Res. Huiquan Wang://nar.oxfordjournals.org Additional information about Nucleic Acids Research, including how to subscribe can be found at Published of superhelical stress imposed on the DNA is determined by the levels of competing DNA topoisomerase enzyme

  18. Theoretical Determination of One-Electron Oxidation Potentials for Nucleic Acid Bases

    E-print Network

    Schlegel, H. Bernhard

    Theoretical Determination of One-Electron Oxidation Potentials for Nucleic Acid Bases Brian T potentials for N-methyl substituted nucleic acid bases guanine, adenine, cytosine, thymine, uracil, xanthine of redox potentials for the standard nucleic acids guanine, adenine, cytosine, thymine, and uracil

  19. SAFA: Semi-automated footprinting analysis software for high-throughput quantification of nucleic acid

    E-print Network

    Herschlag, Dan

    of nucleic acid footprinting experiments RHIJU DAS,1,2,4 , ALAIN LAEDERACH3,4 SAMUEL M. PEARLMAN,4 DANIEL, and kinetics of nucleic acid folding and ligand binding reactions. However, quantitative analysis of the gel and can therefore facilitate the use of quantitative footprinting techniques in nucleic acid laboratories

  20. Selective Nucleic Acid Capture with Shielded Covalent Probes Jeffrey R. Vieregg,

    E-print Network

    Pierce, Niles A.

    Selective Nucleic Acid Capture with Shielded Covalent Probes Jeffrey R. Vieregg, Hosea M. Nelson 91125, United States *S Supporting Information ABSTRACT: Nucleic acid probes are used for diverse binding of nucleic acid targets under conditions where base-pairing is disrupted (e.g., by stringent

  1. Nucleic Acids Research, Vol. 18, No. 18 5533 Ternary interactions of spermine with DNA

    E-print Network

    Williams, Loren

    Nucleic Acids Research, Vol. 18, No. 18 5533 Ternary interactions of spermine with DNA: 4 such as membranes (4,5) and nucleic acids. Polyamines stabilize duplex DNA (6-9), condense DNA (10-13) and chromatin (14,15) and promote the B-DNA to Z- DNA transition (16,17). Molecular aspects of nucleic acid

  2. Oxidative Strand Scission of Nucleic Acids: Routes Initiated by Hydrogen Abstraction from the Sugar Moiety

    E-print Network

    Tullius, Thomas D.

    Oxidative Strand Scission of Nucleic Acids: Routes Initiated by Hydrogen Abstraction from the Sugar ionized by high-energy ra- diation. While the heterocyclic bases of nucleic acids are important sites produces a carbon-based sugar radical that can rearrange, culminating in scission of the nucleic acid

  3. Energy Transfer from Nucleic Acids to Tb(III): Selective Emission Enhancement by Single DNA Mismatches

    E-print Network

    Turro, Claudia

    Energy Transfer from Nucleic Acids to Tb(III): Selective Emission Enhancement by Single DNA energy transfer (EnT) from nucleic acids to Tb3+ has been utilized to investigate the binding of the ions in nucleic acid hybridization assays with applications that range from the determination of genetic

  4. A Theoretical Analysis of Specificity of Nucleic Acid Interactions with Oligonucleotides and Peptide

    E-print Network

    Benedek, George B.

    A Theoretical Analysis of Specificity of Nucleic Acid Interactions with Oligonucleotides and Peptide Nucleic Acids (PNAs) Aleksey Lomakin1 and Maxim D. Frank-Kamenetskii2 * 1 Physics Department theoretically the problem of the speci®city of interaction between nucleic acid and an oligonucleotide, its

  5. Adsorption of Nucleic Acid Components on Rutile (TiO2) Surfaces

    E-print Network

    Sverjensky, Dimitri A.

    Adsorption of Nucleic Acid Components on Rutile (TiO2) Surfaces H. James Cleaves II,1 Caroline M are important because there is a tremendous flux of nucleic acids in the environment due to cell death of nucleic acid components with rutile (TiO2), a mineral common in many terrestrial crustal rocks. Our

  6. PHYSICAL REVIEW E 84, 061912 (2011) Kinetic Monte Carlo method applied to nucleic acid hairpin folding

    E-print Network

    Widom, Michael

    2011-01-01

    PHYSICAL REVIEW E 84, 061912 (2011) Kinetic Monte Carlo method applied to nucleic acid hairpin December 2011) Kinetic Monte Carlo on coarse-grained systems, such as nucleic acid secondary structure states. Secondary structure models of nucleic acids, which record the pairings of complementary

  7. Highly Cooperative Behavior of Peptide Nucleic Acid-Linked DNA-Modified Gold-Nanoparticle and

    E-print Network

    Highly Cooperative Behavior of Peptide Nucleic Acid-Linked DNA-Modified Gold-Nanoparticle and Comb of nucleic acids, proteins, metal ions, and small molecules.[1­10] When complementary mixtures whether particle aggregates can be held together with peptide nucleic acids (PNAs),[15,16] uncharged

  8. Nucleic Acid Sample Preparation Using Spontaneous Biphasic Plug Peter C. Thomas,,

    E-print Network

    Beebe, David J.

    Nucleic Acid Sample Preparation Using Spontaneous Biphasic Plug Flow Peter C. Thomas,,§ Lindsay N States *S Supporting Information ABSTRACT: Nucleic acid (NA) extraction and purification has become was determined. The results demonstrate the utility of the current technique for nucleic acid purification

  9. Bifacial Peptide Nucleic Acid Directs Cooperative Folding and Assembly of Binary, Ternary, and Quaternary DNA Complexes

    E-print Network

    Bong, Dennis

    Bifacial Peptide Nucleic Acid Directs Cooperative Folding and Assembly of Binary, Ternary, which we term bifacial peptide nucleic acid (bPNA), function as a noncovalent template for thymine length. Synthetic bPNA structuring elements may be useful tools for biotechnology. Nucleic acid triplex

  10. Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity

    E-print Network

    Heller, Eric

    Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity Simon of alternative nucleotides would support the assembly of nucleic acid polymers containing nonheritable backbone of heterogeneous nucleic acid molecules could evolve reproducible function. For such evolution to be possible

  11. Integration of On-Chip Isotachophoresis and Functionalized Hydrogels for Enhanced-Sensitivity Nucleic Acid Detection

    E-print Network

    Santiago, Juan G.

    -Sensitivity Nucleic Acid Detection Giancarlo Garcia-Schwarz and Juan G. Santiago* Department of Mechanical Engineering introduce an on-chip electrokinetic assay to perform high-sensitivity nucleic acid (NA) detection- functionalized hydrogel for rapid and sensitive nucleic acid (NA) detection. ITP preconcentrates NAs to enhance

  12. Fluorescent hybridization probes for nucleic acid detection Jia Guo & Jingyue Ju & Nicholas J. Turro

    E-print Network

    Turro, Nicholas J.

    REVIEW Fluorescent hybridization probes for nucleic acid detection Jia Guo & Jingyue Ju & Nicholas widely used to detect nucleic acids both in vivo and in vitro. Molecular beacons (MBs) and binary probes of identifying nucleic acid sequences are critical to biomedical research, disease diagnosis, and drug discovery

  13. Integrated Printed Circuit Board Device for Cell Lysis and Nucleic Acid Extraction

    E-print Network

    Santiago, Juan G.

    Integrated Printed Circuit Board Device for Cell Lysis and Nucleic Acid Extraction Lewis A and an isotachophoresis assay for sample preparation of nucleic acids from biological samples. The device has integrated two 15 L reservoirs. We demonstrated this device by extracting pathogenic nucleic acids from 1 L

  14. Paradigms for computational nucleic acid design Robert M. Dirks, Milo Lin1

    E-print Network

    Winfree, Erik

    Paradigms for computational nucleic acid design Robert M. Dirks, Milo Lin1 , Erik Winfree2®ed approach to nucleic acid design as parameter sets are re®ned further. Finally, we observe that designing systems with increasing functional density. Nucleic acids hold great promise as a design medium

  15. Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids

    E-print Network

    Herschlag, Dan

    Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids Yu Bai, 2007; E-mail: herschla@stanford.edu Abstract: The ion atmosphere around nucleic acids critically theoretical models, can be applied to complex binding and folding equilibria of nucleic acids

  16. A Stochastic Model of Nonenzymatic Nucleic Acid Replication: ``Elongators'' Sequester Replicators

    E-print Network

    Fernando, Chrisantha

    A Stochastic Model of Nonenzymatic Nucleic Acid Replication: ``Elongators'' Sequester Replicators / Accepted: 22 January 2007 [Reviewing Editor: Dr. Niles Lehman] Abstract. The origin of nucleic acid template replication is a major unsolved problem in science. A novel stochastic model of nucleic acid

  17. Software News and Updates NUPACK: Analysis and Design of Nucleic Acid Systems

    E-print Network

    Pierce, Niles A.

    Software News and Updates NUPACK: Analysis and Design of Nucleic Acid Systems JOSEPH N. ZADEH,1 online 19 July 2010 in Wiley Online Library (wileyonlinelibrary.com). Abstract: The Nucleic Acid Package (NUPACK) is a growing software suite for the analysis and design of nucleic acid systems. The NUPACK web

  18. Nucleic Acids Research doi:10.1093/nar/gkn031

    E-print Network

    Paris-Sud XI, Université de

    Nucleic Acids Research doi:10.1093/nar/gkn031 36:1861-1870, 2008. First published 11 Feb 2008;Nucleic Acids Res. Antoine Graindorge, Olivier Le Tonquèze, Raphaël Thuret, Nicolas Pollet, H. Beverley information about Nucleic Acids Research, including how to subscribe can be found at Published on behalf

  19. Nucleic Acids Research, 2009, 112 doi:10.1093/nar/gkp675

    E-print Network

    Hassibi, Arjang

    Nucleic Acids Research, 2009, 1­12 doi:10.1093/nar/gkp675 Real-time DNA microarray analysis Arjang for the analysis of complex nucleic acid samples, use the base pairing of nucleic acid molecules (3) as both

  20. Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures

    E-print Network

    Dietz, Hendrik

    Quantitative prediction of 3D solution shape and flexibility of nucleic acid nanostructures Do designed using nucleic acids. INTRODUCTION Programmable self-assembly of complementary single- stranded nucleic acids is a versatile approach to designing sophisticated nanoscale structures (2­4). Scaffolded

  1. Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation between

    E-print Network

    Heller, Eric

    Enzymatic synthesis of DNA on glycerol nucleic acid templates without stable duplex formation for review May 8, 2007) Glycerol nucleic acid (GNA) is an interesting alternative base- pairing system based is not required for template-dependent polymerization. information transfer polymerase Nucleic acid analogs

  2. APPLICATION OF THE RATE OF NUCLEIC ACID SYNTHESIS TO THE STUDY OF MICROBIAL GROWTH

    E-print Network

    Luther, Douglas S.

    APPLICATION OF THE RATE OF NUCLEIC ACID SYNTHESIS TO THE STUDY OF MICROBIAL GROWTH AND PRODUCTION. Stroup Tom Humphreys #12;ABSTRACT The rate of nucleic acid synthesis was used as a measure of growth grown under controlled conditions. These studies demonstrated that accurate rates of nucleic acid

  3. Mapping nucleic acid structure by hydroxyl radical cleavage Thomas D Tullius1,2

    E-print Network

    Tullius, Thomas D.

    Mapping nucleic acid structure by hydroxyl radical cleavage Thomas D Tullius1,2 and Jason of the first use of the hydroxyl radical as a high-resolution tool for the structural study of nucleic acids [1 for assessing the folded structure of nucleic acids, particularly RNA. The characteristic chemistry

  4. Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution

    E-print Network

    Das, Rhiju

    Probing counterion modulated repulsion and attraction between nucleic acid duplexes in solution Yu for review June 22, 2004) Understanding biological and physical processes involving nucleic acids of the ion atmosphere that surrounds nucleic acids. We have used a simple model DNA system to determine how

  5. A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry

    E-print Network

    Bansal, Manju

    A Standard Reference Frame for the Description of Nucleic Acid Base-pair Geometry Wilma K. Olson Westhof Cynthia Wolberger and Helen M. Berman # 2001 Academic Press Keywords: nucleic acid conformation the three-dimensional arrangements of bases and base-pairs in nucleic acid structures. The different

  6. Honey, I Shrunk the DNA: DNA Length as a Probe for Nucleic-Acid Enzyme Activity

    E-print Network

    Honey, I Shrunk the DNA: DNA Length as a Probe for Nucleic-Acid Enzyme Activity Antoine M. van to manipulate individual DNA molecules17 have allowed a large number of nucleic-acid enzymes to be charac will discuss how changes in the physical properties of DNA can be exploited to study the dynamics of nucleic-acid

  7. The relation of nucleic acids to condition factor in the catfish, Heteropneustes fossilis

    E-print Network

    Paris-Sud XI, Université de

    The relation of nucleic acids to condition factor in the catfish, Heteropneustes fossilis S intermingling red muscle fibers. The fact that red and white muscles differ in nucleic acids and other analysis. For nucleic acid assays dry fat-free tissue was obtained according to the technique of Webb

  8. Using Internal and Collective Variables in Monte Carlo Simulations of Nucleic Acid Structures: Chain

    E-print Network

    Rohs, Remo

    Using Internal and Collective Variables in Monte Carlo Simulations of Nucleic Acid Structures of nucleic acid structures by using the constant bond lengths approximation. The resulting chain breakage simulations; nucleic acid structures; Jacobians Introduction Simplified molecular models with a reduced number

  9. reprinted with permission from Nature magazine A Structure for Deoxyribose Nucleic Acid

    E-print Network

    Gottgens, Hans

    reprinted with permission from Nature magazine A Structure for Deoxyribose Nucleic Acid J. D for the salt of deoxyribose nucleic acid (D.N.A.). This structure has novel features which are of considerable biological interest. A structure for nucleic acid has already been proposed by Pauling (4) and Corey1

  10. RESEARCH Open Access Considerations on the use of nucleic acid-based

    E-print Network

    Paris-Sud XI, Université de

    RESEARCH Open Access Considerations on the use of nucleic acid-based amplification for malaria,4 and Georges Snounou5,6,7* Abstract Background: Nucleic acid amplification provides the most sensitive researchers in different settings to ensure that the nucleic acid amplification protocols they wish to use

  11. Nucleic Acids Research doi:10.1093/nar/gkn148

    E-print Network

    Paris-Sud XI, Université de

    Nucleic Acids Research doi:10.1093/nar/gkn148 36:3214-3225, 2008. First published 16 Apr 2008;Nucleic Acids Res. René Rezsohazy Xavier Lampe, Omar Abdel Samad, Allan Guiguen, Christelle Matis, Sophie://nar.oxfordjournals.org Additional information about Nucleic Acids Research, including how to subscribe can be found at Published

  12. A HANDHELD MAGNETIC SENSING PLATFORM FOR ANTIGEN AND NUCLEIC ACID DETECTION

    E-print Network

    Weinreb, Sander

    A HANDHELD MAGNETIC SENSING PLATFORM FOR ANTIGEN AND NUCLEIC ACID DETECTION A. Pai1* , AM for the protein interferon- (IFN- ). KEYWORDS: Nucleic Acid, Antigen, Biosensor, Magnetic Figure 1: (a) Handheld. 1a) with two fully implemented assays for antigens and nucleic acids (Fig 2a,b). It is based

  13. Bifacial Peptide Nucleic Acid as an Allosteric Switch for Aptamer and Ribozyme Function

    E-print Network

    Bong, Dennis

    Bifacial Peptide Nucleic Acid as an Allosteric Switch for Aptamer and Ribozyme Function Xin Xia demonstrate herein that bifacial peptide nucleic acid (bPNA) hybrid triplexes functionally sub- stitute for duplex DNA or RNA. Structure-function loss in three non-coding nucleic acids was inflicted by replacement

  14. Multiplexed detection of nucleic acids in a combinatorial screening chip Benjamin R. Schudel,ac

    E-print Network

    Kenis, Paul J. A.

    Multiplexed detection of nucleic acids in a combinatorial screening chip Benjamin R. Schudel of the world. Here, we report the multiplexed detection of nucleic acids as disease markers within discrete­25 In this work, we report a combinatorial microfluidic approach for the detec- tion of nucleic acid fragments

  15. Effect of Stalling after Mismatches on the Error Catastrophe in Nonenzymatic Nucleic Acid Replication

    E-print Network

    Heller, Eric

    Effect of Stalling after Mismatches on the Error Catastrophe in Nonenzymatic Nucleic Acid of nonenzymatic, template-directed nucleic acid polymerization. We found that most mismatches decrease the rate rates. Previous work indicates that nonenzymatic, template-directed nucleic acid polymerization has high

  16. Templated Synthesis of Peptide Nucleic Acids via Sequence-Selective Base-Filling Reactions

    E-print Network

    Liu, David R.

    Templated Synthesis of Peptide Nucleic Acids via Sequence-Selective Base-Filling Reactions Jennifer describe the templated synthesis of both native and modified peptide nucleic acids (PNAs) through base, 2009; E-mail: drliu@fas.harvard.edu Template-directed nucleic acid synthesis is an essential compo

  17. Peptide nucleic acid: a versatile tool in genetic diagnostics and molecular biology

    Microsoft Academic Search

    Peter E Nielsen

    2001-01-01

    During the past ten years, the DNA mimic peptide nucleic acid has inspired the development of a variety of hybridisation-based methods for detection, quantification, purification and characterisation of nucleic acids. Most of these methods have taken advantage of the very favourable DNA and RNA hybridisation properties of peptide nucleic acids combined with the unique properties and opportunities offered by peptide

  18. Peptide nucleic acid (PNA): its medical and biotechnical applications and promise for the future

    Microsoft Academic Search

    ARGHYA RAY; BENGT NORDEN

    Synthetic molecules that can bind with high sequence specificity to a chosen target in a gene sequence are of major interest in medicinal and biotechnological contexts. They show promise for the development of gene therapeutic agents, diag- nostic devices for genetic analysis, and as molecular tools for nucleic acid manipulations. Peptide nucleic acid (PNA) is a nucleic acid analog in

  19. Vibrational spectroscopy and principal component analysis for conformational study of virus nucleic acids

    NASA Astrophysics Data System (ADS)

    Dovbeshko, G. I.; Repnytska, O. P.; Pererva, T.; Miruta, A.; Kosenkov, D.

    2004-07-01

    Conformation analysis of mutated DNA-bacteriophages (PLys-23, P23-2, P47- the numbers have been assigned by T. Pererva) induced by MS2 virus incorporated in Ecoli AB 259 Hfr 3000 has been done. Surface enhanced infrared absorption (SEIRA) spectroscopy and principal component analysis has been applied for solving this problem. The nucleic acids isolated from the mutated phages had a form of double stranded DNA with different modifications. The nucleic acid from phage P47 was undergone the structural rearrangement in the most degree. The shape and position ofthe fine structure of the Phosphate asymmetrical band at 1071cm-1 as well as the stretching OH vibration at 3370-3390 cm-1 has indicated to the appearance ofadditional OH-groups. The Z-form feature has been found in the base vibration region (1694 cm-1) and the sugar region (932 cm-1). A supposition about modification of structure of DNA by Z-fragments for P47 phage has been proposed. The P23-2 and PLys-23 phages have showed the numerous minor structural changes also. On the basis of SEIRA spectra we have determined the characteristic parameters of the marker bands of nucleic acid used for construction of principal components. Contribution of different spectral parameters of nucleic acids to principal components has been estimated.

  20. Radiation Inactivation of Enzymes, Nucleic Acids, and Phage Particles

    Microsoft Academic Search

    Ernest Pollard

    1959-01-01

    ABS>Studies directed at cell structure and function are reported. The ; general charactcr of radioinactivation is treated first. The results of ; quantitative studies on proteins and on nucleic acids are presentcd and cvaluated. ; An example of a radiation study on dry protein is given. Studies of virus ; inactivations bacteriophagc changes and Newcastlc discase and influenza virus are

  1. Structure, stability and behaviour of nucleic acids in ionic liquids

    PubMed Central

    Tateishi-Karimata, Hisae; Sugimoto, Naoki

    2014-01-01

    Nucleic acids have become a powerful tool in nanotechnology because of their conformational polymorphism. However, lack of a medium in which nucleic acid structures exhibit long-term stability has been a bottleneck. Ionic liquids (ILs) are potential solvents in the nanotechnology field. Hydrated ILs, such as choline dihydrogen phosphate (choline dhp) and deep eutectic solvent (DES) prepared from choline chloride and urea, are ‘green’ solvents that ensure long-term stability of biomolecules. An understanding of the behaviour of nucleic acids in hydrated ILs is necessary for developing DNA materials. We here review current knowledge about the structures and stabilities of nucleic acids in choline dhp and DES. Interestingly, in choline dhp, A–T base pairs are more stable than G–C base pairs, the reverse of the situation in buffered NaCl solution. Moreover, DNA triplex formation is markedly stabilized in hydrated ILs compared with aqueous solution. In choline dhp, the stability of Hoogsteen base pairs is comparable to that of Watson–Crick base pairs. Moreover, the parallel form of the G-quadruplex is stabilized in DES compared with aqueous solution. The behaviours of various DNA molecules in ILs detailed here should be useful for designing oligonucleotides for the development of nanomaterials and nanodevices. PMID:25013178

  2. Structure, stability and behaviour of nucleic acids in ionic liquids.

    PubMed

    Tateishi-Karimata, Hisae; Sugimoto, Naoki

    2014-08-01

    Nucleic acids have become a powerful tool in nanotechnology because of their conformational polymorphism. However, lack of a medium in which nucleic acid structures exhibit long-term stability has been a bottleneck. Ionic liquids (ILs) are potential solvents in the nanotechnology field. Hydrated ILs, such as choline dihydrogen phosphate (choline dhp) and deep eutectic solvent (DES) prepared from choline chloride and urea, are 'green' solvents that ensure long-term stability of biomolecules. An understanding of the behaviour of nucleic acids in hydrated ILs is necessary for developing DNA materials. We here review current knowledge about the structures and stabilities of nucleic acids in choline dhp and DES. Interestingly, in choline dhp, A-T base pairs are more stable than G-C base pairs, the reverse of the situation in buffered NaCl solution. Moreover, DNA triplex formation is markedly stabilized in hydrated ILs compared with aqueous solution. In choline dhp, the stability of Hoogsteen base pairs is comparable to that of Watson-Crick base pairs. Moreover, the parallel form of the G-quadruplex is stabilized in DES compared with aqueous solution. The behaviours of various DNA molecules in ILs detailed here should be useful for designing oligonucleotides for the development of nanomaterials and nanodevices. PMID:25013178

  3. A netlike rolling circle nucleic acid amplification technique.

    PubMed

    Zhu, Xiaoli; Feng, Chang; Zhang, Bin; Tong, Hui; Gao, Tao; Li, Genxi

    2015-01-01

    A nucleic acid amplification technique termed as netlike rolling circle amplification is proposed by introducing a nicking enzyme into the existing hyperbranched rolling circle amplification system. Surprisingly dense and uniform network morphology is observed; and cubic amplification is achieved for the sensitive detection of a sequence from HIV. PMID:25407326

  4. Mfold web server for nucleic acid folding and hybridization prediction

    Microsoft Academic Search

    Michael Zuker

    2003-01-01

    The abbreviated name,'mfold web server',describes a number of closely related software applications available on the World Wide Web (WWW) for the prediction of the secondary structure of single stranded nucleic acids. The objective of this web server is to provide easy access to RNA and DNA folding and hybridization software to the scientific community at large. By making use of

  5. NPDock: a web server for protein–nucleic acid docking

    PubMed Central

    Tuszynska, Irina; Magnus, Marcin; Jonak, Katarzyna; Dawson, Wayne; Bujnicki, Janusz M.

    2015-01-01

    Protein–RNA and protein–DNA interactions play fundamental roles in many biological processes. A detailed understanding of these interactions requires knowledge about protein–nucleic acid complex structures. Because the experimental determination of these complexes is time-consuming and perhaps futile in some instances, we have focused on computational docking methods starting from the separate structures. Docking methods are widely employed to study protein–protein interactions; however, only a few methods have been made available to model protein–nucleic acid complexes. Here, we describe NPDock (Nucleic acid–Protein Docking); a novel web server for predicting complexes of protein–nucleic acid structures which implements a computational workflow that includes docking, scoring of poses, clustering of the best-scored models and refinement of the most promising solutions. The NPDock server provides a user-friendly interface and 3D visualization of the results. The smallest set of input data consists of a protein structure and a DNA or RNA structure in PDB format. Advanced options are available to control specific details of the docking process and obtain intermediate results. The web server is available at http://genesilico.pl/NPDock. PMID:25977296

  6. NPDock: a web server for protein-nucleic acid docking.

    PubMed

    Tuszynska, Irina; Magnus, Marcin; Jonak, Katarzyna; Dawson, Wayne; Bujnicki, Janusz M

    2015-07-01

    Protein-RNA and protein-DNA interactions play fundamental roles in many biological processes. A detailed understanding of these interactions requires knowledge about protein-nucleic acid complex structures. Because the experimental determination of these complexes is time-consuming and perhaps futile in some instances, we have focused on computational docking methods starting from the separate structures. Docking methods are widely employed to study protein-protein interactions; however, only a few methods have been made available to model protein-nucleic acid complexes. Here, we describe NPDock (Nucleic acid-Protein Docking); a novel web server for predicting complexes of protein-nucleic acid structures which implements a computational workflow that includes docking, scoring of poses, clustering of the best-scored models and refinement of the most promising solutions. The NPDock server provides a user-friendly interface and 3D visualization of the results. The smallest set of input data consists of a protein structure and a DNA or RNA structure in PDB format. Advanced options are available to control specific details of the docking process and obtain intermediate results. The web server is available at http://genesilico.pl/NPDock. PMID:25977296

  7. Nucleic acid probes in diagnosis of viral diseases of man

    Microsoft Academic Search

    J. K. Kulski; Mary Norval

    1985-01-01

    Summary With the recent, rapid advances in recombinant DNA technology, it has become possible to consider the use of nucleic acid probes in diagnosis of human viral diseases. Several examples are discussed which employ techniques of dot blot hybridization, sandwich hybridization andin situ hybridization. Typing of viral strains using restriction endonuclease digestion as an epidemiological tool is considered. Finally, the

  8. Past, present and future of nucleic acids electrochemistry

    Microsoft Academic Search

    Emil Pale?ek

    2002-01-01

    Electrochemistry of nucleic acids was discovered about 40 years ago. During the first 15 years electrochemistry brought early evidence of DNA premelting and polymorphy of the DNA double helix. At present electrochemical methods working with stationary electrodes are able to detect DNA at attomol and in some cases, even at lower levels. A great progress in the development of electrochemical

  9. Nucleic acid amplification: Alternative methods of polymerase chain reaction

    PubMed Central

    Fakruddin, Md; Mannan, Khanjada Shahnewaj Bin; Chowdhury, Abhijit; Mazumdar, Reaz Mohammad; Hossain, Md. Nur; Islam, Sumaiya; Chowdhury, Md. Alimuddin

    2013-01-01

    Nucleic acid amplification is a valuable molecular tool not only in basic research but also in application oriented fields, such as clinical medicine development, infectious diseases diagnosis, gene cloning and industrial quality control. A comperehensive review of the literature on the principles, applications, challenges and prospects of different alternative methods of polymerase chain reaction (PCR) was performed. PCR was the first nucleic acid amplification method. With the advancement of research, a no of alternative nucleic acid amplification methods has been developed such as loop mediated isothermal amplification, nucleic acid sequence based amplification, strand displacement amplification, multiple displacement amplification. Most of the alternative methods are isothermal obviating the need for thermal cyclers. Though principles of most of the alternate methods are relatively complex than that of PCR, they offer better applicability and sensitivity in cases where PCR has limitations. Most of the alternate methods still have to prove themselves through extensive validation studies and are not available in commercial form; they pose the potentiality to be used as replacements of PCR. Continuous research is going on in different parts of the world to make these methods viable technically and economically. PMID:24302831

  10. Synthesis, Analysis, Purification, and Intracellular Delivery of Peptide Nucleic Acids

    Microsoft Academic Search

    Dwaine A. Braasch; David R. Corey

    2001-01-01

    Peptide nucleic acids (PNAs) are nonionic DNA mimics. Their novel chemical properties may facilitate the development of selective and potent antisense and antigene strategies for regulating intracellular processes. Described herein are procedures for the synthesis, purification, handling, and characterization of PNAs. A simple protocol for the lipid-mediated introduction of PNAs into in vitro cultures of mammalian cells is provided.

  11. Liver cell specific targeting of peptide nucleic acid oligomers

    Microsoft Academic Search

    Xiao Zhang; Carla G Simmons; David R Corey

    2001-01-01

    Chimeric molecules consisting of peptide nucleic acid (PNA) and lactose have been synthesized to test the hypothesis that lactose moieties can promote cell-specific uptake of PNAs. We find that lactose modified PNAs rapidly enter liver-derived HepG2 cells while unmodified PNAs do not and that lactose modified PNAs can inhibit cellular telomerase.

  12. Nucleic acids encoding modified human immunodeficiency virus type 1 (HIV-1) group M consensus envelope glycoproteins

    DOEpatents

    Haynes, Barton F. (Durham, NC); Gao, Feng (Durham, NC); Korber, Bette T. (Los Alamos, NM); Hahn, Beatrice H. (Birmingham, AL); Shaw, George M. (Birmingham, AL); Kothe, Denise (Birmingham, AL); Li, Ying Ying (Hoover, AL); Decker, Julie (Alabaster, AL); Liao, Hua-Xin (Chapel Hill, NC)

    2011-12-06

    The present invention relates, in general, to an immunogen and, in particular, to an immunogen for inducing antibodies that neutralizes a wide spectrum of HIV primary isolates and/or to an immunogen that induces a T cell immune response. The invention also relates to a method of inducing anti-HIV antibodies, and/or to a method of inducing a T cell immune response, using such an immunogen. The invention further relates to nucleic acid sequences encoding the present immunogens.

  13. Nucleic acid molecules conferring enhanced ethanol tolerance and microorganisms having enhanced tolerance to ethanol

    SciTech Connect

    Brown, Steven; Guss, Adam; Yang, Shihui; Karpinets, Tatiana; Lynd, Lee; Shao, Xiongjun

    2014-01-14

    The present invention provides isolated nucleic acid molecules which encode a mutant acetaldehyde-CoA/alcohol dehydrogenase or mutant alcohol dehydrogenase and confer enhanced tolerance to ethanol. The invention also provides related expression vectors, genetically engineered microorganisms having enhanced tolerance to ethanol, as well as methods of making and using such genetically modified microorganisms for production of biofuels based on fermentation of biomass materials.

  14. The use of Sonogashira coupling for the synthesis of modified uracil peptide nucleic acid

    Microsoft Academic Search

    Robert H. E Hudson; Ge Li; Joseph Tse

    2002-01-01

    Palladium-catalyzed Sonogashira coupling has been shown to be compatible with PNA monomers as illustrated by the reaction of 5-iodouracil peptide nucleic acid monomer (IU-PNA) with several terminal alkynes. These reactions have been performed in the solution phase and with IU-PNA linked to an insoluble polymer support. The results presented herein show that while the isolated yields from the solution phase

  15. Study of the interaction of nucleic acids with acridine red and CTMAB by a resonance light scattering technique and determination of nucleic acids at nanogram levels

    Microsoft Academic Search

    Min Wang; Jinghe Yang; Xia Wu; Fang Huang

    2000-01-01

    In this paper, a determinating method of nucleic acids at nanogram levels by a resonance light scattering (RLS) technique with a common spectrofluorometer has been reported. The characteristics of RLS spectra of acridine red (AR) with nucleic acids, the effective factors and the optimum conditions have been studied. In the pH range 6.40–7.10, nucleic acids and surfactant CTMAB can jointly

  16. Present status of protein and nucleic acid database activities in the world

    NASA Astrophysics Data System (ADS)

    Tsugita, Akira

    The first protein database was founded in 1965, followed by the establishment of nucleic acid databases from 1971. Presently there are six major sequence databases, located in Japan, USA and the FRG-three for protein data and three for nucleic acid data. International cooperation between the protein databases and between the nucleic acid databases have greatly facilitated compilation and dissemination of data. Coordination between these protein and nucleic acid databases have progressed with the support of the CODATA Task Group and the International Advisory Board for Nucleic Acid Databases. In the protein field, several additional database activities are initiated to contribute to protein engineering and structure-activity relationships.

  17. Volume10Number121982 Nucleic Acids Research~~~~~~~

    E-print Network

    Haseloff, Jim

    Volume10Number121982 Nucleic Acids Research~~~~~~~ Comparative sequence and structure of viroid, England. 3681 0305-1048/82/1012-3681$2.00/0 Nucleic Acids ResearchVolume 10 Number 12 1982 #12;Nucleic tobacco mottle virus and solanum nodiflorum mottle virus, have been determined. RNA 2 of solanum

  18. NUCLEIC ACID SYNTHESIS MEASURM,IEII]S IN SEDIMENT MICROBIAI CO}O{UNITIES

    E-print Network

    Luther, Douglas S.

    by NUCLEIC ACID SYNTHESIS MEASURM,IEII]S IN SEDIMENT MICROBIAI CO}O{UNITIES: I microbial communities. Biomass-specific raEes of nucleic acid synthesis in sediment microbial communities for measuring rates of nucleic acj-d synthesis in sedimentary microbial communi-ties has been adapted from

  19. The effect of confinement on dynamics and rheology of dilute deoxyribose nucleic acid solutions. II. Effective

    E-print Network

    Shaqfeh, Eric

    The effect of confinement on dynamics and rheology of dilute deoxyribose nucleic acid solutions. II the effect of confinement on deoxyribose nucleic acid rheology and chain dynamics. We present results these findings to microchannel flows to study the rhe- ology and chain dynamics of dilute deoxyribose nucleic

  20. Nucleic-acid characterization of the identity and activity of subsurface microorganisms

    Microsoft Academic Search

    E. L. Madsen

    2000-01-01

    Nucleic-acid approaches to characterizing naturally occurring microorganisms in their habitats have risen to prominence during the last decade. Extraction of deoxyribonucleic-acid (DNA) and ribonucleic-acid (RNA) biomarkers directly from environmental samples provides a new means of gathering information in microbial ecology. This review article defines: (1) the subsurface habitat; (2) what nucleic-acid procedures are; and (3) the types of information nucleic-acid

  1. Determination of Three-Bond 1H3?– 31P Couplings in Nucleic Acids and Protein–Nucleic Acid Complexes by Quantitative JCorrelation Spectroscopy

    Microsoft Academic Search

    G. Marius Clore; Elizabeth C. Murphy; Angela M. Gronenborn; Ad Bax

    1998-01-01

    A new sensitive two-dimensional quantitativeJcorrelation experiment is described for measuring3JH3?–Pcouplings in nucleic acids and protein–nucleic acid complexes. The method is based on measuring the change in intensity of the1H–1H cross peaks in a constant-time1H–1H COSY experiment which occurs in the presence and absence of3JH3?–Pdephasing during the constant-time evolution period. For protein–nucleic acid complexes where the protein is13C-labeled but the nucleic

  2. Detection of nucleic acid hybrids by prolonged chemiluminescence

    SciTech Connect

    Dattagupta, N.; Clemens, A.H.

    1988-12-27

    A method for determining a particular single stranded polynucleotide sequence in a test medium, comprising the steps of: (a) immobilizing on a solid support single stranded nucleic acids in the test medium, (b) contacting the immobilized nucleic acids with a polynucleotide probe having a base sequence substantially complementary to the sequence to be determined and the contacting being under conditions favorable to hybridization between the probe and the sequence to be determined, wherein the probe is labeled with a chemiluminescence enhancer, (c) separating the immobilized hybrids from the unhybridized probe, (d) initiating a chemiluminescent reaction by contacting the separated, labeled, immobilized hybrids with an oxidant, a 2.3-dihydro-1,4-phthalazinedione chemiluminescence precursor, and a peroxidase enzyme, (e) detecting the resulting light emission, and (f) relating the amount of emitted light to the amount of the single stranded polynucleotide sequence.

  3. Phase Transitions in Sequence Matches and Nucleic Acid Structure

    NASA Astrophysics Data System (ADS)

    Waterman, Michael S.; Gordon, Louis; Arratia, Richard

    1987-03-01

    Analyses of phase transitions in biopolymers have previously been restricted to studies of average behavior along macromolecules. Extremal properties, such as longest helical region, can now be studied with a new family of probability distributions [Arratia, R., Gordon, L. & Waterman, M. S. (1986) Ann. Stat. 14, 971-993]. Not only is such extremal behavior analyzed with great precision, but new phase transitions are determined. One phase transition occurs when behavior of the free energy of the longest helical region abruptly changes from proportional to logarithm of the sequence length to proportional to sequence length. The annealing of two single-stranded molecules and the melting of a double helix are both considered. These results, initially suggested by studies of optimal matching of random DNA sequences [Smith, T. F., Waterman, M. S. & Burks, C. (1985) Nucleic Acids Res. 13, 645-656], also have importance for significance tests in comparison of nucleic acid or protein sequences.

  4. Selected Nucleic Acid Precursors in Studies of Aquatic Microbial Ecology

    PubMed Central

    Karl, David M.

    1982-01-01

    The use of radiolabeled nucleosides and nucleic acid bases to estimate the rates of RNA and DNA synthesis in naturally occurring microbial assemblages requires numerous assumptions, several of which are evaluated herein. Comparative time series analyses of the uptake and incorporation, labeling specificity, and extent of catabolism of [2-3H]adenine, [methyl-3H]thymidine, and [5-3H]uridine were performed with pure bacterial and algal cultures, as well as with environmental samples. [3H]thymidine yielded the most variable results, especially with regard to the extent of nonspecific macromolecular labeling. The pathways of [3H]thymidine and [3H]adenine metabolism were further evaluated by isotope dilution methods and by comparing incorporation patterns of thymidine labeled at different sites of the molecule. The advantages, uncertainties, and limitations of the use of radiolabeled nucleic acid precursors in studies of aquatic microbial ecology are discussed and a prospectus for future studies presented. PMID:16346114

  5. 7-Azidomethoxy Coumarins as Profluorophores for Templated Nucleic Acid Detection

    PubMed Central

    Franzini, Raphael M.

    2012-01-01

    Templated nucleic acid detection is an emerging bioanalytical method that makes use of the target DNA or RNA strand to initiate a fluorogenic reaction. The Staudinger reduction holds particular promise for templated sensing of nucleic acids because the involved functional groups are highly chemoselective. Here, the azidomethoxy group, which can be removed under Staudinger conditions, is used to cage 7-hydroxycoumarin fluorophores. The reduction by phosphines and the subsequent loss of the azidomethoxy substituent induce a significant bathochromic shift of the major absorbance band in the near UV region. When excited at the appropriate wavelength, this change in the absorbance spectrum translates into a substantial fluorescence turn-on signal. The described profluorophores are readily conjugated to amino-modified DNAs and are rapidly uncaged by a triphenylphosphine-DNA probe under the control of a DNA template. In addition, turnover of the probes on the target strand is demonstrated, yielding substantial signal amplification. PMID:19035374

  6. Ultrasensitive nucleic acid sequence detection by single-molecule electrophoresis

    SciTech Connect

    Castro, A; Shera, E.B.

    1996-09-01

    This is the final report of a one-year laboratory-directed research and development project at Los Alamos National Laboratory. There has been considerable interest in the development of very sensitive clinical diagnostic techniques over the last few years. Many pathogenic agents are often present in extremely small concentrations in clinical samples, especially at the initial stages of infection, making their detection very difficult. This project sought to develop a new technique for the detection and accurate quantification of specific bacterial and viral nucleic acid sequences in clinical samples. The scheme involved the use of novel hybridization probes for the detection of nucleic acids combined with our recently developed technique of single-molecule electrophoresis. This project is directly relevant to the DOE`s Defense Programs strategic directions in the area of biological warfare counter-proliferation.

  7. Synthetic nucleic Acid delivery systems: present and perspectives.

    PubMed

    Draghici, Bogdan; Ilies, Marc A

    2015-05-28

    Self-assembled synthetic gene delivery systems represent the bottom-up approach to gene delivery and gene silencing, in which scientists are designing novel cationic and procationic amphiphiles that can pack, transport, and deliver nucleic acids to various targets in the body in a controlled manner. These supramolecular assemblies are safer than viruses, but they are lagging behind them in efficiency. We are presenting recent progress that has narrowed this gap through better understanding the delivery barriers and incorporation of this knowledge in the design of novel synthetic amphiphiles, formulations, and revolutionary screening and optimization processes. Structure-properties and structure-activity relationships were drawn within each amphiphile class, presenting the cellular and animal models used to generate them. We are also revealing pertinent in vitro/in vivo correlations that emphasize promising amphiphiles and successful formulation optimization efforts for efficient in vivo nucleic acid delivery, together with main organ targets and diseases treatable with these revolutionary technologies. PMID:25658858

  8. A rapid multiplex assay for nucleic acid-based diagnostics.

    PubMed

    Deshpande, Alina; Gans, Jason; Graves, Steven W; Green, Lance; Taylor, Laura; Kim, Heung Bok; Kunde, Yuliya A; Leonard, Pascale M; Li, Po-E; Mark, Jacob; Song, Jian; Vuyisich, Momchilo; White, P Scott

    2010-02-01

    We have developed a rapid (under 4 hours), multiplex, nucleic acid assay, adapted to a microsphere array detection platform. We call this assay multiplex oligonucleotide ligation-PCR (MOL-PCR). Unlike other ligation-based assays that require multiple steps, our protocol consists of a single tube reaction, followed by hybridization to a Luminex microsphere array for detection. We demonstrate the ability of this assay to simultaneously detect diverse nucleic acid signatures (e.g., unique sequences, single nucleotide polymorphisms) in a single multiplex reaction. Detection probes consist of modular components that enable target detection, probe amplification, and subsequent capture onto microsphere arrays. To demonstrate the utility of our assay, we applied it to the detection of three biothreat agents, B. anthracis, Y. pestis, and F. tularensis. Combined with the ease and robustness of this assay, the results presented here show a strong potential of our assay for use in diagnostics and surveillance. PMID:20006656

  9. Nucleic Acid Aptamers: Research Tools in Disease Diagnostics and Therapeutics

    PubMed Central

    Yadava, Pramod K.

    2014-01-01

    Aptamers are short sequences of nucleic acid (DNA or RNA) or peptide molecules which adopt a conformation and bind cognate ligands with high affinity and specificity in a manner akin to antibody-antigen interactions. It has been globally acknowledged that aptamers promise a plethora of diagnostic and therapeutic applications. Although use of nucleic acid aptamers as targeted therapeutics or mediators of targeted drug delivery is a relatively new avenue of research, one aptamer-based drug “Macugen” is FDA approved and a series of aptamer-based drugs are in clinical pipelines. The present review discusses the aspects of design, unique properties, applications, and development of different aptamers to aid in cancer diagnosis, prevention, and/or treatment under defined conditions. PMID:25050359

  10. Design of antisense oligonucleotides stabilized by locked nucleic acids

    Microsoft Academic Search

    Jens Kurreck; Eliza Wyszko; Clemens Gillen; Volker A. Erdmann

    2002-01-01

    The design of antisense oligonucleotides containing locked nucleic acids (LNA) was optimized and compared to intensively studied DNA oligonucleotides, phosphorothioates and 2'-O-methyl gapmers. In contradiction to the literature, a stretch of seven or eight DNA monomers in the center of a chimeric DNA\\/LNA oligonucleotide is necessary for full activation of RNase H to cleave the target RNA. For 2'-O-methyl gapmers

  11. Spontaneous Mutual Ordering of Nucleic Acids and Proteins

    NASA Astrophysics Data System (ADS)

    Wills, Peter R.

    2014-12-01

    It is proposed that the prebiotic ordering of nucleic acid and peptide sequences was a cooperative process in which nearly random populations of both kinds of polymers went through a codependent series of self-organisation events that simultaneously refined not only the accuracy of genetic replication and coding but also the functional specificity of protein catalysts, especially nascent aminoacyl-tRNA synthetase "urzymes".

  12. Prospects for antisense peptide nucleic acid (PNA) therapies for HIV

    PubMed Central

    Pandey, Virendra N.; Upadhyay, Alok; Chaubey, Binay

    2009-01-01

    Since the discovery and synthesis of a novel DNA mimic, peptide nucleic acid (PNA) in 1991, PNAs have attracted tremendous interest and have shown great promise as potential antisense drugs. They have been used extensively as tools for specific modulation of genes expression by targeting translation or transcription processes. This review discusses the present and future therapeutic potential of this class of compound as anti-HIV-1 drugs. PMID:19534584

  13. Method and apparatus for staining immobilized nucleic acids

    DOEpatents

    Ramsey, J. Michael (Knoxville, TN); Foote, Robert S. (Oak Ridge, TN); Jacobson, Stephen C. (Knoxville, TN)

    2000-01-01

    A method for staining immobilized nucleic acids includes the steps of affixing DNA probes to a solid substrate, moving target DNA material into proximity with the DNA probes, whereby the target DNA hybridized with specific ones of the DNA probes, and moving a fluorescent dye into proximity with the hybridized target DNA, whereby the fluorescent dye binds to the hybridized DNA to enable subsequent detection of fluorescence.

  14. NanoDrop microvolume quantitation of nucleic acids.

    PubMed

    Desjardins, Philippe; Conklin, Deborah

    2010-01-01

    Biomolecular assays are continually being developed that use progressively smaller amounts of material, often precluding the use of conventional cuvette-based instruments for nucleic acid quantitation for those that can perform microvolume quantitation. The NanoDrop microvolume sample retention system (Thermo Scientific NanoDrop Products) functions by combining fiber optic technology and natural surface tension properties to capture and retain minute amounts of sample independent of traditional containment apparatus such as cuvettes or capillaries. Furthermore, the system employs shorter path lengths, which result in a broad range of nucleic acid concentration measurements, essentially eliminating the need to perform dilutions. Reducing the volume of sample required for spectroscopic analysis also facilitates the inclusion of additional quality control steps throughout many molecular workflows, increasing efficiency and ultimately leading to greater confidence in downstream results. The need for high-sensitivity fluorescent analysis of limited mass has also emerged with recent experimental advances. Using the same microvolume sample retention technology, fluorescent measurements may be performed with 2 ?L of material, allowing fluorescent assays volume requirements to be significantly reduced. Such microreactions of 10 ?L or less are now possible using a dedicated microvolume fluorospectrometer. Two microvolume nucleic acid quantitation protocols will be demonstrated that use integrated sample retention systems as practical alternatives to traditional cuvette-based protocols. First, a direct A260 absorbance method using a microvolume spectrophotometer is described. This is followed by a demonstration of a fluorescence-based method that enables reduced-volume fluorescence reactions with a microvolume fluorospectrometer. These novel techniques enable the assessment of nucleic acid concentrations ranging from 1 pg/ ?L to 15,000 ng/ ?L with minimal consumption of sample. PMID:21189466

  15. Molecular Dynamics Simulations of Cyclohexyl Modified Peptide Nucleic Acids (PNA)

    Microsoft Academic Search

    Smriti Sharma; Uddhavesh B. Sonavane; Rajendra R. Joshi

    2010-01-01

    Peptide Nucleic Acids (PNA) that bind sequence specifically to DNA\\/RNA are of major interest in the field of molecular biology and could form the basis for gene-targeted drugs. Molecular dynamics simulations are aimed to characterize the structural and dynamical features to understand the effect of backbone modification on the structure and dynamics along with the stability of the resulting 10mer

  16. Nucleic acid-based tissue biomarkers of urologic malignancies.

    PubMed

    Dietrich, Dimo; Meller, Sebastian; Uhl, Barbara; Ralla, Bernhard; Stephan, Carsten; Jung, Klaus; Ellinger, Jörg; Kristiansen, Glen

    2014-08-01

    Molecular biomarkers play an important role in the clinical management of cancer patients. Biomarkers allow estimation of the risk of developing cancer; help to diagnose a tumor, ideally at an early stage when cure is still possible; and aid in monitoring disease progression. Furthermore, they hold the potential to predict the outcome of the disease (prognostic biomarkers) and the response to therapy (predictive biomarkers). Altogether, biomarkers will help to avoid tumor-related deaths and reduce overtreatment, and will contribute to increased survival and quality of life in cancer patients due to personalized treatments. It is well established that the process of carcinogenesis is a complex interplay between genomic predisposition, acquired somatic mutations, epigenetic changes and genomic aberrations. Within this complex interplay, nucleic acids, i.e. RNA and DNA, play a fundamental role and therefore represent ideal candidates for biomarkers. They are particularly promising candidates because sequence-specific hybridization and amplification technologies allow highly accurate and sensitive assessment of these biomarker levels over a broad dynamic range. This article provides an overview of nucleic acid-based biomarkers in tissues for the management of urologic malignancies, i.e. tumors of the prostate, testis, kidney, penis, urinary bladder, renal pelvis, ureter and other urinary organs. Special emphasis is put on genomic, transcriptomic and epigenomic biomarkers (SNPs, mutations [genomic and mitochondrial], microsatellite instabilities, viral and bacterial DNA, DNA methylation and hydroxymethylation, mRNA expression, and non-coding RNAs [lncRNA, miRNA, siRNA, piRNA, snRNA, snoRNA]). Due to the multitude of published biomarker candidates, special focus is given to the general applicability of different molecular classes as biomarkers and some particularly promising nucleic acid biomarkers. Furthermore, specific challenges regarding the development and clinical implementation of nucleic acid-based biomarkers are discussed. PMID:24878394

  17. Inhibition of a DNA-helicase by peptide nucleic acids

    Microsoft Academic Search

    Lionel Bastide; Paul E. Boehmer; Giuseppe Villani; Bernard Lebleu

    1999-01-01

    Bis-peptide nucleic acid (bis-PNA) binding results in D-loop formation by strand displacement at comple- mentary homopurine stretches in DNA duplexes. Transcription and replication in intact cells is mediated by multienzymatic complexes involving several proteins other than polymerases. The behaviour of the highly stable clamp structure formed by bis-PNAs has thus far been studied with respect to their capacity to arrest

  18. DNA-like double helix formed by peptide nucleic acid

    Microsoft Academic Search

    Pernilla Wittung; Peter E. Nielsen; Ole Buchardt; Michael Egholm; Bengt Nordén

    1994-01-01

    ALTHOUGH the importance of the nucleobases in the DNA double helix is well understood, the evolutionary significance of the deoxyribose phosphate backbone and the contribution of this chemical entity to the overall helical structure and stability of the double helix is not so clear. Peptide nucleic acid (PNA)1-7 is a DNA analogue with a backbone consisting of N-(2-aminoethyl)glycine units (Fig.

  19. Inhibiting transcription of chromosomal DNA with antigene peptide nucleic acids

    Microsoft Academic Search

    Bethany A Janowski; Kunihiro Kaihatsu; Kenneth E Huffman; Jacob C Schwartz; Rosalyn Ram; Daniel Hardy; Carole R Mendelson; David R Corey

    2005-01-01

    Synthetic molecules that recognize specific sequences within cellular DNA are potentially powerful tools for investigating chromosome structure and function. Here, we designed antigene peptide nucleic acids (agPNAs) to target the transcriptional start sites for the human progesterone receptor B (hPR-B) and A (hPR-A) isoforms at sequences predicted to be single-stranded within the open complex of chromosomal DNA. We found that

  20. Determination of nucleic acids in acidic medium by enhanced light scattering of large particles

    Microsoft Academic Search

    Zhengping Li; Ke’an Li; Shenyang Tong

    2000-01-01

    The large particle light scattering technique was first developed as a sensitive and convenient analysis method for microdetermination of nucleic acids by using a common spectrofluorometer. In 0.1 mol l?1 HCl, H2SO4, or HNO3 solution, the nucleic acids can aggregate to form large particles whose dimensions are comparable to the wavelength of UV-Vis light. The large particles can result in

  1. Interaction of cetylpyridine bromide with nucleic acids and determination of nucleic acids at nanogram levels based on the enhancement of resonance Rayleigh light scattering

    Microsoft Academic Search

    Rutao Liu; Jinghe Yang; Xia Wu

    2002-01-01

    Resonance Rayleigh light scattering (RRLS) spectra of cetylpyridine bromide (CPB)–nucleic acid system and their analytical application have been first studied. The effective factors and optimum conditions of the reaction have been investigated. After CPB and nucleic acid are mixed together, a new absorption peak located at 300 nm appeared, which is due to the formation of new ion associate of

  2. Deep ultraviolet mapping of intracellular protein and nucleic acid in femtograms per pixel.

    PubMed

    Cheung, Man C; Evans, James G; McKenna, Brian; Ehrlich, Daniel J

    2011-11-01

    By using imaging spectrophotometry with paired images in the 200- to 280-nm wavelength range, we have directly mapped intracellular nucleic acid and protein distributions across a population of Chinese hamster ovary (CHO-K1) cells. A broadband 100× objective with a numerical aperture of 1.2 NA (glycerin immersion) and a novel laser-induced-plasma point source generated high-contrast images with short (?100 ms) exposures and a lateral resolution nearing 200 nm that easily resolves internal organelles. In a population of 420 CHO-K1 cells and 477 nuclei, we found a G1 whole-cell nucleic acid peak at 26.6 pg, a nuclear-isolated total nucleic acid peak at 11.4 pg, and, as inferred by RNase treatment, a G1 total DNA mass of 7.4 pg. At the G1 peak, we found a whole-cell protein mass of 95.6 pg, and a nuclear-isolated protein mass of 39.3 pg. An algorithm for protein quantification that senses peptide-bond (220-nm) absorbance was found to have a higher signal-to-noise ratio and to provide more reliable nucleic acid and protein determinations when compared to more classical 280/260-nm algorithms when used for intracellular mass mapping. Using simultaneous imaging with common nuclear stains (Hoechst 33342, Syto-14, and Sytox Orange), we have compared staining patterns to deep-UV images of condensed chromatin and have confirmed bias of these common nuclear stains related to nuclear packaging. The approach allows absolute mass measurements with no special sample preparation or staining. It can be used in conjunction with normal fluorescence microscopy and with relatively modest modification of the microscope. PMID:21796773

  3. Devices and approaches for generating specific high-affinity nucleic acid aptamers

    NASA Astrophysics Data System (ADS)

    Szeto, Kylan; Craighead, Harold G.

    2014-09-01

    High-affinity and highly specific antibody proteins have played a critical role in biological imaging, medical diagnostics, and therapeutics. Recently, a new class of molecules called aptamers has emerged as an alternative to antibodies. Aptamers are short nucleic acid molecules that can be generated and synthesized in vitro to bind to virtually any target in a wide range of environments. They are, in principal, less expensive and more reproducible than antibodies, and their versatility creates possibilities for new technologies. Aptamers are generated using libraries of nucleic acid molecules with random sequences that are subjected to affinity selections for binding to specific target molecules. This is commonly done through a process called Systematic Evolution of Ligands by EXponential enrichment, in which target-bound nucleic acids are isolated from the pool, amplified to high copy numbers, and then reselected against the desired target. This iterative process is continued until the highest affinity nucleic acid sequences dominate the enriched pool. Traditional selections require a dozen or more laborious cycles to isolate strongly binding aptamers, which can take months to complete and consume large quantities of reagents. However, new devices and insights from engineering and the physical sciences have contributed to a reduction in the time and effort needed to generate aptamers. As the demand for these new molecules increases, more efficient and sensitive selection technologies will be needed. These new technologies will need to use smaller samples, exploit a wider range of chemistries and techniques for manipulating binding, and integrate and automate the selection steps. Here, we review new methods and technologies that are being developed towards this goal, and we discuss their roles in accelerating the availability of novel aptamers.

  4. Nucleic Acids Research, Vol. 18, No. 22 6587 Purification of RNA and RNA-protein complexes by an

    E-print Network

    Wickens, Marv

    Nucleic Acids Research, Vol. 18, No. 22 6587 Purification of RNA and RNA-protein complexes by an R purification methods exist for the isolation of RNA- protein complexes formed in vitro (1-4). In one17 coat protein affinity method Vivian J.Bardwell1 and Marvin Wickens' 2* 0Cell and Molecular Biology

  5. Imperfectly matched nucleic acid complexes and their biochemical manifestation

    NASA Astrophysics Data System (ADS)

    Zenkova, M. A.; Karpova, G. G.

    1993-04-01

    The review is devoted to the analysis of experimental data on the selectivity of the interaction of nucleic acid with antisense oligonucleotides and their derivatives, which lead to the prospect of achieving a highly selective influence on many biochemical and molecular-genetic processes in living organisms. Theoretical estimates of the level of specificity of the interactions of nucleic acids and the thermodynamic parameters of the formation of perfectly and imperfectly matched complementary complexes are examined in the review. Attention is concentrated on the complementation accuracy of the interaction of DNA and RNA with oligonucleotides and their derivatives in various model systems both in vitro and in vivo. Data on the specificity of the inhibition of translation with the aid of antisense oligonucleotides in model systems in vitro are analysed. The question of the influence of the steric structure of the nucleic acid molecule on the accuracy and efficiency of the interactions with antisense oligonucleotides and their derivatives is discussed. The bibliography includes 247 references.

  6. The role of immunostimulatory nucleic acids in septic shock

    PubMed Central

    Bleiblo, Farag; Michael, Paul; Brabant, Danielle; Ramana, Chilakamarti V; Tai, TC; Saleh, Mazen; Parrillo, Joseph E; Kumar, Anand; Kumar, Aseem

    2012-01-01

    Sepsis and its associated syndromes represent the systemic host response to severe infection and is manifested by varying degrees of hypotension, coagulopathy, and multiorgan dysfunction. Despite great efforts being made to understand this condition and designing therapies to treat sepsis, mortality rates are still high in septic patients. Characterization of the complex molecular signaling networks between the various components of host-pathogen interactions, highlights the difficulty in identifying a single driving force responsible for sepsis. Although triggering the inflammatory response is generally considered as protective against pathogenic threats, the interplay between the signaling pathways that are induced or suppressed during sepsis may harm the host. Numerous surveillance mechanisms have evolved to discriminate self from foreign agents and accordingly provoke an effective cellular response to target the pathogens. Nucleic acids are not only an essential genetic component, but sensing their molecular signature is also an important quality control mechanism which has evolved to maintain the integrity of the human genome. Evidence that has accumulated recently indicated that distinct pattern recognition receptors sense nucleic acids released from infectious organisms or from damaged host cells, resulting in the modulation of intracellular signalling cascades. Immunoreceptor-mediated detection of these nucleic acids induces antigen-specific immunity, secretion of proinflammatory cytokines and reactive oxygen/nitrogen species and thus are implicated in a range of diseases including septic shock. PMID:22328944

  7. Aptamers to explore prion protein interactions with nucleic acids.

    PubMed

    Marc, Daniel

    2010-01-01

    A misfolded isoform of the prion protein (PrP) is the essential component of the prion diseases' agent. The prion concept has progressively gained acceptance, in a large part thanks to the realization that it played a role not only in the transmissible spongiform encephalopathies, but also in the non-Mendelian propagation of self-perpetuating phenotypes of the yeast Saccharomyces cerevisiae. Uncertainties about the nature of the agent and the function of PrP have fostered searches of nucleic acid ligands of the protein. In vitro methods of nucleic acid evolutions have been used to identify RNAs or DNAs that bind PrP, towards the triple objective of i) setting up new diagnostic tools, ii) identifying nucleic acids with which PrP may interact, as part of its physiological or pathological function, and iii) elucidating the pathological transconformation of PrP. This review will focus on these studies, their methods, the knowledge acquired from them about the prion protein, and the possibilities that they offer in the areas of diagnosis and therapy of prion diseases. PMID:20036833

  8. Nucleic acid-induced antiviral immunity in shrimp.

    PubMed

    Wang, Pei-Hui; Yang, Li-Shi; Gu, Zhi-Hua; Weng, Shao-Ping; Yu, Xiao-Qiang; He, Jian-Guo

    2013-09-01

    Vertebrates detect viral infection predominantly by sensing viral nucleic acids to produce type I interferon (IFN). In invertebrates, it has been believed that the IFN system is absent and RNA interference is a sequence-specific antiviral pathway. In this study, we found that injection of nucleic acid mimics poly(I:C), poly(C:G), CL097, poly C and CpG-DNA, afforded shrimp antiviral immunity, which is similar to the vertebrate IFN system. Using suppression subtractive hybridization (SSH) method, 480 expression sequence tags were identified to be involved in the poly(I:C)-induced antiviral immunity of the model crustacean Litopenaeus vannamei, and 41% of them were new genes. In the SSH libraries, several IFN system-related genes such as dsRNA-dependent protein kinase PKR, Toll-like receptor 3 (TLR3) and IFN?-inducible protein 30 were identified. L. vannamei IKK?, whose vertebrate homologs are central regulators of the IFN-producing pathway, could significantly activate IFN reporter genes in HEK293T cells. In crustacean databases, many genes homologous to genes of the vertebrate IFN response, such as IRFs, PKR, ADAR (adenosine deaminase, RNA-specific) and other interferon-stimulated genes (ISGs) were discovered. These results suggest that shrimp may possess nucleic acid-induced antiviral immunity. PMID:23773856

  9. Computational design of nucleic acid feedback control circuits.

    PubMed

    Yordanov, Boyan; Kim, Jongmin; Petersen, Rasmus L; Shudy, Angelina; Kulkarni, Vishwesh V; Phillips, Andrew

    2014-08-15

    The design of synthetic circuits for controlling molecular-scale processes is an important goal of synthetic biology, with potential applications in future in vitro and in vivo biotechnology. In this paper, we present a computational approach for designing feedback control circuits constructed from nucleic acids. Our approach relies on an existing methodology for expressing signal processing and control circuits as biomolecular reactions. We first extend the methodology so that circuits can be expressed using just two classes of reactions: catalysis and annihilation. We then propose implementations of these reactions in three distinct classes of nucleic acid circuits, which rely on DNA strand displacement, DNA enzyme and RNA enzyme mechanisms, respectively. We use these implementations to design a Proportional Integral controller, capable of regulating the output of a system according to a given reference signal, and discuss the trade-offs between the different approaches. As a proof of principle, we implement our methodology as an extension to a DNA strand displacement software tool, thus allowing a broad range of nucleic acid circuits to be designed and analyzed within a common modeling framework. PMID:25061797

  10. IN VITRO SELECTION OF FUNCTIONAL NUCLEIC ACIDS

    Microsoft Academic Search

    David S. Wilson; Jack W. Szostak

    1999-01-01

    ? Abstract In vitro selection allows rare functional RNA or DNA molecules to be isolated from pools of over 10 15 different sequences. This approach has been used to identify RNA and DNA ligands for numerous small molecules, and recent three- dimensional structure solutions have revealed the basis for ligand recognition in sev- eral cases. By selecting high-affinity and -specificity

  11. PAPER www.rsc.org/analyst | The Analyst A double-stranded molecular probe for homogeneous nucleic acid analysis

    E-print Network

    Wong, Pak Kin

    fluorogenic conformational change upon hybridization to its complementary nucleic acid target. The molecular of specific nucleic acid molecules. In this sensing scheme, a fluorophore-conjugated nucleic acid sequencePAPER www.rsc.org/analyst | The Analyst A double-stranded molecular probe for homogeneous nucleic

  12. Backscattering light detection of nucleic acids with tetraphenylporphyrin–Al(III)–nucleic acids at liquid\\/liquid interface

    Microsoft Academic Search

    Yong Hong Wang; Hong Ping Guo; Ke Jun Tan; Cheng Zhi Huang

    2004-01-01

    A backscattering light (BSL) detection assembly is constructed and applied to the determination of nucleic acids with high sensitivity and selectivity based on the measurements of BSL signals at water\\/tetrachloromethane (H2O\\/CCl4) interface. In aqueous medium of pH 3, the binary complex of of Al(III)–DNAs could be formed by the interaction of Al(III) with the phosphate group of DNAs, which then

  13. Nucleic Acid Homologies Among Species of Saccharomyces

    PubMed Central

    Bicknell, J. N.; Douglas, Howard C.

    1970-01-01

    Evolutionary divergence among species of the yeast genus Saccharomyces was estimated from measurements of deoxyribonucleic acid (DNA)/DNA and ribosomal ribonucleic acid (RNA)/DNA homology. Much diversity was found in the DNA base sequences with several species showing little or no homology to the three reference species, S. cerevisiae, S. lactis, and S. fragilis. These three reference species also showed little or no homology to each other. On the other hand the diversity among ribosomal RNA base sequences was small since most species showed a high degree of homology to the reference species. The arrangement of species based on ribosomal RNA homologies agrees in most cases with current taxonomic groupings. A yeast hybrid (S. fragilis × S. lactis) was shown to contain two nonhomologous genomes. A minimum genome size of 9.2 × 109 daltons for S. cerevisiae was calculated from the rate of DNA renaturation. PMID:5413823

  14. Innate immune recognition of nucleic acids

    Microsoft Academic Search

    Tsan Xiao

    2009-01-01

    The innate immune system employs a number of pattern recognition receptor families in response to DNAs and RNAs, either from\\u000a invading microbes or within the hosts. These include the Toll-like receptors (TLRs), the retinoic acid inducible gene I (RIG-I)\\u000a like receptors (RLRs), and the nucleotide-binding domain leucine-rich repeat\\/NOD-like receptor (NLRs), among other potential\\u000a sensors in the cytoplasm. These receptors are

  15. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    SciTech Connect

    Marcia, Marco, E-mail: marco.marcia@yale.edu; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas [Yale University, New Haven, CT 06511 (United States); Rajashankar, Kanagalaghatta [Argonne National Laboratory, Argonne, IL 60439 (United States); Pyle, Anna Marie, E-mail: marco.marcia@yale.edu [Yale University, New Haven, CT 06511 (United States); Yale University, New Haven, CT 06511 (United States); Howard Hughes Medical Institute, Chevy Chase, MD 20815 (United States)

    2013-11-01

    Strategies for phasing nucleic acid structures by molecular replacement, using both experimental and de novo designed models, are discussed. Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts.

  16. Spectrofluorimetric Determination of Nucleic Acids with Aluminum(III)\\/8Hydroxyquinoline Complex

    Microsoft Academic Search

    Cheng Zhi Huang; Yuan Fang Li; Shen Yang Tong

    1997-01-01

    On the basis of the fluorescence enhancement effect of nucleic acids on the aluminum (III) \\/ 8-hydroxyquinoline (8-HQ) complex, a spectrofluorimetric method for nucleic acids is proposed in the present paper. In the pH range 5.8–7.0, the fluorescence of the Al(III)\\/8-HQ complex, excited at 265 nm or at 365 nm, is enhanced by nucleic acids. The calibration curve was linear

  17. RESONANCE LIGHT SCATTERING FOR THE DETERMINATION OF NUCLEIC ACIDS WITH METHYL VIOLET

    Microsoft Academic Search

    Wu Juan Zhang; Hong Ping Xu; Chun Xia Xue; Xing Guo Chen; Zhi De Hu

    2001-01-01

    For the first time, methyl violet (MV) was used to determine nucleic acids with a resonance light scattering (RLS) technique. The interactions of MV with nucleic acids give strong signals of RLS at 327.0, 490.0 and 651.0 nm. Based on this reaction, a new quantitative determination method for nucleic acids in aqueous solutions has been developed. At pH 7.51 and

  18. Spectrofluorimetric determination of nucleic acids as 8-hydroxyquinoline\\/ yttrium ternary complexes

    Microsoft Academic Search

    Cheng Zhi Huang; Ke An Li; Shen Yang Tong

    1997-01-01

    The formation of nucleic acids\\/8-hydroxyquinoline\\/yttrium(III) ternary complexes and their fluorescent properties have been studied. The nucleic acids studied include native and thermally denatured calf thymus DNA, fish sperm DNA and yeast RNA. In the range of pH 7.6–8.5, controlled by NH3-NH4C1 buffer, ternary complexes are formed that fluoresce at different wavelengths with different nucleic acids. Based on the fluorescence reactions,

  19. Silver nanoparticles fluorescence enhancement effect for determination of nucleic acids with kaempferol–Al(III)

    Microsoft Academic Search

    Yinghua Cao; Xia Wu; Minqin Wang

    2011-01-01

    Nucleic acids can greatly enhance fluorescence intensity of the kaempferol (Km)–Al(III) system in the presence of silver nanoparticles (AgNPs). Based on this, a novel method for the determination of nucleic acids is proposed. Under studied conditions, there are linear relationships between the extent of fluorescence enhancement and the concentration of nucleic acids in the range of 5.0×10?9 to 2.0×10?6gmL?1 for

  20. Determination of nucleic acids at nanogram level using resonance light scattering technique with Congo Red

    Microsoft Academic Search

    Xia Wu; Yuebo Wang; Minqin Wang; Shuna Sun; Jinghe Yang; Yuxia Luan

    2005-01-01

    Based on the enhancement of the resonance light scattering (RLS) of Congo Red (CR) by nucleic acid, a new quantitative method for nucleic acid is developed. In the Tris–HCl buffer (pH 10.5), the weak light scattering of CR is greatly enhanced by addition of nucleic acid and CTMAB, the maximum peak is at 560nm and the enhanced intensity of RLS

  1. Design of Multi-Stable Nucleic Acid Sequences Ingrid G. Abfalter1

    E-print Network

    Stadler, Peter F.

    Design of Multi-Stable Nucleic Acid Sequences Ingrid G. Abfalter1 , Christoph Flamm1 , Peter F nucleic acid-structure [6]. GCGGAUU U AG C U C A G U UG G G A G A G CG CCAGA C UG A A GAUCUGG A G GUCC U G. (below) bracket-dot-representation. 1 #12;Multi-Stable Nucleic Acid Structures 2 1 5 10 15 20 1 5 10 15

  2. Origin of Overstretching Transitions in Single-Stranded Nucleic Acids

    NASA Astrophysics Data System (ADS)

    Scholl, Zackary N.; Rabbi, Mahir; Lee, David; Manson, Laura; S-Gracz, Hanna; Marszalek, Piotr E.

    2013-11-01

    We combined single-molecule force spectroscopy with nuclear magnetic resonance measurements and molecular mechanics simulations to examine overstretching transitions in single-stranded nucleic acids. In single-stranded DNA and single-stranded RNA there is a low-force transition that involves unwinding of the helical structure, along with base unstacking. We determined that the high-force transition that occurs in polydeoxyadenylic acid single-stranded DNA is caused by the cooperative forced flipping of the dihedral angle formed between four atoms, O5’-C5’-C4’-C3’ (? torsion), in the nucleic acid backbone within the canonical B-type helix. The ? torsion also flips under force in A-type helices, where the helix is shorter and wider as compared to the B-type helix, but this transition is less cooperative than in the B type and does not generate a high-force plateau in the force spectrums of A-type helices. We find that a similar high-force transition can be induced in polyadenylic acid single-stranded RNA by urea, presumably due to disrupting the intramolecular hydrogen bonding in the backbone. We hypothesize that a pronounced high-force transition observed for B-type helices of double stranded DNA also involves a cooperative flip of the ? torsion. These observations suggest new fundamental relationships between the canonical structures of single-and double-stranded DNA and the mechanism of their molecular elasticity.

  3. HPLC measurement of guanine for the determination of nucleic acids (RNA) in yeasts

    Microsoft Academic Search

    Bryan Todd; Jian Zhao; Graham Fleet

    1995-01-01

    A method based upon the assay of guanine is described for the determination of nucleic acid content in yeasts. Total nucleic acids are hydrolysed by hot perchloric acid and the resultant quantitative release of guanine is measured by reverse-phase HPLC. Due to the high RNA:DNA ratio in yeasts, the method can be used to estimate the RNA concentration in yeasts.

  4. BGL5 .beta.-glucosidase and nucleic acids encoding the same

    DOEpatents

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-02-28

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl5, and the corresponding BGL5 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL5, recombinant BGL5 proteins and methods for producing the same.

  5. BGL3 beta-glucosidase and nucleic acids encoding the same

    DOEpatents

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2008-04-01

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl3, and the corresponding BGL3 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL3, recombinant BGL3 proteins and methods for producing the same.

  6. BGL3 beta-glucosidase and nucleic acids encoding the same

    DOEpatents

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2007-09-25

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl3, and the corresponding BGL3 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL3, recombinant BGL3 proteins and methods for producing the same.

  7. BGL4 beta-glucosidase and nucleic acids encoding the same

    DOEpatents

    Dunn-Coleman, Nigel (Los Gatos, CA) [Los Gatos, CA; Goedegebuur, Frits (Vlaardingen, NL) [Vlaardingen, NL; Ward, Michael (San Francisco, CA) [San Francisco, CA; Yao, Jian (Sunnyvale, CA) [Sunnyvale, CA

    2008-01-22

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl4, and the corresponding BGL4 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL4, recombinant BGL4 proteins and methods for producing the same.

  8. BGL5 .beta.-glucosidase and nucleic acids encoding the same

    DOEpatents

    Dunn-Coleman, Nigel (Los Gatos, CA); Goedegebuur, Frits (Vlaardingen, NL); Ward, Michael (San Francisco, CA); Yao, Jian (Sunnyvale, CA)

    2008-03-18

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl5, and the corresponding BGL5 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL5, recombinant BGL5 proteins and methods for producing the same.

  9. BGL4 .beta.-glucosidase and nucleic acids encoding the same

    DOEpatents

    Dunn-Coleman, Nigel; Goedegebuur, Frits; Ward, Michael; Yao, Jian

    2006-05-16

    The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl4, and the corresponding BGL4 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL4, recombinant BGL4 proteins and methods for producing the same.

  10. Point of Attachment and Sequence of Immobilized Peptide-Acridine Conjugates Control Affinity for Nucleic Acids

    E-print Network

    Beal, Peter A.

    for Nucleic Acids Coby B. Carlson and Peter A. Beal* Department of Chemistry, UniVersity of Utah, 315 South of peptide-acridine conjugates (PACs) featuring a novel 9-anilinoacridine amino acid that we wish to screen if immobilization of a PAC affects binding to RNA targets. Similar compounds have been shown to bind nucleic acids

  11. Nonenzymatic catalytic signal amplification for nucleic acid hybridization assays

    NASA Technical Reports Server (NTRS)

    Fan, Wenhong (Inventor); Cassell, Alan M. (Inventor); Han, Jie (Inventor)

    2006-01-01

    Devices, methods, and kits for amplifying the signal from hybridization reactions between nucleic acid probes and their cognate targets are presented. The devices provide partially-duplexed, immobilized probe complexes, spatially separate from and separately addressable from immobilized docking strands. Cognate target acts catalytically to transfer probe from the site of probe complex immobilization to the site of immobilized docking strand, generating a detectable signal. The methods and kits of the present invention may be used to identify the presence of cognate target in a fluid sample.

  12. Fluorecently labeled bionanotransporters of nucleic acid based on carbon nanotubes

    E-print Network

    Novopashina, D S; Venyaminova, A G

    2012-01-01

    Here we propose the approach to design of the new type of hybrids of oligonucleotides with fluorescein-functionalized single-walled carbon nanotubes. The approach is based on stacking interactions of functionalized nanotubes with pyrene residues in conjugates of oligonucleotides. The amino- and fluorescein-modified single-walled carbon nanotubes were obtained, and their physico-chemical properties were investigated. The effect of carbon nanotubes functionalization type on the efficacy of sorption of pyrene conjugates of oligonucleotides was examined. Proposed non-covalent hybrids of fluorescein-labeled carbon nanotubes with oligonucleotides may be used for intracellular transport of functional nucleic acids.

  13. Interaction of bleomycin and its oligonucleotide derivatives with nucleic acids

    NASA Astrophysics Data System (ADS)

    Sergeyev, D. S.; Zarytova, V. F.

    1996-04-01

    Various aspects of interaction of the antitumour glycopeptide antibiotic bleomycin with nucleic acids are considered. Data on equilibrium binding parameters obtained by various physicochemical methods have been collected and compared. The contribution of N- and C-terminal domains of the glycopeptide molecule to the binding with DNA and sequence specificity of DNA cleavage are discussed. Data on a recently created new class of compounds — bleomycin — oligonucleotide conjugates — are presented. These compounds, like antibiotics, possess DNA-cleaving activity (also in a catalytic manner) together with high selectivity towards a selected nucleotide sequence. The bibliography includes 267 references.

  14. Nucleic acid programmed polymeric nanomaterials for biological communication

    NASA Astrophysics Data System (ADS)

    Rush, Anthony Michael

    A number of nucleic acid-polymer conjugates were synthesized, resulting in amphiphilic polymer-nucleic acid conjugates with the capability to self-assemble into a range of discrete nanoscale architectures. These nanomaterials, termed DNA-polymer amphiphile nanoparticles (DPA NPs), were studied with respect to their enzymatic processing by both endo- and exonucleases and further deployed as antisense genetic regulatory elements in live cultured human cells. DPA NPs were designed to act as substrates for both non sequence-specific exonucleases and a sequence-specific endonuclease. In all cases, nucleic acids arranged in the corona of spherical nanoparticles exhibited increased resistance to nucleolytic cleavage as compared to native single- or double-stranded analogues. For the exonucleases studied (Exonuclease III from E. Coli and phosphodiesterase I from Crotalus adamanteus), nanoparticle display retarded enzymatic processing by roughly a factor of five. For the endonuclease studied (Nt.CviPII), nanoparticle display prohibited virtually all enzyme activity on oligonucleotides within the nanoparticle shell. To test the ability of these materials to regulate mRNA levels in live cultured human cells, LPA (LNA-polymer amphiphile) NPs were designed to be perfectly complementary to a 20-base region of mRNA encoding the anti-apoptosis protein survivin. In this study two key observations were made. The first observation is that packaging LNA into spherical micellar nanoparticles serves to dramatically enhance cellular uptake of LNA based on flow cytometry and fluorescence microscopy data. The second observation is that LPA NPs are capable of regulating mRNA levels by what is hypothesized to be activation of target mRNA for catalytic RNase H-mediated degradation. These materials represent a unique class of DNA delivery system capable of rendering nucleic acids with natural backbone chemistry resistant to nuclease degradation and further serving to deliver DNA into cells to facilitate depletion of mRNA levels in a sequence-specific fashion. Notably, the use of detergents, charge-neutralizing, or DNA-sequestering components are not required for these materials to be effective in cells.

  15. Targeting Nucleic Acid Secondary Structures by Antisense Oligonucleotides Designed through in vitro Selection

    NASA Astrophysics Data System (ADS)

    Mishra, Rakesh K.; Le Tinevez, Rejane; Toulme, Jean-Jacques

    1996-10-01

    Using an in vitro selection approach, we have isolated oligonucleotides that can bind to a DNA hairpin structure. Complex formation of these oligonucleotides with the target hairpin involves some type of triple-stranded structure with noncanonical interaction, as indicated by band-shift assays and footprinting studies. The selected oligomers can block restriction endonuclease cleavage of the target hairpin in a sequence-specific manner. We demonstrate that in vitro selection can extend the antisense approach to functional targeting of secondary structure motifs. This could provide a basis for interfering with regulatory processes mediated by a variety of nucleic acid structures.

  16. Single-molecule characterization and engineering of the surfaces of nucleic acid sensors

    NASA Astrophysics Data System (ADS)

    Josephs, Eric Alan

    The advent of personalized medicine will require biosensors capable of reliably detecting small levels of disease biomarkers. In microarrays and sensors for nucleic acids, hybridization events between surface-tethered DNA probes and the nucleic acids of interest (targets) are transduced into a detectable signal. However, target-binding ultimately occurs as a result of molecular motions and interactions between the probe and target at the nanometer scale, and common characterization methods either lack the resolution to characterize the sensors at this scale or provide only limited information about their interactions with their nanoscale chemical environment. In this dissertation I argue that an impediment to the development of more reliable and practical biosensors is the lack of knowledge and control of the nanometer length-scale structure of biosensor surfaces, which has a profound impact on molecular recognition and reactions for detection. After reviewing the fundamental surface chemistry and structural motifs of biosensors in Chapter 1, in Chapter 2 I use electrochemical atomic force microscopy (EC-AFM) to characterize in situ a common class of model nucleic acid sensors---thiolated DNA attached to a gold electrode which has been passivated by an alkanethiol self-assembled monolayer---with single-molecule resolution. This level of detail allows me to observe both the conformations of individual probes and their spatial distribution at the nanoscale, then determine how these are affected by assembly conditions, probe structure, and interactions with co-adsorbates. I also determine how these nanoscale details affect the dynamic response of probes to electric fields, which have been commonly used in sensing schemes, and ultimately the ability of the surface-tethered probes to bind with target nucleic acids. In Chapter 3, I demonstrate and optimize the nanoscale patterning of individual DNA molecules into isolated, chemically well-defined niches on the surface, and the use of these patterned probes as a single-molecule `nano-array' able to bind with target nucleic acids. Additionally, an outstanding issue is the expense of the high-quality substrates used in these studies. In Chapter 4, I discuss the development of single-crystal gold micro-plates with controllable surface chemistries as high-quality substrates for biotechnological platforms at a fraction of the cost.

  17. Molecular polarization potential maps of the nucleic acid bases

    SciTech Connect

    Alkorta, I. [Instituto de Quimica Medica, Madrid (Spain)] [Instituto de Quimica Medica, Madrid (Spain); Perez, J.J. [ETS d`Enginyers Industrials, Barcelona (Spain)] [ETS d`Enginyers Industrials, Barcelona (Spain)

    1996-01-05

    Ab initio calculations at the SCF level were carried out to compute the polarization potential map NM of the nucleic acid bases: cytosine, thymine, uracil, adedine, and guanine. For this purpose, the Dunning`s 9s5p basis set contracted to a split-valence, was selected to perform the calculations. The molecular polarization potential (MPP) at each point was evaluated by the difference between the interaction energy of the molecule with a unit point charge and the molecular electrostatic potential (MEP) at that point. MEPS and MPPS for the different molecules were computed with a density of 5 points/{Angstrom}{sup 2} on the van der Waals surface of each molecule, defined using the van der Waals radii. Due to the symmetry of the molecules, only half the points were computed. The total number of points calculated was 558 for cytosine, 621 for thymine, 526 for uracil, 666 for adenine, and 699 for guanine. The results of these calculations are analyzed in terms of their implications on the molecular interactions between pairs of nucleic acid bases. 23 refs., 5 figs., 1 tab.

  18. Radiation-induced electron migration in nucleic acids.

    PubMed

    Fuciarelli, A F; Sisk, E C; Miller, J H; Zimbrick, J D

    1994-11-01

    Radiation-induced electron migration along DNA is a mechanism by which randomly produced stochastic energy deposition events can lead to non-random types of damage along DNA manifested distal to the sites of the initial energy deposition. Radiation-induced electron migration in nucleic acids has been examined using oligonucleotides containing 5-bromouracil (5-BrU). Interaction of 5-BrU with solvated electrons results in release of bromide ions and formation or uracil-5-yl radicals. Monitoring either bromide ion release or uracil formation provides an opportunity to study electron migration processes in model nucleic acid systems. Using this approach we have discovered that electron migration along oligonucleotides is significantly influenced by the base sequence and strandedness. Migration along 7 base pairs in oligonucleotides containing guanine bases was observed for oligonucleotides irradiated in solution, which compares with mean migration distances of 6-10 bp for Escherichia coli DNA irradiated in solution and 5.5 bp for E. coli DNA irradiated in cells. Evidence also suggests that electron migration can occur preferentially in the 5' to 3' direction along a double-stranded oligonucleotide containing a region of purine bases adjacent to the 5-BrU moiety. Our continued efforts will provide information regarding the contribution of electron transfer along DNA to formation of locally multiply damaged sites created in DNA by exposure to ionizing radiation. PMID:7983438

  19. UNAFold: software for nucleic acid folding and hybridization.

    PubMed

    Markham, Nicholas R; Zuker, Michael

    2008-01-01

    The UNAFold software package is an integrated collection of programs that simulate folding, hybridization, and melting pathways for one or two single-stranded nucleic acid sequences. The name is derived from "Unified Nucleic Acid Folding." Folding (secondary structure) prediction for single-stranded RNA or DNA combines free energy minimization, partition function calculations and stochastic sampling. For melting simulations, the package computes entire melting profiles, not just melting temperatures. UV absorbance at 260 nm, heat capacity change (C(p)), and mole fractions of different molecular species are computed as a function of temperature. The package installs and runs on all Unix and Linux platforms that we have looked at, including Mac OS X. Images of secondary structures, hybridizations, and dot plots may be computed using common formats. Similarly, a variety of melting profile plots is created when appropriate. These latter plots include experimental results if they are provided. The package is "command line" driven. Underlying compiled programs may be used individually, or in special combinations through the use of a variety of Perl scripts. Users are encouraged to create their own scripts to supplement what comes with the package. This evolving software is available for download at http://www.bioinfo.rpi.edu/applications/hybrid/download.php . PMID:18712296

  20. A Small Unstructured Nucleic Acid Disrupts a Trinucleotide Repeat Hairpin

    PubMed Central

    Ávila-Figueroa, Amalia; Cattie, Douglas; Delaney, Sarah

    2011-01-01

    A variety of neurodegenerative disorders are associated with the expansion of trinucleotide repeat (TNR) sequences. These repetitive sequences are prone to adopting non-canonical structures, such as intrastrand stem-loop hairpins. Indeed, the formation and persistence of these hairpins during DNA replication and/or repair have been proposed as factors that facilitate TNR expansion. Given this proposed contribution of TNR hairpins to the expansion mechanism, disruption of such structures via strand invasion offers a potential means to negate the disease-initiating expansion. In this work, we investigated the strand invading abilities of a (CTG)3 unstructured nucleic acid on a (CAG)10 TNR hairpin. Using fluorescence, optical, and electrophoretic methods, instantaneous disruption of the (CAG)10 hairpin by (CTG)3 was observed at low temperatures. Additionally, we have identified three distinct duplex-like species that form between (CAG)10 and (CTG)3; these include 1, 2, or 3 (CTG)3 sequences hybridized to (CAG)10. The results presented here showcase (CTG)3 as an invader of a TNR hairpin and suggest that unstructured nucleic acids could serve as a scaffold to design agents to prevent TNR expansion. PMID:21924238

  1. Analyzing and Building Nucleic Acid Structures with 3DNA

    PubMed Central

    Colasanti, Andrew V.; Lu, Xiang-Jun; Olson, Wilma K.

    2013-01-01

    The 3DNA software package is a popular and versatile bioinformatics tool with capabilities to analyze, construct, and visualize three-dimensional nucleic acid structures. This article presents detailed protocols for a subset of new and popular features available in 3DNA, applicable to both individual structures and ensembles of related structures. Protocol 1 lists the set of instructions needed to download and install the software. This is followed, in Protocol 2, by the analysis of a nucleic acid structure, including the assignment of base pairs and the determination of rigid-body parameters that describe the structure and, in Protocol 3, by a description of the reconstruction of an atomic model of a structure from its rigid-body parameters. The most recent version of 3DNA, version 2.1, has new features for the analysis and manipulation of ensembles of structures, such as those deduced from nuclear magnetic resonance (NMR) measurements and molecular dynamic (MD) simulations; these features are presented in Protocols 4 and 5. In addition to the 3DNA stand-alone software package, the w3DNA web server, located at http://w3dna.rutgers.edu, provides a user-friendly interface to selected features of the software. Protocol 6 demonstrates a novel feature of the site for building models of long DNA molecules decorated with bound proteins at user-specified locations. PMID:23644419

  2. Design, preparation and application of nucleic acid delivery carriers.

    PubMed

    Yang, Jun; Liu, Hongmei; Zhang, Xin

    2014-01-01

    Gene delivery vectors must deliver their cargoes into the cytosol or the nucleus, where DNA or siRNA functions in vivo. Therefore it is crucial for the rational design of the nucleic acid delivery carriers. Compared with viral vectors, non-viral vectors have overcome some fatal defections in gene therapy. Whereas the most important issue for the non-viral vectors is the low transfection efficiency, which hinders the progress of non-viral carriers. Sparked by the structures of the virus and understanding of the process of virus infection, various biomimic structures of non-viral carriers were designed and prepared to improve the transfection issues in vitro and in vivo. However, less impressive results are achieved. In this review, we will investigate the evolution of the virus-mimicking carriers of nucleic acids for gene therapy, especially in cancer therapy; explore and discuss the relationship between the structures, materials and functions of the carriers, to provide guidance for establishing safe and highly efficient non-viral carriers for gene therapy. PMID:24239630

  3. New Approaches Towards Recognition of Nucleic Acid Triple Helices

    PubMed Central

    Arya, Dev P.

    2012-01-01

    We show that groove recognition of nucleic acid triple helices can be achieved with aminosugars. Among these aminosugars, neomycin is the most effective aminoglycoside (groove binder) for stabilizing a DNA triple helix. It stabilizes both the T·A·T triplex and mixed-base DNA triplexes better than known DNA minor groove binders (which usually destabilize the triplex) and polyamines. Neomycin selectively stabilizes the triplex (T·A·T and mixed base) without any effect on the DNA duplex. The selectivity of neomycin likely originates from its potential and shape complementarity to the triplex Watson–Hoogsteen groove, making it the first molecule that selectively recognizes a triplex groove over a duplex groove. The groove recognition of aminoglycosides is not limited to DNA triplexes, but also extends to RNA and hybrid triple helical structures. Intercalator–neomycin conjugates are shown to simultaneously probe the base stacking and groove surface in the DNA triplex. Calorimetric and spectrosocopic studies allow the quantification of the effect of surface area of the intercalating moiety on binding to the triplex. These studies outline a novel approach to the recognition of DNA triplexes that incorporates the use of non-competing binding sites. These principles of dual recognition should be applicable to the design of ligands that can bind any given nucleic acid target with nanomolar affinities and with high selectivity. PMID:21073199

  4. Nucleic acid sequence detection using multiplexed oligonucleotide PCR

    DOEpatents

    Nolan, John P. (Santa Fe, NM); White, P. Scott (Los Alamos, NM)

    2006-12-26

    Methods for rapidly detecting single or multiple sequence alleles in a sample nucleic acid are described. Provided are all of the oligonucleotide pairs capable of annealing specifically to a target allele and discriminating among possible sequences thereof, and ligating to each other to form an oligonucleotide complex when a particular sequence feature is present (or, alternatively, absent) in the sample nucleic acid. The design of each oligonucleotide pair permits the subsequent high-level PCR amplification of a specific amplicon when the oligonucleotide complex is formed, but not when the oligonucleotide complex is not formed. The presence or absence of the specific amplicon is used to detect the allele. Detection of the specific amplicon may be achieved using a variety of methods well known in the art, including without limitation, oligonucleotide capture onto DNA chips or microarrays, oligonucleotide capture onto beads or microspheres, electrophoresis, and mass spectrometry. Various labels and address-capture tags may be employed in the amplicon detection step of multiplexed assays, as further described herein.

  5. A method to find palindromes in nucleic acid sequences.

    PubMed

    Anjana, Ramnath; Shankar, Mani; Vaishnavi, Marthandan Kirti; Sekar, Kanagaraj

    2013-01-01

    Various types of sequences in the human genome are known to play important roles in different aspects of genomic functioning. Among these sequences, palindromic nucleic acid sequences are one such type that have been studied in detail and found to influence a wide variety of genomic characteristics. For a nucleotide sequence to be considered as a palindrome, its complementary strand must read the same in the opposite direction. For example, both the strands i.e the strand going from 5' to 3' and its complementary strand from 3' to 5' must be complementary. A typical nucleotide palindromic sequence would be TATA (5' to 3') and its complimentary sequence from 3' to 5' would be ATAT. Thus, a new method has been developed using dynamic programming to fetch the palindromic nucleic acid sequences. The new method uses less memory and thereby it increases the overall speed and efficiency. The proposed method has been tested using the bacterial (3891 KB bases) and human chromosomal sequences (Chr-18: 74366 kb and Chr-Y: 25554 kb) and the computation time for finding the palindromic sequences is in milli seconds. PMID:23515654

  6. A Simple Glycol Nucleic Acid Lilu Zhang, Adam Peritz, and Eric Meggers*

    E-print Network

    Meggers, Eric

    with an acyclic three-carbon propylene glycol phos- phodiester backbone (Figure 1). Groundbreaking studiesA Simple Glycol Nucleic Acid Lilu Zhang, Adam Peritz, and Eric Meggers* Department of Chemistry. The discovered glycol nucleic acid (GNA) uses the canonical Watson-Crick base pairing scheme combined

  7. Application of Vitamin K3 as a Photochemical Fluorescence Probe in the Determination of Nucleic Acids

    Microsoft Academic Search

    Wen-You Li; Jin-Gou Xu; Xiang-Qun Guo; Qing-Zhi Zhu; Yi-Bing Zhao

    1997-01-01

    An in situ photochemical fluorescence probe method for the determination of nucleic acids with vitamin k3(VK3) as the photochemical fluorescence probe was developed for the first time. It was based on the conversion of VK3 into an intensively fluorescent product on irradiating with UV radiation. The photochemical reaction is decelerated by nucleic acids. The determination can be carried out by

  8. Further analysis of nucleic acids in purified scrapie prion preparations by improved return refocusing gel electrophoresis

    Microsoft Academic Search

    Klaus Kellings; Norbert Meyer; Carol Mirenda; Detlev Riesner

    1992-01-01

    Although increasingly unlikely, the possibility of a scrapie-specific nucleic acid carried by infectious prion particles is still unresolved. Return refocusing gel electrophoresis was developed to detect homogeneous and heterogeneous nucleic acids extracted from highly purified scrapie prion preparations. This method was improved with respect to the size range from 13 to 1100 nucleotides (nt) over which analyses could be per-

  9. Quantitative determination of nucleic acids in salmonidae milt by various methods

    Microsoft Academic Search

    V. A. Karklinya; I. A. Birska; Yu. A. Limarenko

    1989-01-01

    Procedures for the determination of total nucleic acids from ultraviolet absorption and for the separate determination of DNA and RNA by means of color reactions using the same tissue extracts have been developed. The results of the total and separate determination of the nucleic acids and the analysis of milts preserved by various methods are given. The discrepancies between the

  10. Nucleic acid templated uncaging of fluorophores using Ru-catalyzed photoreduction with visible light.

    PubMed

    Röthlingshöfer, Manuel; Gorska, Katarzyna; Winssinger, Nicolas

    2012-01-20

    Hybridization-based reactions have attracted significant attention. The nucleic acid templated photocatalyzed azide reduction using catalytic amounts of a [Ru(bpy)(2)phen](2+) conjugate is reported. The reaction could be performed with as little as 2% of the Ru nucleic acid probe and was shown to productively unquench 7-azido-coumarin as well as uncage a small molecule. PMID:22206275

  11. Nucleic Acid Helix Stability: Effects of Salt Concentration, Cation Valence and Size, and Chain Length

    Microsoft Academic Search

    Zhi-Jie Tan; Shi-Jie Chen

    2006-01-01

    Metal ions play crucial roles in thermal stability and folding kinetics of nucleic acids. For ions (especially multivalent ions) in the close vicinity of nucleic acid surface, interion correlations and ion-binding mode fluctuations may be important. Poisson-Boltzmann theory ignores these effects whereas the recently developed tightly bound ion (TBI) theory explicitly accounts for these effects. Extensive experimental data demonstrate that

  12. The Definition of Generalized Helicoidal Parameters and of Axis Curvature for Irregular Nucleic Acids

    Microsoft Academic Search

    Richard Lavery; Heinz Sklenar

    1988-01-01

    An algorithm is presented which solves the problem of obtaining a rigorous helicoidal description of an irregular nucleic acid segment. Central to this approach is the definition of a function describing simultaneously the curvature of the nucleic acid segment in question and the corresponding stepwise variation of helicoidal parameters along the segment. Minimisation of this function leads to an optimal

  13. Use of Nucleic-Acid Homologies in the Taxonomy of Anaerobic Bacteria

    Microsoft Academic Search

    JOHN L. JOHNSON

    1973-01-01

    Nucleic acid homology studies are providing a common base for establishing bacterial groups. Few phenotypic characteristics have consistently correlated with homology data among the various groups of organisms that we have investigated. However, there are correlations that are specific for a given group of bacteria such that nucleic-acid homology data can be used to select those phenotypic properties that will

  14. Comparative Assessment of Automated Nucleic Acid Sample Extraction Equipment for Biothreat Agents

    PubMed Central

    Kalina, Warren Vincent; Douglas, Christina Elizabeth; Coyne, Susan Rajnik

    2014-01-01

    Magnetic beads offer superior impurity removal and nucleic acid selection over older extraction methods. The performances of nucleic acid extraction of biothreat agents in blood or buffer by easyMAG, MagNA Pure, EZ1 Advanced XL, and Nordiag Arrow were evaluated. All instruments showed excellent performance in blood; however, the easyMAG had the best precision and versatility. PMID:24452173

  15. Telomerase inhibition by peptide nucleic acids reverses `immortality' of transformed human cells

    Microsoft Academic Search

    Masood A Shammas; Carla G Simmons; David R Corey; Robert J Shmookler Reis; RJS Reis

    1999-01-01

    Telomerase activity, the ability to add telomeric repeats to the ends of chromosomes, has been detected in most immortal cell lines including tumor cells, but is low or absent in most diploid, mortal cells such as those of somatic tissues. Peptide nucleic acids (PNAs), analogs of DNA or RNA which bind to complementary nucleic acids with very high affinity, were

  16. Information transfer from DNA to peptide nucleic acids by template- directed syntheses

    Microsoft Academic Search

    G. Schmidt; Leif Christensen; Peter E. Nielsen; Leslie E. Orgel

    1997-01-01

    Peptide nucleic acids (PNAs) are analogs of nucleic acids in which the ribose-phosphate backbone is replaced by a backbone held together by amide bonds. PNAs are interesting as models of alternative genetic systems because they form potentially informational base paired helical structures. Oligocytidylates have been shown to act as templates for formation of longer oligomers of G from PNA G2

  17. LNA (Locked Nucleic Acids): Synthesis of the adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil bicyclonucleoside monomers, oligomerisation, and unprecedented nucleic acid recognition

    Microsoft Academic Search

    Alexei A. Koshkin; Sanjay K. Singh; Poul Nielsen; Vivek K. Rajwanshi; Ravindra Kumar; Michael Meldgaard; Carl Erik Olsen; Jesper Wengel

    1998-01-01

    LNA (Locked Nucleic Acids), consisting of 2?-O,4?-C-methylene bicyclonucleoside monomers, is efficiently synthesized and its nucleic acid recognition potential evaluated for six different nucleobases, namely adenine, cytosine, guanine, 5-methylcytosine, thymine and uracil. Unprecedented increases (+3 to +8 °C per modification) in the thermal stability of duplexes towards both DNA and RNA were obtained when evaluating mixed sequences of partly or fully

  18. Study on the resonance light-scattering spectrum of anionic dye xylenol orange-cetyltrimethylammonium-nucleic acids system and determination of nucleic acids at nanogram levels

    Microsoft Academic Search

    Xiaoming Chen; Changqun Cai; He ‘an Luo; Guanghuo Zhang

    2005-01-01

    The interaction of xylenol orange (XO) and nucleic acids in the presence of cetyltrimethylammonium bromide (CTMAB) in aqueous solution has been studied by a resonance light-scattering (RLS) technique with a common spectrofluorometer. In hexamethylenetetramine (HMTA) buffer (pH7.30), XO and nucleic acids react with cetyltrimethylammonium bromide to form large particles of three-component complex, which results in strong enhanced RLS signals characterized

  19. Interactions of Nile Blue Sulphate with Nucleic Acids as Studied by Resonance Light-Scattering Measurements and Determination of Nucleic Acids at Nanogram Levels

    Microsoft Academic Search

    Cheng Zhi Huang; Yuan Fang Li; Qing Hai Pu; Liang Jun Lai

    1999-01-01

    The interactions of nile blue sulphate (NBS) with nucleic acids, including calf thymus DNA, fish sperm DNA and yeast RNA, were characterized with resonance light-scattering (RLS) measurements by using a common spectrofluorometer. Accordingly a method for the determination of nucleic acids at nanogram levels was established. At pH's of 7.20?7.60 and ionic strengths lower than 0.012, the interactions of NBS

  20. Gefitinib for non-small-cell lung cancer patients with epidermal growth factor receptor gene mutations screened by peptide nucleic acid-locked nucleic acid PCR clamp

    Microsoft Academic Search

    A Sutani; Y Nagai; K Udagawa; Y Uchida; N Koyama; Y Murayama; T Tanaka; H Miyazawa; M Nagata; M Kanazawa; K Hagiwara; K Kobayashi

    2006-01-01

    This study was prospectively designed to evaluate a phase II study of gefitinib for non-small-cell lung cancer (NSCLC) patients with epidermal growth factor receptor (EGFR) mutations. Clinical samples were tested for EGFR mutations by peptide nucleic acid-locked nucleic acid PCR clamp, and patients having EGFR mutations were given gefitinib 250 mg daily as the second treatment after chemotherapy. Poor PS

  1. Molecular Dynamic Modeling of Nanodiamond (ND) PEI Interaction Towards Delivery of Nucleic Acids Goal: Understand the interaction between NDs and

    E-print Network

    Chen, Wei

    of Nucleic Acids Goal: Understand the interaction between NDs and polyethylenimine (PEI) towards delivery nucleic acids into cells in an invivo environment. ND PEI combines the efficacy of industry standard

  2. Digestion of Nucleic Acids Starts in the Stomach

    PubMed Central

    Liu, Yu; Zhang, Yanfang; Dong, Ping; An, Ran; Xue, Changhu; Ge, Yinlin; Wei, Liangzhou; Liang, Xingguo

    2015-01-01

    The ingestion of nucleic acids (NAs) as a nutritional supplement or in genetically modified food has attracted the attention of researchers in recent years. Discussions over the fate of NAs led us to study their digestion in the stomach. Interestingly, we found that NAs are digested efficiently by human gastric juice. By performing digests with commercial, recombinant and mutant pepsin, a protein-specific enzyme, we learned that the digestion of NAs could be attributed to pepsin rather than to the acidity of the stomach. Further study showed that pepsin cleaved NAs in a moderately site-specific manner to yield 3?-phosphorylated fragments and the active site to digest NAs is probably the same as that used to digest protein. Our results rectify the misunderstandings that the digestion of NAs in the gastric tract begins in the intestine and that pepsin can only digest protein, shedding new light on NA metabolism and pepsin enzymology. PMID:26168909

  3. Solving nucleic acid structures by molecular replacement: examples from group II intron studies.

    PubMed

    Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-11-01

    Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts. PMID:24189228

  4. Solving nucleic acid structures by molecular replacement: examples from group II intron studies

    PubMed Central

    Marcia, Marco; Humphris-Narayanan, Elisabeth; Keating, Kevin S.; Somarowthu, Srinivas; Rajashankar, Kanagalaghatta; Pyle, Anna Marie

    2013-01-01

    Structured RNA molecules are key players in ensuring cellular viability. It is now emerging that, like proteins, the functions of many nucleic acids are dictated by their tertiary folds. At the same time, the number of known crystal structures of nucleic acids is also increasing rapidly. In this context, molecular replacement will become an increasingly useful technique for phasing nucleic acid crystallographic data in the near future. Here, strategies to select, create and refine molecular-replacement search models for nucleic acids are discussed. Using examples taken primarily from research on group II introns, it is shown that nucleic acids are amenable to different and potentially more flexible and sophisticated molecular-replacement searches than proteins. These observations specifically aim to encourage future crystallographic studies on the newly discovered repertoire of noncoding transcripts. PMID:24189228

  5. Nucleic Acid Encoding A Lectin-Derived Progenitor Cell Preservation Factor

    DOEpatents

    Colucci, M. Gabriella (Dugenta, IT); Chrispeels, Maarten J. (La Jolla, CA); Moore, Jeffrey G. (New York, NY)

    2001-10-30

    The invention relates to an isolated nucleic acid molecule that encodes a protein that is effective to preserve progenitor cells, such as hematopoietic progenitor cells. The nucleic acid comprises a sequence defined by SEQ ID NO:1, a homolog thereof, or a fragment thereof. The encoded protein has an amino acid sequence that comprises a sequence defined by SEQ ID NO:2, a homolog thereof, or a fragment thereof that contains an amino acid sequence TNNVLQVT. Methods of using the encoded protein for preserving progenitor cells in vitro, ex vivo, and in vivo are also described. The invention, therefore, include methods such as myeloablation therapies for cancer treatment wherein myeloid reconstitution is facilitated by means of the specified protein. Other therapeutic utilities are also enabled through the invention, for example, expanding progenitor cell populations ex vivo to increase chances of engraftation, improving conditions for transporting and storing progenitor cells, and facilitating gene therapy to treat and cure a broad range of life-threatening hematologic diseases.

  6. A simple and sensitive assay of nucleic acids based on the enhanced resonance light scattering of zwitterionics

    Microsoft Academic Search

    Zhanguang Chen; Weifeng Ding; Fenglian Ren; Jinbin Liu; Yizeng Liang

    2005-01-01

    A new assay of nucleic acids at nanogram level was established based on the enhanced resonance light scattering (RLS) signals of two zwitterionics cocamidopropyl hydroxysultaine (HSB) and lauryl betaine (BS-12). Under optimum conditions, the weak RLS signal of HSB is enhanced by nucleic acids, and the enhanced RLS intensity is proportional to the concentration of nucleic acids in the range

  7. Helicases and nucleic acid translocases are a diverse group of motor proteins that function in nearly all

    E-print Network

    Lohman, Timothy M.

    Helicases and nucleic acid translocases are a diverse group of motor proteins that function in nearly all aspects of nucleic acid metabolism. Helicases use the binding and hydrolysis of nucleoside triphosphates (NTPs) to catalyse the separation of double-stranded (ds) nucleic acids into their complementary

  8. Molecular evolution allows chemists and biologists to generate nucleic acids with tailor-made binding or catalytic activities.

    E-print Network

    Liu, David R.

    367 Molecular evolution allows chemists and biologists to generate nucleic acids with tailor-made binding or catalytic activities. Recent examples of nucleic acid evolution in vitro provide insights. Efforts to expand the scope of nucleic acid evolution are also underway, including the development

  9. CINT Science Highlight September 22, 2010 NanoCluster Beacon detects specific nucleic acid target sequence for diagnostics

    E-print Network

    CINT Science Highlight ­ September 22, 2010 NanoCluster Beacon detects specific nucleic acid target studies, where removal of unbound probes is difficult. Molecular beacons are hairpin-shaped nucleic acid probes that fluoresce upon hybridization with specific nucleic acid targets. While molecular beacons

  10. Vibrational Stark Effect Probes for Nucleic Acids Lisa N. Silverman, Michael E. Pitzer, Peter O. Ankomah, Steven G. Boxer,*, and

    E-print Network

    Boxer, Steven G.

    Vibrational Stark Effect Probes for Nucleic Acids Lisa N. Silverman, Michael E. Pitzer, Peter O of infrared probes. To explore the use of VSE in nucleic acids, we investigated the Stark spectroscopy of nine in nucleic acids have been studied extensively by a variety of theoretical methods,1-7 often with conflicting

  11. Volume 10 Number 24 1982 Nucleic Acids Research An algorithm for the disply of nudeic aad secondary sbtcture

    E-print Network

    Sankoff, David

    Volume 10 Number 24 1982 Nucleic Acids Research An algorithm for the disply of nudeic aad secondary A simple algorithm is presented for the graphic display of nucleic acid secondary structure. Examples display of secondary structures of nucleic acids. THE DATA AND THE ALGORITHM The data for the algorithm

  12. Fundamental differences between the nucleic acid chaperone activities of HIV-1 nucleocapsid protein and Gag or Gag-derived

    E-print Network

    Levin, Judith G.

    Fundamental differences between the nucleic acid chaperone activities of HIV-1 nucleocapsid protein nucleocapsid (NC). Although mature NC and NC embedded in Gag are nucleic acid chaperones (proteins that remodel nucleic acid structure), few studies include detailed analysis of the chaperone activity of partially

  13. The C-Terminal Domain of Nucleolin Accelerates Nucleic Acid Annealing L. A. Hanakahi,*,, Zimei Bu,,| and Nancy Maizels,,#

    E-print Network

    Maizels, Nancy

    The C-Terminal Domain of Nucleolin Accelerates Nucleic Acid Annealing L. A. Hanakahi,*,,§ Zimei Bu protein nucleolin accelerates nucleic acid annealing. Nucleolin accelerates annealing of complementary it independently accelerate annealing. Acceleration of nucleic acid annealing by nucleolin is likely to depend

  14. Nucleic acids in disease and disorder: Understanding the language of life emerging from the `ABC' of DNA

    E-print Network

    Bansal, Manju

    Nucleic acids in disease and disorder: Understanding the language of life emerging from the `ABC in, and contributing towards, understanding the structure and dynamics of nucleic acids com- pared structure and dynamics of nucleic acids (Jayaraman and Yathindra 1981; Maiti et al. 1983; Malathi

  15. Aminoglycoside (Neomycin) Preference Is for A-Form Nucleic Acids, Not Just RNA: Results from a Competition Dialysis Study

    E-print Network

    Stuart, Steven J.

    Aminoglycoside (Neomycin) Preference Is for A-Form Nucleic Acids, Not Just RNA: Results from added to the number of nucleic acids (other than RNA) that aminoglycosides have been shown to target for host triplex, duplex DNA, single-stranded (DNA/RNA), and other possible nucleic acid targets (tetraplex

  16. Efficient and Rapid Template-Directed Nucleic Acid Copying Using 2-Amino-2,3-dideoxyribonucleoside-5-Phosphorimidazolide

    E-print Network

    Heller, Eric

    Efficient and Rapid Template-Directed Nucleic Acid Copying Using 2-Amino-2,3-dideoxyribonucleoside@molbio.mgh.harvard.edu Abstract: The development of a sequence-general nucleic acid copying system is an essential step of a series of nucleic acid templates using 2-amino-2,3-dideoxynucle- otide-5-phosphorimidazolides

  17. Alteration of Nucleic Acid Structure and Stability Modulates the Efficiency of Minus-Strand Transfer Mediated by the

    E-print Network

    Levin, Judith G.

    Alteration of Nucleic Acid Structure and Stability Modulates the Efficiency of Minus with minus-strand transfer. To investigate the relationship between nucleic acid sec- ondary structure and NC) NC is a small, highly basic, nucleic acid-binding protein with two zinc fingers, each containing

  18. The Effect of Dye-Dye Interactions on the Spatial Resolution of Single-Molecule FRET Measurements in Nucleic Acids

    E-print Network

    in Nucleic Acids Nicolas Di Fiori and Amit Meller * Department of Physics and Department of Biomedical, these results are useful when deciding which dye pairs to use for nucleic acids analyses using FRET and dynamics of proteins and nucleic acids, DNA-protein interactions, RNA catalysis, and many other systems (5

  19. Cascade of Reduced Speed and Accuracy after Errors in Enzyme-Free Copying of Nucleic Acid Sequences

    E-print Network

    Chen, Irene

    Cascade of Reduced Speed and Accuracy after Errors in Enzyme-Free Copying of Nucleic Acid Sequences, template-directed synthesis of nucleic acids is a paradigm for self-replicating systems. The evolutionary. On the basis of these data, we simulated nucleic acid replication in silico, which indicated that a primer

  20. Inhibitory effect of crocetin on intracellular nucleic acid and protein synthesis in malignant cells.

    PubMed

    Abdullaev, F I

    1994-02-01

    The possibility that dietary intake of diverse naturally occurring compounds may influence the occurrence of cancer is receiving considerable scientific attention. Previously, it was reported that an extract (Crocus sativus), which contains carotenoids, had an antitumor effect and inhibited colony formation and nucleic acid synthesis by malignant human cells. Epidemiological and experimental research has indicated that carotenoids might act as antitumor agents. We have studied crocetin, a carotenoid isolated from saffron, which has been shown to have biological activity. In our experiments we utilized three malignant human cell lines: HeLa (cervical epitheloid carcinoma), A549 (lung adenocarcinoma) and VA13 (SV-40 transformed fetal lung fibroblast) cells. The effect of crocetin on colony formation and cellular DNA, RNA and protein synthesis in these cells has been examined. Incubation of these cells with crocetin for 3 h caused a dose-dependent inhibition of nucleic acid and protein synthesis. Crocetin also had a dose-dependent inhibitory effect on DNA and RNA synthesis in isolated nuclei and suppressed the activity of purified RNA polymerase II. PMID:8296327

  1. Polysaccharide-free nucleic acids and proteins of Abelmoschus esculentus for versatile molecular studies.

    PubMed

    Manoj-Kumar, A; Reddy, K N; Manjulatha, M; Blanco, L

    2012-01-01

    Abelmoschus esculentus (okra) is one of the polysaccharide rich crop plants. The polysaccharides interfere with nucleic acids and protein isolation thereby affecting the downstream molecular analysis. So, to understand the molecular systematics of okra, high quality DNA, RNA and proteins are essential. In this study we present a method for extracting genomic DNA, RNA and proteins from polysaccharide rich okra tissues. The conventional extraction procedures were integrated with purification treatments with pectinase, RNase and proteinase K, which improved the quality and quantity of DNA as well. Using SDS, additional washes with CIA and NaCl precipitation improved the RNA isolation both quantitatively and qualitatively. Finally, ammonium acetate mediated protein precipitation and re-solubilization increased the quality of total protein extracts from the okra leaves. All of the methods above not only eliminated the impurities but also improved the quality and quantity of nucleic acids and proteins. Further, we subjected these samples to versatile downstream molecular analyses such as restriction endonuclease digestion, RAPD, Southern, reverse transcription-PCR and Western analysis and were proved to be successful. PMID:23113348

  2. Microgel Tethering For Microarray-Based Nucleic Acid Diagnostics

    NASA Astrophysics Data System (ADS)

    Dai, Xiaoguang

    Molecular diagnostics (MDx) have radically changed the process of clinical microbial identification based on identifying genetic information, MDx approaches are both specific and fast. They can identify microbes to the species and strain level over a time scale that can be as short as one hour. With such information clinicians can administer the most effective and appropriate antimicrobial treatment at an early time point with substantial implications both for patient well-being and for easing the burden on the health-care system. Among the different MDx approaches, such as fluorescence in-situ hybridization, microarrays, next-generation sequencing, and mass spectrometry, point-of-care MDx platforms are drawing particular interest due to their low cost, robustness, and wide application. This dissertation develops a novel MDx technology platform capable of high target amplification and detection performance. For nucleic acid target detection, we fabricate an array of electron-beam-patterned microgels on a standard glass microscope slide. The microgels can be as small as a few hundred nanometers. The unique way of energy deposition during electron-beam lithography provides the microgels with a very diffuse water -gel interface that enables them to not only serve as substrates to immobilize DNA probes but do so while preserving them in a highly hydrated environment that optimizes their performance. Benefiting from the high spatial resolution provided by such techniques as position-sensitive microspotting and dip-pen nanolithography, multiple oligonucleotide probes known as molecular beacons (MBs) can be patterned on microgels. Furthermore, nucleic acid target amplification can be conducted in direct contact with the microgel-tethered detection array. Specifically, we use an isothermal RNA amplification reaction - nucleic acid sequence-based amplification (NASBA). ssRNA amplicons of from the NASBA reaction can directly hybridize with microgel-tethered MBs, and the fluorescence response can be monitored in real-time without any additional labeling. With the properties of low complexity, high sensitivity and specificity, this platform holds important possibilities for commercialization. To further de-risk this MDx approach, future research includes enhancing the multiplexity of target amplification and detection by solid-phase NASBA, as well as combining the platform into a microfluidic device that can both process and handle small sample sizes.

  3. Advances in the Determination of Nucleic Acid Conformational Ensembles

    NASA Astrophysics Data System (ADS)

    Salmon, Loïc; Yang, Shan; Al-Hashimi, Hashim M.

    2014-04-01

    Conformational changes in nucleic acids play a key role in the way genetic information is stored, transferred, and processed in living cells. Here, we describe new approaches that employ a broad range of experimental data, including NMR-derived chemical shifts and residual dipolar couplings, small-angle X-ray scattering, and computational approaches such as molecular dynamics simulations to determine ensembles of DNA and RNA at atomic resolution. We review the complementary information that can be obtained from diverse sets of data and the various methods that have been developed to combine these data with computational methods to construct ensembles and assess their uncertainty. We conclude by surveying RNA and DNA ensembles determined using these methods, highlighting the unique physical and functional insights obtained so far.

  4. Imaging of nucleic acids with atomic force microscopy

    PubMed Central

    Lyubchenko, Yuri L.; Shlyakhtenko, Luda S.; Ando, Toshio

    2011-01-01

    Atomic force microscopy (AFM) is a key tool of nanotechnology with great importance in applications to DNA nanotechnology and to the recently emerging field of RNA nanotechnology. Advances in the methodology of AFM now enable reliable and reproducible imaging of DNA of various structures, topologies, and DNA and RNA nanostructures. These advances are reviewed here with emphasis on methods utilizing modification of mica to prepare the surfaces enabling reliable and reproducible imaging of DNA and RNA nanostructures. Since the AFM technology for DNA is more mature, AFM imaging of DNA is introduced in this review to provide experience and background for the improvement of AFM imaging of RNA. Examples of imaging different structures of RNA and DNA are discussed and illustrated. Special attention is given to the potential use of AFM to image the dynamics of nucleic acids at the nanometer scale. As such, we review recent advances with the use of time-lapse AFM. PMID:21310240

  5. Nucleic acid-metal organic framework (MOF) nanoparticle conjugates.

    PubMed

    Morris, William; Briley, William E; Auyeung, Evelyn; Cabezas, Maria D; Mirkin, Chad A

    2014-05-21

    Nanoparticles of a metal-organic framework (MOF), UiO-66-N3 (Zr6O4OH4(C8H3O4-N3)6), were synthesized. The surface of the MOF was covalently functionalized with oligonucleotides, utilizing a strain promoted click reaction between DNA appended with dibenzylcyclooctyne and azide-functionalized UiO-66-N3 to create the first MOF nanoparticle-nucleic acid conjugates. The structure of the framework was preserved throughout the chemical transformation, and the surface coverage of DNA was quantified. Due to the small pore sizes, the particles are only modified on their surfaces. When dispersed in aqueous NaCl, they exhibit increased stability and enhanced cellular uptake when compared with unfunctionalized MOF particles of comparable size. PMID:24818877

  6. Circulating and stool nucleic acid analysis for colorectal cancer diagnosis

    PubMed Central

    De Maio, Giulia; Rengucci, Claudia; Zoli, Wainer; Calistri, Daniele

    2014-01-01

    In recent years, the need to identify molecular markers characterized by high sensitivity and specificity in detecting and monitoring early and colorectal cancer lesions has increased. Up to now, none of the markers or panels of markers analyzed have met the rigorous standards required of a screening program. The important discovery of circulating nucleic acids in biological fluids has aroused intense scientific interest because of their usefulness in malignant and non malignant diseases. Over time, their yield and stability have been identified and compared with other “standard” biomarkers. The analysis of circulating DNA from blood and stool is a relatively simple and non-invasive procedure, representing a very attractive marker to detect genetic and epigenetic mutations and to monitor disease progression. A correlation between blood and stool biomarkers could also help to enhance currently available diagnostic approaches. However, various processing and analytic problems need to be resolved before such an approach can be applied in clinical practice. PMID:24574768

  7. Circulating and stool nucleic acid analysis for colorectal cancer diagnosis.

    PubMed

    De Maio, Giulia; Rengucci, Claudia; Zoli, Wainer; Calistri, Daniele

    2014-01-28

    In recent years, the need to identify molecular markers characterized by high sensitivity and specificity in detecting and monitoring early and colorectal cancer lesions has increased. Up to now, none of the markers or panels of markers analyzed have met the rigorous standards required of a screening program. The important discovery of circulating nucleic acids in biological fluids has aroused intense scientific interest because of their usefulness in malignant and non malignant diseases. Over time, their yield and stability have been identified and compared with other "standard" biomarkers. The analysis of circulating DNA from blood and stool is a relatively simple and non-invasive procedure, representing a very attractive marker to detect genetic and epigenetic mutations and to monitor disease progression. A correlation between blood and stool biomarkers could also help to enhance currently available diagnostic approaches. However, various processing and analytic problems need to be resolved before such an approach can be applied in clinical practice. PMID:24574768

  8. Clinical applications of nucleic acid aptamers in cancer

    PubMed Central

    PEI, XIAOYU; ZHANG, JUN; LIU, JIE

    2014-01-01

    Nucleic acid aptamers are small single-stranded DNA or RNA oligonucleotide segments, which bind to their targets with high affinity and specificity via unique three-dimensional structures. Aptamers are generated by an iterative in vitro selection process, termed as systematic evolution of ligands by exponential enrichment. Owing to their specificity, non-immunogenicity, non-toxicity, easily modified chemical structure and wide range of targets, aptamers appear to be ideal candidates for various clinical applications (diagnosis or treatment), such as cell detection, target diagnosis, molecular imaging and drug delivery. Several aptamers have entered the clinical pipeline for applications in diseases such as macular degeneration, coronary artery bypass graft surgery and various types of cancer. The aim of this review was to summarize and highlight the clinical applications of aptamers in cancer diagnosis and treatment. PMID:24772298

  9. A novel nucleic acid analogue shows strong angiogenic activity

    SciTech Connect

    Tsukamoto, Ikuko, E-mail: tukamoto@med.kagawa-u.ac.jp [Department of Pharmaco-Bio-Informatics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)] [Department of Pharmaco-Bio-Informatics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan); Sakakibara, Norikazu; Maruyama, Tokumi [Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193 (Japan)] [Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193 (Japan); Igarashi, Junsuke; Kosaka, Hiroaki [Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)] [Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan); Kubota, Yasuo [Department of Dermatology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)] [Department of Dermatology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan); Tokuda, Masaaki [Department of Cell Physiology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)] [Department of Cell Physiology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan); Ashino, Hiromi [The Tokyo Metropolitan Institute of Medical Science, 1-6 Kamikitazawa2-chome, Setagaya-ku, Tokyo 156-8506 (Japan)] [The Tokyo Metropolitan Institute of Medical Science, 1-6 Kamikitazawa2-chome, Setagaya-ku, Tokyo 156-8506 (Japan); Hattori, Kenichi; Tanaka, Shinji; Kawata, Mitsuhiro [Teikoku Seiyaku Co., Ltd., Sanbonmatsu, Higashikagawa, Kagawa 769-2695 (Japan)] [Teikoku Seiyaku Co., Ltd., Sanbonmatsu, Higashikagawa, Kagawa 769-2695 (Japan); Konishi, Ryoji [Department of Pharmaco-Bio-Informatics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)] [Department of Pharmaco-Bio-Informatics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)

    2010-09-03

    Research highlights: {yields} A novel nucleic acid analogue (2Cl-C.OXT-A, m.w. 284) showed angiogenic potency. {yields} It stimulated the tube formation, proliferation and migration of HUVEC in vitro. {yields} 2Cl-C.OXT-A induced the activation of ERK1/2 and MEK in HUVEC. {yields} Angiogenic potency in vivo was confirmed in CAM assay and rabbit cornea assay. {yields} A synthesized small angiogenic agent would have great clinical therapeutic value. -- Abstract: A novel nucleic acid analogue (2Cl-C.OXT-A) significantly stimulated tube formation of human umbilical endothelial cells (HUVEC). Its maximum potency at 100 {mu}M was stronger than that of vascular endothelial growth factor (VEGF), a positive control. At this concentration, 2Cl-C.OXT-A moderately stimulated proliferation as well as migration of HUVEC. To gain mechanistic insights how 2Cl-C.OXT-A promotes angiogenic responses in HUVEC, we performed immunoblot analyses using phospho-specific antibodies as probes. 2Cl-C.OXT-A induced robust phosphorylation/activation of MAP kinase ERK1/2 and an upstream MAP kinase kinase MEK. Conversely, a MEK inhibitor PD98059 abolished ERK1/2 activation and tube formation both enhanced by 2Cl-C.OXT-A. In contrast, MAP kinase responses elicited by 2Cl-C.OXT-A were not inhibited by SU5416, a specific inhibitor of VEGF receptor tyrosine kinase. Collectively these results suggest that 2Cl-C.OXT-A-induces angiogenic responses in HUVEC mediated by a MAP kinase cascade comprising MEK and ERK1/2, but independently of VEGF receptor tyrosine kinase. In vivo assay using chicken chorioallantoic membrane (CAM) and rabbit cornea also suggested the angiogenic potency of 2Cl-C.OXT-A.

  10. BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE

    PubMed Central

    Rao, Archana N.; Grainger, David W.

    2014-01-01

    Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA’s persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools. PMID:24765522

  11. Single molecule DNA interaction kinetics of retroviral nucleic acid chaperone proteins

    NASA Astrophysics Data System (ADS)

    Williams, Mark

    2010-03-01

    Retroviral nucleocapsid (NC) proteins are essential for several viral replication processes including specific genomic RNA packaging and reverse transcription. The nucleic acid chaperone activity of NC facilitates the latter process. In this study, we use single molecule biophysical methods to quantify the DNA interactions of wild type and mutant human immunodeficiency virus type 1 (HIV-1) NC and Gag and human T-cell leukemia virus type 1 (HTLV-1) NC. We find that the nucleic acid interaction properties of these proteins differ significantly, with HIV-1 NC showing rapid protein binding kinetics, significant duplex destabilization, and strong DNA aggregation, all properties that are critical components of nucleic acid chaperone activity. In contrast, HTLV-1 NC exhibits significant destabilization activity but extremely slow DNA interaction kinetics and poor aggregating capability, which explains why HTLV-1 NC is a poor nucleic acid chaperone. To understand these results, we developed a new single molecule method for quantifying protein dissociation kinetics, and applied this method to probe the DNA interactions of wild type and mutant HIV-1 and HTLV-1 NC. We find that mutations to aromatic and charged residues strongly alter the proteins' nucleic acid interaction kinetics. Finally, in contrast to HIV-1 NC, HIV-1 Gag, the nucleic acid packaging protein that contains NC as a domain, exhibits relatively slow binding kinetics, which may negatively impact its ability to act as a nucleic acid chaperone.

  12. Onset of nucleic acid synthesis during germination of Pisum sativum L

    Microsoft Academic Search

    Nigel E. Robinson; John A. Bryant

    1975-01-01

    Measurments of total nucleic acid content of the embryonic axis indicated that massive net synthesis of both DNA and RNA was initiated at approximately 30 h after the onset of germination. The onset of net nucleic acid synthesis was marked by an increase in the rate of incorporation of [3H]thymidine into DNA, and of [3H]orotic acid and [3H]uridine into both

  13. Voltage-induced release of nucleic acids from palaeontological samples.

    PubMed

    Bachmann, L; Scholz, M; Broghammer, M; Giddings, I; Pusch, C M

    2000-05-01

    Most of the protocols for the recovery of ancient DNA from palaeontological specimens are time-consuming and tend to yield inconsistent polymerase chain reaction (PCR) results. "Voltage-induced release" is a novel and rapid approach for the extraction of ancient DNA. Nucleic acids are directly electrophoresed out of powder derived from hard and soft tissues. This technique is much faster than other methods in which pulverized tissue conventionally undergoes time-consuming crude lysis steps. The total preparation time is 5-6 h. The reliability of the voltage-induced release method was validated by (i) measuring the ratio of D-to L-enantiomers of the amino acids aspartic acid, alanine, and leucine, and (ii) by specific PCR amplification of four single-copy markers of human chromosome 17 and 18. We compare voltage-induced release to a frequently used silica-based protocol. DNA extracted employing voltage-induced release was more effective in PCR amplifications, which may be attributed to the effective removal of PCR inhibitors. PMID:10832878

  14. Specificity of protein — Nucleic acid interaction and the biochemical evolution

    NASA Astrophysics Data System (ADS)

    Podder, S. K.; Basu, H. S.

    1984-12-01

    The water soluble carbodiimide mediated condensation of dipeptides of the general form Gly-X was carried out in the presence of mono- and poly-nucleotides. The observed yield of the tetrapeptide was found to be higher for peptide-nucleotide system of higher interaction specificity following mainly the anticodon-amino acid relationship (Basu, H.S. & Podder, S.K., 1981, Ind. J. Biochem. Biophys., 19, 251 253). The yield of the condensation product of L-peptide was more because of its higher interaction specificity. The extent of the racemization during the condensation of Gly-L-Phe, Gly-L-Tyr and Gly-D-Phe was found to be dependent on the specificity of the interaction —the higher the specificity, the lesser the racemization. The product formed was shown to have a catalytic effect on the condensation reaction. These data thus provide a mechanism showing how the specific interaction between amino acids/dipeptides and nucleic acids could lead to the formation of the ‘primitive’ translation machinery.

  15. Adsorption of amino acids and nucleic acid bases onto minerals: a few suggestions for prebiotic chemistry experiments

    NASA Astrophysics Data System (ADS)

    Zaia, Dimas A. M.

    2012-10-01

    Amino acids and nucleic acid bases are very important for the living organisms. Thus, their protection from decomposition, selection, pre-concentration and formation of biopolymers are important issues for understanding the origin of life on the Earth. Minerals could have played all of these roles. This paper discusses several aspects involving the adsorption of amino acids and nucleic acid bases onto minerals under conditions that could have been found on the prebiotic Earth; in particular, we recommend the use of minerals, amino acids, nucleic acid bases and seawater ions in prebiotic chemistry experiments. Several experiments involving amino acids, nucleic acid bases, minerals and seawater ions are also suggested, including: (a) using well-characterized minerals and the standardization of the mineral synthesis methods; (b) using primary chondrite minerals (olivine, pyroxene, etc.) and clays modified with metals (Cu, Fe, Ni, Mo, Zn, etc.); (c) determination of the possible products of decomposition due to interactions of amino acids and nucleic acid bases with minerals; (d) using minerals with more organophilic characteristics; (e) using seawaters with different concentrations of ions (i.e. Na+, Ca2+, Mg2+, SO4 2- and Cl-) (f) using non-protein amino acids (AIB, ?-ABA, ?-ABA, ?-ABA and ?-Ala and g) using nucleic acid bases other than adenine, thymine, uracil and cytosine. These experiments could be useful to clarify the role played by minerals in the origin of life on the Earth.

  16. Carbon composite micro- and nano-tubes-based electrodes for detection of nucleic acids

    PubMed Central

    2011-01-01

    The first aim of this study was to fabricate vertically aligned multiwalled carbon nanotubes (MWCNTs). MWCNTs were successfully prepared by using plasma enhanced chemical vapour deposition. Further, three carbon composite electrodes with different content of carbon particles with various shapes and sizes were prepared and tested on measuring of nucleic acids. The dependences of adenine peak height on the concentration of nucleic acid sample were measured. Carbon composite electrode prepared from a mixture of glassy and spherical carbon powder and MWCNTs had the highest sensitivity to nucleic acids. Other interesting result is the fact that we were able to distinguish signals for all bases using this electrode. PMID:21711910

  17. New substituted aryldiazomethyl labels for high density DNA chip-based nucleic acid testing.

    PubMed

    Laurent, Alain; Kotera, Mitsuharu; Burr, Arnaud; Lasnet, Frederick; Martin, Thibault; Laayoun, Ali

    2008-01-01

    DNA and RNA labeling and detection are key steps in nucleic acid testing, particularly for molecular diagnostics applications. Here, we report a new class of aryldiazomethyl labels that include in their structure a biotin moiety as a detectable unit and a nitro substituted phenyl diazomethyl as a reactive group. The greatest reactivity towards phosphates of nucleic acids, the water solubility and the stability of these new molecules were demonstrated. These very important properties, which are the main requirements for nucleic acid labeling in aqueous conditions using automated protocols within integrated diagnostic devices, make them the perfect labeling tools for hybridization-based analysis, especially for high-density DNA chips. PMID:18776349

  18. Carbon composite micro- and nano-tubes-based electrodes for detection of nucleic acids.

    PubMed

    Prasek, Jan; Huska, Dalibor; Jasek, Ondrej; Zajickova, Lenka; Trnkova, Libuse; Adam, Vojtech; Kizek, Rene; Hubalek, Jaromir

    2011-01-01

    The first aim of this study was to fabricate vertically aligned multiwalled carbon nanotubes (MWCNTs). MWCNTs were successfully prepared by using plasma enhanced chemical vapour deposition. Further, three carbon composite electrodes with different content of carbon particles with various shapes and sizes were prepared and tested on measuring of nucleic acids. The dependences of adenine peak height on the concentration of nucleic acid sample were measured. Carbon composite electrode prepared from a mixture of glassy and spherical carbon powder and MWCNTs had the highest sensitivity to nucleic acids. Other interesting result is the fact that we were able to distinguish signals for all bases using this electrode. PMID:21711910

  19. Brnsted Acids The Strongest Isolable Acid**

    E-print Network

    Reed, Christopher A.

    Brønsted Acids The Strongest Isolable Acid** Mark Juhasz, Stephan Hoffmann, Evgenii Stoyanov, Kee-Chan Kim, and Christopher A. Reed* Acids based on carborane anions as conjugate bases (Figure 1) are a new class of Brønsted (protic) acids, notable for their "strong yet gentle" qualities.[1] For example

  20. a,b-D-Constrained Nucleic Acids Are Strong Terminators of Thermostable DNA Polymerases in Polymerase Chain

    E-print Network

    Paris-Sud XI, Université de

    a,b-D-Constrained Nucleic Acids Are Strong Terminators of Thermostable DNA Polymerases, RP) a,b-D- Constrained Nucleic Acids (CNA) are dinucleotide building blocks that can feature either B. Citation: Marti´nez O, Ecochard V, Mahe´o S, Gross G, Bodin P, et al. (2011) a,b-D-Constrained Nucleic

  1. Strategies for automated sample preparation, nucleic acid purification, and concentration of low-target-number nucleic acids in environmental and food processing samples

    NASA Astrophysics Data System (ADS)

    Bruckner-Lea, Cynthia J.; Holman, David A.; Schuck, Beatrice L.; Brockman, Fred J.; Chandler, Darrell P.

    1999-01-01

    The purpose of this work is to develop a rapid, automated system for nucleic acid purification and concentration from environmental and food processing samples. Our current approach involves off-line filtration and cell lysis (ballistic disintegration) functions in appropriate buffers followed by automated nucleic acid capture and purification on renewable affinity matrix microcolumns. Physical cell lysis and renewable affinity microcolumns eliminate the need for toxic organic solvents, enzyme digestions or other time- consuming sample manipulations. Within the renewable affinity microcolumn, we have examined nucleic acid capture and purification efficiency with various microbead matrices (glass, polymer, paramagnetic), surface derivitization (sequence-specific capture oligonucleotides or peptide nucleic acids), and DNA target size and concentration under variable solution conditions and temperatures. Results will be presented comparing automated system performance relative to benchtop procedures for both clean (pure DNA from a laboratory culture) and environmental (soil extract) samples, including results which demonstrate 8 minute purification and elution of low-copy nucleic acid targets from a crude soil extract in a form suitable for PCR or microarray-based detectors. Future research will involve the development of improved affinity reagents and complete system integration, including upstream cell concentration and cell lysis functions and downstream, gene-based detectors. Results of this research will ultimately lead to improved processes and instrumentation for on-line, automated monitors for pathogenic micro-organisms in food, water, air, and soil samples.

  2. 70967108 Nucleic Acids Research, 2007, Vol. 35, No. 21 Published online 16 October 2007 doi:10.1093/nar/gkm750

    E-print Network

    Levin, Judith G.

    7096­7108 Nucleic Acids Research, 2007, Vol. 35, No. 21 Published online 16 October 2007 doi:10 of Vif, displays cytidine deaminase and single- stranded (ss) nucleic acid binding activities. HIV-1 nucleocapsid protein (NC) also binds nucleic acids and has a unique property, nucleic acid chaperone activity

  3. Intracellular Nucleic Acid Delivery by the Supercharged Dengue Virus Capsid Protein

    PubMed Central

    Freire, João Miguel; Veiga, Ana Salomé; Conceição, Thaís M.; Kowalczyk, Wioleta; Mohana-Borges, Ronaldo; Andreu, David; Santos, Nuno C.; Da Poian, Andrea T.; Castanho, Miguel A. R. B.

    2013-01-01

    Supercharged proteins are a recently identified class of proteins that have the ability to efficiently deliver functional macromolecules into mammalian cells. They were first developed as bioengineering products, but were later found in the human proteome. In this work, we show that this class of proteins with unusually high net positive charge is frequently found among viral structural proteins, more specifically among capsid proteins. In particular, the capsid proteins of viruses from the Flaviviridae family have all a very high net charge to molecular weight ratio (> +1.07/kDa), thus qualifying as supercharged proteins. This ubiquity raises the hypothesis that supercharged viral capsid proteins may have biological roles that arise from an intrinsic ability to penetrate cells. Dengue virus capsid protein was selected for a detailed experimental analysis. We showed that this protein is able to deliver functional nucleic acids into mammalian cells. The same result was obtained with two isolated domains of this protein, one of them being able to translocate lipid bilayers independently of endocytic routes. Nucleic acids such as siRNA and plasmids were delivered fully functional into cells. The results raise the possibility that the ability to penetrate cells is part of the native biological functions of some viral capsid proteins. PMID:24339931

  4. Nucleic Acid Aptamers as Potential Therapeutic and Diagnostic Agents for Lymphoma

    PubMed Central

    Shum, Ka-To; Zhou, Jiehua; Rossi, John J.

    2014-01-01

    Lymphomas are cancers that arise from white blood cells and usually present as solid tumors. Treatment of lymphoma often involves chemotherapy, and can also include radiotherapy and/or bone marrow transplantation. There is an un-questioned need for more effective therapies and diagnostic tool for lymphoma. Aptamers are single stranded DNA or RNA oligonucleotides whose three-dimensional structures are dictated by their sequences. The immense diversity in function and structure of nucleic acids enable numerous aptamers to be generated through an iterative in vitro selection technique known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Aptamers have several biochemical properties that make them attractive tools for use as potential diagnostic and pharmacologic agents. Isolated aptamers may directly inhibit the function of target proteins, or they can also be formulated for use as delivery agents for other therapeutic or imaging cargoes. More complex aptamer identification methods, using whole cancer cells (Cell-SELEX), may identify novel targets and aptamers to affect them. This review focuses on recent advances in the use of nucleic acid aptamers as diagnostic and therapeutic agents and as targeted delivery carriers that are relevant to lymphoma. Some representative examples are also discussed. PMID:25057429

  5. Detection of piscine nodaviruses by real-time nucleic acid sequence based amplification (NASBA).

    PubMed

    Starkey, William G; Millar, Rose Mary; Jenkins, Mary E; Ireland, Jacqueline H; Muir, K Fiona; Richards, Randolph H

    2004-05-01

    Nucleic acid sequence based amplification (NASBA) is an isothermal nucleic acid amplification procedure based on target-specific primers and probes, and the co-ordinated activity of 3 enzymes: AMV reverse transcriptase, RNase H, and T7 RNA polymerase. We have developed a real-time NASBA procedure for detection of piscine nodaviruses, which have emerged as major pathogens of marine fish. Viral RNA was isolated by guanidine thiocyanate lysis followed by purification on silica particles. Primers were designed to target sequences in the nodavirus capsid protein gene, yielding an amplification product of 120 nucleotides. Amplification products were detected in real-time with a molecular beacon (FAM labelled/methyl-red quenched) that recognised an internal region of the target amplicon. Amplification and detection were performed at 41 degrees C for 90 min in a Corbett Research Rotorgene. Based on the detection of cell culture-derived nodavirus, and a synthetic RNA target, the real-time NASBA procedure was approximately 100-fold more sensitive than single-tube RT-PCR. When used to test a panel of 37 clinical samples (negative, n = 18; positive, n = 19), the real-time NASBA assay correctly identified all 18 negative and 19 positive samples. In comparison, the RT-PCR procedure identified all 18 negative samples, but only 16 of the positive samples. These results suggest that real-time NASBA may represent a sensitive and specific diagnostic procedure for piscine nodaviruses. PMID:15212274

  6. Synthesis and characterization of peptide nucleic acid platinum nanoclusters

    NASA Astrophysics Data System (ADS)

    Wang, Xu; Pandey, Rajeev R.; Singh, Krishna V.; Senthil Andavan, G. T.; Tsai, Chunglin; Lake, Roger; Ozkan, Mihrimah; Ozkan, Cengiz S.

    2006-03-01

    Peptide nucleic acid (PNA) is an analogue of deoxyribonucleic acid (DNA) and possesses a neutral backbone that affords stronger hybridization, greater stability and higher specificity in base pairing. However, it has not been explored as much as DNA in self-assembling functional nanostructures or nanoelectronic devices. We report here for the first time the metallization of PNA with platinum (Pt) nanoparticles via chemical binding, reduction and deposition. Pt ions from a precursor salt solution are allowed to bind over the PNA fragments followed by a reduction and then growth into metal nanoparticles. PNA-Pt complexes form chains several hundred nanometres in length and by varying the duration of chemical reduction step, the dimension of the Pt nanoparticles can be controlled. The structural features and chemical composition of PNA-Pt nanoparticles have been characterized via scanning electron microscopy, transmission electron microscopy and Fourier transform-infrared spectroscopy. These results are also supported by modelling and analysis of the nature of high-lying molecular orbitals on PNA using density functional theory (DFT) method.

  7. Simple and sensitive determination of nucleic acids using palladium(II) complex with 2-(2-thiazolylazo)-5-dimethylaminobenzoic acid

    Microsoft Academic Search

    Yong-Mei Hao; Han-Xi Shen

    2000-01-01

    The paper describes the use of the palladium(II) complex with 2-(2-thiazolylazo)-5-dimethylamino-benzoic acid (TAMB) for the spectrophotometric determination of nucleic acids with the detection limit at ng levels. At pH 5.9, Pd(II), TAMB and nucleic acids interact rapidly at room temperature to form a supermolecular complex, leading to absorbance decreases at 621 and 675nm of the palladium(II)–TAMB complex. With 675nm as

  8. Development of polymer and lipid materials for enhanced delivery of nucleic acids and proteins

    E-print Network

    Eltoukhy, Ahmed Atef

    2013-01-01

    The development of synthetic vectors enabling efficient intracellular delivery of macromolecular therapeutics such as nucleic acids and proteins could potentially catalyze the clinical translation of many gene and protein-based ...

  9. Two-dimensional infrared spectroscopy of nucleic acids : application to tautomerism and DNA aptamer unfolding dynamics

    E-print Network

    Peng, Chunte Sam

    2014-01-01

    The structural dynamics of nucleic acids are intimately related to their biological functions; however, our ability to study these molecular dynamics has been largely impeded by the lack of techniques that possess both ...

  10. Beyond H&E: integration of nucleic acid-based analyses into diagnostic pathology.

    PubMed

    Maes, R K; Langohr, I M; Wise, A G; Smedley, R C; Thaiwong, T; Kiupel, M

    2014-01-01

    Veterinary pathology of infectious, particularly viral, and neoplastic diseases has advanced significantly with the advent of newer molecular methodologies that can detect nucleic acid of infectious agents within microscopic lesions, differentiate neoplastic from nonneoplastic cells, or determine the suitability of a targeted therapy by detecting specific mutations in certain cancers. Polymerase chain reaction-based amplification of DNA or RNA and in situ hybridization are currently the most commonly used methods for nucleic acid detection. In contrast, the main methodology used for protein detection within microscopic lesions is immunohistochemistry. Other methods that allow for analysis of nucleic acids within a particular cell type or individual cells, such as laser capture microdissection, are also available in some laboratories. This review gives an overview of the factors that influence the accurate analysis of nucleic acids in formalin-fixed tissues, as well as of different approaches to detect such targets. PMID:24129897

  11. Peptide nucleic acid-encoded libraries for microarray-based high-throughput screening 

    E-print Network

    Planonth, Songsak

    2012-06-22

    Peptide nucleic acids (PNAs) were used as encoding tags to enable the analysis of peptide libraries by PNA/DNA hybridisation onto DNA microarrays. This allowed entire peptide libraries to be organised and sorted in a two ...

  12. Nucleic Acids Research, 2009, 112 doi:10.1093/nar/gkp407

    E-print Network

    Pervouchine, Dmitri D.

    Nucleic Acids Research, 2009, 1­12 doi:10.1093/nar/gkp407 Modulation of alternative splicing/exon definition requires a network of pro- tein­protein and protein­RNA interactions to ensure that the correct

  13. Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score

    PubMed Central

    Miao, Zhichao; Westhof, Eric

    2015-01-01

    We describe a general binding score for predicting the nucleic acid binding probability in proteins. The score is directly derived from physicochemical and evolutionary features and integrates a residue neighboring network approach. Our process achieves stable and high accuracies on both DNA- and RNA-binding proteins and illustrates how the main driving forces for nucleic acid binding are common. Because of the effective integration of the synergetic effects of the network of neighboring residues and the fact that the prediction yields a hierarchical scoring on the protein surface, energy funnels for nucleic acid binding appear on protein surfaces, pointing to the dynamic process occurring in the binding of nucleic acids to proteins. PMID:25940624

  14. Method for detection of polymorphic restriction sites and nucleic acid sequences

    SciTech Connect

    Saiki, R.K.; Erlich, H.A.

    1987-07-28

    A method is detected for detecting the presence or absence of at least one specific restriction site in a specific nucleic acid sequence comprising the steps of: (a) hybridizing the nucleic acid sequence in solution with an oligonucleotide probe for each restriction site detected. A probe is complementary to a region in the nucleic acid sequence spanning the respective restriction site of the probe is labeled at the end which is nearer to the respective restriction site than the other end of the probe; (b) digesting the hybridized nucleic acid sequence with a restriction endonuclease for each restriction site detected by each probe capable of cleaving its respective probe at the restriction site being detected. This produces labeled and unlabeled oligomer fragments.; (c) separating any labeled cleaved oligomer fragments from labeled uncleaved oligomers, and (d) detecting the presence or absence of labeled oligomer fragments.

  15. Gene Therapy for Advanced Melanoma: Selective Targeting and Therapeutic Nucleic Acids

    PubMed Central

    Viola, Joana R.; Rafael, Diana F.; Wagner, Ernst; Besch, Robert; Ogris, Manfred

    2013-01-01

    Despite recent advances, the treatment of malignant melanoma still results in the relapse of the disease, and second line treatment mostly fails due to the occurrence of resistance. A wide range of mutations are known to prevent effective treatment with chemotherapeutic drugs. Hence, approaches with biopharmaceuticals including proteins, like antibodies or cytokines, are applied. As an alternative, regimens with therapeutically active nucleic acids offer the possibility for highly selective cancer treatment whilst avoiding unwanted and toxic side effects. This paper gives a brief introduction into the mechanism of this devastating disease, discusses the shortcoming of current therapy approaches, and pinpoints anchor points which could be harnessed for therapeutic intervention with nucleic acids. We bring the delivery of nucleic acid nanopharmaceutics into perspective as a novel antimelanoma therapeutic approach and discuss the possibilities for melanoma specific targeting. The latest reports on preclinical and already clinical application of nucleic acids in melanoma are discussed. PMID:23634303

  16. Understanding barriers to efficient nucleic acid delivery with bioresponsive block copolymers

    E-print Network

    Bonner, Daniel Kenneth

    2012-01-01

    The delivery of nucleic acids has the potential to revolutionize medicine by allowing previously untreatable diseases to be clinically addressed. Viral delivery systems have been held back by immunogenicity and toxicity ...

  17. Electrochemical control of reversible DNA hybridisation : for future use in nucleic acid amplification 

    E-print Network

    Syed, Shahida Nina

    2014-06-28

    Denaturation and renaturation is indispensable for the biological function of nucleic acids in many cellular processes, such as for example transcription for the synthesis of RNA and DNA replication during cell division. ...

  18. Prediction of nucleic acid binding probability in proteins: a neighboring residue network based score.

    PubMed

    Miao, Zhichao; Westhof, Eric

    2015-06-23

    We describe a general binding score for predicting the nucleic acid binding probability in proteins. The score is directly derived from physicochemical and evolutionary features and integrates a residue neighboring network approach. Our process achieves stable and high accuracies on both DNA- and RNA-binding proteins and illustrates how the main driving forces for nucleic acid binding are common. Because of the effective integration of the synergetic effects of the network of neighboring residues and the fact that the prediction yields a hierarchical scoring on the protein surface, energy funnels for nucleic acid binding appear on protein surfaces, pointing to the dynamic process occurring in the binding of nucleic acids to proteins. PMID:25940624

  19. Extraction of total nucleic acids from ticks for the detection of bacterial and viral pathogens.

    PubMed

    Crowder, Chris D; Rounds, Megan A; Phillipson, Curtis A; Picuri, John M; Matthews, Heather E; Halverson, Justina; Schutzer, Steven E; Ecker, David J; Eshoo, Mark W

    2010-01-01

    Ticks harbor numerous bacterial, protozoal, and viral pathogens that can cause serious infections in humans and domestic animals. Active surveillance of the tick vector can provide insight into the frequency and distribution of important pathogens in the environment. Nucleic-acid based detection of tick-borne bacterial, protozoan, and viral pathogens requires the extraction of both DNA and RNA (total nucleic acids) from ticks. Traditional methods for nucleic acid extraction are limited to extraction of either DNA or the RNA from a sample. Here we present a simple bead-beating based protocol for extraction of DNA and RNA from a single tick and show detection of Borrelia burgdorferi and Powassan virus from individual, infected Ixodes scapularis ticks. We determined expected yields for total nucleic acids by this protocol for a variety of adult tick species. The method is applicable to a variety of arthropod vectors, including fleas and mosquitoes, and was partially automated on a liquid handling robot. PMID:20180313

  20. In-silico design of computational nucleic acids for molecular information processing

    PubMed Central

    2013-01-01

    Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the regulatory networks within living cells has increasingly been revealed. Molecular computers are attractive due to their ability to function within a biological system; an application area extraneous to the present information technology paradigm. The existence of natural information processing architectures (predominately exemplified by protein) demonstrates that computing based on physical substrates that are radically different from silicon is feasible. Two key principles underlie molecular level information processing in organisms: conformational dynamics of macromolecules and self-assembly of macromolecules. Nucleic acids support both principles, and moreover computational design of these molecules is practicable. This study demonstrates the simplicity with which one can construct a set of nucleic acid computing units using a new computational protocol. With the new protocol, diverse classes of nucleic acids imitating the complete set of boolean logical operators were constructed. These nucleic acid classes display favourable thermodynamic properties and are significantly similar to the approximation of successful candidates implemented in the laboratory. This new protocol would enable the construction of a network of interconnecting nucleic acids (as a circuit) for molecular information processing. PMID:23647621

  1. Electrochemical microfluidic biosensor for the detection of nucleic acid sequences.

    PubMed

    Goral, Vasiliy N; Zaytseva, Natalya V; Baeumner, Antje J

    2006-03-01

    A microfluidic biosensor with electrochemical detection for the quantification of nucleic acid sequences was developed. In contrast to most microbiosensors that are based on fluorescence for signal generation, it takes advantage of the simplicity and high sensitivity provided by an amperometric and coulorimetric detection system. An interdigitated ultramicroelectrode array (IDUA) was fabricated in a glass chip and integrated directly with microchannels made of poly(dimethylsiloxane) (PDMS). The assembly was packaged into a Plexiglas housing providing fluid and electrical connections. IDUAs were characterized amperometrically and using cyclic voltammetry with respect to static and dynamic responses for the presence of a reversible redox couple-potassium hexacyanoferrate (ii)/hexacyanoferrate (iii) (ferri/ferrocyanide). A combined concentration of 0.5 microM of ferro/ferricyanide was determined as lower limit of detection with a dynamic range of 5 orders of magnitude. Background signals were negligible and the IDUA responded in a highly reversible manner to the injection of various volumes and various concentrations of the electrochemical marker. For the detection of nucleic acid sequences, liposomes entrapping the electrochemical marker were tagged with a DNA probe, and superparamagnetic beads were coated with a second DNA probe. A single stranded DNA target sequence hybridized with both probes. The sandwich was captured in the microfluidic channel just upstream of the IDUA via a magnet located in the outside housing. Liposomes were lysed using a detergent and the amount of released ferro/ferricyanide was quantified while passing by the IDUA. Optimal location of the magnet with respect to the IDUA was investigated, the effect of dextran sulfate on the hybridization reaction was studied and the amount of magnetic beads used in the assay was optimized. A dose response curve using varying concentrations of target DNA molecules was carried out demonstrating a limit of detection at 1 fmol assay(-1) and a dynamic range between 1 and 50 fmol. The overall assay took 6 min to complete, plus 15-20 min of pre-incubation and required only a simple potentiostat for signal recording and interpretation. PMID:16511625

  2. Resonance Double Light Scattering Method for the Determination of Nucleic Acids with Cetylpyridine Bromide

    Microsoft Academic Search

    Rutao Liu; Jinghe Yang; Changxia Sun; Xia Wu; Xibao Gao; Yang Liu; Shufang Liu; Benyu Su

    2004-01-01

    Cetylpyridine bromide (CPB) was used as a novel probe to determine nucleic acids by the resonance double light scattering technique in this paper. Under the optimum conditions, different nucleic acids have different binding properties with CPB. The sensitivity of this method decreases in the following order: ctDNA>yRNA>fsDNA. The detection limits are 8.9, 12.7 and 18.7?ng?mL -1, respectively. Synthetic samples were

  3. Determination of nucleic acids with a near infrared cyanine dye using resonance light scattering technique

    Microsoft Academic Search

    Fang Fang; Hong Zheng; Ling Li; Yuqin Wu; Jinlong Chen; Shujuan Zhuo; Changqing Zhu

    2006-01-01

    A new method for the determination of nucleic acids has been developed based on the enhancement effect of resonance light scattering (RLS) with a cationic near infrared (NIR) cyanine dye. Under the optimal conditions, the enhanced RLS intensity at 823nm is proportional to the concentration of nucleic acids in the range of 0–400ngmL?1 for both calf thymus DNA (CT DNA)

  4. The sensitive determination of nucleic acids using resonance light scattering quenching method

    Microsoft Academic Search

    Zhen Jia; Jinghe Yang; Xia Wu; Changxia Sun; Shufang Liu; Fei Wang; Zongshan Zhao

    2006-01-01

    It is found that in hexamethylene tetramine (HMTA)–HCl buffer of pH 7.00, nucleic acids can quench the resonance light scattering (RLS) of europium (III) (Eu3+)–2-thenoyltrifluoroacetne (TTA)–1,10-phenanthroline (Phen) system. Based on this, a sensitive method for the determination of nucleic acids is proposed. The experiments indicate that under the optimum conditions, the quenched RLS intensity is in proportion to the concentration

  5. Cationic cyanine as a near-infrared fluorescent probe for the determination of nucleic acids

    Microsoft Academic Search

    Hong Zheng; Dong-Hui Li; Chang-Qing Zhu; Xiao-Lan Chen; Jin-Gou Xu

    2000-01-01

    A new method with a cationic near-IR cyanine as fluorescent probe was developed for the determination of nucleic acids. The\\u000a near-IR cyanine shows maximum excitation and emission wavelengths at 765 and 790 nm, respectively, in aqueous solution. The\\u000a method is based on the fluorescence decrease of near-IR cyanine in the presence of nucleic acids. Under optimal conditions,\\u000a the ratio of

  6. Effect of brassinosteroids on nucleic acids and protein content in cultured cells of Chlorella vulgaris

    Microsoft Academic Search

    Andrzej Bajguz

    2000-01-01

    This study was conducted to investigate changes of nucleic acids and protein levels in response to brassinosteroid (BR) effect in the green alga Chlorella vulgaris Beijerinck. BRs had the greatest effect on growth and metabolism of algae between 24 and 36 h after treatment in the range from 10–12 to 10–8 M. The highest growth of the content of nucleic acids and

  7. Plasmacytoid dendritic cells: sensing nucleic acids in viral infection and autoimmune diseases

    Microsoft Academic Search

    Michel Gilliet; Wei Cao; Yong-Jun Liu

    2008-01-01

    Plasmacytoid dendritic cells (pDCs) are important mediators of antiviral immunity through their ability to produce large amounts of type I interferons (IFNs) on viral infection. This function of pDCs is linked to their expression of Toll-like receptor 7 (TLR7) and TLR9, which sense viral nucleic acids within the early endosomes. Exclusion of self nucleic acids from TLR-containing early endosomes normally

  8. Affinity Purification of DNA and RNA from Environmental Samples with Peptide Nucleic Acid Clamps

    Microsoft Academic Search

    DARRELL P. CHANDLER; JENNIE R. STULTS; SHARON CEBULA; BEATRICE L. SCHUCK; DEREK W. WEAVER; KEVIN K. ANDERSON; MICHAEL EGHOLM; FRED J. BROCKMAN

    2000-01-01

    Bispeptide nucleic acids (bis-PNAs; PNA clamps), PNA oligomers, and DNA oligonucleotides were evaluated as affinity purification reagents for subfemtomolar 16S ribosomal DNA (rDNA) and rRNA targets in soil, sed- iment, and industrial air filter nucleic acid extracts. Under low-salt hybridization conditions (10 mM NaPO4, 5 mM disodium EDTA, and 0.025% sodium dodecyl sulfate (SDS)) a PNA clamp recovered significantly more

  9. Inhibition of the bovine papillomavirus E2 protein activity by peptide nucleic acid

    Microsoft Academic Search

    Reet Kurg; Ülo Langel; Mart Ustav

    2000-01-01

    The bovine papillomavirus type-1 E2 protein is the master regulator of the papillomavirus transcription and replication, the activity of which is regulated through sequence-specific DNA binding. Peptide nucleic acid (PNA) is a nucleic acid analogue, which associates with high affinity to complementary DNA, RNA or PNA, yielding in formation of stable complexes. The potential use of PNA as a sequence-specific

  10. Simple Protocol for Secondary School Hands-On Activity: Electrophoresis of Pre-Stained Nucleic Acids on Agar-Agar Borate Gels

    ERIC Educational Resources Information Center

    Britos, Leticia; Goyenola, Guillermo; Orono, Silvia Umpierrez

    2004-01-01

    An extremely simple, inexpensive, and safe method is presented, which emulates nucleic acids isolation and electrophoretic analysis as performed in a research environment, in the context of a secondary school hands-on activity. The protocol is amenable to an interdisciplinary approach, taking into consideration the electrical and chemical…

  11. Evaluation of the QIAsymphony SP Workstation for Magnetic Particle–Based Nucleic Acid Purification From Different Sample Types for Demanding Downstream Applications

    Microsoft Academic Search

    Mogens Kruhøffer; Thorsten Voss; Katharina Beller; Mario Scherer; Janina Cramer; Thomas Deutschmann; Cordula Homberg; Martin Schlumpberger; Christian Lenz

    2010-01-01

    We evaluated automated nucleic acid (NA) extraction from a variety of different biological specimens using the QIAsymphony SP instrument. QIAsymphony DNA kits were used for DNA purification from human blood and from diverse human and animal tissue specimens. RNA was isolated from human blood stabilized in PAXgene Blood RNA tubes with the QIAsymphony PAXgene Blood RNA kit, and from human

  12. Self-assembly of stable monomolecular nucleic acid lipid particles with a size of 30 nm.

    PubMed

    Rudorf, Sophia; Rädler, Joachim O

    2012-07-18

    The design of efficient nucleic acid complexes is key to progress in genetic research and therapies based on RNA interference. For optimal transport within tissue and across extracellular barriers, nucleic acid carriers need to be small and stable. In this Article, we prepare and characterize mono-nucleic acid lipid particles (mono-NALPs). The particles consist of single short double-stranded oligonucleotides or single siRNA molecules each encapsulated within a closed shell of a cationic-zwitterionic lipid bilayer, furnished with an outer polyethylene glycol (PEG) shield. The particles self-assemble by solvent exchange from a solution containing nucleic acid mixed with the four lipid components DOTAP, DOPE, DOPC, and DSPE-PEG(2000). Using fluorescence correlation spectroscopy, we monitor the formation of mono-NALPs from short double-stranded oligonucleotides or siRNA and lipids into monodisperse particles of approximately 30 nm in diameter. Small angle neutron and X-ray scattering and transmission electron microscopy experiments substantiate a micelle-like core-shell structure of the particles. The PEGylated lipid shell protects the nucleic acid core against degradation by nucleases, sterically stabilizes the mono-NALPs against disassembly in collagen networks, and prevents nonspecific binding to cells. Hence, PEG-lipid shielded mono-NALPs are the smallest stable siRNA lipid system possible and may provide a structural design to be built upon for the development of novel nucleic acid delivery systems with enhanced biodistribution in vivo. PMID:22694262

  13. Elucidation of nucleic acid-drug interactions by tandem mass spectrometry.

    PubMed

    Hari, Yvonne; Nyakas, Adrien; Stucki, Silvan R; Schürch, Stefan

    2014-01-01

    In continuation of the long tradition of mass spectrometric research at the University of Bern, our group focuses on the characterization of nucleic acids as therapeutic agents and as drug targets. This article provides a short overview of our recent work on platinated single-stranded and higher-order nucleic acids. Nearly three decades ago the development of soft ionization techniques opened a whole new chapter in the mass spectrometric analysis of not only nucleic acids themselves, but also their interactions with potential drug candidates. In contrast to modern next generation sequencing approaches, though, the goal of the tandem mass spectrometric investigation of nucleic acids is by no means the complete sequencing of genetic DNA, but rather the characterization of short therapeutic and regulatory oligonucleotides and the elucidation of nucleic acid-drug interactions. The influence of cisplatin binding on the gas-phase dissociation of nucleic acids was studied by the means of electrospray ionization tandem mass spectrometry. Experiments on native and modified DNA and RNA oligomers confirmed guanine base pairs as the preferred platination site and laid the basis for the formulation of a gas-phase fragmentation mechanism of platinated oligonucleotides. The study was extended to double-stranded DNA and DNA quadruplexes. While duplexes are believed to be the main target of cisplatin in vivo, the recently discovered DNA quadruplexes constitute another promising target for anti-tumor drugs owing to their regulatory functions in the cell cycle. PMID:24801849

  14. Stability of free and mineral-protected nucleic acids: Implications for the RNA world

    NASA Astrophysics Data System (ADS)

    Swadling, Jacob B.; Coveney, Peter V.; Christopher Greenwell, H.

    2012-04-01

    Using molecular dynamics simulations we study the structural stability of three different nucleic acids intercalated within a magnesium aluminium layered double hydroxide (LDH) mineral, at varying degrees of hydration, and free in aqueous solution. The nucleotides investigated are ribose nucleic acid (RNA), deoxyribose nucleic acid (DNA) and peptide nucleic acid (PNA), all in duplex form. Our simulations show that DNA has enhanced Watson-Crick hydrogen-bonding when intercalated within the LDH clay interlayers, compared with intercalated RNA and PNA, whilst the reverse trend is found for the nucleic acids in bulk water. The tendency for LDH to alter the stability of the three nucleic acids persists for higher temperature and pressure conditions. The uncharged protein backbone of PNA is found to have a detrimental effect on the overall stability of the duplex, as it experiences a greatly reduced electrostatic interaction with the charged LDH sheets compared to RNA and DNA. Assuming an RNA world, in which RNA preceded the DNA/protein world, at some point in time DNA must have taken over the role as the information storage molecule from RNA. These results suggest that a mineral based origin of life may have favoured DNA as the information-storage biomolecule over potentially competing RNA and PNA, providing a route to modern biology from the RNA world.

  15. Electron Microscopy of the Nucleic Acid of Mouse Mammary Tumor Virus

    PubMed Central

    Sarkar, Nurul H.; Moore, Dan H.

    1970-01-01

    Mouse mammary tumor virus (MTV) was isolated from the milk of RIII mice by density-gradient centrifugation in Ficoll. The homogeneity of the preparation was demonstrated in electron micrographs. The nucleic acid was extracted with phenol in the presence of Pronase. Its viral origin was attested by failure of ribo-nuclease and deoxyribonuclease treatment of the virus preparation to destroy the filamentous molecules; after phenol extraction, the molecules were destroyed by ribonuclease but not by deoxyribonuclease. Rotary shadowed preparations were examined in the electron microscope. The length distribution of the RNA filaments showed peaks at 1.2, 2.4, and 3.6 ?m. The molecular weight of the longest molecule of MTV-RNA was estimated as 3.6 × 106 daltons. Images PMID:4317350

  16. Linear and nonlinear optical properties of nucleic acid bases

    NASA Astrophysics Data System (ADS)

    Alparone, Andrea

    2013-01-01

    Electronic and vibrational (hyper)polarizabilities of neutral nucleic acid bases (uracil, thymine, cytosine, adenine, hypoxanthine and guanine) were determined using Hartree-Fock, correlated MPn (n = 2, 4), CCSD and DFT (B3LYP, B97-1, CAM-B3LYP) methods. The computations were performed in gaseous and aqueous phases for the most stable tautomeric forms. Frequency-dependent second-order hyperpolarizabilities were calculated for the OKE, IDRI, EFISHG and THG nonlinear optical processes at the wavelength of 1064 nm. The results show that the average electronic polarizabilities increase in the order uracil < cytosine < thymine < hypoxanthine < adenine < guanine. This order is also maintained for the electronic hyperpolarizabilities, with the inversion between cytosine and thymine. The response electric properties for the tautomers are almost similar to each other, whereas group substitution and solvation effects are much more significant. Among the DFT methods, the long-range corrected CAM-B3LYP functional gives the better performances, reproducing satisfactorily the correlated ab initio (hyper)polarizability data.

  17. Nucleic acid aptamers: clinical applications and promising new horizons

    PubMed Central

    Ni, Xiaohua; Castanares, Mark; Mukherjee, Amarnath; Lupold, Shawn E.

    2011-01-01

    Aptamers are a special class of nucleic acid molecules that are beginning to be investigated for clinical use. These small RNA/DNA molecules can form secondary and tertiary structures capable of specifically binding proteins or other cellular targets; they are essentially a chemical equivalent of antibodies. Aptamers have the advantage of being highly specific, relatively small in size, and non-immunogenic. Since the discovery of aptamers in the early 1990s, great efforts have been made to make them clinically relevant for diseases like cancer, HIV, and macular degeneration. In the last two decades, many aptamers have been clinically developed as inhibitors for targets such as vascular endothelial growth factor (VEGF) and thrombin. The first aptamer based therapeutic was FDA approved in 2004 for the treatment of age-related macular degeneration and several other aptamers are currently being evaluated in clinical trials. With advances in targeted-therapy, imaging, and nanotechnology, aptamers are readily considered as potential targeting ligands because of their chemical synthesis and ease of modification for conjugation. Preclinical studies using aptamer-siRNA chimeras and aptamer targeted nanoparticle therapeutics have been very successful in mouse models of cancer and HIV. In summary aptamers are in several stages of development, from pre-clinical studies to clinical trials and even as FDA approved therapeutics. In this review, we will discuss the current state of aptamers in clinical trials as well as some promising aptamers in pre-clinical development. PMID:21838685

  18. Proposed Ancestors of Phage Nucleic Acid Packaging Motors (and Cells)

    PubMed Central

    Serwer, Philip

    2011-01-01

    I present a hypothesis that begins with the proposal that abiotic ancestors of phage RNA and DNA packaging systems (and cells) include mobile shells with an internal, molecule-transporting cavity. The foundations of this hypothesis include the conjecture that current nucleic acid packaging systems have imprints from abiotic ancestors. The abiotic shells (1) initially imbibe and later also bind and transport organic molecules, thereby providing a means for producing molecular interactions that are links in the chain of events that produces ancestors to the first molecules that are both information carrying and enzymatically active, and (2) are subsequently scaffolds on which proteins assemble to form ancestors common to both shells of viral capsids and cell membranes. Emergence of cells occurs via aggregation and merger of shells and internal contents. The hypothesis continues by using proposed imprints of abiotic and biotic ancestors to deduce an ancestral thermal ratchet-based DNA packaging motor that subsequently evolves to integrate a DNA packaging ATPase that provides a power stroke. PMID:21994778

  19. Solution influence on biomolecular equilibria - Nucleic acid base associations

    NASA Technical Reports Server (NTRS)

    Pohorille, A.; Pratt, L. R.; Burt, S. K.; Macelroy, R. D.

    1984-01-01

    Various attempts to construct an understanding of the influence of solution environment on biomolecular equilibria at the molecular level using computer simulation are discussed. First, the application of the formal statistical thermodynamic program for investigating biomolecular equilibria in solution is presented, addressing modeling and conceptual simplications such as perturbative methods, long-range interaction approximations, surface thermodynamics, and hydration shell. Then, Monte Carlo calculations on the associations of nucleic acid bases in both polar and nonpolar solvents such as water and carbon tetrachloride are carried out. The solvent contribution to the enthalpy of base association is positive (destabilizing) in both polar and nonpolar solvents while negative enthalpies for stacked complexes are obtained only when the solute-solute in vacuo energy is added to the total energy. The release upon association of solvent molecules from the first hydration layer around a solute to the bulk is accompanied by an increase in solute-solvent energy and decrease in solvent-solvent energy. The techniques presented are expectd to displace less molecular and more heuristic modeling of biomolecular equilibria in solution.

  20. Rapid genotyping using pyrene?perylene locked nucleic acid complexes

    PubMed Central

    Kumar, T. Santhosh; Myznikova, Anna; Samokhina, Evgeniya; Astakhova, Irina Kira

    2013-01-01

    We have developed an assay for single strand DNA and RNA detection which is based on novel pyrene?perylene FRET pairs attached to short LNA/DNA probes. The assay is based on ratiometric emission upon binding of target DNA/RNA by three combinations of fluorescent LNA/DNA reporter strands. Specific geometry of the pyrene fluorophore attached to the 2?-amino group of 2?-amino-LNA in position 4 allows for the first time to efficiently utilize dipole?dipole orientation parameter for sensing of single-nucleotide polymorphisms (SNPs) in nucleic acid targets by FRET. Using novel probes, SNP detection is achieved with advantages of large Stokes shift (115 nm), high fluorescence quantum yields and low limit of target detection values (< 5 nM). Rapid and accurate genotyping of highly polymorphic HIV Pol cDNA and RNA fragments performed herein proves the possibility for broad application of the novel pyrene?perylene FRET pairs, e.g., in imaging and clinical diagnostics. PMID:24044052

  1. Locked nucleic acid oligomers as handles for single molecule manipulation

    PubMed Central

    Berezney, John P.; Saleh, Omar A.

    2014-01-01

    Single-molecule manipulation (SMM) techniques use applied force, and measured elastic response, to reveal microscopic physical parameters of individual biomolecules and details of biomolecular interactions. A major hurdle in the application of these techniques is the labeling method needed to immobilize biomolecules on solid supports. A simple, minimally-perturbative labeling strategy would significantly broaden the possible applications of SMM experiments, perhaps even allowing the study of native biomolecular structures. To accomplish this, we investigate the use of functionalized locked nucleic acid (LNA) oligomers as biomolecular handles that permit sequence-specific binding and immobilization of DNA. We find these probes form bonds with DNA with high specificity but with varied stability in response to the direction of applied mechanical force: when loaded in a shear orientation, the bound LNA oligomers were measured to be two orders of magnitude more stable than when loaded in a peeling, or unzipping, orientation. Our results show that LNA provides a simple, stable means to functionalize dsDNA for manipulation. We provide design rules that will facilitate their use in future experiments. PMID:25159617

  2. Reticuloendotheliosis Virus Nucleic Acid Sequences in Cellular DNA

    PubMed Central

    Kang, Chil-Yong; Temin, Howard M.

    1974-01-01

    Reticuloendotheliosis virus 60S RNA labeled with 125I, or reticuloendotheliosis virus complementary DNA labeled with 3H, were hybridized to DNAs from infected chicken and pheasant cells. Most of the sequences of the viral RNA were found in the infected cell DNAs. The reticuloendotheliosis viruses, therefore, replicate through a DNA intermediate. The same labeled nucleic acids were hybridized to DNA of uninfected chicken, pheasant, quail, turkey, and duck. About 10% of the sequences of reticuloendotheliosis virus RNA were present in the DNA of uninfected chicken, pheasant, quail, and turkey. None were detected in DNA of duck. The specificity of the hybridization was shown by competition between unlabeled and 125I-labeled viral RNAs and by determination of melting temperatures. In contrast, 125I-labeled RNA of Rous-associated virus-O, an avian leukosis-sarcoma virus, hybridized 55% to DNA of uninfected chicken, 20% to DNA of uninfected pheasant, 15% to DNA of uninfected quail, 10% to DNA of uninfected turkey, and less than 1% to DNA of uninfected duck. PMID:4372393

  3. Guanine base stacking in G-quadruplex nucleic acids

    PubMed Central

    Lech, Christopher Jacques; Heddi, Brahim; Phan, Anh Tuân

    2013-01-01

    G-quadruplexes constitute a class of nucleic acid structures defined by stacked guanine tetrads (or G-tetrads) with guanine bases from neighboring tetrads stacking with one another within the G-tetrad core. Individual G-quadruplexes can also stack with one another at their G-tetrad interface leading to higher-order structures as observed in telomeric repeat-containing DNA and RNA. In this study, we investigate how guanine base stacking influences the stability of G-quadruplexes and their stacked higher-order structures. A structural survey of the Protein Data Bank is conducted to characterize experimentally observed guanine base stacking geometries within the core of G-quadruplexes and at the interface between stacked G-quadruplex structures. We couple this survey with a systematic computational examination of stacked G-tetrad energy landscapes using quantum mechanical computations. Energy calculations of stacked G-tetrads reveal large energy differences of up to 12 kcal/mol between experimentally observed geometries at the interface of stacked G-quadruplexes. Energy landscapes are also computed using an AMBER molecular mechanics description of stacking energy and are shown to agree quite well with quantum mechanical calculated landscapes. Molecular dynamics simulations provide a structural explanation for the experimentally observed preference of parallel G-quadruplexes to stack in a 5?–5? manner based on different accessible tetrad stacking modes at the stacking interfaces of 5?–5? and 3?–3? stacked G-quadruplexes. PMID:23268444

  4. An Efficient Biodelivery System for Antisense Polyamide Nucleic Acid (PNA)

    PubMed Central

    Mehiri, Mohamed; Upert, Gregory; Tripathi, Snehlata; Di Giorgio, Audrey; Condom, Roger

    2008-01-01

    With the aim of developing a general and straightforward procedure for the intracellular delivery of naked peptide nucleic acids (PNAs), we designed an intracellularly biodegradable triphenylphosphonium (TPP) cation based transporter system. In this system, TPP is linked, via a biolabile disulfide bridge, to an activated mercaptoethoxycarbonyl moiety, allowing its direct coupling to the N-terminal extremity of a free PNA through a carbamate bond. We found that such TPP-PNA-carbamate conjugates were highly stable in a cell culture medium containing fetal calf serum. In a glutathione-containing medium mimicking the cytosol, the conjugates were rapidly degraded into an unstable intermediate, which spontaneously decomposed, releasing the free PNA. Using a fluorescence-labeled PNA–TPP conjugate, we demonstrated that conjugates were taken up by cells. Efficient cellular uptake and release of the PNA into the cytosol was further confirmed by the anti-HIV activity measured for the TPP-conjugate of a 16-mer PNA targeting the TAR region of the HIV-1 genome. This conjugate exhibited an IC50 value of 1 ?M, while the free 16-mer PNA did not inhibit replication of HIV in the same cellular test. PMID:18707540

  5. Method for producing labeled single-stranded nucleic acid probes

    DOEpatents

    Dunn, John J. (Bellport, NY); Quesada, Mark A. (Middle Island, NY); Randesi, Matthew (Upton, NY)

    1999-10-19

    Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

  6. Improved nucleic acid descriptors for siRNA efficacy prediction

    PubMed Central

    Sciabola, Simone; Cao, Qing; Orozco, Modesto; Faustino, Ignacio; Stanton, Robert V.

    2013-01-01

    Although considerable progress has been made recently in understanding how gene silencing is mediated by the RNAi pathway, the rational design of effective sequences is still a challenging task. In this article, we demonstrate that including three-dimensional descriptors improved the discrimination between active and inactive small interfering RNAs (siRNAs) in a statistical model. Five descriptor types were used: (i) nucleotide position along the siRNA sequence, (ii) nucleotide composition in terms of presence/absence of specific combinations of di- and trinucleotides, (iii) nucleotide interactions by means of a modified auto- and cross-covariance function, (iv) nucleotide thermodynamic stability derived by the nearest neighbor model representation and (v) nucleic acid structure flexibility. The duplex flexibility descriptors are derived from extended molecular dynamics simulations, which are able to describe the sequence-dependent elastic properties of RNA duplexes, even for non-standard oligonucleotides. The matrix of descriptors was analysed using three statistical packages in R (partial least squares, random forest, and support vector machine), and the most predictive model was implemented in a modeling tool we have made publicly available through SourceForge. Our implementation of new RNA descriptors coupled with appropriate statistical algorithms resulted in improved model performance for the selection of siRNA candidates when compared with publicly available siRNA prediction tools and previously published test sets. Additional validation studies based on in-house RNA interference projects confirmed the robustness of the scoring procedure in prospective studies. PMID:23241392

  7. Nanodelivery systems for nucleic acid therapeutics in drug resistant tumors.

    PubMed

    Iyer, Arun K; Duan, Zhenfeng; Amiji, Mansoor M

    2014-08-01

    Development of intrinsic and acquired drug resistance in cancer is a significant clinical challenge for effective therapeutic outcomes. Multidrug resistance (MDR) in solid tumors is especially difficult to overcome due to the many different factors that influence clinically manifested refractory disease. Genetic profiling of MDR tumors can provide for more specific control through RNA interference (RNAi) therapy. However, there are multiple barriers to effective in vivo delivery of functional nucleic acid constructs, such as small interfering RNAs (siRNAs) and micro RNAs (miRNAs or miRs). In this review, we have briefly described the principles and mechanisms based on the RNA interference phenomenon and the barriers to its successful clinical translation. The principles of active and passive tumor targeting using nanoparticles systems are also discussed. Furthermore, illustrative examples of miRNA, siRNA, and gene-drug combination delivery using nanoparticle systems that have shown promising potentials for the treatment of diseases such as MDR cancers are covered. PMID:24661041

  8. Membrane Protected Apoptotic Trophoblast Microparticles Contain Nucleic Acids

    PubMed Central

    Orozco, Aaron F.; Jorgez, Carolina J.; Horne, Cassandra; Marquez-Do, Deborah A.; Chapman, Matthew R.; Rodgers, John R.; Bischoff, Farideh Z.; Lewis, Dorothy E.

    2008-01-01

    Microparticles (MPs) that circulate in blood may be a source of DNA for molecular analyses, including prenatal genetic diagnoses. Because MPs are heterogeneous in nature, however, further characterization is important before use in clinical settings. One key question is whether DNA is either bound to aggregates of blood proteins and lipid micelles or intrinsically associated with MPs from dying cells. To test the latter hypothesis, we asked whether MPs derived in vitro from dying cells were similar to those in maternal plasma. JEG-3 cells model extravillous trophoblasts, which predominate during the first trimester of pregnancy when prenatal diagnosis is most relevant. MPs were derived from apoptosis and increased over 48 hours. Compared with necrotic MPs, DNA in apoptotic MPs was more fragmented and resistant to plasma DNases. Membrane-specific dyes indicated that apoptotic MPs had more membranous material, which protects nucleic acids, including RNA. Flow cytometry showed that MPs derived from dying cells displayed light scatter and DNA staining similar to MPs found in maternal plasma. Quantification of maternal MPs using characteristics defined by MPs generated in vitro revealed a significant increase of DNA+ MPs in the plasma of women with preeclampsia compared with plasma from women with normal pregnancies. Apoptotic MPs are therefore a likely source of stable DNA that could be enriched for both early genetic diagnosis and monitoring of pathological pregnancies. PMID:18974299

  9. Search algorithm for pattern match analysis of nucleic acid sequences.

    PubMed Central

    Harr, R; Häggström, M; Gustafsson, P

    1983-01-01

    A new type of search algorithm to find biological information inherited in nucleic acid sequences was developed. The algorithm is of pattern match type and is based on the fact that genetic information often is a function of a predictable statistical occurrence of the four bases within parts of the sequence. The search algorithm compares the known statistical pattern of bases in e.g. a promoter, with an unknown sequence and calculates the statistical significance of the match at all positions in the unknown sequence. The program was tested on 54 published prokaryotic promoters. 44 or 49 could be found with 1 or 4 false answers, respectively. The program was also used on plasmid pBR322. All promoters functioning in an in vitro transcription system were found (tet, anti-tet, p4, bla and ori) except the so called p5 promoter. A search for donor and acceptor sites was performed in a human HLA genomic sequence that contains six introns. Five of the possible six donor and acceptor sites were found. PMID:6344023

  10. Biolistic inoculation of plants with viroid nucleic acids.

    PubMed

    Matousek, J; Orctová, L; Steger, G; Riesner, D

    2004-12-15

    Parameters for biolistic transfer of viroid nucleic acids using a Helios Gene Gun device were assayed. The main achievement of this method is high efficiency of inoculation with linear monomeric viroid cDNAs and RNAs. This greatly facilitates the study of mutated sequence variants, viroid libraries and mixed populations. The lower limits for efficient inoculation of monomeric cDNA fragments with the sequence of potato spindle tuber viroid (PSTVd) and native PSTVd RNA as detected 21 days p.i. are in the range of 50 ng and 200 pg per tomato plant, respectively. At a higher dose, i.e. 2 ng of native RNA per plant, biolistic transfer causes drastic stunting compared to conventional mechanical inoculation, which points to higher PSTVd titers after the biolistic transfer. Infection is readily achieved with exact length monomeric RNA transcripts having 5'-triphosphate and 3'-OH termini in amounts ranging from 2 to 20 ng per plant, suggesting no need for any supplementary modifications of ends or RNA circularization. The biolistic transfer is efficient for viroid "thermomutants", which exhibit low or no infectivity with conventional mechanical inoculation with Carborundum. The biolistic inoculation is also efficient for two other members of the Pospiviroidae family, hop stunt and hop latent viroid. PMID:15542139

  11. Nucleic Acids for Ultra-Sensitive Protein Detection

    PubMed Central

    Janssen, Kris P. F.; Knez, Karel; Spasic, Dragana; Lammertyn, Jeroen

    2013-01-01

    Major advancements in molecular biology and clinical diagnostics cannot be brought about strictly through the use of genomics based methods. Improved methods for protein detection and proteomic screening are an absolute necessity to complement to wealth of information offered by novel, high-throughput sequencing technologies. Only then will it be possible to advance insights into clinical processes and to characterize the importance of specific protein biomarkers for disease detection or the realization of “personalized medicine”. Currently however, large-scale proteomic information is still not as easily obtained as its genomic counterpart, mainly because traditional antibody-based technologies struggle to meet the stringent sensitivity and throughput requirements that are required whereas mass-spectrometry based methods might be burdened by significant costs involved. However, recent years have seen the development of new biodetection strategies linking nucleic acids with existing antibody technology or replacing antibodies with oligonucleotide recognition elements altogether. These advancements have unlocked many new strategies to lower detection limits and dramatically increase throughput of protein detection assays. In this review, an overview of these new strategies will be given. PMID:23337338

  12. NUCLEIC ACIDS OF CHLOROPLASTS AND MITOCHONDRIA IN SWISS CHARD.

    PubMed

    KISLEV, N; SWIFT, H; BOGORAD, L

    1965-05-01

    Nucleic acids in young leaves of Swiss chard have been studied by light and electron microscope techniques. Leaf DNA has also been characterized by density gradient centrifugation and shown to contain a minor band of higher guanine plus cytosine (GC) content, presumably attributable to chloroplasts. The chloroplasts were faintly stained by the Feulgen reaction; radioautography demonstrated the incorporation of tritiated thymidine in the cytoplasm and in some nuclei. The Feulgen stainability and most of the radioactivity were removable with DNase. Under the electron microscope, both mitochondria and chloroplasts were found to contain filamentous and particulate components within the matrix areas. The morphology of the filamentous component was dependent on the fixation, being partially clumped after OSO(4) or formalin, but finely filamentous after Kellenberger fixation. The filaments were stainable with uranyl acetate, and were extractable with DNase following formalin fixation under conditions in which nuclear DNA was also extracted. The particulate component, after formalin fixation and uranyl staining, was prominent in chloroplasts from young leaves, but was only sparsely distributed in mitochondria. The stainability was removed with ribonuclease. We have concluded that chloroplasts and mitochondria of Swiss chard possess a filamentous component that contains DNA, probably responsible for both cytoplasmic thymidine incorporation and the minor band in CsCl centrifugation. A particulate ribosome-like component that contains RNA is also present. PMID:14287184

  13. Relevance of nucleic acid amplification techniques for diagnosis of respiratory tract infections in the clinical laboratory.

    PubMed Central

    Ieven, M; Goossens, H

    1997-01-01

    Clinical laboratories are increasingly receiving requests to perform nucleic acid amplification tests for the detection of a wide variety of infectious agents. In this paper, the efficiency of nucleic acid amplification techniques for the diagnosis of respiratory tract infections is reviewed. In general, these techniques should be applied only for the detection of microorganisms for which available diagnostic techniques are markedly insensitive or nonexistent or when turnaround times for existing tests (e.g., viral culture) are much longer than those expected with amplification. This is the case for rhinoviruses, coronaviruses, and hantaviruses causing a pulmonary syndrome, Bordetella pertussis, Chlamydia pneumoniae, Mycoplasma pneumoniae, and Coxiella burnetii. For Legionella spp. and fungi, contamination originating from the environment is a limiting factor in interpretation of results, as is the difficulty in differentiating colonization and infection. Detection of these agents in urine or blood by amplification techniques remains to be evaluated. In the clinical setting, there is no need for molecular diagnostic tests for the diagnosis of Pneumocystis carinii. At present, amplification methods for Mycobacterium tuberculosis cannot replace the classical diagnostic techniques, due to their lack of sensitivity and the absence of specific internal controls for the detection of inhibitors of the reaction. Also, the results of interlaboratory comparisons are unsatisfactory. Furthermore, isolates are needed for susceptibility studies. Additional work remains to be done on sample preparation methods, comparison between different amplification methods, and analysis of results. The techniques can be useful for the rapid identification of M. tuberculosis in particular circumstances, as well as the rapid detection of most rifampin-resistant isolates. The introduction of diagnostic amplification techniques into a clinical laboratory implies a level of proficiency for excluding false-positive and false-negative results. PMID:9105753

  14. Integration of On-chip Isotachophoresis and Functionalized Hydrogels for Enhanced-Sensitivity Nucleic Acid Detection

    E-print Network

    Santiago, Juan G.

    for Enhanced-Sensitivity Nucleic Acid Detection Giancarlo Garcia-Schwarz and Juan G. Santiago* Department% perchloric acid from Sigma-Aldrich (St. Louis, MO). We purchased the photoinitiator 2,2- azobis[2-methyl-N-(2-hydroxyethyl) propionamide] (VA-086) from Wako Chemicals (Richmond, VA). We also purchased hydrochloric acid

  15. Nucleic Acids Research, 2007, 19 doi:10.1093/nar/gkm623

    E-print Network

    Steve Kemp

    Nucleic Acids Research, 2007, 1­9 doi:10.1093/nar/gkm623 A systematic strategy for large within the Tir1 QTL region. Subsequent re-sequencing in Daxx identified a deletion of an amino acid subsequently changes the primary amino acid structure of the gene. In other cases the polymorphism may lie

  16. The interaction of poly(ethylenimine) with nucleic acids and its use in determination of nucleic acids based on light scattering

    Microsoft Academic Search

    Ying-lin Zhou; Yuan-zong Li

    2004-01-01

    For the first time, poly(ethylenimine) (PEI) was used to determine nucleic acids with a light scattering technique using a common spectrofluorometer. The interaction of PEI with DNA results in greatly enhanced intensity of light scattering at 300 nm, which is caused by the formation of the big particles between DNA and PEI. Based on this, a new quantitative method for

  17. Determination of a universal nucleic acid extraction procedure for PCR detection of gastroenteritis viruses in faecal specimens

    Microsoft Academic Search

    Nassar B. G Rasool; Stephan S Monroe; Roger I Glass

    2002-01-01

    Four nucleic acid extraction protocols were examined for their suitability for extraction of the ssRNA, dsRNA and dsDNA genomes of gastroenteritis viruses, for PCR detection. Protocol (A), employed specimen lysis with guanidinium thiocyanate, extraction with phenol–chloroform–isoamyl alcohol and nucleic acid purification by size-fractionated silica particles. Protocol (B), utilised specimen lysis with guanidinium thiocyanate and nucleic acid purification by silica, followed

  18. Rapid and Sensitive Determination of Nucleic Acids by Enhanced Resonance Light Scattering Spectroscopy of Tetraphenyl Porphyrin Cobalt(II)Chloride

    Microsoft Academic Search

    Zhanguang Chen; Jinbin Liu; Fenglian Ren; Weifeng Ding

    2006-01-01

    A novel probe, tetraphenyl porphyrin Cobalt(II)chloride (CoTPPCl), was first developed for the determination of nucleic acids at a nanogram level by a resonance light scattering (RLS) technique. Under optimum conditions, the weak RLS signal of CoTPPCl was enhanced greatly by nucleic acids at 444.0 nm; the enhanced RLS intensity is proportional to the concentration of nucleic acids in the range of

  19. [Genotoxic modification of nucleic acid bases and biological consequences of it. Review and prospects of experimental and computational investigations

    NASA Technical Reports Server (NTRS)

    Poltev, V. I.; Bruskov, V. I.; Shuliupina, N. V.; Rein, R.; Shibata, M.; Ornstein, R.; Miller, J.

    1993-01-01

    The review is presented of experimental and computational data on the influence of genotoxic modification of bases (deamination, alkylation, oxidation) on the structure and biological functioning of nucleic acids. Pathways are discussed for the influence of modification on coding properties of bases, on possible errors of nucleic acid biosynthesis, and on configurations of nucleotide mispairs. The atomic structure of nucleic acid fragments with modified bases and the role of base damages in mutagenesis and carcinogenesis are considered.

  20. Cationic Lipid-Nucleic Acid Complexes (Lipoplexes): from Physicochemical Properties to In Vitro and In Vivo Transfection Kits

    Microsoft Academic Search

    Dmitri Simberg; Danielle Hirsch-Lerner; Nicolaas-Jan Zuidam; Simcha Even-Chen; Miryam Kerner; Hagit Eliyahu; Natalie Servel; Sarah Weisman; Alla Plis-Finarov; Yeshayahu Talmon; Yechezkel Barenholz

    \\u000a Lipoplexes are complexes formed spontaneously upon mixing of negatively charged nucleic acids (or other polyelectrolytes such\\u000a as proteins) with positively-charged lipid assemblies [1]( for definitions see [2]). The relevant nucleic acids include plasmid DNA (pDNA), linear DNA, single chain DNA, oligonucleotide (ODN), messenger\\u000a RNA, and silencing double stranded short RNA (siRNA) [1–3] The lipoplex-mediated nucleic acid delivery appears to be

  1. NAIL: Nucleic Acid detection using Isotachophoresis and Loop-mediated isothermal amplification.

    PubMed

    Borysiak, Mark D; Kimura, Kevin W; Posner, Jonathan D

    2015-04-01

    Nucleic acid amplification tests are the gold standard for many infectious disease diagnoses due to high sensitivity and specificity, rapid operation, and low limits of detection. Despite the advantages of nucleic acid amplification tests, they currently offer limited point-of-care (POC) utility due to the need for complex instruments and laborious sample preparation. We report the development of the Nucleic Acid Isotachophoresis LAMP (NAIL) diagnostic device. NAIL uses isotachophoresis (ITP) and loop-mediated isothermal amplification (LAMP) to extract and amplify nucleic acids from complex matrices in less than one hour inside of an integrated chip. ITP is an electrokinetic separation technique that uses an electric field and two buffers to extract and purify nucleic acids in a single step. LAMP amplifies nucleic acids at constant temperature and produces large amounts of DNA that can be easily detected. A mobile phone images the amplification results to eliminate the need for laser fluorescent detection. The device requires minimal user intervention because capillary valves and heated air chambers act as passive valves and pumps for automated fluid actuation. In this paper, we describe NAIL device design and operation, and demonstrate the extraction and detection of pathogenic E. coli O157:H7 cells from whole milk samples. We use the Clinical and Laboratory Standards Institute (CLSI) limit of detection (LoD) definitions that take into account the variance from both positive and negative samples to determine the diagnostic LoD. According to the CLSI definition, the NAIL device has a limit of detection (LoD) of 1000 CFU mL(-1) for E. coli cells artificially inoculated into whole milk, which is two orders of magnitude improvement to standard tube-LAMP reactions with diluted milk samples and comparable to lab-based methods. The NAIL device potentially offers significant reductions in the complexity and cost of traditional nucleic acid diagnostics for POC applications. PMID:25666345

  2. Experimental characterization of the human non-sequence-specific nucleic acid interactome

    PubMed Central

    2013-01-01

    Background The interactions between proteins and nucleic acids have a fundamental function in many biological processes, including gene transcription, RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins that bind individual mRNAs in mammalian cells has been greatly augmented by recent surveys, no systematic study on the non-sequence-specific engagement of native human proteins with various types of nucleic acids has been reported. Results We designed an experimental approach to achieve broad coverage of the non-sequence-specific RNA and DNA binding space, including methylated cytosine, and tested for interaction potential with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high-confidence direct binders, 139 of which were novel and 237 devoid of previous experimental evidence. We could assign specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and individual domains. The evolutionarily conserved protein YB-1, previously associated with cancer and drug resistance, was shown to bind methylated cytosine preferentially, potentially conferring upon YB-1 an epigenetics-related function. Conclusions The dataset described here represents a rich resource of experimentally determined nucleic acid-binding proteins, and our methodology has great potential for further exploration of the interface between the protein and nucleic acid realms. PMID:23902751

  3. Multiplexed analysis of genes using nucleic acid-stabilized silver-nanocluster quantum dots.

    PubMed

    Enkin, Natalie; Wang, Fuan; Sharon, Etery; Albada, H Bauke; Willner, Itamar

    2014-11-25

    Luminescent nucleic acid-stabilized Ag nanoclusters (Ag NCs) are applied for the optical detection of DNA and for the multiplexed analysis of genes. Two different sensing modules including Ag NCs as luminescence labels are described. One sensing module involves the assembly of a three-component sensing module composed of a nucleic acid-stabilized Ag NC and a quencher-modified nucleic acid hybridized with a nucleic acid scaffold that is complementary to the target DNA. The luminescence of the Ag NCs is quenched in the sensing module nanostructure. The strand displacement of the scaffold by the target DNA separates the nucleic acid-functionalized Ag NCs, leading to the turned-on luminescence of the NCs and to the optical readout of the sensing process. By implementing two different-sized Ag NC-modified sensing modules, the parallel multiplexed analysis of two genes (the Werner Syndrome gene and the HIV, human immunodeficiency, gene), using 615 and 560 nm luminescent Ag NCs, is demonstrated. The second sensing module includes the nucleic acid functionalized Ag NCs and the quencher-modified nucleic acid hybridized with a hairpin DNA scaffold. The luminescence of the Ag NCs is quenched in the sensing module. Opening of the hairpin by the target DNA triggers the luminescence of the Ag NCs, due to the spatial separation of the Ag NCs/quencher units. The system is applied for the optical detection of the BRAC1 gene. In addition, by implementing two-sized Ag NCs, the multiplexed analysis of two genes by the hairpin sensing module approach is demonstrated. PMID:25327411

  4. Chance and necessity in the selection of nucleic acid catalysts

    NASA Technical Reports Server (NTRS)

    Lorsch, J. R.; Szostak, J. W.

    1996-01-01

    In Tom Stoppard's famous play [Rosencrantz and Guildenstern are Dead], the ill-fated heroes toss a coin 101 times. The first 100 times they do so the coin lands heads up. The chance of this happening is approximately 1 in 10(30), a sequence of events so rare that one might argue that it could only happen in such a delightful fiction. Similarly rare events, however, may underlie the origins of biological catalysis. What is the probability that an RNA, DNA, or protein molecule of a given random sequence will display a particular catalytic activity? The answer to this question determines whether a collection of such sequences, such as might result from prebiotic chemistry on the early earth, is extremely likely or unlikely to contain catalytically active molecules, and hence whether the origin of life itself is a virtually inevitable consequence of chemical laws or merely a bizarre fluke. The fact that a priori estimates of this probability, given by otherwise informed chemists and biologists, ranged from 10(-5) to 10(-50), inspired us to begin to address the question experimentally. As it turns out, the chance that a given random sequence RNA molecule will be able to catalyze an RNA polymerase-like phosphoryl transfer reaction is close to 1 in 10(13), rare enough, to be sure, but nevertheless in a range that is comfortably accessible by experiment. It is the purpose of this Account to describe the recent advances in combinatorial biochemistry that have made it possible for us to explore the abundance and diversity of catalysts existing in nucleic acid sequence space.

  5. Remote Enantioselection Transmitted by an Achiral Peptide Nucleic Acid Backbone

    NASA Technical Reports Server (NTRS)

    Kozlov, Igor A.; Orgel, Leslie E.; Nielsen, Peter E.

    2000-01-01

    short homochiral segment of DNA into a PNA helix could have guaranteed that the next short segment of DNA to be incorporated would have the same handedness as the first. Once two segments of the same handedness were present, the probability that a third segment would have the same handedness would increase, and so on. Evolution could then slowly dilute out the PNA part. This scenario would ultimately allow the formation of a chiral oligonucleotide by processes that are largely resistant to enantiomeric crossinhibition. It is important to note that the ligation of homochiral dinucleotides on a nucleic acid template would probably be at least as enantiospecific as the reaction that we have studied. The disadvantage of using chiral monomers as components of a replicating system arises from the difficulty of generating a first long homochiral template from a racemic mixture of monomers, although results of experiments designed to overcome this difficulty by employing homochiral tetramers have been reported.l l The probability of obtaining a homochiral n-mer from achiral substrates is approximately 1P-I if the nontemplate-directed extension of the primer is not enantioselective. Hence, it would be very hard to get started with a homochiral 40-mer, for example. No such difficulty exists in a scenario that originates with an achiral genetic material and in which the incorporation of very few chiral monomers in this achiral background gradually progresses towards homochirality. It seems possible that some PNA sequences could act as catalysts, analogous to ribozymes, even though PNA lacks clear metal binding sites. Although such catalysts could not be enantioselective, the incorporation of as few as two chiral nucleotides could then impose chiral specificity on the system. Furthermore, such patch chimeras could help to bridge the gap in catalytic potential between PNA and RNA, while guaranteeing enantioselectivity.

  6. Variables Influencing Extraction of Nucleic Acids from Microbial Plankton (Viruses, Bacteria, and Protists) Collected on Nanoporous Aluminum Oxide Filters

    PubMed Central

    Mueller, Jaclyn A.; Culley, Alexander I.

    2014-01-01

    Anodic aluminum oxide (AAO) filters have high porosity and can be manufactured with a pore size that is small enough to quantitatively capture viruses. These properties make the filters potentially useful for harvesting total microbial communities from water samples for molecular analyses, but their performance for nucleic acid extraction has not been systematically or quantitatively evaluated. In this study, we characterized the flux of water through commercially produced nanoporous (0.02 ?m) AAO filters (Anotop; Whatman) and used isolates (a virus, a bacterium, and a protist) and natural seawater samples to test variables that we expected would influence the efficiency with which nucleic acids are recovered from the filters. Extraction chemistry had a significant effect on DNA yield, and back flushing the filters during extraction was found to improve yields of high-molecular-weight DNA. Using the back-flush protocol, the mass of DNA recovered from microorganisms collected on AAO filters was ?100% of that extracted from pellets of cells and viruses and 94% ± 9% of that obtained by direct extraction of a liquid bacterial culture. The latter is a minimum estimate of the relative recovery of microbial DNA, since liquid cultures include dissolved nucleic acids that are retained inefficiently by the filter. In conclusion, we demonstrate that nucleic acids can be extracted from microorganisms on AAO filters with an efficiency similar to that achievable by direct extraction of microbes in suspension or in pellets. These filters are therefore a convenient means by which to harvest total microbial communities from multiple aqueous samples in parallel for subsequent molecular analyses. PMID:24747903

  7. Diagnostic Value of Monitoring Human Cytomegalovirus Late pp67 mRNA Expression in Renal-Allograft Recipients by Nucleic Acid Sequence-Based Amplification

    Microsoft Academic Search

    MARINUS J. BLOK; VALERE J. GOOSSENS; SABINA J. V. VANHERLE; BERT TOP; NICOLE TACKEN; JAAP M. MIDDELDORP; MAARTEN H. L. CHRISTIAANS; JOHANNES P. VAN HOOFF; CATHRIEN A. BRUGGEMAN

    1998-01-01

    The diagnostic value of monitoring human cytomegalovirus (HCMV) late pp67 mRNA expression by nucleic acid sequence-based amplification (NASBA) after renal-allograft transplantation was evaluated. RNAs were isolated from 489 whole-blood specimens of 42 patients for the specific amplification of the late pp67 (UL65) mRNA. NASBA results were compared to results from the pp65 antigenemia assay, virus isolation by cell culture, and

  8. Nucleic acid-induced antiviral immunity in invertebrates: an evolutionary perspective.

    PubMed

    Wang, Pei-Hui; Weng, Shao-Ping; He, Jian-Guo

    2015-02-01

    Nucleic acids derived from viral pathogens are typical pathogen associated molecular patterns (PAMPs). In mammals, the recognition of viral nucleic acids by pattern recognition receptors (PRRs), which include Toll-like receptors (TLRs) and retinoic acid-inducible gene (RIG)-I-like receptors (RLRs), induces the release of inflammatory cytokines and type I interferons (IFNs) through the activation of nuclear factor ?B (NF-?B) and interferon regulatory factor (IRF) 3/7 pathways, triggering the host antiviral state. However, whether nucleic acids can induce similar antiviral immunity in invertebrates remains ambiguous. Several studies have reported that nucleic acid mimics, especially dsRNA mimic poly(I:C), can strongly induce non-specific antiviral immune responses in insects, shrimp, and oyster. This behavior shows multiple similarities to the hallmarks of mammalian IFN responses. In this review, we highlight the current understanding of nucleic acid-induced antiviral immunity in invertebrates. We also discuss the potential recognition and regulatory mechanisms that confer non-specific antiviral immunity on invertebrate hosts. PMID:24685509

  9. Biomedical publications of Prof. David N. Nikogosyan, made in UCC UV-induced nucleic acid-protein cross-linking

    E-print Network

    Nikogosyan, David N.

    Biomedical publications of Prof. David N. Nikogosyan, made in UCC UV-induced nucleic acid-protein cross-linking 1. E.N. Dobrov, D.N. Nikogosyan: UV-induced nucleic acid-protein cross-linking: manual acids in collagen. J. Photochem. Photobiol. B: Biol., 47(1), 63-67 (1998) 2. D.N. Nikogosyan, H. Görner

  10. Influence of Plasma Processing on Recovery and Analysis of Circulating Nucleic Acids

    PubMed Central

    Zahra, Nathalie; Primrose, Lindsay; Elshaw, Shona R.; Pringle, J. Howard; Blighe, Kevin; Marchese, Stephanie D.; Hills, Allison; Woodley, Laura; Stebbing, Justin; Coombes, R. Charles; Shaw, Jacqueline A.

    2013-01-01

    Circulating nucleic acids (CNAs) are under investigation as a liquid biopsy in cancer. However there is wide variation in blood processing and methods for isolation of circulating free DNA (cfDNA) and microRNAs (miRNAs). Here we compare the extraction efficiency and reproducibility of 4 commercially available kits for cfDNA and 3 for miRNA using spike-in of reference templates. We also compare the effects of increasing time between venepuncture and centrifugation and differential centrifugation force on recovery of CNAs. cfDNA was quantified by TaqMan qPCR and targeted deep sequencing. miRNA profiles were assessed with TaqMan low-density arrays and assays. The QIAamp® DNA Blood Mini and Circulating nucleic acid kits gave the highest recovery of cfDNA and efficient recovery (>90%) of a 564bp spike-in. Moreover, targeted sequencing revealed overlapping cfDNA profiles and variant depth, including detection of HER2 gene amplification, using the Ion AmpliSeq™Cancer Hotspot Panel v2. Highest yields of miRNA and the synthetic Arabidopsis thaliana miR-159a spike-in were obtained using the miRNeasy Serum/Plasma kit, with saturation above 200 µl of plasma. miRNA profiles showed significant variation with increasing time before centrifugation (p<0.001) and increasing centrifugation force, with depletion of platelet associated miRNAs, whereas cfDNA was unaffected. However, sample replicates showed excellent reproducibility on TaqMan low density arrays (? = 0.96, p<0.0001). We also successfully generated miRNA profiles for plasma samples stored > 12 years, highlighting the potential for analysis of stored sample biobanks. In the era of the liquid biopsy, standardisation of methods is required to minimise variation, particularly for miRNA. PMID:24205045

  11. Adsorption of Nucleic Acid Components on Rutile (TiO2) Surfaces

    NASA Astrophysics Data System (ADS)

    Cleaves, H. James; Jonsson, Caroline M.; Jonsson, Christopher L.; Sverjensky, Dimitri A.; Hazen, Robert M.

    2010-04-01

    Nucleic acids, the storage molecules of genetic information, are composed of repeating polymers of ribonucleotides (in RNA) or deoxyribonucleotides (in DNA), which are themselves composed of a phosphate moiety, a sugar moiety, and a nitrogenous base. The interactions between these components and mineral surfaces are important because there is a tremendous flux of nucleic acids in the environment due to cell death and horizontal gene transfer. The adsorption of mono-, oligo-, and polynucleotides and their components on mineral surfaces may have been important for the origin of life. We have studied here interactions of nucleic acid components with rutile (TiO2), a mineral common in many terrestrial crustal rocks. Our results suggest roles for several nucleic acid functional groups (including sugar hydroxyl groups, the phosphate group, and extracyclic functional groups on the bases) in binding, in agreement with results obtained from studies of other minerals. In contrast with recent studies of nucleotide adsorption on ZnO, aluminum oxides, and hematite, our results suggest a different preferred orientation for the monomers on rutile surfaces. The conformations of the molecules bound to rutile surfaces appear to favor specific interactions, which in turn may allow identification of the most favorable mineral surfaces for nucleic acid adsorption.

  12. Nano-vectors for the Ocular Delivery of Nucleic Acid-based Therapeutics

    PubMed Central

    Khar, R. K.; Jain, G. K.; Warsi, M. H.; Mallick, N.; Akhter, S; Pathan, S. A.; Ahmad, F. J.

    2010-01-01

    Nucleic acid-based therapeutics have gained a lot of interest for the treatment of diverse ophthalmic pathologies. The first to enter in clinic has been an oligonucleotide, Vitravene® for the treatment of cytomegalovirus infection. More recently, research on aptamers for the treatment of age related macular degeneration has led to the development of Macugen®. Despite intense potential, effective ocular delivery of nucleic acids is a major challenge since therapeutic targets for nucleic acid-based drugs are mainly located in the posterior eye segment, requiring repeated invasive administration. Of late, nanotechnology-based nano-vectors have been developed in order to overcome the drawbacks of viral and other non-viral vectors. The diversity of nano-vectors allows for ease of use, flexibility in application, low-cost of production, higher transfection efficiency and enhanced genomic safety. Using nano-vector strategies, nucleic acids can be delivered either encapsulated or complexed with cationic lipids, polymers or peptides forming sustained release systems, which can be tailored according to the ocular tissue being targeted. The present review focuses on developments and advances in various nano-vectors for the ocular delivery of nucleic acid-based therapeutics, the barriers that such delivery systems face and methods to overcome them. PMID:21969738

  13. Cationic liposome-nucleic acid complexes: liquid crystal phases with applications in gene therapy

    PubMed Central

    Safinya, C. R.; Ewert, K. K.; Leal, Cecília

    2011-01-01

    Cationic liposome (CL) carriers of nucleic acids are primarily studied because of their applications in gene delivery and gene silencing with CL-DNA and CL-siRNA (short-interfering RNA) complexes, respectively, and their implications to ongoing clinical gene therapy trials worldwide. A series of synchrotron-based small-angle-x-ray scattering studies, dating back to 1997, has revealed that CL-nucleic acid complexes spontaneously assemble into distinct novel liquid crystalline phases of matter. Significantly, transfection efficiency (TE; a measure of expression of an exogenous gene that is transferred into the cell by the lipid carrier) has been found to be dependent on the liquid crystalline structure of complexes, with lamellar complexes showing strong dependence on membrane charge density (?M) and non-lamellar complexes exhibiting TE behavior independent of?M. The review describes our current understanding of the structures of different liquid crystalline CL-nucleic acid complexes including the recently described gyroid cubic phase of CL-siRNA complexes used in gene silencing. It further makes apparent that the long-term goal of developing optimized liquid crystalline CL-nucleic acid complexes for successful medical applications requires a comprehensive understanding of the nature of the interactions of distinctly structured complexes with cell membranes and events leading to release of active nucleic acids within the cell cytoplasm. PMID:22778490

  14. Nucleic acid/quantum dots (QDs) hybrid systems for optical and photoelectrochemical sensing.

    PubMed

    Freeman, Ronit; Girsh, Julia; Willner, Itamar

    2013-04-24

    Nucleic acid/semiconductor quantum dots (QDs) hybrid systems combine the recognition and catalytic properties of nucleic acids with the unique photophysical features of QDs. These functions of nucleic acid/QDs hybrids are implemented to develop different optical sensing platforms for the detection of DNA, aptamer-substrate complexes, and metal ions. Different photophysical mechanisms including fluorescence, electron transfer quenching, fluorescence resonance energy transfer (FRET), and chemiluminescence resonance energy transfer (CRET) are used to develop the sensor systems. The size-controlled luminescence properties of QDs are further implemented for the multiplexed, parallel analysis of several DNAs, aptamer-substrate complexes, or mixtures of ions. Similarly, methods to amplify the sensing events through the biocatalytic regeneration of the analyte were developed. An additional paradigm in the implementation of nucleic acid/QDs hybrids for sensing applications involves the integration of the systems with electrodes, and the generation of photocurrents as transduction signals for the sensing events. Finally, semiconductor QDs conjugated to functional DNA machines, such as "walker" systems, provide an effective optical label for probing the dynamics and mechanical functions of the molecular devices. The present article addresses the recent advances in the application of nucleic acid/QDs hybrids for sensing applications and DNA nanotechnology, and discusses future perspectives of these hybrid materials. PMID:23425022

  15. Nucleic Acids Research, 2014 1 doi: 10.1093/nar/gku1059

    E-print Network

    Akhmedov, Azer

    Nucleic Acids Research, 2014 1 doi: 10.1093/nar/gku1059 KnotProt: a database of proteins with knots protein and permits users to determine, for example, the minimal length of the knotted regions (knot's core size) or the depth of a knot, i.e. how many amino acids can be removed from either end

  16. Fluorescence enhancement of yttrium(III)-rutin by nucleic acids in the presence of cetyltrimethylammonium bromide

    NASA Astrophysics Data System (ADS)

    Wu, Xia; Guo, Changying; Wang, Fei; Yang, Jinghe; Ran, Dehuan; Zheng, Jinhua; Wu, Jinbo

    2006-11-01

    It is found that nucleic acids can enhance the fluorescence intensity of yttrium(III) (Y 3+)-rutin in presence of cetyltrimethylammonium bromide (CTMAB) system. In hexamethylenetetramine (HMTA)-HCl buffer, the maximum enhanced fluorescence is produced, with maximum excitation and emission wavelengths at 452 and 520 nm, respectively. Based on this, a new fluorimetric method of determination of nucleic acids is proposed. Under optimum conditions, the enhanced fluorescence intensity is proportion to the concentration of nucleic acids in the range of 1.0 × 10 -7 to 1.0 × 10 -5 g/ml for fish sperm DNA (fsDNA), 1.0 × 10 -7 to 4.6 × 10 -6 g/ml for yeast RNA (yRNA), their detection limits (S/N = 3) are 7.5 × 10 -8, 8.0 × 10 -8 g/ml, respectively. The interaction mechanism is also studied.

  17. Advances in polymeric and inorganic vectors for nonviral nucleic acid delivery

    PubMed Central

    Sunshine, Joel C; Bishop, Corey J; Green, Jordan J

    2014-01-01

    Nonviral systems for nucleic acid delivery offer a host of potential advantages compared with viruses, including reduced toxicity and immunogenicity, increased ease of production and less stringent vector size limitations, but remain far less efficient than their viral counterparts. In this article we review recent advances in the delivery of nucleic acids using polymeric and inorganic vectors. We discuss the wide range of materials being designed and evaluated for these purposes while considering the physical requirements and barriers to entry that these agents face and reviewing recent novel approaches towards improving delivery with respect to each of these barriers. Furthermore, we provide a brief overview of past and ongoing nonviral gene therapy clinical trials. We conclude with a discussion of multifunctional nucleic acid carriers and future directions. PMID:22826857

  18. Salt Contribution to the Flexibility of Single-stranded Nucleic Acid of Finite Length

    E-print Network

    Wang, Feng-Hua; Tan, Zhi-Jie

    2012-01-01

    Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this paper, the salt effects on the flexibility of single stranded (ss) nucleic acid chain ranging from 12 to 120 nucleotides are investigated systematically by the coarse grained Monte Carlo simulations where the salt ions are considered explicitly and the ss chain is modeled with the virtual bond structural model. Our calculations show that, the increase of ion concentration causes the structural collapse of ss chain and multivalent ions are much more efficient in causing such collapse, and trivalent and small divalent ions can both induce more compact state than a random relaxation state. We found that monovalent, divalent and trivalent ions can all overcharge ss chain, and the dominating source for such overcharging changes from ion exclusion volume effect to ion Coulomb correlations. In addition, the predicted Na and Mg dependent persistence length lp of ss nucleic acid a...

  19. Spherical Nucleic Acid Nanoparticle Conjugates Enhance G-Quadruplex Formation and Increase Serum Protein Interactions**

    PubMed Central

    Chinen, Alyssa B.; Guan, Chenxia M.

    2014-01-01

    To understand the effect of three-dimensional oligonucleotide structure on protein corona formation, we studied the identity and quantity of human serum proteins that bind to spherical nucleic acid (SNA) nanoparticle conjugates. SNAs exhibit cellular uptake properties that are remarkably different from those of linear nucleic acids, which have been related to their interaction with certain classes of proteins. Through a proteomic analysis, this work shows that the protein binding properties of SNAs are sequence-specific and supports the conclusion that the oligonucleotide tertiary structure can significantly alter the chemical composition of the SNA protein corona. This knowledge will impact our understanding of how nucleic acid-based nanostructures, and SNAs in particular, function in complex biological milieu. PMID:25393322

  20. Templated Synthesis of Peptide Nucleic Acids via Sequence-Selective Base-Filling Reactions

    PubMed Central

    2009-01-01

    The templated synthesis of nucleic acids has previously been achieved through the backbone ligation of preformed nucleotide monomers or oligomers. In contrast, here we demonstrate templated nucleic acid synthesis using a base-filling approach in which individual bases are added to abasic sites of a peptide nucleic acid (PNA). Because nucleobase substrates in this approach are not self-reactive, a base-filling approach may reduce the formation of nontemplated reaction products. Using either reductive amination or amine acylation chemistries, we observed efficient and selective addition of each of the four nucleobases to an abasic site in the middle of the PNA strand. We also describe the addition of single nucleobases to the end of a PNA strand through base filling, as well as the tandem addition of two bases to the middle of the PNA strand. These findings represent an experimental foundation for nonenzymatic information transfer through base filling. PMID:19722647

  1. Beyond DNA origami: A look on the bright future of nucleic acid nanotechnology

    PubMed Central

    Michelotti, Nicole; Johnson-Buck, Alexander; Manzo, Anthony J.

    2012-01-01

    Nucleic acid nanotechnology exploits the programmable molecular recognition properties of natural and synthetic nucleic acids to assemble structures with nanometer-scale precision. In 2006, DNA origami transformed the field by providing a versatile platform for self-assembly of arbitrary shapes from one long DNA strand held in place by hundreds of short, site-specific (spatially addressable) DNA ”staples”. This revolutionary approach has led to the creation of a multitude of 2D and 3D scaffolds that form the basis for functional nanodevices. Not limited to nucleic acids, these nanodevices can incorporate other structural and functional materials, such as proteins and nanoparticles, making them broadly useful for current and future applications in emerging fields such as nanomedicine, nanoelectronics, and alternative energy. PMID:22131292

  2. Microwell array-mediated delivery of lipoplexes containing nucleic acids for enhanced therapeutic efficacy.

    PubMed

    Wu, Yun; Gallego-Perez, Daniel; Lee, L James

    2015-01-01

    Many delivery methods have been developed to improve the therapeutic efficacy and facilitate the clinical translation of nucleic acids-based therapeutics. We present a facile microwell array to mediate the delivery of nucleic acids carried by lipoplexes, which combines the advantages of lipoplexes as an efficient carrier system, the surface mediated delivery, and the control of surface topography. This method shows much higher transfection efficiency than conventional transfection method for oligodeoxynucleotides and microRNAs, and thus significantly reduces the effective therapeutic dosages. Microwell array is also a very flexible platform. Multifunctional lipoplexes containing both nucleic acid therapeutics and imaging reagents can be easily prepared in the microwell array and efficiently delivered to cells, demonstrating its potential applications in theranostic medicine. PMID:25319649

  3. Development of Chemiluminescent Lateral Flow Assay for the Detection of Nucleic Acids

    PubMed Central

    Wang, Yuhong; Fill, Catherine; Nugen, Sam R.

    2012-01-01

    Rapid, sensitive detection methods are of utmost importance for the identification of pathogens related to health and safety. Herein we report the development of a nucleic acid sequence-based lateral flow assay which achieves a low limit of detection using chemiluminescence. On-membrane enzymatic signal amplification is used to reduce the limit of detection to the sub-femtomol level. To demonstrate this assay, we detected synthetic nucleic acid sequences representative of Trypanosoma mRNA, the causative agent for African sleeping sickness, with relevance in human and animal health in sub-Saharan Africa. The intensity of the chemiluminescent signal was evaluated by using a charge-coupled device as well as a microtiter plate reader. We demonstrated that our lateral flow chemiluminescent assay has a very low limit of detection and is easy to use. The limit of detection was determined to be 0.5 fmols of nucleic acid target. PMID:25585630

  4. Nucleic-acid-binding properties of the C2-L1Tc nucleic acid chaperone encoded by L1Tc retrotransposon.

    PubMed

    Heras, Sara R; Thomas, M Carmen; Macias, Francisco; Patarroyo, Manuel E; Alonso, Carlos; López, Manuel C

    2009-12-15

    It has been reported previously that the C2-L1Tc protein located in the Trypanosoma cruzi LINE (long interspersed nuclear element) L1Tc 3' terminal end has NAC (nucleic acid chaperone) activity, an essential activity for retrotransposition of LINE-1. The C2-L1Tc protein contains two cysteine motifs of a C2H2 type, similar to those present in TFIIIA (transcription factor IIIA). The cysteine motifs are flanked by positively charged amino acid regions. The results of the present study show that the C2-L1Tc recombinant protein has at least a 16-fold higher affinity for single-stranded than for double-stranded nucleic acids, and that it exhibits a clear preference for RNA binding over DNA. The C2-L1Tc binding profile (to RNA and DNA) corresponds to a non-co-operative-binding model. The zinc fingers present in C2-L1Tc have a different binding affinity to nucleic acid molecules and also different NAC activity. The RRR and RRRKEK [NLS (nuclear localization sequence)] sequences, as well as the C2H2 zinc finger located immediately downstream of these basic stretches are the main motifs responsible for the strong affinity of C2-L1Tc to RNA. These domains also contribute to bind single- and double-stranded DNA and have a duplex-stabilizing effect. However, the peptide containing the zinc finger situated towards the C-terminal end of C2-L1Tc protein has a slight destabilization effect on a mismatched DNA duplex and shows a strong preference for single-stranded nucleic acids, such as C2-L1Tc. These results provide further insight into the essential properties of the C2-L1Tc protein as a NAC. PMID:19751212

  5. Nucleic-acid-binding properties of the C2-L1Tc nucleic acid chaperone encoded by L1Tc retrotransposon

    PubMed Central

    Heras, Sara R.; Thomas, M. Carmen; Macias, Francisco; Patarroyo, Manuel E.; Alonso, Carlos; López, Manuel C.

    2009-01-01

    It has been reported previously that the C2-L1Tc protein located in the Trypanosoma cruzi LINE (long interspersed nuclear element) L1Tc 3? terminal end has NAC (nucleic acid chaperone) activity, an essential activity for retrotransposition of LINE-1. The C2-L1Tc protein contains two cysteine motifs of a C2H2 type, similar to those present in TFIIIA (transcription factor IIIA). The cysteine motifs are flanked by positively charged amino acid regions. The results of the present study show that the C2-L1Tc recombinant protein has at least a 16-fold higher affinity for single-stranded than for double-stranded nucleic acids, and that it exhibits a clear preference for RNA binding over DNA. The C2-L1Tc binding profile (to RNA and DNA) corresponds to a non-co-operative-binding model. The zinc fingers present in C2-L1Tc have a different binding affinity to nucleic acid molecules and also different NAC activity. The RRR and RRRKEK [NLS (nuclear localization sequence)] sequences, as well as the C2H2 zinc finger located immediately downstream of these basic stretches are the main motifs responsible for the strong affinity of C2-L1Tc to RNA. These domains also contribute to bind single- and double-stranded DNA and have a duplex-stabilizing effect. However, the peptide containing the zinc finger situated towards the C-terminal end of C2-L1Tc protein has a slight destabilization effect on a mismatched DNA duplex and shows a strong preference for single-stranded nucleic acids, such as C2-L1Tc. These results provide further insight into the essential properties of the C2-L1Tc protein as a NAC. PMID:19751212

  6. Determination of nucleic acid by its enhancement effect on the fluorescence of Ellagic acid – Cationic surfactant system

    Microsoft Academic Search

    Feng Wang; Wei Huang; Yanwei Wang; Bo Tang

    2010-01-01

    In this paper, nucleic acid can greatly enhance the fluorescence of Ellagic acid (EA) in the presence of cetylpyridine bromide (CPB). Experiments indicate that under the optimum conditions, the enhanced intensity of fluorescence is proportional to the concentration of nucleic acid in the range of 5.0×10?9–3.5×10?5gmL?1 for hsDNA, 5.0×10?9–3.5×10?5gmL?1 for ctDNA and 5.0×10?9–3.5×10?5gmL?1 for yRNA. Their detection limits (S\\/N=3) are

  7. Detecting and genotyping Escherichia coli O157:H7 using multiplexed PCR and nucleic acid microarrays

    SciTech Connect

    Call, Douglas R.; Brockman, Fred J.; Chandler, Darrell P.

    2001-07-05

    Rapid detection and characterization of food borne pathogens such as Escherichia coli O157:H7 is crucial for epidemiological investigations and food safety surveillance. As an alternative to conventional technologies, we examined the sensitivity and specificity of nucleic acid microarrays for detecting and genotyping E. coli O157:H7. The array was composed of oligonucleotide probes (25-30 mer) complementary to four virulence loci (intimin, Shiga-like toxins I and II, and hemolysin A). Target DNA was amplified from whole cells or from purified DNA via single or multiplexed polymerase chain reaction (PCR), and PCR products were hybridized to the array without further modification or purification. The array was 32-fold more sensitive than gel electrophoresis and capable of detecting amplification products from < 1 cell equivalent of genomic DNA (1 fg). Immunomagnetic capture, PCR and a microarray were subsequently used to detect 55 CFUs ml-1 (E. coli O157:H7) from chicken rinsate without the aid of pre-enrichment. Four isolates of E. coli O157:H7 and one isolate of O91:H2, for which genotypic data were available, were unambiguously genotyped with this array. Glass based microarrays are relatively simple to construct and provide a rapid and sensitive means to detect multiplexed PCR products and the system is amenable to automation.

  8. Detecting and Genotyping Escherichia coli O157:H7 using multiplexed PCR and nucleic acid microarrays

    SciTech Connect

    Call, Douglas R. (Michigan, Univ Of - Ann Arbor); Brockman, Fred J. (BATTELLE (PACIFIC NW LAB)); Chandler, Darrell P. (Pacific Northwest National Laboratory)

    2000-12-01

    Rapid detection and characterization of food borne pathogens such as Escherichia coli O157:H7 is crucial for epidemiological investigations and food safety surveillance. As an alternative to conventional technologies, we examined the sensitivity and specificity of nucleic acid microarrays for detecting and genotyping E. coli O157:H7. The array was composed of oligonucleotide probes (25-30 mer) complementary to four virulence loci (intimin, Shiga-like toxins I and II, and hemolysin A). Target DNA was amplified from whole cells or from purified DNA via single or multiplexed polymerase chain reaction (PCR), and PCR products were hybridized to the array without further modification or purification. The array was 32-fold more sensitive than gel electrophoresis and capable of detecting amplification products from < 1 cell equivalent of genomic DNA (1 fg). Immunomagnetic capture, PCR and a microarray were subsequently used to detect 55 CFU ml-1 (E. coli O157:H7) from chicken rinsate without the aid of pre-enrichment. Four isolates of E. coli O157:H7 and one isolate of O91:H2, for which genotypic data were available, were unambiguously genotyped with this array. Glass based microarrays are relatively simple to construct and provide a rapid and sensitive means to detect multiplexed PCR products and the system is amenable to automation.

  9. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures

    PubMed Central

    šponer, Ji?í; Cang, Xiaohui; Cheatham, Thomas E.

    2013-01-01

    The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids. PMID:22525788

  10. Reducible Poly(amido ethylenimine)s for Nucleic Acid Delivery

    E-print Network

    Christensen, Lane

    2006-10-26

    1 Reducible Poly(amido ethylenimine)s for Nucleic Acid Delivery GPEN 2006 L.V. Christensen 1 , C.-W. Chang 1 , J.H. Jeong 1 , Z. Zhong 2 , J. Feijen 2 , and S.W. Kim 1 1 Department of Pharmaceutics and Pharmaceutical Chemistry, University of Utah... e n t r a t i o n Therapeutic Window Traditional Pharmaceutical Approach MTC MEC Gene Delivery 3 Vector Systems for Nucleic Acid Delivery ? Ability to deliver a diverse range of genetic material #1; RNAi, shRNA, oligos, pDNA ? Chemistry allows...

  11. Highly selective and sensitive nucleic acid detection based on polysaccharide-functionalized silver nanoparticles

    NASA Astrophysics Data System (ADS)

    Yan, Jing-Kun; Ma, Hai-Le; Cai, Pan-Fu; Wu, Jian-Yong

    2015-01-01

    Polysaccharide-functionalized silver nanoparticles (Oc-AgNPs) with a mean diameter of 15 nm were utilized as a novel and effective fluorescence-sensing platform for nucleic acid detection. Tests on the oligonucleotide sequences associated with the human immunodeficiency virus as a model system showed that the Oc-AgNPs effectively absorbed and quenched dye-labeled single-stranded DNA through strong hydrogen bonding interactions and slight electrostatic attractive interactions. The proposed system efficiently differentiated between complementary and mismatched nucleic acid sequences with high selectivity and good reproducibility at room temperature.

  12. Sfold: Software for Statistical Folding and Rational Design of Nucleic Acids

    NSDL National Science Digital Library

    Available free of charge to any researcher for non-commercial applications, Sfold "predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids." Sfold is offered through the Wadsworth center of the New York State Department of Health. Sfold application modules allow users to target accessibility prediction and rational design of siRNA, antisense oligonucelotides and nucleic acid probes, _trans_-cleaving ribozymes, and to generate general features and output for statistical RNA folding.

  13. Counter-current chromatographic separation of nucleic acid constituents with an extremely hydrophilic solvent system

    PubMed Central

    Shibusawa, Yoichi; Shoji, Atsushi; Suzuka, Chihiro; Yanagida, Akio; Ito, Yoichiro

    2010-01-01

    Nucleic acid constituents such as nucleobases, nucleosides and nucleotides were separated by counter-current chromatography using a type J coil planet centrifuge. The separation was performed with an extremely hydrophilic solvent system composed of 1-propanol/800 mM potassium phosphate buffer (pH 7.4) (1 : 1) by eluting the lower aqueous phase at a flow-rate of 0.5 ml/min. Eight kinds of nucleic acid constituents, including UMP, AMP, deoxyAMP, uridine, urasile, 2’ deoxy uridine, adenosine and adenine were well resolved within 170 min. PMID:20362294

  14. Nucleic Acid-based Detection of Bacterial Pathogens Using Integrated Microfluidic Platform Systems

    PubMed Central

    Lui, Clarissa; Cady, Nathaniel C.; Batt, Carl A.

    2009-01-01

    The advent of nucleic acid-based pathogen detection methods offers increased sensitivity and specificity over traditional microbiological techniques, driving the development of portable, integrated biosensors. The miniaturization and automation of integrated detection systems presents a significant advantage for rapid, portable field-based testing. In this review, we highlight current developments and directions in nucleic acid-based micro total analysis systems for the detection of bacterial pathogens. Recent progress in the miniaturization of microfluidic processing steps for cell capture, DNA extraction and purification, polymerase chain reaction, and product detection are detailed. Discussions include strategies and challenges for implementation of an integrated portable platform. PMID:22412335

  15. Fluoride ion catalyzed alkylation of nucleic acid derivatives using trialkyl phosphates, dialkyl sulfates and alkyl methanesulfonates.

    PubMed Central

    Ogilvie, K K; Beaucage, S L; Gillen, M F; Entwistle, D W

    1979-01-01

    Trimethyl phosphate, dimethyl and diethyl sulfate and methyl and ethyl methanesulfonate all give high yields of alkylation on purines and pyrimidines in the presence of tetrabutylammonium fluoride. Trimethyl phosphate produces near quantitative yields of diesters of nucleic acids but gives virtually no triester formation. The alkyl sulfates produce very high yields of triesters of nucleic acids including cyclic phosphates while the alkyl methanesulfonates are intermediate in reactivity. It was observed that in the absence of fluoride ion the dialkylsulfates gave reasonable yields of thymidine monosulfates. PMID:223127

  16. Ordered Self-Assembled Monolayers of Peptide Nucleic Acids with DNA Recognition Capability

    NASA Astrophysics Data System (ADS)

    Briones, C.; Mateo-Marti, E.; Gómez-Navarro, C.; Parro, V.; Román, E.; Martín-Gago, J. A.

    2004-11-01

    We report on the formation of ordered self-assembled monolayers (SAMs) of single-stranded peptide nucleic acids (ssPNA). In spite of their remarkable length (7nm) thiolated PNAs assemble standing up on gold surfaces similarly to the SAMs of short alkanethiols. SAMs of ssPNA recognize complementary nucleic acids, acting as specific biosensors that discriminate even a point mutation in target ssDNA. These results are obtained by surface characterization techniques that avoid labeling of the target molecule: x-ray photoemission, x-ray absorption and atomic force microscopy.

  17. 4344-4347 Nucleic Acids Research, 1993, Vol. 21, No. 18 Cloning and characterization of the C.elegans histidyl-

    E-print Network

    Baillie, David

    4344-4347 Nucleic Acids Research, 1993, Vol. 21, No. 18 Cloning and characterization of the C recommended by the manufacturer. * To whom correspondence should be addressed #12;Nucleic Acids Research, 1993 genomic sequence, and most of the cDNA sequence, of this gene is now determined. The gene size including

  18. 1997 Oxford University Press850860 Nucleic Acids Research, 1997, Vol. 25, No. 4 Quantitative analysis of electrophoresis data: novel

    E-print Network

    Tullius, Thomas D.

    © 1997 Oxford University Press850­860 Nucleic Acids Research, 1997, Vol. 25, No. 4 Quantitative is employed for the separation of proteins and nucleic acids. Methods available for quantitation analysis of electrophoresis data: novel curve fitting methodology and its application to the determination

  19. The EMBO Journal vol.8 no.1 pp.1 -4, 1989 Definitions and nomenclature of nucleic acid structure

    E-print Network

    Bansal, Manju

    The EMBO Journal vol.8 no.1 pp.1 -4, 1989 Definitions and nomenclature of nucleic acid structure-15 September 1988, two sessions were scheduled on definitions of parameters used to describe the geometry of nucleic acid chains and helices, and a common nomenclature for these parameters. The most widely used

  20. "cgDNAmanuscriptfinal" --2014/9/5 --8:05 --page 1 --#1 Published online Nucleic Acids Research, , Vol. , No. 18

    E-print Network

    Gonzalez, Oscar

    "cgDNAmanuscriptfinal" -- 2014/9/5 -- 8:05 -- page 1 -- #1 Published online Nucleic Acids Research), and (11, a webserver to access various databases and models of nucleic acid flexibility). c The Author