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1

Silicon dioxide thin film mediated single cell nucleic acid isolation.  

PubMed

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

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

2013-07-10

2

Silicon Dioxide Thin Film Mediated Single Cell Nucleic Acid Isolation  

PubMed Central

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.

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

2013-01-01

3

Nucleic acid molecule  

US Patent & Trademark Office Database

The invention relates to an isolated nucleic acid molecule encoding a polypeptide capable of producing a triterpenoid hydrocarbon. The invention also relates to the encoded polypeptide, a vector comprising the nucleic acid molecule, a recombinant non-human organism comprising the nucleic acid molecule, and to methods of producing a triterpenoid hydrocarbon or an intermediate of biofuel using the nucleic acid molecule, polypeptide or recombinant organism.

Ball; Andrew (Bedford Park, AU); Moore; Robert (Bedford Park, AU); Knowles; Gregory (Bedford Park, AU); Qin; Jian (Bedford Park, AU)

2011-10-11

4

Isolated nucleic acids encoding autoactivated resistance proteins and uses thereof  

US Patent & Trademark Office Database

The invention relates to nucleic acid, which codes for an autoactivated resistance protein for creating a resistance to pathogens in plants, characterized in that the nucleic acid has a limited portion of an NBS-LRR resistance gene, which extends from the 5'-end of the coded region of the NBS-LRR resistance downstream to the beginning of the NBS domain of the NBS-LRR resistance gene, the NBS-LRR resistance gene not being a TIR-NBS-LRR resistance gene.

2011-12-20

5

Rapid and Efficient Isolation of High Quality Nucleic Acids from Plant Tissues Rich in Polyphenols and Polysaccharides  

Microsoft Academic Search

Isolation of high quality nucleic acids from plant tissues rich in polysaccharides and polyphenols is often difficult. The\\u000a presence of these substances can affect the quality and\\/or quantity of the nucleic acids isolated. Here, we describe a rapid\\u000a and efficient nucleic acids extraction protocol that in contrast to other methods tested, effectively purify high quality\\u000a nucleic acids from plant tissues

Reza Heidari Japelaghi; Raheem Haddad; Ghasem-Ali Garoosi

6

Detection and isolation of nucleic acid sequences using a bifunctional hybridization probe  

DOEpatents

A method for detecting and isolating a target sequence in a sample of nucleic acids is provided using a bifunctional hybridization probe capable of hybridizing to the target sequence that includes a detectable marker and a first complexing agent capable of forming a binding pair with a second complexing agent. A kit is also provided for detecting a target sequence in a sample of nucleic acids using a bifunctional hybridization probe according to this method.

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

2000-01-01

7

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

Microsoft Academic Search

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.

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

2003-01-01

8

Comparison of nucleic acid-based detection of avian influenza H5N1 with virus isolation  

Microsoft Academic Search

Nucleic acid sequence-based amplification with electrochemiluminescent detection (NASBA\\/ECL) of avian influenza virus was compared with viral culture in embryonated chicken eggs. Virus was isolated from blood or anal swabs of chickens artificially infected with highly pathogenic avian influenza A\\/Chicken\\/Hong Kong\\/1000\\/97 (H5N1). Viral nucleic acid was detected in blood samples by NASBA\\/ECL immediately prior to death, whilst nucleic acid extracted from

Songhua Shan; Lung-Sang Ko; Richard A. Collins; Zhongliang Wu; Jiahua Chen; Ka-Yun Chan; Jun Xing; Lok-Ting Lau; Albert Cheung-Hoi Yub

2003-01-01

9

The peptide nucleic acids: a new way for chromosomal investigation on isolated cells?  

Microsoft Academic Search

The development of nucleic acid analogues has become an important feature due to the potential use of this new biomolecular tool in genetic diagnostics and investigations. Among all the synthetic oligonucleotides designed, the peptide nucleic acids (PNA) constitute a remarkable class of nucleic acid mimics, with important physico-chemical properties which have been exploited to develop a wide range of powerful

F. Pellestor; P. Paulasova; M. Macek; S. Hamamah

2004-01-01

10

Detection and isolation of nucleic acid sequences using competitive hybridization probes  

DOEpatents

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.

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

1997-04-01

11

Detection and isolation of nucleic acid sequences using competitive hybridization probes  

DOEpatents

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.

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

1997-01-01

12

Nucleic Acids for Computation  

NASA Astrophysics Data System (ADS)

Nucleic acids have many features that are ideal for molecular computation. Using nucleic acids, we have constructed a full set of molecular logic gates, with modular stem-loop-controlled deoxyribozymes as switches and single-stranded oligonucleotides as inputs and outputs. These gates have been combined to form basic computational circuits, including a half- and a full-adder, and can also be assembled into automata to perform complex computational tasks such as game playing. Our most advanced automaton to-date integrates more than 100 nucleic acid logic gates to play a complete game of tic-tac-toe encompassing 76 possible game plays. Inputs and outputs can also be coupled with upstream and downstream components, such as aptamers, sensors, secondary gate activation, and small-molecule release, indicating the potential for nucleic acid computation in the engineering of autonomous therapeutic and diagnostic molecular devices.

MacDonald, Joanne; Stojanovic, Milan N.

13

Nucleic Acids for Computation  

Microsoft Academic Search

\\u000a Nucleic acids have many features that are ideal for molecular computation. Using nucleic acids, we have constructed a full\\u000a set of molecular logic gates, with modular stem-loop-controlled deoxyribozymes as switches and single-stranded oligonucleotides\\u000a as inputs and outputs. These gates have been combined to form basic computational circuits, including a half- and a full-adder,\\u000a and can also be assembled into automata

Joanne MacDonald; Milan N. Stojanovic

2009-01-01

14

Nucleic acid detection method  

US Patent & Trademark Office Database

A method of detecting a target nucleotide sequence in a nucleic acid molecule, which comprises: (a) binding of an oligonucleotide probe to said nucleic acid molecule; (b) selective labelling of the bound oligonucleotide probe in the presence of said target nucleotide sequence; (c) hybridization of the labelled oligonucleotide to a complementary sequence; and (d) subsequent detection of the label; such methods being suitable for qualitative and quantitative assays of microbiological populations.

Rudi; Knut (Oslo, NO); Jakobsen; Kjetill Sigurd (Olso, NO)

2003-09-09

15

Portable nucleic acid thermocyclers.  

PubMed

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

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

2013-10-21

16

Efficient isolation of high quality nucleic acids from different tissues of Taxus baccata L.  

PubMed

Improved and efficient methods were developed for isolating high quality DNA and RNA from different sources of Iranian Yew (Taxus baccata L.). The methods were based on CTAB extraction buffer added with high levels of polyvinylpyrrolidone (PVP) and beta-mercaptoethanol to properly remove polysaccharides and prevent oxidation of phenolics. The pellets obtained by ethanol precipitation were washed only with Chloroform: isoamyl alcohol (24:1). So, we could successfully eliminate the dangerous phenol/chloroform extraction steps from the isolation procedure. Both spectrophotometric (A(260)/A(280) and A(260)/A(230) ratios) and agarose electrophoresis analysis of isolated nucleic acids (DNA and RNA) indicated good results. DNA with the average yield of 100-300 microg/g leaf and stem tissue and total RNA with an average yield of 20-30 microg/g cell culture and 80-100 microg/g leaf and stem tissue of Iranian yew could be obtained. Successful amplification of pam and pds by PCR and RT-PCR, showed the integrity of isolated DNA and RNA, respectively. PMID:19578976

Abbasi Kejani, Abolghasem; Hosseini Tafreshi, Sayed Ali; Khayyam Nekouei, Sayed Mojtaba; Mofid, Mohammad Reza

2009-07-04

17

Polyvalent Nucleic Acid Nanostructures  

PubMed Central

Polyvalent oligonucleotide-nanoparticle conjugates possess several unique emergent properties including enhanced cellular uptake, high antisense bioactivity, and nuclease resistance, which hypothetically originate from the dense packing and orientation of oligonucleotides on the surface of the nanoparticle. In this communication, we describe a new class of polyvalent nucleic acid nanostructures (PNANs), which comprise only crosslinked and oriented nucleic acids. We demonstrate that these particles are capable of effecting high cellular uptake and gene regulation without the need of a cationic polymer co-carrier. The PNANs also exhibit cooperative binding behavior and nuclease resistance properties.

Cutler, Joshua I.; Zhang, Ke; Zheng, Dan; Auyeung, Evelyn; Prigodich, Andrew E.

2011-01-01

18

Immunostimulatory Nucleic Acid Molecules.  

National Technical Information Service (NTIS)

Nucleic acids containing unmethylated CpG dinucleotides and therapeutic utilities based on their ability to stimulate an immune response and to redirect a Th2 response to a Th1 response in a subject are disclosed. Methods for treating atopic diseases, inc...

A. D. Steinberg A. M. Krieg D. Klinman J. Kline

2005-01-01

19

Composition for nucleic acid sequencing  

DOEpatents

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 followed in real time. The sequence is deduced by identifying which base is being incorporated into the growing complementary strand of the target nucleic acid by the catalytic activity of the nucleic acid polymerizing enzyme at each step in the sequence of base additions. A polymerase on the target nucleic acid molecule complex is provided in a position suitable to move along the target nucleic acid molecule and extend the oligonucleotide primer at an active site. A plurality of labelled types of nucleotide analogs are provided proximate to the active site, with each distinguishable type of nucleotide analog being complementary to a different nucleotide in the target nucleic acid sequence. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand at the active site, where the nucleotide analog being added is complementary to the nucleotide of the target nucleic acid at the active site. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The steps of providing labelled nucleotide analogs, polymerizing the growing nucleic acid strand, and identifying the added nucleotide analog are repeated so that the nucleic acid strand is further extended and the sequence of the target nucleic acid is determined.

Korlach, Jonas (Ithaca, NY); Webb, Watt W. (Ithaca, NY); Levene, Michael (Ithaca, NY); Turner, Stephen (Ithaca, NY); Craighead, Harold G. (Ithaca, NY); Foquet, Mathieu (Ithaca, NY)

2008-08-26

20

Isolation of nucleic acids and cultures from fossil ice and permafrost.  

PubMed

Owing to their constant low temperatures, glacial ice and permafrost might contain the oldest nucleic acids and microbial cells on Earth, which could prove key to reconstructing past ecosystems and for the planning of missions to other planets. However, recent claims concerning viable cells and microbial nucleic acids obtained from ice- and permafrost cores from hundreds of thousands to millions of years old are not properly authenticated and the findings could be the result of contamination. Here, we discuss the processes that restrict the long-term survival of DNA and/or RNA molecules in ice and permafrost, and highlight sources of contamination that could result in false claims. Additionally, we present a set of precautions, controls and criteria to help ensure that future cultures and sequences are authentic. PMID:16701245

Willerslev, Eske; Hansen, Anders J; Poinar, Hendrik N

2004-03-01

21

Lna (Locked Nucleic Acid)  

Microsoft Academic Search

LNA (Locked Nucleic Acid) forms duplexes with complementary DNA, RNA or LNA with unprecedented thermal affinities. CD spectra show that duplexes involving fully modified LNA (especially LNA:RNA) structurally resemble an A-form RNA:RNA duplex. NMR examination of an LNA:DNA duplex confirm the 3?-endo conformation of an LNA monomer. Recognition of double-stranded DNA is demonstrated suggesting strand invasion by LNA. Lipofectin-mediated efficient

Jesper Wengel; Alexei Koshkin; Sanjay K. Singh; Poul Nielsen; Michael Meldgaard; Vivek K. Rajwanshi; Ravindra Kumar; Jan Skouv; Christina B. Nielsen; Jens Peter Jacobsen; Nana Jacobsen; Carl E. Olsen

1999-01-01

22

Comparison of nucleic acid-based detection of avian influenza H5N1 with virus isolation.  

PubMed

Nucleic acid sequence-based amplification with electrochemiluminescent detection (NASBA/ECL) of avian influenza virus was compared with viral culture in embryonated chicken eggs. Virus was isolated from blood or anal swabs of chickens artificially infected with highly pathogenic avian influenza A/Chicken/Hong Kong/1000/97 (H5N1). Viral nucleic acid was detected in blood samples by NASBA/ECL immediately prior to death, whilst nucleic acid extracted from anal swabs was detected from the day following artificial infection until death. Thus, blood and/or anal swabs are a suitable source of material for the detection of avian influenza in dead birds, but anal swabs are more suitable for detection of viral genetic material in live birds. Dilution of a known viral standard was used to determine the limit of sensitivity for both NASBA/ECL and egg culture detection methods. The NASBA/ECL method was equivalent in sensitivity to egg culture. The NASBA/ECL results agreed with egg culture data in 71/94 (75.5%) tissue samples obtained from artificially infected birds. PMID:12604358

Shan, Songhua; Ko, Lung-Sang; Collins, Richard A; Wu, Zhongliang; Chen, Jiahua; Chan, Ka-Yun; Xing, Jun; Lau, Lok-Ting; Yu, Albert Cheung-Hoi

2003-03-01

23

Nucleic acid arrays and methods of synthesis  

Microsoft Academic Search

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

Chandran R. Sabanayagam; Takeshi Sano; John Misasi; Anson Hatch; Charles Cantor

2001-01-01

24

Isolation of phosphatidylethanolamine as a solitary cofactor for prion formation in the absence of nucleic acids  

PubMed Central

Infectious prions containing the pathogenic conformer of the mammalian prion protein (PrPSc) can be produced de novo from a mixture of the normal conformer (PrPC) with RNA and lipid molecules. Recent reconstitution studies indicate that nucleic acids are not required for the propagation of mouse prions in vitro, suggesting the existence of an alternative prion propagation cofactor in brain tissue. However, the identity and functional properties of this unique cofactor are unknown. Here, we show by purification and reconstitution that the molecule responsible for the nuclease-resistant cofactor activity in brain is endogenous phosphatidylethanolamine (PE). Synthetic PE alone facilitates conversion of purified recombinant (rec)PrP substrate into infectious recPrPSc molecules. Other phospholipids, including phosphatidylcholine, phosphatidylserine, phosphatidylinositol, and phosphatidylglycerol, were unable to facilitate recPrPSc formation in the absence of RNA. PE facilitated the propagation of PrPSc molecules derived from all four different animal species tested including mouse, suggesting that unlike RNA, PE is a promiscuous cofactor for PrPSc formation in vitro. Phospholipase treatment abolished the ability of brain homogenate to reconstitute the propagation of both mouse and hamster PrPSc molecules. Our results identify a single endogenous cofactor able to facilitate the formation of prions from multiple species in the absence of nucleic acids or other polyanions.

Deleault, Nathan R.; Piro, Justin R.; Walsh, Daniel J.; Wang, Fei; Ma, Jiyan; Geoghegan, James C.; Supattapone, Surachai

2012-01-01

25

Nucleic acid detection methods  

DOEpatents

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{prime}-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be easily distinguish from nuclease uncleaved heteroduplexes by differential labeling. Probes and target can be differentially labeled with detectable labels. Matched target can be detected by cleaving resulting loops from the hybridized target and creating free 3-hydroxyl groups. These groups are recognized and extended by polymerases added into the reaction system which also adds or releases one label into solution. Analysis of the resulting products using either solid phase or solution. These methods can be used to detect characteristic nucleic acid sequences, to determine target sequence and to screen for genetic defects and disorders. Assays can be conducted on solid surfaces allowing for multiple reactions to be conducted in parallel and, if desired, automated. 18 figs.

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

1998-05-19

26

Perfectly Complementary Nucleic Acid Enzymes  

Microsoft Academic Search

The ability to maximize the use of available nucleic acid sequence space would have been crucial during the presumed RNA world and confers selective advantage in many contemporary organisms. One way to access sequence space at a higher density would be to make use of both strands of a duplex nucleic acid for the production of functional molecules. As a

Scott T. Kuhns; Gerald F. Joyce

2003-01-01

27

Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same  

DOEpatents

In one aspect, the present invention provides isolated nucleic acid molecules that each encode a geranyl diphosphate synthase protein, wherein each isolated nucleic acid molecule hybridizes to a nucleic acid molecule consisting of the sequence set forth in SEQ ID NO:1 under conditions of 5.times.SSC at 45.degree. C. for one hour. The present invention also provides isolated geranyl diphosphate synthase proteins, and methods for altering the level of expression of geranyl diphosphate synthase protein in a host cell.

Croteau, Rodney Bruce (Pullman, WA); Burke, Charles Cullen (Moscow, ID)

2008-06-24

28

Nucleic acid arrays and methods of synthesis  

DOEpatents

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.

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

29

Nucleic acid based molecular devices.  

PubMed

In biology, nucleic acids are carriers of molecular information: DNA's base sequence stores and imparts genetic instructions, while RNA's sequence plays the role of a messenger and a regulator of gene expression. As biopolymers, nucleic acids also have exciting physicochemical properties, which can be rationally influenced by the base sequence in myriad ways. Consequently, in recent years nucleic acids have also become important building blocks for bottom-up nanotechnology: as molecules for the self-assembly of molecular nanostructures and also as a material for building machinelike nanodevices. In this Review we will cover the most important developments in this growing field of nucleic acid nanodevices. We also provide an overview of the biochemical and biophysical background of this field and the major "historical" influences that shaped its development. Particular emphasis is laid on DNA molecular motors, molecular robotics, molecular information processing, and applications of nucleic acid nanodevices in biology. PMID:21432950

Krishnan, Yamuna; Simmel, Friedrich C

2011-03-28

30

Biopolymers: Protein and Nucleic Acids.  

National Technical Information Service (NTIS)

The work focuses on learning the principles that govern interactions between proteins and nucleic acids. With these principles as guides we are synthesizing peptides (of about 50 amino acids) that bind to specific regions of DNA. Various reactive function...

J. H. Richards J. N. Abelson L. E. Hood M. I. Simon J. L. Campbell

1987-01-01

31

Immunoseparation and Immunodetection of Nucleic Acids Labeled with Halogenated Nucleotides  

Microsoft Academic Search

A novel methodology for labeling, isolation, and detection of nucleic acids is described. Nucleic acid isolation is based onin vivoorin vitroincorporation of BrU or BrdU to either RNA or DNA, respectively, followed by immunoprecipitation of the labeled nucleic acid utilizing anti-BrdU MoAb, which crossreacts with BrU, attached to solid particles. Filter-bound bromine-labeled DNA or RNA was detected by immunoblotting with

S. Raza Haider; Gloria Juan; Frank Traganos; Zbigniew Darzynkiewicz

1997-01-01

32

Biopolymers: Proteins and Nucleic Acids.  

National Technical Information Service (NTIS)

Our work focuses on molecular recognition by biopolymers as a model for interactions between macromolecules in general. Specifically we are learning the rules that govern protein-nucleic acid (both DNA and RNA) binding. Chemical synthesis, molecular genet...

J. H. Richards J. N. Abelson P. B. Dervan L. E. Hood M. I. Simon

1990-01-01

33

Enzymatic labeling of nucleic acids  

Microsoft Academic Search

Enzymatic labeling of nucleic acids is a fundamental tool in molecular biology with virtually every aspect of nucleic acid\\u000a hybridization technique involving the use of labeled probes. Different methods for enzymatic labeling of DNA, RNA and oligonucleotide\\u000a probes are available today. In this review, we will describe both radioactive and nonradioactive labeling methods, yet the\\u000a choice of system for labeling

Jamal Temsamani; Sudhir Agrawal

1996-01-01

34

Comparison of 3 nucleic acid isolation methods for the quantification of HIV1 RNA by Cobas Taqman real-time polymerase chain reaction system  

Microsoft Academic Search

Quantification of human immunodeficiency virus type 1 (HIV-1) RNA viral load in blood is a clinically validated tool for the management and follow-up of patients infected with this virus. HIV-1 RNA quantification can be performed by several kinds of commercially available polymerase chain reaction (PCR) assays. The sensitivity of these assays is affected by the nucleic acid isolation procedures that

Alpaslan Alp; Gülsen Hascelik

2009-01-01

35

Nucleic acid aptamers in cancer medicine  

Microsoft Academic Search

Many signalling proteins involved in diverse functions such as cell growth and differentiation can act as oncogenes and cause cellular transformation. These molecules represent attractive targets for cancer diagnosis or therapy and are therefore subject to intensive investigation. Aptamers are small nucleic acid molecules, isolated from combinatorial libraries by a procedure termed SELEX, that bind to a target molecule by

Laura Cerchia; Jörg Hamm; Domenico Libri; Bertrand Tavitian; Vittorio de Franciscis

2002-01-01

36

Novel FDRG Protein and Nucleic Acid Molecules and Uses Therefor.  

National Technical Information Service (NTIS)

Novel FDRG polypeptides, proteins, and nucleic acid molecules are disclosed. In addition to isolated, full-length FDRG proteins, the invention further provides isolated FDRG fusion proteins, antigenic peptides and anti-FDRG antibodies. The invention also ...

B. M. Speigelman C. H. Yoon D. A. Holtzman

2004-01-01

37

Biopolymers: Protein and Nucleic Acids.  

National Technical Information Service (NTIS)

The work focuses on learning the principles that govern interactions between proteins and nucleic acids both DNA and RNA (specifically tRNA). With these principles as guides we are synthesizing peptides (of about 50 amino acids) that bind to specific regi...

J. H. Richards J. N. Abelson L. H. Hood M. I. Simon P. B. Dervan

1988-01-01

38

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.

1998-01-01

39

Amyloid-Associated Nucleic Acid Hybridisation  

Microsoft Academic Search

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

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

2011-01-01

40

Cell Response to Nucleic Acid Penetration.  

National Technical Information Service (NTIS)

Employing the Haemophilus influenzae bacterial transformation system, the immediate response of cells to the penetration by nucleic acids is being analyzed. The investigation involves the study of the fate of absorbed nucleic acids, especially their degra...

J. H. Stuy

1969-01-01

41

Replica amplification of nucleic acid arrays  

DOEpatents

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.

Church, George M. (Brookline, MA)

2002-01-01

42

Noninstrumented nucleic acid amplification assay  

NASA Astrophysics Data System (ADS)

We have developed components of a diagnostic disposable platform that has the dual purpose of providing molecular diagnostics at the point of care (POC) as well as stabilizing specimens for further analysis via a centralized surveillance system. This diagnostic is targeted for use in low-resource settings by minimally trained health workers. The disposable device does not require any additional instrumentation and will be almost as rapid and simple to use as a lateral flow strip test - yet will offer the sensitivity and specificity of nucleic acid amplification tests (NAATs). The low-cost integrated device is composed of three functional components: (1) a sample-processing subunit that generates clean and stabilized DNA from raw samples containing nucleic acids, (2) a NA amplification subunit, and (3) visual amplicon detection sub-unit. The device integrates chemical exothermic heating, temperature stabilization using phase-change materials, and isothermal nucleic acid amplification. The aim of developing this system is to provide pathogen detection with NAAT-level sensitivity in low-resource settings where there is no access to instrumentation. If a disease occurs, patients would be tested with the disposable in the field. A nucleic acid sample would be preserved within the spent disposable which could be sent to a central laboratory facility for further analysis if needed.

Weigl, Bernhard H.; Domingo, Gonzalo; Gerlach, Jay; Tang, Dennis; Harvey, Darrel; Talwar, Nick; Fichtenholz, Alex; van Lew, Bill; LaBarre, Paul

2008-03-01

43

The promise of nucleic acid vaccines  

Microsoft Academic Search

Establishing the effective use of ‘naked’ nucleic acids as vaccines would undoubtedly be one of the most important advances in the history of vaccinology. While nucleic acids show much promise for use as vaccine vectors in experimental animals, not a single naked nucleic acid vector has been approved for use in humans. Indeed, data from human clinical trials is scant:

N P Restifo; H Ying; L Hwang; W W Leitner

2000-01-01

44

Nucleic acid hydration: a volumetric perspective  

Microsoft Academic Search

Hydration represents a major force governing the conformational preferences and drug binding properties of nucleic acids. Volumetric measurements have proven useful in characterizing the hydration properties of nucleic acid structures and their complexes with other molecules. In this paper, we present an overview of recent developments in the field of volumetric investigations of nucleic acids. We discuss, in particular, the

Tigran V. Chalikian; Robert B. Macgregor

2007-01-01

45

Circulating nucleic acids in cancer and pregnancy  

Microsoft Academic Search

Circulating nucleic acids are present in the blood of humans and other vertebrates. During the last 10 years researchers actively studied cell-free nucleic acids present in plasma or serum with great expectations of their use as potential biomarkers for cancer and other pathologic conditions. In the present manuscript the main findings related to the principal characteristics of circulating nucleic acids,

Pamela Pinzani; Francesca Salvianti; Mario Pazzagli; Claudio Orlando

2010-01-01

46

Chemical etiology of nucleic acid structure  

Microsoft Academic Search

The synthesis of potentially natural nucleic acid alternatives and comparison of some of their chemical properties with those of RNA and DNA have led to findings that we consider to be relevant in the context of a chemical etiology of nucleic acid structure. Chemical etiology of nucleic acid structure refers to systematic experimental studies aimed at narrowing the diversity of

A. Eschenmoser; R. Krishnamurthy

2000-01-01

47

An international collaborative study on the detection of an HIV-1 genotype B field isolate by nucleic acid amplification techniques.  

PubMed

An international collaborative study to assess inter-laboratory variation in the sensitivity of gene amplification assays for the detection of HIV-1 RNA sequences was conducted using a panel of eight duplicate dilutions of an HIV-1 genotype B clinical isolate and negative control samples. Twenty-five laboratories participated in the study and used a variety of in-house assays and commercial assay systems. With few exceptions, the assays were more sensitive than a p24 antigen assay. Overall, the PCR-based Amplicor Monitor assay was the most sensitive and gave the highest mean copy number for any one sample. Some of the in-house assays gave results comparable with the Monitor assay whilst the NASBA and bDNA assays appeared to be less sensitive. As a result of this study, an HIV-1 Working Reagent for the standardisation of nucleic acid amplification assays was developed and assessed in a subsequent study. Similar differences in sensitivity between the different assay systems was observed. The discrepancies in viral copy number obtained using the Working Reagent highlights the need for an International Standard against which all Working Reagents may be calibrated. PMID:10204694

Bootman, J; Heath, A B; Hughes, P; Holmes, H

1999-03-01

48

Nucleic Acid Detection using MNAzymes  

PubMed Central

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.

Gerasimova, Yulia V.; Kolpashchikov, Dmitry M.

2010-01-01

49

Nucleic acids, compositions and uses thereof  

DOEpatents

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.

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

50

Nucleic acid binding properties of the nucleic acid chaperone domain of hepatitis delta antigen  

Microsoft Academic Search

The N terminal region of hepatitis delta antigen (HDAg), referred to here as NdAg, has a nucleic acid chaperone activity that modulates the ribozyme activity of hepatitis delta virus (HDV) RNA and stimulates hammerhead ribozyme catalysis. We characterized the nucleic acid binding properties of NdAg, identified the structural and sequence domains important for nucleic acid binding, and studied the correlation

Chun-Chung Wang; Tsung-Cheng Chang; Ching-Wen Lin; Hsiu-Ling Tsui; B. C. Chu; Bo-Shun Chen; Zhi-Shun Huang; Huey-Nan Wu

2003-01-01

51

STUDIES ON NUCLEIC ACID METACHROMASY  

PubMed Central

Acrolein-fixed, polyester wax-embedded tissue sections showed excellent preservation of light microscopic architecture and, when stained with toluidine blue, intense color contrast between DNA, which stained orthochromatically, and RNA, which stained metachromatically. This method has practical value for differentiating DNA from RNA in the same section. The color contrast was impaired by substituting formaldehyde for acrolein or paraffin for polyester wax, and was negligible in tissues fixed in formaldehyde or Carnoy's fluid and embedded in paraffin. Quality of structural preservation paralleled degree of color contrast. Metachromatic staining can be analysed, by the quantitative parameters of Bradley and colleagues, to provide inferences regarding the conformation of biopolymers in tissue sections. Comparison of the nucleic acid color contrasts in toluidine blue-stained sections with titrations of fixative-treated nucleic acids against toluidine blue in solution indicated a greater difference in conformation between DNA- and RNA-protein in acrolein-polyester sections than between acrolein-treated free DNA and RNA in solution. This is supported by recent evidence that the conformation of ribosomal RNA is quite different in whole ribosomes from that assumed by the same RNA free in solution. The acrolein-polyester method may enhance color contrast by providing superior preservation of ordered nucleoprotein conformations.

Feder, Ned; Wolf, Merrill K.

1965-01-01

52

STUDIES ON NUCLEIC ACID METACHROMASY  

PubMed Central

The stacking coefficients (K's) of nucleic acids have been thought to influence the color contrast between DNA and RNA in tissue sections stained with metachromatic dyes. This idea was tested by titrating toluidine blue (TB) and acridine orange (AO) in solution against DNA and RNA, native or treated with formaldehyde, acrolein, or Carnoy's fluid. Absorption spectra at varying polymer-dye ratios were used to compute K values by the methods of Bradley and colleagues. Results with both dyes fit Bradley's stacking equations. Fixatives did not block dye-binding sites but markedly altered K values. K of DNA was low, unaffected by aldehyde fixative, increased by Carnoy's fluid or heat denaturation. K of RNA was higher than that of DNA and was increased greatly by formaldehyde, almost as much by acrolein, considerably less by Carnoy's fluid. Aldehyde effects were partially reversed upon removal of aldehyde by dialysis. These observations accord with known effects of aldehydes and denaturation upon nucleic acid conformation. Differences between K's of DNA and RNA were greater after aldehyde treatment than after Carnoy's, and were greater with AO than with TB. This is generally consistent with the magnitude of the color contrasts observed in tissues. Additional factors must contribute to the intense color contrast observed in acrolein-fixed tissues stained with TB.

Lamm, Michael E.; Childers, Lillian; Wolf, Merrill K.

1965-01-01

53

Cell-free fetal nucleic acids in amniotic fluid  

PubMed Central

BACKGROUND Research into cell-free fetal (cff) nucleic acids has primarily focused on maternal plasma; however, cff DNA and RNA are also detectable in other body fluids such as amniotic fluid (AF). In AF, cff DNA is present in much greater concentrations than in maternal plasma and represents a pure fetal sample uncontaminated by maternal- and trophoblast-derived nucleic acids. The aim of this review was to summarize the current knowledge on cff nucleic acids in AF and to outline future research directions. METHODS MEDLINE and PREMEDLINE were searched up to August 2010 for original investigations of cell-free RNA or DNA in AF. Sixteen studies were included in the review. RESULTS AF cff DNA represents a physiologically separate pool from cff DNA in maternal plasma. The placenta is not a major source of nucleic acids in AF. It is feasible to isolate cff nucleic acids from small volumes of discarded AF supernatant in sufficient quality and quantity to perform microarray studies and downstream applications such as pathway analysis. This ‘discovery-driven approach’ has resulted in new information on the pathogenesis of Down syndrome and polyhydramnios. There is otherwise a paucity of information relating to the basic biology and clinical applications of cff nucleic acids in AF. CONCLUSIONS AF supernatant is a valuable and widely available but under-utilized biological resource. Further studies of cff nucleic acids in AF may lead to new insights into human fetal development and ultimately new approaches to antenatal treatment of human disease.

Hui, L.; Bianchi, D.W.

2011-01-01

54

21 CFR 866.3225 - Enterovirus nucleic acid assay.  

Code of Federal Regulations, 2010 CFR

...2009-04-01 2009-04-01 false Enterovirus nucleic acid assay. 866.3225...Serological Reagents § 866.3225 Enterovirus nucleic acid assay. (a) Identification . An enterovirus nucleic acid assay is a device...

2009-04-01

55

21 CFR 866.3225 - Enterovirus nucleic acid assay.  

Code of Federal Regulations, 2010 CFR

...2010-04-01 2010-04-01 false Enterovirus nucleic acid assay. 866.3225...Serological Reagents § 866.3225 Enterovirus nucleic acid assay. (a) Identification . An enterovirus nucleic acid assay is a device...

2010-04-01

56

Progress of Spectral Probes for Nucleic Acids  

Microsoft Academic Search

Spectral probes have been widely used for the structural and quantitative study of nucleic acids. Traditional probes including absorption-type, fluorescent, and chemiluminescent probes continue to be developed. Of them, near infrared (NIR) dyes, ruthenium(II), and rare earth complexes are especially suitable for the investigation and determination of biomacromolecules including nucleic acids, so their developments are rapid. Resonance light scattering and

Yuebo Wang; Jinghe Yang; Xia Wu; Lei Li; Shuna Sun; Benyu Su; Zongshan Zhao

2003-01-01

57

Inhibition and Facilitation of Nucleic Acid Amplification  

Microsoft Academic Search

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

IAN G. WILSON

1997-01-01

58

Adaptive Recognition by Nucleic Acid Aptamers  

Microsoft Academic Search

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

Thomas Hermann; Dinshaw J. Patel

2000-01-01

59

Locked nucleic acids (LNA) and medical applications  

Microsoft Academic Search

Locked Nucleic Acid (LNA) is a novel, third generation DNA analogue that has the potentialto impact strongly on the future\\u000a development of a diversity of nucleic acid based technologies.The present chapter reviews the known biochemical properties\\u000a of LNA and exemplifies how thesehave been used to improve both DNA diagnostic technologies and antisense therapeutics.

Henrik Ørum; Andreas Wolter; Lars Kongsbak

2003-01-01

60

Nucleic acid driven sterile inflammation.  

PubMed

The etiology of sterile inflammatory conditions is complex and affected by a variety of genetic, environmental and stochastic factors. But despite this overt complexity, progress has been made in elucidating mechanisms underlying disease pathogenesis. An intriguing new finding that has emerged over the past years was the realization that innate immune receptors participate in driving or aggravating disease manifestation. Originally identified as sensors of pathogens and as initiators of antimicrobial immune responses, receptors of the innate immune system recognize a variety of highly conserved microbe associated molecular patterns (MAMPs), including nucleic acids (NAs). While the sensing of DNA and RNA enables detection of a broad range of pathogens this strategy comes at a cost. Indeed, the capacity of NAs to accidentally activate innate sensors significantly contributes to inappropriate responses to self. In this review we will discuss recent findings based on established disease models. PMID:23419883

Ablasser, Andrea; Hertrich, Carola; Waßermann, Ruth; Hornung, Veit

2013-01-19

61

Nucleic acid binding properties of the nucleic acid chaperone domain of hepatitis delta antigen  

PubMed Central

The N terminal region of hepatitis delta antigen (HDAg), referred to here as NdAg, has a nucleic acid chaperone activity that modulates the ribozyme activity of hepatitis delta virus (HDV) RNA and stimulates hammerhead ribozyme catalysis. We characterized the nucleic acid binding properties of NdAg, identified the structural and sequence domains important for nucleic acid binding, and studied the correlation between the nucleic acid binding ability and the nucleic acid chaperone activity. NdAg does not recognize the catalytic core of HDV ribozyme specifically. Instead, NdAg interacts with a variety of nucleic acids and has higher affinities to longer nucleic acids. The studies with RNA homopolymers reveal that the binding site size of NdAg is around nine nucleotides long. The extreme N terminal portion of NdAg, the following coiled-coil domain and the basic amino acid clusters in these regions are important for nucleic acid binding. The nucleic acid–NdAg complex is stabilized largely by electrostatic interactions. The formation of RNA–protein complex appears to be a prerequisite for facilitating hammerhead ribozyme catalysis of NdAg and its derivatives. Mutations that reduce the RNA binding activity or high ionic strength that destabilizes the RNA–protein complex, reduce the nucleic acid chaperone activity of NdAg.

Wang, Chun-Chung; Chang, Tsung-Cheng; Lin, Ching-Wen; Tsui, Hsiu-Ling; Chu, Page B. C.; Chen, Bo-Shun; Huang, Zhi-Shun; Wu, Huey-Nan

2003-01-01

62

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

DOEpatents

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. 14 figs.

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

1998-03-24

63

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

DOEpatents

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.

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

1998-01-01

64

The search for scrapie agent nucleic acid.  

PubMed Central

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.

Aiken, J M; Marsh, R F

1990-01-01

65

Methods for detecting modification resistant nucleic acids  

US Patent & Trademark Office Database

Methods are provided for, inter alia, detecting nucleic acid molecules resistant to degradation, such as a plurality of RNA molecules bound to a ribosome, using various technologies including deep sequencing.

2013-07-16

66

Polysaccharide-based nucleic acid nanoformulations.  

PubMed

Therapeutic application of nucleic acids requires their encapsulation in nanosized carriers that enable safe and efficient intracellular delivery. Before the desired site of action is reached, drug-loaded nanoparticles (nanomedicines) encounter numerous extra- and intracellular barriers. Judicious nanocarrier design is highly needed to stimulate nucleic acid delivery across these barriers and maximize the therapeutic benefit. Natural polysaccharides are widely used for biomedical and pharmaceutical applications due to their inherent biocompatibility. At present, there is a growing interest in applying these biopolymers for the development of nanomedicines. This review highlights various polysaccharides and their derivatives, currently employed in the design of nucleic acid nanocarriers. In particular, recent progress made in polysaccharide-assisted nucleic acid delivery is summarized and the specific benefits that polysaccharides might offer to improve the delivery process are critically discussed. PMID:23680381

Raemdonck, Koen; Martens, Thomas F; Braeckmans, Kevin; Demeester, Jo; De Smedt, Stefaan C

2013-05-13

67

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

SciTech Connect

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.

Bavykin, Sergei (Darien, IL)

2011-01-18

68

Nucleic acid visualization with UCSF Chimera  

Microsoft Academic Search

With the increase in the number of large, 3D, high-resolution nucleic acid structures, particularly of the 30S and 50S ribosomal subunits and the intact bacterial ribosome, advancements in the visualiza- tion of nucleic acid structural features are essential. Large molecular structures are complicated and detailed, and one goal of visualization software is to allow the user to simplify the display

Gregory S. Couch; Donna K. Hendrix; Thomas E. Ferrin

2006-01-01

69

Oral Delivery of Nucleic Acid Drugs  

Microsoft Academic Search

Nucleic acid molecules have emerged as versatile tools with promising utility in a variety of biochemical, diagnostic, and\\u000a therapeutic applications. A parenteral administration of a nucleic acid is inconvenient because of pain, fear, and risks being\\u000a associated with this type of application. The intestinal epithelium is considered to be an attractive site for oral delivery\\u000a of therapeutic genes.\\u000a \\u000a The successful

Ronny Martien

70

A plastic microchip for nucleic acid purification  

Microsoft Academic Search

A microchip for purifying nucleic acids from bacterial pathogens was designed and fabricated in plastic. The fabricated plastic\\u000a microchips were tested for their ability to purify nucleic acids from the bacteria Listeria monocytogenes (L. monocytogenes), Escherichia coli (E. coli), and Salmonella typhimurium (S. typhimurium). These chips were constructed using rapid and low-cost plastic fabrication techniques including hot embossing and plastic

Yuxin Liu; Nathaniel C. Cady; Carl A. Batt

2007-01-01

71

Structure of Pna-Nucleic Acid Complexes  

Microsoft Academic Search

The solution structure of the PNA-DNA hybrid H-GCTATGTC-NH2d(GACATAGC), determined by NMR methods, shows a new conformation which has elements of both A- and B-form DNA. Comparison with other PNA-nucleic acid complexes points to common structural features, but also demonstrates the ability of PNA to conform to nucleic acid partners of different conformations.

Magdalena Eriksson

1997-01-01

72

Nucleic Acids Hybridization: Potentials and Limitations  

Microsoft Academic Search

Several nucleic acids hybridization-based approaches, such as microarray, competitive genomic, and Southern or Northern blot\\u000a hybridization, have become popular tools for specialists in biochemistry and in biomedicine, and are now in routine use. However,\\u000a the potential of in-solution nucleic acids hybridization-based experimental techniques seems to be underestimated now. Examples\\u000a are subtractive hybridization (SH), which allows one to efficiently find differences

ANTON A. BUZDIN

73

Amplification of trace amounts of nucleic acids  

DOEpatents

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).

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

2008-06-17

74

Perfect Strangers: Inorganic Photochemistry and Nucleic Acids  

NASA Astrophysics Data System (ADS)

The applications of inorganic photochemistry to nucleic acid chemistry are discussed. A brief review of nucleic acid structure is given. Methods for probing DNA using emissive inorganic complexes are discussed. Photoreactions that damage DNA by hydrogen atom transfer from sugar or electron abstraction from guanine are presented. The method of photochemical footprinting using a diplatinum photocatalyst is described. The final section discusses advances in combinatorial selection experiments that increase the urgency for rapid screening methods such as those derived from inorganic photochemistry.

Carter, Pamela J.; Ciftan, Suzanne A.; Sistare, Mark F.; Holden Thorp, H.

1997-06-01

75

MOLECULAR HYBRIDIZATION TECHNIQUES OF NUCLEIC ACIDS  

Microsoft Academic Search

The nucleic acid hybridization is the process wherein two DNA or RNA single chains (mono-stranded) from different biological sources, make the double catenary configuration, based on contingent sequence homology of the two sources, resulting DNA-DNA, RNA-RNA or DNA-RNA hybrids. The purpose is identification or localization of certain nucleic acid sequences (genes) in the genome of some species. The target molecule

Vasilica BARBU

2007-01-01

76

Method of Identifying a Base in a Nucleic Acid  

DOEpatents

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.

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

1999-01-01

77

Hybridization and sequencing of nucleic acids using base pair mismatches  

SciTech Connect

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.

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

2001-01-01

78

Probe kit for identifying a base in a nucleic acid  

SciTech Connect

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.

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

2001-01-01

79

Cell cycle nucleic acids, polypeptides and uses thereof  

DOEpatents

The invention provides isolated nucleic acids and their encoded proteins that are involved in cell cycle regulation. The invention further provides recombinant expression cassettes, host cells, transgenic plants, and antibody compositions. The present invention provides methods and compositions relating to altering cell cycle protein content, cell cycle progression, cell number and/or composition of plants.

Gordon-Kamm, William J. (Urbandale, IA); Lowe, Keith S. (Johnston, IA); Larkins, Brian A. (Tucson, AZ); Dilkes, Brian R. (Tucson, AZ); Sun, Yuejin (Westfield, IN)

2007-08-14

80

Interaction of Nucleic Acids with the Glycocalyx  

PubMed Central

Mammalian cells resist the uptake of nucleic acids. The lipid bilayer of the plasma membrane presents one barrier. Here, we report on a second physicochemical barrier for uptake. To create a sensitive probe for nucleic acid–cell interactions, we synthesized fluorescent conjugates in which lipids are linked to DNA oligonucleotides. We found that these conjugates incorporate readily into the plasma membrane but are not retained there. Expulsion of lipid–oligonucleotide conjugates from the plasma membrane increases with oligonucleotide length. Conversely, the incorporation of conjugates increases markedly in cells that lack the major anionic components of the glycocalyx—sialic acid and glycosaminoglycans, and in cells that had incorporated highly cationic lipids into their plasma membrane. We conclude that anionic oligosaccharides provide a formidable barrier to the uptake of nucleic acids by mammalian cells. This conclusion has implications for genomic stability, as well as the delivery of genes and siRNAs into mammalian cells.

Palte, Michael J.; Raines, Ronald T.

2012-01-01

81

Nucleic acid visualization with UCSF Chimera  

PubMed Central

With the increase in the number of large, 3D, high-resolution nucleic acid structures, particularly of the 30S and 50S ribosomal subunits and the intact bacterial ribosome, advancements in the visualization of nucleic acid structural features are essential. Large molecular structures are complicated and detailed, and one goal of visualization software is to allow the user to simplify the display of some features and accent others. We describe an extension to the UCSF Chimera molecular visualization system for the purpose of displaying and highlighting nucleic acid characteristics, including a new representation of sugar pucker, several options for abstraction of base geometries that emphasize stacking and base pairing, and an adaptation of the ribbon backbone to accommodate the nucleic acid backbone. Molecules are displayed and manipulated interactively, allowing the user to change the representations as desired for small molecules, proteins and nucleic acids. This software is available as part of the UCSF Chimera molecular visualization system and thus is integrated with a suite of existing tools for molecular graphics.

Couch, Gregory S.; Hendrix, Donna K.; Ferrin, Thomas E.

2006-01-01

82

Nucleic acid visualization with UCSF Chimera.  

PubMed

With the increase in the number of large, 3D, high-resolution nucleic acid structures, particularly of the 30S and 50S ribosomal subunits and the intact bacterial ribosome, advancements in the visualization of nucleic acid structural features are essential. Large molecular structures are complicated and detailed, and one goal of visualization software is to allow the user to simplify the display of some features and accent others. We describe an extension to the UCSF Chimera molecular visualization system for the purpose of displaying and highlighting nucleic acid characteristics, including a new representation of sugar pucker, several options for abstraction of base geometries that emphasize stacking and base pairing, and an adaptation of the ribbon backbone to accommodate the nucleic acid backbone. Molecules are displayed and manipulated interactively, allowing the user to change the representations as desired for small molecules, proteins and nucleic acids. This software is available as part of the UCSF Chimera molecular visualization system and thus is integrated with a suite of existing tools for molecular graphics. PMID:16478715

Couch, Gregory S; Hendrix, Donna K; Ferrin, Thomas E

2006-02-14

83

Nucleic acid biosensors for environmental pollution monitoring.  

PubMed

Nucleic acid-based biosensors are finding increasing use for the detection of environmental pollution and toxicity. A biosensor is defined as a compact analytical device incorporating a biological or biologically-derived sensing element either integrated within or intimately associated with a physicochemical transducer. A nucleic acid-based biosensor employs as the sensing element an oligonucleotide, with a known sequence of bases, or a complex structure of DNA or RNA. Nucleic acid biosensors can be used to detect DNA/RNA fragments or either biological or chemical species. In the first application, DNA/RNA is the analyte and it is detected through the hybridization reaction (this kind of biosensor is also called a genosensor). In the second application, DNA/RNA plays the role of the receptor of specific biological and/or chemical species, such as target proteins, pollutants or drugs. Recent advances in the development and applications of nucleic acid-based biosensors for environmental application are reviewed in this article with special emphasis on functional nucleic acid elements (aptamers, DNAzymes, aptazymes) and lab-on-a-chip technology. PMID:18575633

Palchetti, Ilaria; Mascini, Marco

2008-06-02

84

Detection of nucleic acid sequences by invader-directed cleavage  

SciTech Connect

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.

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

85

Novel biochip platform for nucleic acid analysis.  

PubMed

This manuscript describes the use of a novel biochip platform for the rapid analysis/identification of nucleic acids, including DNA and microRNAs, with very high specificity. This approach combines a unique dynamic chemistry approach for nucleic acid testing and analysis developed by DestiNA Genomics with the STMicroelectronics In-Check platform, which comprises two microfluidic optimized and independent PCR reaction chambers, and a sequential microarray area for nucleic acid capture and identification by fluorescence. With its compact bench-top "footprint" requiring only a single technician to operate, the biochip system promises to transform and expand routine clinical diagnostic testing and screening for genetic diseases, cancers, drug toxicology and heart disease, as well as employment in the emerging companion diagnostics market. PMID:22969389

Pernagallo, Salvatore; Ventimiglia, Giorgio; Cavalluzzo, Claudia; Alessi, Enrico; Ilyine, Hugh; Bradley, Mark; Diaz-Mochon, Juan J

2012-06-11

86

Multicenter Evaluation of a Candida albicans Peptide Nucleic Acid Fluorescent In Situ Hybridization Probe for Characterization of Yeast Isolates from Blood Cultures  

PubMed Central

We evaluated aliquots from 244 clinical blood culture bottles that demonstrated yeasts on Gram stain using a Candida albicans peptide nucleic acid (PNA) fluorescent in situ hybridization (FISH) probe. The sensitivity, specificity, positive predictive value, and negative predictive value of the C. albicans PNA FISH test in this study were 99%, 100%, 100%, and 99.3%, respectively.

Wilson, D. A.; Joyce, M. J.; Hall, L. S.; Reller, L. B.; Roberts, G. D.; Hall, G. S.; Alexander, B. D.; Procop, G. W.

2005-01-01

87

Method for identifying and quantifying nucleic acid sequence aberrations  

DOEpatents

A method for detecting nucleic acid sequence aberrations by detecting nucleic acid sequences having both a first and a second nucleic acid sequence type, the presence of the first and second sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. The method uses a first hybridization probe which includes a nucleic acid sequence that is complementary to a first sequence type and a first complexing agent capable of attaching to a second complexing agent and a second hybridization probe which includes a nucleic acid sequence that selectively hybridizes to the second nucleic acid sequence type over the first sequence type and includes a detectable marker for detecting the second hybridization probe.

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

1998-01-01

88

Zorro locked nucleic acid induces sequence-specific gene silencing  

Microsoft Academic Search

Locked nucleic acids (LNAs) are syn- thetic analogs of nucleic acids that contain a bridging methylene carbon between the 2 and 4 positions of the ribose ring. In this study, we generated a novel sequence-specific antigene molecule \\

Rongbin Ge; Juhana E. Heinonen; Mathias G. Svahn; Abdalla J. Mohamed; Karin E. Lundin; C. I. Edvard Smith

2007-01-01

89

ACCURUN 803 Nucleic Acid Negative Quality Control (HIV ...  

Center for Biologics Evaluation and Research (CBER)

... Approved Products. Substantially Equivalent 510(k ... Nucleic Acid Negative Quality Control (HIV, HCV ... Product: ACCURUN 803 Nucleic Acid Negative ... More results from www.fda.gov/biologicsbloodvaccines/bloodbloodproducts/approvedproducts

90

Nucleic acids encoding IL13 mutants  

US Patent & Trademark Office Database

This invention provides nucleic acid molecules encoding mutant human interleukin 13 molecules showing varying specificity for the restricted (IL4 independent) IL13 receptor. The mutant hIL13 molecules include those made by substituting the amino acid residues that occur in the alpha-helix regions of native hIL13 with various other amino acid residues. Some of the mutants retain the ability to bind and cause signaling through IL13 receptors, while other mutants do not.

2009-10-06

91

Nucleic acid amplification using microfluidic systems.  

PubMed

In the post-human-genome-project era, the development of molecular diagnostic techniques has advanced the frontiers of biomedical research. Nucleic-acid-based technology (NAT) plays an especially important role in molecular diagnosis. However, most research and clinical protocols still rely on the manual analysis of individual samples by skilled technicians which is a time-consuming and labor-intensive process. Recently, with advances in microfluidic designs, integrated micro total-analysis-systems have emerged to overcome the limitations of traditional detection assays. These microfluidic systems have the capability to rapidly perform experiments in parallel and with a high-throughput which allows a NAT analysis to be completed in a few hours or even a few minutes. These features have a significant beneficial influence on many aspects of traditional biological or biochemical research and this new technology is promising for improving molecular diagnosis. Thus, in the foreseeable future, microfluidic systems developed for molecular diagnosis using NAT will become an important tool in clinical diagnosis. One of the critical issues for NAT is nucleic acid amplification. In this review article, recent advances in nucleic acid amplification techniques using microfluidic systems will be reviewed. Different approaches for fast amplification of nucleic acids for molecular diagnosis will be highlighted. PMID:23407669

Chang, Chen-Min; Chang, Wen-Hsin; Wang, Chih-Hung; Wang, Jung-Hao; Mai, John D; Lee, Gwo-Bin

2013-04-01

92

Nucleic acid-coupled colorimetric analyte detectors  

US Patent & Trademark Office Database

The present invention relates to methods and compositions for the direct detection of analytes and membrane conformational changes through the detection of color changes in biopolymeric materials. In particular, the present invention provide for the direct colorimetric detection of analytes using nucleic acid ligands at surfaces of polydiacetylene liposomes and related molecular layer systems.

2001-10-23

93

Common structural features of nucleic acid polymerases  

Microsoft Academic Search

Summary Structures of multisubunit RNA polymerases strongly differ from the many known structures of single subunit DNA and RNA polymerases. However, in functional complexes of these diverse enzymes, nucleic acids take a similar course through the active center. This finding allows superposition of diverse polymerases and reveals features that are functionally equivalent. The entering DNA duplex is bent by almost

P. Cramer

2002-01-01

94

Synthetic nucleic acid analogs preparation and interaction  

Microsoft Academic Search

In order to prepare simply designed nucleic acid models with high functionality, a series of polymeric compounds containing purine and pyrimidine bases as pendant, functional side groups were prepared successfully from their corresponding monomers by either polymerization or polycondensation techniques. As for the functionality of the polymers prepared, specific base-base interactions were studied in detail by measuring UV, NMR and

Kiichi Takemoto; Yoshiaki Inaki

95

Nucleic acids in the classification of campylobacters  

Microsoft Academic Search

The importance of campylobacters in human disease has stimulated improvements in the methods for identification of strains from hospitals and the environment, Reliable and accurate identification depends on a sound classification for which nucleic acid analyses provide fundamental information about species relationships. Studies on the genusCampylobacter show that the genome DNA of species have base compositions of 29 to 38

R. J. Owen

1983-01-01

96

Efficient Method for Matching Nucleic Acid Sequences.  

National Technical Information Service (NTIS)

A method of computing the fraction of matches between two nucleic acid sequences at all possible alignments is described. It makes use of the Fast Fourier Transform. It should be particularly efficient for very long sequences, achieving its result in a nu...

J. Felsenstein S. A. Sawyer R. Kochin

1981-01-01

97

Algorithms for Nucleic Acid Sequence Design  

NASA Astrophysics Data System (ADS)

Motivated by a growing field of research focused on programming function into biomolecules, we seek to decrease the cost of high-quality rational nucleic acid sequence design while increasing its versatility and availability. We begin by describing an algorithm for designing the sequence of one or more interacting nucleic acid strands intended to adopt a target secondary structure at equilibrium. Using ensemble defect optimization, we seek to minimize the average number of incorrectly paired nucleotides at equilibrium, calculated over the entire ensemble of unpseudoknotted secondary structures. Empirically, the algorithm exhibits asymptotic optimality and costs 4/3 the time of a single objective function evaluation for large structures. We then extend this algorithm to design multi-state systems with an arbitrary number of linked targets and demonstrate its efficacy on systems invented by molecular engineers. To improve the ease of use and availability of nucleic acid analysis and design tools, we present NUPACK, a web application already in wide use that allows the international research community to share a high-performance compute cluster for the analysis and design of systems of interacting nucleic acids.

Zadeh, Joseph N.

98

Nucleic acid oxidation in Alzheimer disease  

Microsoft Academic Search

Increasing evidence suggests that oxidative stress is intimately associated with Alzheimer disease pathophysiology. Nucleic acids (nuclear DNA, mitochondrial DNA, and RNA) are one of the several cellular macromolecules damaged by reactive oxygen species, particularly the hydroxyl radical. Because neurons are irreplaceable and survive as long as the organism does, they need elaborate defense mechanisms to ensure their longevity. In Alzheimer

Paula I. Moreira; Akihiko Nunomura; Masao Nakamura; Atsushi Takeda; Justin C. Shenk; Gjumrakch Aliev; Mark A. Smith; George Perry

2008-01-01

99

Nucleic Acid Hybridization Detected by Piezoelectric Resonance  

Microsoft Academic Search

Ordinary AT-cut, quartz, piezoelectric crystals as commonly used in watches, radios, computers, etc., were used to detect the hybridization of complementary strands of synthetic RNA's. The method is based on the large absolute mass increase accompanying hybridization. Nucleic acid strands were covalently attached to the polymer-modified surface of a piezoelectric crystal. When these immobilized probe strands were melted and then

Newton C. Fawcett; Jeffrey A. Evans; Liang-Chy Chien; Naomi Flowers

1988-01-01

100

Carbon nanotubes and nucleic acids: tools and targets  

Microsoft Academic Search

Nucleic acids, with their intrinsic structural properties as well as their high specificity, are playing an important role in the rapid development of nano-technologies. In turn, these new technologies and their efficient performance enable fast and precise methods for detection of nucleic acids, improving the diagnosis of diseases and identification of pathogens. We discuss the use of nucleic acids to

Bibiana Onoa; Ming Zheng; Mildred S. Dresselhaus; Bruce A. Diner

2006-01-01

101

Nucleic acid structure analysis: Local, mathematically rigorous, comparable  

Microsoft Academic Search

A more sophisticated mathematical treatments for analyzing nucleic acid coordinate data is presented. The methodology is both rigorous and comparable for parameterizing nucleic acids in terms of the local structural morphology of complementary and neighboring base pairs. Chapter 1 clearly defines the problems of nucleic acid structure parameterization by examining the consequences of the EMBO workshop guidelines published in 1989.

Babcock

1993-01-01

102

Localized nucleic acid delivery to living cells using nanobiotechnology approaches  

Microsoft Academic Search

Nucleic acids delivered to cells are powerful research tools and promising therapeutics. Spatial and temporal control of delivery is essential for the efficacy, safety and specificity of the application. The shuttles for nucleic acid delivery, so-called vectors, are nanometric biological or synthetic entities comprising complex biological functionalities. We localize nucleic acid delivery exploiting carrier materials. These are on the one

Christian Plank; U. Schillinger; C. Hacker; T. Brill; C. Rudolph; F. Krotz; J. Hirschberger; A. Stemberger; B. Gansbacher

2004-01-01

103

Synthesis and Nucleic Acids Binding Properties of Diastereomeric Aminoethylprolyl Peptide Nucleic Acids (aepPNA)  

Microsoft Academic Search

A general synthetic method for Fmoc-protected monomers of all four diastereomeric aminoethyl peptide nucleic acid (aepPNA) has been developed. The key reaction is the coupling of nucleobase-modified proline derivatives and Fmoc-protected aminoacetaldehyde by reductive alkylation. Oligomerization of the aepPNAs up to 10mer was achieved by Fmoc-solid phase peptide synthesis methodology. Preliminary binding studies of these aepPNA oligomers with nucleic acids

Patcharee Ngamwiriyawong; Tirayut Vilaivan

2011-01-01

104

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

Microsoft Academic Search

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

Cheng Zhi Huang; Ke An Li; Shen Yang Tong

1996-01-01

105

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

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.

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

2010-01-01

106

Enzyme-based colorimetric detection of nucleic acids using peptide nucleic acid-immobilized microwell plates.  

PubMed

The development of label-free or nonlabeling assays for nucleic acids is important in basic biological research and biomedical diagnosis. In this study, we have developed an enzyme-based colorimetric assay for nucleic acids, which combines the robustness of nonlabeling of DNA and RNA samples and the adequate sensitivity of enzymatic reactions. The core of this assay is the use of neutral peptide nucleic acid (PNA) as capture probe and the electrostatic adsorption of horseradish peroxidase (HRP) on hybridized, negatively charged nucleic acids to report the hybridization events, through HRP-catalyzed color reactions of 3,3',5,5'-tetramethylbenzidine and H(2)O(2). The proposed assay has been validated with fully complementary and single base-mismatched DNAs of different chain lengths. The proposed assay has also been validated with total RNA samples extracted from two human cancer cell lines (A 549 lung cancer cell and HeLa cell) for microRNA detection in real samples. Through extensive optimizations of HRP adsorption and nucleic acid hybridization conditions, detection limits of 0.1-0.2 nM for DNA (depending on chain length) and approximately 2 microg of total RNA have been achieved. Surface plasmon resonance spectroscopy has been used to elucidate the HRP adsorption and PNA-nucleic acid hybridizations through real-time measurements and to provide guidance for the development of the colorimetric assay. PMID:17708676

Su, Xiaodi; Teh, Huey Fang; Lieu, Xiaohui; Gao, Zhiqiang

2007-08-21

107

Detection of nucleic acids by multiple sequential invasive cleavages  

DOEpatents

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.

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

1999-01-01

108

Detection of nucleic acids by multiple sequential invasive cleavages 02  

DOEpatents

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.

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

2002-01-01

109

Nucleic acids encoding antifungal polypeptides and uses thereof  

DOEpatents

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.

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

110

Easy to use and rapid isolation and detection of a viral nucleic acid by using paramagnetic microparticles and carbon nanotubes-based screen-printed electrodes  

Microsoft Academic Search

A method that is easy to use, rapid, with a low cost of detecting viral nucleic acid in a biological sample represents the\\u000a essential tool in targeted therapy. In this study, we report the use of paramagnetic microparticles covered by streptavidin\\u000a and modified by an oligonucleotide probe with a specific viral sequence labeled by biotin to detect human immunodeficiency\\u000a virus

Vojtech Adam; Dalibor Huska; Jaromir Hubalek; Rene Kizek

2010-01-01

111

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

PubMed

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

Hida, Kaoru; Kulka, Michael; Papafragkou, Efstathia

2012-12-28

112

Intracellular Nucleic Acid Sensors and Autoimmunity  

PubMed Central

A collection of molecular sensors has been defined by studies in the last decade that can recognize a diverse array of pathogens and initiate protective immune and inflammatory responses. However, if the molecular signatures recognized are shared by both foreign and self-molecules, as is the case of nucleic acids, then the responses initiated by these sensors may have deleterious consequences. Notably, this adverse occurrence may be of primary importance in autoimmune disease pathogenesis. In this case, microbe-induced damage or mishandled physiologic processes could lead to the generation of microparticles containing self-nucleic acids. These particles may inappropriately gain access to the cytosol or endolysosomes and, hence, engage resident RNA and DNA sensors. Evidence, as reviewed here, strongly indicates that these sensors are primary contributors to autoimmune disease pathogenesis, spearheading efforts toward development of novel therapeutics for these disorders.

Kono, Dwight H.; Beutler, Bruce

2011-01-01

113

Topological constraints in nucleic acid hybridization kinetics  

PubMed Central

A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures suggests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechanism of ‘helix-driven wrapping’. Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates the potential for topological effects to influence the kinetics and function of nucleic acid strands. An experimental study of metastable complementary ‘kissing hairpins’ demonstrates that the topological constraint of zero linking number between the loops effectively prevents conversion to the minimum free energy helical state. Introduction of short catalyst strands that break the topological constraint causes rapid conversion to full duplex.

Bois, Justin S.; Venkataraman, Suvir; Choi, Harry M. T.; Spakowitz, Andrew J.; Wang, Zhen-Gang; Pierce, Niles A.

2005-01-01

114

NPIDB: nucleic acid--protein interaction database  

PubMed Central

The Nucleic acid—Protein Interaction DataBase (http://npidb.belozersky.msu.ru/) contains information derived from structures of DNA–protein and RNA–protein complexes extracted from the Protein Data Bank (3846 complexes in October 2012). It provides a web interface and a set of tools for extracting biologically meaningful characteristics of nucleoprotein complexes. The content of the database is updated weekly. The current version of the Nucleic acid—Protein Interaction DataBase is an upgrade of the version published in 2007. The improvements include a new web interface, new tools for calculation of intermolecular interactions, a classification of SCOP families that contains DNA–binding protein domains and data on conserved water molecules on the DNA–protein interface.

Kirsanov, Dmitry D.; Zanegina, Olga N.; Aksianov, Evgeniy A.; Spirin, Sergei A.; Karyagina, Anna S.; Alexeevski, Andrei V.

2013-01-01

115

Therapeutic Potential of Antisense Nucleic Acid Molecules  

NSDL National Science Digital Library

Elucidation of many disease-related signal transduction and gene expression pathways has provided unparalleled opportunities for the development of targeted therapeutics. The types of molecules in development are increasingly varied and include small-molecule enzyme inhibitors, humanized antibodies to cell surface receptors, and antisense nucleic acids for silencing the expression of specific genes. This Perspective reviews the basis for various antisense strategies for modulating gene expression, including RNA interference, and discusses the prospects for their clinical use.

Joanna B. Opalinska (Pommeranian Medical Academy;Department of Hematology REV); Alan M. Gewirtz (University of Pennsylvania School of Medicine;Division of Hematology and Oncology REV)

2003-10-28

116

Nucleic Acid Sequence-Based Amplification  

Microsoft Academic Search

\\u000a Nucleic acid sequence-based amplification (NASBA; bioMérieux, Boxtel, The Netherlands) is a commercially available amplification\\u000a procedure that uses RNA as the target. It makes use of the simultaneous enzymatic activities of avian myeloblastosis virus\\u000a reverse transcriptase (AMV-RT), RNase H, and T7 RNA polymerase, under isothermal conditions. The constant temperature maintained\\u000a throughout the amplification reaction allows each step of the reaction to

Katherine Loens; D. Ursi; H. Goossens; M. Ieven

117

Peptide-templated nucleic acid ligation.  

PubMed

Short oligonucleotide and peptide replicators have been described. To determine whether cross-replication could have occurred between such systems, we have attempted to show that peptides can specifically template the ligation of nucleic acids. A complex between a 35-mer anti-Rev RNA aptamer and a 17-mer arginine-rich motif (ARM) peptide from the HIV-1 Rev protein served as a model system. Aptamer half-molecules were activated for ligation via two activation chemistries, representing two distinct kinetic possibilities for early replicators. Cyanogen bromide activation was transient relative to oligonucleotides that terminated with a 5'-iodine and a 3'phosphorothioate, respectively. The Rev ARM specifically enhanced the degree or rate of ligation by both methods: there was a 10-fold increase in the production of full-length aptamer in the presence of cyanogen bromide and a 5.9- to 7.6-fold enhancement in the rate of ligation for stably activated aptamer half-molecules. These results support the possibility that life could have originated with peptide replicators and transitioned to nucleic acid replicators or that peptide and nucleic acid replicators could have been interdependent. PMID:12698297

Levy, Matthew; Ellington, Andrew D

2003-05-01

118

Single-molecule fluorescence of nucleic acids.  

PubMed

Single-molecule fluorescence studies of nucleic acids are revolutionizing our understanding of fundamental cellular processes related to DNA and RNA processing mechanisms. Detailed molecular insights into DNA repair, replication, transcription, and RNA folding and function are continuously being uncovered by using the full repertoire of single-molecule fluorescence techniques. The fundamental reason behind the stunning growth in the application of single-molecule techniques to study nucleic acid structure and dynamics is the unmatched ability of single-molecule fluorescence, and mostly single-molecule FRET, to resolve heterogeneous static and dynamic populations and identify transient and low-populated states without the need for sample synchronization. New advances in DNA and RNA synthesis, post-synthetic dye-labeling methods, immobilization and passivation strategies, improved dye photophysics, and standardized analysis methods have enabled the implementation of single-molecule techniques beyond specialized laboratories. In this chapter, we introduce the practical aspects of applying single-molecule techniques to investigate nucleic acid structure, dynamics, and function. PMID:24108654

McCluskey, Kaley; Shaw, Euan; Lafontaine, Daniel A; Penedo, J Carlos

2014-01-01

119

Methods for nucleic acid mapping and identification of fine-structural-variations in nucleic acids  

US Patent & Trademark Office Database

A method of juxtaposing sequence tags (GVTs) that are unique positional markers along the length of a population of target nucleic acid molecules is provided, the method comprising: fragmenting the target nucleic acid molecule to form target DNA insert; ligating the target DNA insert to a DNA vector or backbone to create a circular molecule; digesting the target DNA insert endonuclease to cleave the target DNA insert at a distance from each end of the target DNA insert yielding two GVTs comprising terminal sequences of the target DNA insert attached to an undigested linear backbone; recircularizing the linear backbone with the attached GVTs to obtain a circular DNA containing a GVT-pair having two juxtaposed GVTs; and recovering the GVT-pair DNA by nucleic acid amplification or digestion with endonuclease having sites flanking the GVT-pair. Cosmid vectors are provided for creating GVT-pairs of .about.45- to 50-kb separation sequencable by next-generation DNA sequencers.

Lok; Si (Honk Kong, CN)

2012-12-11

120

Use of Nucleic Acid Analogs for the Study of Nucleic Acid Interactions  

PubMed Central

Unnatural nucleosides have been explored to expand the properties and the applications of oligonucleotides. This paper briefly summarizes nucleic acid analogs in which the base is modified or replaced by an unnatural stacking group for the study of nucleic acid interactions. We also describe the nucleoside analogs of a base pair-mimic structure that we have examined. Although the base pair-mimic nucleosides possess a simplified stacking moiety of a phenyl or naphthyl group, they can be used as a structural analog of Watson-Crick base pairs. Remarkably, they can adopt two different conformations responding to their interaction energies, and one of them is the stacking conformation of the nonpolar aromatic group causing the site-selective flipping of the opposite base in a DNA double helix. The base pair-mimic nucleosides can be used to study the mechanism responsible for the base stacking and the flipping of bases out of a nucleic acid duplex.

Nakano, Shu-ichi; Fujii, Masayuki; Sugimoto, Naoki

2011-01-01

121

Lipid-based Nanoparticles for Nucleic Acid Delivery  

Microsoft Academic Search

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

Weijun Li; Francis C. Szoka Jr

2007-01-01

122

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids  

Microsoft Academic Search

The improvements of the force fields and the more accurate treatment of long-range interactions are providing more reliable molecular dynamics simulations of nucleic acids. The abilities of certain nucleic acid force fields to represent the structural and conformational properties of nucleic acids in solution are compared. The force fields are AMBER 4.1, BMS, CHARMM22, and CHARMM27; the comparison of the

Swarnalatha Y. Reddy; Fabrice Leclerc; Martin Karplus

2003-01-01

123

Nucleic acid and amino acid sequences relating to Acinetobacter baumannii for diagnostics and therapeutics  

US Patent & Trademark Office Database

The invention provides isolated polypeptide and nucleic acid sequences derived from Acinetobacter mirabilis that are useful in diagnosis and therapy of pathological conditions; antibodies against the polypeptides; and methods for the production of the polypeptides. The invention also provides methods for the detection, prevention and treatment of pathological conditions resulting from bacterial infection.

2003-05-13

124

CRC handbook of chromatography: Nucleic acids and related compounds  

SciTech Connect

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.

Krstulovic, A.M.

1987-01-01

125

Promising nucleic acid analogs and mimics: characteristic features and applications of PNA, LNA, and morpholino  

Microsoft Academic Search

Nucleic acid analogs and mimics are commonly the modifications of native nucleic acids at the nucleobase, the sugar ring, or the phosphodiester backbone. Many forms of promising nucleic acid analogs and mimics are available, such as locked nucleic acids (LNAs), peptide nucleic acids (PNAs), and morpholinos. LNAs, PNAs, and morpholinos can form both duplexes and triplexes and have improved biostability.

Shantanu Karkare; Deepak Bhatnagar

2006-01-01

126

Symmetry in nucleic acid structure and its role in protein--nucleic acid interactions  

Microsoft Academic Search

It is clear that symmetry concepts will play an increasingly important role in understanding the structural aspects of many protein--nucleic acid interactions. This review summarizes current data and concepts along these lines. Exact crystallographic symmetries are rarely expected to occur in biological systems, and the departures from symmetry that occur may eventually prove to play important roles in modulating physiological

H M Sobell

1976-01-01

127

Enzyme-Free Isothermal Exponential Amplification of Nucleic Acids and Nucleic Acid Analog Signals.  

National Technical Information Service (NTIS)

An enzyme-free, isothermal method of generating an amplification signal indicative of a target nucleic acid molecule is provided, as are compositions for performing such a method. An advantage of the detection system is that it is very sensitive, and can ...

B. Yurke D. Zhang E. Winfree

2004-01-01

128

EGVI endoglucanase and nucleic acids encoding the same  

SciTech Connect

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.

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

2010-10-12

129

EGVI endoglucanase and nucleic acids encoding the same  

DOEpatents

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.

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

2010-10-05

130

EGVI endoglucanase and nucleic acids encoding the same  

DOEpatents

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.

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

2008-04-01

131

EGVII endoglucanase and nucleic acids encoding the same  

DOEpatents

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.

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

2013-07-16

132

EGVII endoglucanase and nucleic acids encoding the same  

DOEpatents

The present invention provides an 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.

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

2009-05-05

133

Yields of Viral and Circulating Cell-Free Nucleic Acids Using the QIAamp ® Circulating Nucleic Acid Kit  

Microsoft Academic Search

\\u000a Fragmented DNA and RNA circulate as cell-free nucleic acids in plasma, serum, urine and other body fluids. Access to these\\u000a molecules for analysis may allow for detection of certain disease states based on a blood sample. In this study the extraction\\u000a efficiency of a large volume nucleic acid extraction kit for circulating and viral nucleic acids was assayed with different

Martin Horlitz; Tanja Hartinger; Simone Graf; Annabelle Lucas; Annette Nocon; Markus Sprenger-Haussels

134

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

Microsoft Academic Search

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

Eveline Lescrinier; Matheus Froeyen; Piet Herdewijn

2003-01-01

135

Detection of North American Eastern and Western Equine Encephalitis Viruses by Nucleic Acid Amplification Assays  

Microsoft Academic Search

We have developed nucleic acid sequence-based amplification (NASBA), standard reverse transcription PCR (RT-PCR), and TaqMan nucleic acid amplification assays for the rapid detection of North American eastern equine encephalitis (EEE) and western equine encephalitis (WEE) viral RNAs from samples collected in the field and clinical samples. The sensitivities of these assays have been compared to that of virus isolation. While

Amy J. Lambert; Denise A. Martin; Robert S. Lanciotti

136

Cyclohexenyl nucleic acids: conformationally flexible oligonucleotides  

PubMed Central

Cyclohexenyl nucleic acid (CeNA) is a nucleic acid mimic, where the (deoxy)ribose sugar has been replaced by cyclohexenyl moieties. In order to study the conformation of cyclohexenyl nucleosides by NMR, the HexRot program was developed to calculate conformations from scalar coupling constants of cyclohexenyl compounds, analogous to the methods applied for (deoxy)ribose nucleosides. The conformational equilibria and the values of the thermodynamic parameters are very similar between a cyclohexenyl nucleoside [energy difference between 2H3 (N-type) and 2H3 (S-type) is 1.8 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 10.9 kJ/mol] and a natural ribose nucleoside (energy difference between N-type and S-type is 2 kJ/mol and equilibrium occurs via the eastern hemisphere with a barrier of 4–20 kJ/mol). The flexibility of the cyclohexenyl nucleoside was demonstrated by the fast equilibrium between two conformational states that was observed in a CeNA-U monomer, combined with the 2H3 conformation of the cyclohexene moiety when incorporated into a Dickerson dodecamer and the 2H3 conformation when incorporated in a d(5?-GCGT*GCG-3?)/d(5?-CGCACGC-3?) duplex, as determined by the NMR spectroscopy. This represents the first example of a synthetic nucleoside that adopts different conformations when incorporated in different double-stranded DNA sequences.

Nauwelaerts, Koen; Lescrinier, Eveline; Sclep, Gert; Herdewijn, Piet

2005-01-01

137

Nucleic acid interactions with pyrite surfaces  

NASA Astrophysics Data System (ADS)

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.

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

2008-09-01

138

Recombination between endogenous and exogenous RNA tumor virus genes as analyzed by nucleic acid hybridization.  

PubMed Central

Certain chicken cells that do not spontaneously release virus particles have been shown to produce a subgroup E avian RNA tumor virus, Rous-associated virus 60 (RAV-60), after infection with viruses of other subgroups. The nucleic acids of RAV-60 were analyzed for sequence homologies with the viral nucleic acids contained in the uninfected cell and with those of RAV-2, the exogenous virus used for the preparation of this particular RAV-60 isolate. In addition, these nucleic acids were compared with those of RAV-0, an endogenous virus spontaneously released from line 100 chicken cells. RAV-60 appears to be intermediate between RAV-0 and RAV-2 in its genetic composition, based on the pattern of hybridization obtained with the nucleic acids of these viruses and on the melting profiles of the various hybrid combinations. Of the three viruses tested, RAV-0 appears to have the greatest sequence homology with the viral nucleic acids of the uninfected cell. Hybridization between RAV-60 3-H-labeled complementary DNA and either DNA or RNA from the uninfected cell indicates that RAV-60 contains some nucleic acid sequences which are not present in the cell. In addition, some RAV-60 sequences which hybridize with the cell nucleic acid contain significant amounts of mismatching, as indicated by the lower thermal stability of these hybrid duplexes. Hybrid formation between these partially homologous sequences was excluded under stringent annealing conditions. The data indicate that RAV-60 is a recombinant between exogenous and endogenous viral genes.

Hayward, W S; Hanafusa, H

1975-01-01

139

Immunoseparation and immunodetection of nucleic acids labeled with halogenated nucleotides.  

PubMed

A novel methodology for labeling, isolation, and detection of nucleic acids is described. Nucleic acid isolation is based on in vivo or in vitro incorporation of BrU or BrdU to either RNA or DNA, respectively, followed by immunoprecipitation of the labeled nucleic acid utilizing anti-BrdU MoAb, which crossreacts with BrU, attached to solid particles. Filter-bound bromine-labeled DNA or RNA was detected by immunoblotting with anti-BrdU MoAb, by a combined Southern/Western or Northern/Western approach, respectively. This method was applied to isolate and detect rRNA and mRNA from human cells, plasmid DNA from bacterial cells, and in vitro synthesized DNA. Newly transcribed BrU-labeled mRNA was recovered from the immunoprecipitates and analyzed by RT-PCR to study phorbol ester-mediated regulation of interleukin 1 gene transcription in human leukemic HL-60 or lymphoma U937 cells. The plasmid DNAs were isolated by immunoprecipitation from transformed bacterial cultures that were grown in the presence of BrdU and were detected immunochemically on filters. Likewise, the products of RT-PCR and Klenow polymerase-catalyzed DNA synthesis in which dTTP was replaced with BrdUTP were detected by immunoblotting. Since the method allows one to selectively separate or detect nucleic acids only synthesized during a pulse of the precursor, it can uniquely be used to identify nascent gene transcripts or the transcripts synthesized within specific time windows, e.g., after induction of differentiation, carcinogenesis, or drug treatment, and distinguish such transcripts from preexisting ones. In addition, this approach offers a simple and inexpensive alternative for preparing labeled DNA as well as RNA probes for use in a variety of hybridization protocols. Due to the low toxicity of BrU and BrdU, this approach can be used in analysis of gene transcription or DNA replication in vivo. PMID:9260920

Haider, S R; Juan, G; Traganos, F; Darzynkiewicz, Z

1997-08-01

140

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

Code of Federal Regulations, 2010 CFR

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

2010-04-01

141

21 CFR 866.5910 - Quality control material for cystic fibrosis nucleic acid assays.  

Code of Federal Regulations, 2010 CFR

... Quality control material for cystic fibrosis nucleic acid assays. 866... Quality control material for cystic fibrosis nucleic acid assays. (a...Quality control material for cystic fibrosis nucleic acid assays. A...

2010-04-01

142

21 CFR 866.5910 - Quality control material for cystic fibrosis nucleic acid assays.  

Code of Federal Regulations, 2010 CFR

... Quality control material for cystic fibrosis nucleic acid assays. 866... Quality control material for cystic fibrosis nucleic acid assays. (a...Quality control material for cystic fibrosis nucleic acid assays. A...

2009-04-01

143

21 CFR 866.5910 - Quality control material for cystic fibrosis nucleic acid assays.  

Code of Federal Regulations, 2013 CFR

... Quality control material for cystic fibrosis nucleic acid assays. 866... Quality control material for cystic fibrosis nucleic acid assays. (a...Quality control material for cystic fibrosis nucleic acid assays. A...

2013-04-01

144

Altered nucleic acid partitioning during phenol extraction or silica adsorption by guanidinium and potassium salts.  

PubMed

Nucleic acids were found to partition into the phenol phase during phenol extraction in the presence of guanidinium at certain concentrations under acidic conditions. The guanidinium-concentration-dependent nucleic acid partitioning patterns were analogous to those of the nucleic acid adsorption/partitioning onto silica mediated by guanidinium, which implied that phenol and silica interact with nucleic acids through similar mechanisms. A competition effect was observed in which the nucleic acids that had partitioned into the phenol phase or onto the silica solid phase could be recovered to the aqueous phases by potassium in a molecular weight-salt concentration-dependent manner (the higher molecular weight nucleic acids needed higher concentrations of potassium to be recovered, and vice versa). Methods were developed based on these findings to isolate total RNA from Escherichia coli. By controlling the concentrations of guanidinium and potassium salts used before phenol extraction or silica adsorption, we can selectively recover total RNA but not the high molecular weight genomic DNA in the aqueous phases. Genomic DNA-free total RNA obtained by our methods is suitable for RT-PCR or other purposes. The methods can also be adapted to isolate small RNAs or RNA in certain molecular weight ranges by changing the salt concentrations used. PMID:21925480

Xu, Lei; Lv, Jun; Ling, Liefeng; Wang, Peng; Song, Ping; Su, Ruirui; Zhu, Guoping

2011-08-31

145

Nature and Magnitude of Aromatic Stacking of Nucleic Acid Bases  

Microsoft Academic Search

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

Jiri Sponer; Kevin E. Riley; Pavel Hobza

2008-01-01

146

Study on the interaction between nucleic acids and cationic surfactants  

Microsoft Academic Search

The interactions of nucleic acids and cationic surfactants (cetylpyridine bromide (CPB) and cetyltrimethylammonium bromide (CTMAB)) in aqueous solution have been studied using the techniques of resonance light scattering (RLS) spectroscopy, the absorption spectroscopy, zeta potential assay and NMR assignment measurement. It is considered that CPB or CTMAB can assemble on the surface of nucleic acid via electrostatic and hydrophobic forces,

Rutao Liu; Jinghe Yang; Changxia Sun; Xia Wu; Lei Li; Benyu Su

2004-01-01

147

AN EXTENDED DOT-BRACKET-NOTATION FOR FUNCTIONAL NUCLEIC ACIDS  

Microsoft Academic Search

Functional nucleic acids are an attractive substrate for molecular computing. A nucleic acid molecule is a linear chain of covalently bound building blocks assembled in arbitrary order from a set of typically four nucleotides. Certain pairs of nucleotides weakly attract each other through short-range electrostatic interaction and, accordingly, complementary sequences of nucleotides can bind to each other. The complementary stretches

I. Ramlan; Klaus-Peter Zauner

2008-01-01

148

Magnetic particles for the separation and purification of nucleic acids  

Microsoft Academic Search

Nucleic acid separation is an increasingly important tool for molecular biology. Before modern technologies could be used, nucleic acid separation had been a time- and work-consuming process based on several extraction and centrifugation steps, often limited by small yields and low purities of the separation products, and not suited for automation and up-scaling. During the last few years, specifically functionalised

Sonja Berensmeier

2006-01-01

149

De Novo Design of Sequences for Nucleic Acid Structural Engineering  

Microsoft Academic Search

An interactive procedure has been developed to assign sequences for the design of nucleic acid secondary structure. The primary goal of the procedure is to facilitate macromolecular architecture studies through the design of branched nucleic acid mono- and oligo-junction constructs in a convenient fashion. The essential feature of the sequence-symmetry minimization algorithm employed is the treatment of short sequences as

Nadrian C. Seeman

1990-01-01

150

Pseudointrinsic probes for generating spectrally enhanced proteins and nucleic acids  

Microsoft Academic Search

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

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

1995-01-01

151

Application of peptide nucleic acid towards development of nanobiosensor arrays  

Microsoft Academic Search

Peptide nucleic acid (PNA) is the modified DNA or DNA analogue with a neutral peptide backbone instead of a negatively charged sugar phosphate. PNA exhibits chemical stability, resistant to enzymatic degradation inside living cell, recognizing specific sequences of nucleic acid, formation of stable hybrid complexes like PNA\\/DNA\\/PNA triplex, strand invasion, extraordinary thermal stability and ionic strength, and unique hybridization relative

Ravindra P. Singh; Byung-Keun Oh; Jeong-Woo Choi

2010-01-01

152

The Effect of Nucleic Acid Geometry on Counterion Association  

Microsoft Academic Search

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

Martha C. Olmsted

1996-01-01

153

Nucleic acid and nucleotide-mediated synthesis of inorganic nanoparticles  

Microsoft Academic Search

Since the advent of practical methods for achieving DNA metallization, the use of nucleic acids as templates for the synthesis of inorganic nanoparticles (NPs) has become an active area of study. It is now widely recognized that nucleic acids have the ability to control the growth and morphology of inorganic NPs. These biopolymers are particularly appealing as templating agents as

Lorenzo Berti; Glenn A. Burley

2008-01-01

154

Genetic Algorithm Based Approach for Nucleic Acid Pattern Extraction  

Microsoft Academic Search

Finding a common pattern among nucleic acid sequences in a given database is an important yet relatively difficult problem in computational biology. Such a pattern is useful for describing the characteristics of a certain family of nucleic acid sequences, and can also be used for classification purposes as well as examine the closeness of two organisms. In this paper, we

Miao Liu; Hai-Feng Guo; Zhengxin Chen

2005-01-01

155

Nucleic Acid Amplification Testing in Suspected Child Sexual Abuse  

ERIC Educational Resources Information Center

|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…

Esernio-Jenssen, Debra; Barnes, Marilyn

2011-01-01

156

Nucleic Acid Isothermal Amplification Technologies—A Review  

Microsoft Academic Search

Nucleic acid amplification technologies are used in the field of molecular biology and recombinant DNA technologies. These techniques are used as leading methods in detecting and analyzing a small quantity of nucleic acids. The polymerase chain reaction (PCR) is the most widely used method for DNA amplification for detection and identification of infectious diseases, genetic disorders and other research purposes.

Pooria Gill; Amir Ghaemi

2008-01-01

157

Cell-free nucleic acids as biomarkers in cancer patients  

Microsoft Academic Search

DNA, mRNA and microRNA are released and circulate in the blood of cancer patients. Changes in the levels of circulating nucleic acids have been associated with tumour burden and malignant progression. In the past decade a wealth of information indicating the potential use of circulating nucleic acids for cancer screening, prognosis and monitoring of the efficacy of anticancer therapies has

Heidi Schwarzenbach; Dave S. B. Hoon; Klaus Pantel

2011-01-01

158

Topics in Nucleic Acids Structure: Noncanonical Helices and RNA Structure  

Microsoft Academic Search

\\u000a This chapter builds upon nucleic acid concepts introduced in the prior two chapters to include a description of alternative\\u000a hydrogen bonding schemes in nucleic acids, non-canonical helical and hybrid structures, DNA mimics, overstretched and understretched\\u000a DNA, and RNA structure and folding, including secondary and tertiary-structure RNA modeling.

Tamar Schlick

159

Nucleic acid amplification testing in suspected child sexual abuse.  

PubMed

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. PMID:22126105

Esernio-Jenssen, Debra; Barnes, Marilyn

2011-11-01

160

The nucleic acid content of some edible mushrooms  

Microsoft Academic Search

An improved method for the determination of nucleic acid content in edible mushrooms is described. Details of tissue homogenization and extraction are also included. In regard to the limit suggested by the Protein Advisory Group of the United Nations System, the amount of nucleic acids found in Agaricus bisporus, Pleurotus cystidiosus, Pleurotus sajor-caju and Volvariella volvacea indicates that it is

G. S. F. Li; S. T. Chang

1982-01-01

161

Multiplex SNP genotyping using Locked Nucleic Acid and microfluidics  

Microsoft Academic Search

Locked Nucleic Acid's or LNA are a new class of bicyclic DNA analogues that have a high affinity and specificity towards complementary nucleic acids. LNA containing oligonucleotides were used to develop a multiplex SNP genotyping assay based entirely on hybridization between capture probe and target. The approach incorporates a polymer microarray platform, photochemistry for immobilization of oligonucleotides onto microarrays, and

Yoanna Choleva; Mikkel Nørholm; Susanne Pedersen; Peter Mouritzen; Poul E. Høiby; Alex. T. Nielsen; Søren Møller; Mogens H. Jakobsen; Lars Kongsbak

2001-01-01

162

Nucleic acid based fluorescent sensor for mercury detection  

DOEpatents

A nucleic acid enzyme comprises an oligonucleotide containing thymine bases. The nucleic acid enzyme is dependent on both Hg.sup.2+and a second ion as cofactors, to produce a product from a substrate. The substrate comprises a ribonucleotide, a deoxyribonucleotide, or both.

Lu, Yi; Liu, Juewen

2013-02-05

163

Nucleic acid polymerases use a general acid for nucleotidyl transfer  

Microsoft Academic Search

Nucleic acid polymerases catalyze the formation of DNA or RNA from nucleoside-triphosphate precursors. Amino acid residues in the active site of polymerases are thought to contribute only indirectly to catalysis by serving as ligands for the two divalent cations that are required for activity or substrate binding. Two proton-transfer reactions are necessary for polymerase-catalyzed nucleotidyl transfer: deprotonation of the 3?-hydroxyl

Christian Castro; Eric D Smidansky; Jamie J Arnold; Kenneth R Maksimchuk; Ibrahim Moustafa; Akira Uchida; Matthias Götte; William Konigsberg; Craig E Cameron

2009-01-01

164

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

Microsoft Academic Search

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

Nicke Svanvik; Gunnar Westman; Dongyuan Wang; Mikael Kubista

2000-01-01

165

Highly Stable Duplex Formation by Artificial Nucleic Acids Acyclic Threoninol Nucleic Acid (aTNA) and Serinol Nucleic Acid (SNA) with Acyclic Scaffolds.  

PubMed

The stabilities of duplexes formed by strands of novel artificial nucleic acids composed of acyclic threoninol nucleic acid (aTNA) and serinol nucleic acid (SNA) building blocks were compared with duplexes formed by the acyclic glycol nucleic acid (GNA), peptide nucleic acid (PNA), and native DNA and RNA. All acyclic nucleic acid homoduplexes examined in this study had significantly higher thermal stability than DNA and RNA duplexes. Melting temperatures of homoduplexes were in the order of aTNA>PNA?GNA?SNA?RNA>DNA. Thermodynamic analyses revealed that high stabilities of duplexes formed by aTNA and SNA were due to large enthalpy changes upon formation of duplexes compared with DNA and RNA duplexes. The higher stability of the aTNA homoduplex than the SNA duplex was attributed to the less flexible backbone due to the methyl group of D-threoninol on aTNA, which induced clockwise winding. Unlike aTNA, the more flexible SNA was able to cross-hybridize with RNA and DNA. Similarly, the SNA/PNA heteroduplex was more stable than the aTNA/PNA duplex. A 15-mer SNA/RNA was more stable than an RNA/DNA duplex of the same sequence. PMID:24038212

Murayama, Keiji; Tanaka, Yoshihiro; Toda, Takasuke; Kashida, Hiromu; Asanuma, Hiroyuki

2013-08-23

166

Towards biomedical applications for nucleic acid nanodevices.  

PubMed

DNA and RNA can be used to construct artificial nanodevices with strong potential for future biomedical applications. DNA nanodevices can function as biosensors, which detect and report the presence of proteins and naturally occurring nucleic acids, such as mRNA or microRNAs. Complex sensors can be realized by supporting DNA devices with DNA-based information processing. Artificial DNA-based reaction networks can be created that amplify molecular signals or evaluate logical functions to report the simultaneous presence of several disease-related molecules. Other applications for DNA nanodevices are found in controlled release and drug delivery. DNA can be used to build nanocontainers for drugs or switchable hydrogels, which can trap and release compounds. For in vivo applications of DNA nanodevices, techniques for efficient packaging and delivery have been developed and the first examples of intracellular RNA-based nanodevices have already been demonstrated. PMID:18095848

Simmel, Friedrich C

2007-12-01

167

ENDOCYTOSIS PATHWAYS FOR NUCLEIC ACID THERAPEUTICS  

PubMed Central

The development of nanoscale delivery vehicles for siRNAs is a current topic of considerable importance. However, little is understood about the exact trafficking mechanisms for siRNA-vehicle complexes across the plasma membrane and into the cytoplasm. While some information can be gleaned from studies on delivery of plasmid DNA, the different delivery requirements for these two vehicles makes drawing specific conclusions a challenge. However, using chemical inhibitors of different endocytosis pathways, studies on which endocytotic pathways are advantageous and deleterious for the delivery of nucleic acid drugs are emerging. Using this information as a guide, it is expected that the future development of effective siRNA delivery vehicles and therapeutics will be greatly improved.

MALEFYT, AMANDA P.; WALTON, S. PATRICK; CHAN, CHRISTINA

2013-01-01

168

Nucleic acid adjuvants: toward an educated vaccine.  

PubMed

Two striking facts surround the practice of vaccination: It is the sole medical approach to have fully annihilated a disease, yet the development of most effective vaccines took place without considering the intricate cellular processes they wish to effectuate. While extremely potent vaccines have been developed that can protect practically a lifetime after a single dose, numerous other vaccines have utterly failed or provide only marginal protection. Here, we aim to illustrate why this difference in efficacy exists, and underline why specific cytotoxic T cell-inducing vaccines could combat persistent major diseases. Moreover, we discuss how the combinatorial use of nucleic acid adjuvants in vaccines could aid the development of the latter and move vaccine design from the empirical stage into an era of "educated design." PMID:22449776

van den Boorn, Jasper G; Barchet, Winfried; Hartmann, Gunther

2012-01-01

169

Nucleic Acid Recognition by Tandem Helical Repeats  

PubMed Central

Protein domains constructed from tandem ?-helical repeats have until recently been primarily associated with protein scaffolds or RNA recognition. Recent crystal structures of human mitochondrial termination factor MTERF1 and Bacillus cereus alkylpurine DNA glycosylase AlkD bound to DNA revealed two new superhelical tandem repeat architectures capable of wrapping around the double helix in unique ways. Unlike DNA sequence recognition motifs that rely mainly on major groove read-out, MTERF and ALK motifs locate target sequences and aberrant nucleotides within DNA by resculpting the double-helix through extensive backbone contacts. Comparisons between MTERF and ALK repeats, together with recent advances in ssRNA recognition by Pumilio/FBF (PUF) domains, provide new insights into the fundamental principles of protein-nucleic acid recognition.

Rubinson, Emily H.; Eichman, Brandt F.

2013-01-01

170

Guidance for Industry: Use of Nucleic Acid Tests on Pooled ...  

Center for Biologics Evaluation and Research (CBER)

Text Version... 1) FDA has licensed nucleic acid tests (NAT) as tests to screen blood donors for HIV-1 ribonucleic acid (RNA), and HCV RNA; and ... More results from www.fda.gov/downloads/biologicsbloodvaccines/guidancecomplianceregulatoryinformation

171

Poisson-Boltzmann calculations for nucleic acids and nucleic acids complexes  

Microsoft Academic Search

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

Krystyna Zakrzewska; Andrea Madami; Richard Lavery

1996-01-01

172

Nucleic acids of the human ABCC11 gene, vectors containing such nucleic acids and uses thereof  

US Patent & Trademark Office Database

The present invention relates to nucleic acids corresponding to various exons of the ABCC11 gene as well as the cDNA encoding the novel full length of ABCC11 protein. The invention also relates to means for the detection of polymorphisms in general, and of mutations in particular, in the ABCC11 gene or in the corresponding protein produced by the allelic form of the ABCC11 gene.

Rosier; Marie (Antony, FR); Prades; Catherine (Thiais, FR); Arnould; Isabelle (Chennevieres sur Marne, FR); Dean; Michael (Frederick, MD); Allikmets; Rando (Cornwall-on

2005-05-17

173

Locked nucleic acids: a family of high affinity nucleic acid probes  

Microsoft Academic Search

The structure and synthesis of LNA (locked nucleic acid) is presented. LNA is defined as an oligonucleotide containing one or more 2'-O, 4'-C-methylene-beta-D-ribofuranosyl nucleotide monomer(s). The improved synthesis of the thymine LNA monomer is shown. The LNA molecular family is presented and the member classes are described in relation to their chemical structures. The hybridization property of each member is

T. Koch

2003-01-01

174

Nucleic Acid Metabolism in Germinating Onion: I. Changes in Root Tip Nucleic Acid during Germination.  

PubMed

Nucleic acid synthesis in the G(1) cell population of the 1-millimeter apex of the Allium cepa embryo was studied during the initial 73 hours of germination. Quantitative data indicate that the total amount of RNA per cell began to increase after 18 hours of germination while the initial DNA per cell increase did not occur until some 20 hours later. Polyacrylamide gel electrophoresis patterns of (3)H-uridine-labeled total nucleic acid samples indicated that synthesis of all detectable RNA fractions present in the pre-emergent 1-millimeter apex (i.e., cytoplasmic and "chloroplast-like" RNA) began at approximately the same time (18 hours). Synthesis of the various cytoplasmic RNA fractions continued throughout the germination period. Data indicating synthesis of the "chloroplast-like" RNA were obtained only for the initial 36 hours of germination. Specific radioactivity of (3)H-uridine-labeled total nucleic acid increased during the first 41.5 hours of germination but then decreased while the accumulation of RNA per cell continued to increase throughout the 73-hour period. In addition, a method is described which reduced the bacterial contamination of Allium seed to a level not detectable by incorporation of radioactive precursors into bacterial ribosomal RNA. PMID:16657739

Melera, P W

1971-07-01

175

Fluorescent complexes of nucleic acids/8-hydroxyquinoline/lanthanum(III) and the fluorometry of nucleic acids  

SciTech Connect

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 NH{sub 3}-NH{sub 4}Cl buffer) ternary fluorescent complexes are formed which emit at 485.0 nm for calf thymus DNA and at 480.0 nm for fish sperm DNA when excited at 265.0 nm. Based on the fluorescence reactions sensitive fluorometric methods for nucleic acids were proposed. Using optimal conditions, the calibration curves were linear in the range of 0.4 --3.6 {mu}g{sup .}ml{sup -1} for calf thymus DNA, 0.4 -- 4.0 {mu}g{sup .}ml{sup -1} for fish sperm DNA and 0.4 --4.0{mu}g{sup .}ml{sup -1} for yeast RNA, respectively. Five synthetic samples were determined with satisfaction.

Cheng Zhi Huang; Ke An Li; Shen Yang Tong [Peking Univ., Beijing (China)

1996-07-01

176

Nucleic acid-binding polymers as anti-inflammatory agents.  

PubMed

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

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

2011-08-15

177

Nucleic acid-binding polymers as anti-inflammatory agents  

PubMed Central

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.

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

2011-01-01

178

Peptide-modified vectors for nucleic acid delivery to neurons  

PubMed Central

Neuron-targeted, nucleic acid delivery systems are important technologies for realizing the potential of gene therapy for nervous system disorders. However, neurons are difficult cells to transfect using non-viral vectors due in part to the specific and unique delivery challenges present in these cells. We have investigated several bioactive peptides for their ability to assist in overcoming delivery barriers in mammalian cells. We summarize here our recent progress in developing and applying peptide-modified polycations for nucleic acid delivery. In addition, we present data demonstrating the potential of using multicomponent, peptide-modified polycations for nucleic acid delivery to neurons.

Kwon, E.J.; Bergen, J.M.; Park, I.K.; Pun, S.H.

2008-01-01

179

Artificial and natural nucleic acid self-assembling systems  

NASA Astrophysics Data System (ADS)

Nucleic acids are good candidates for nanomachine construction. They participate in all the processes of life, and so can function as structural building blocks and dynamic catalysts. However, to use nucleic acids as nanomachines, a better understanding of their material properties, how to design structures using them, and their dynamics is needed. We have tried to address these issues, in a small way, with nucleic acid force field development, an attempt at nanostructural design and synthesis using DNA, and a study of the RNA/protein regulatory dynamics of the tryptophan regulatory attenuation protein.

Wood, Marcus

180

Point-of-care nucleic acid detection using nanotechnology.  

PubMed

Recent developments in nanotechnology have led to significant advancements in point-of-care (POC) nucleic acid detection. The ability to sense DNA and RNA in a portable format leads to important applications for a range of settings, from on-site detection in the field to bedside diagnostics, in both developing and developed countries. We review recent innovations in three key process components for nucleic acid detection: sample preparation, target amplification, and read-out modalities. We discuss how the advancements realized by nanotechnology are making POC nucleic acid detection increasingly applicable for decentralized and accessible testing, in particular for the developing world. PMID:24057263

Hartman, Mark R; Ruiz, Roanna C H; Hamada, Shogo; Xu, Chuanying; Yancey, Kenneth G; Yu, Yan; Han, Wei; Luo, Dan

2013-09-13

181

Point-of-care nucleic acid detection using nanotechnology  

NASA Astrophysics Data System (ADS)

Recent developments in nanotechnology have led to significant advancements in point-of-care (POC) nucleic acid detection. The ability to sense DNA and RNA in a portable format leads to important applications for a range of settings, from on-site detection in the field to bedside diagnostics, in both developing and developed countries. We review recent innovations in three key process components for nucleic acid detection: sample preparation, target amplification, and read-out modalities. We discuss how the advancements realized by nanotechnology are making POC nucleic acid detection increasingly applicable for decentralized and accessible testing, in particular for the developing world.

Hartman, Mark R.; Ruiz, Roanna C. H.; Hamada, Shogo; Xu, Chuanying; Yancey, Kenneth G.; Yu, Yan; Han, Wei; Luo, Dan

2013-10-01

182

Detection of dengue virus RNA using nucleic acid hybridization.  

PubMed

Conditions for using slot-blot nucleic acid hybridization to quantitatively detect dengue-2 virus using a radiolabelled cDNA probe, pVV17, were determined. As little as 11 plaque-forming units of virus were detected using a hybridization mixture without formamide and performing the test at 70 degrees C. While predominantly serotype-specific using stringent (65 degrees C) washing conditions, the probe detected all four dengue virus serotypes using astringent (28 degrees C) washing conditions. No significant qualitative differences were detected using Thai dengue-2 viruses isolated over a 10-year period. High titered, anti-flavivirus antibodies blocked virus detection by an antigen capture, enzyme-linked, immunosorbent assay or by intrathoracic inoculation of Toxorhyncites mosquitoes, but not by nucleic acid hybridization. The appearance of virus-specified RNA coincided with the detection of antigen in infected C6/36 (Aedes albopictus) cells by immunofluorescence, or in cell culture supernatants by the antigen capture method. The method has potential as a diagnostic tool for identifying dengue viruses in clinical and field specimens. PMID:2881940

Henchal, E A; Narupiti, S; Feighny, R; Padmanabhan, R; Vakharia, V

1987-02-01

183

Effect of Berenil on Nucleic Acid Synthesis in Trypanosoma brucei.  

National Technical Information Service (NTIS)

The present study was undertaken to examine (a) the effect of diaminazene on the growth and cellular morphology of monomorphic bloodstream trypanosomes; (b) the effect of diaminazene on nucleic acid and protein synthesis of these trypanosomes; and (c) the...

M. S. Zahalsky A. C. Zahalsky

1979-01-01

184

Sharing and archiving nucleic acid structure mapping data  

PubMed Central

Nucleic acids are particularly amenable to structural characterization using chemical and enzymatic probes. Each individual structure mapping experiment reveals specific information about the structure and/or dynamics of the nucleic acid. Currently, there is no simple approach for making these data publically available in a standardized format. We therefore developed a standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments, or SNRNASMs. We propose a schema for sharing nucleic acid chemical probing data that uses generic public servers for storing, retrieving, and searching the data. We have also developed a consistent nomenclature (ontology) within the Ontology of Biomedical Investigations (OBI), which provides unique identifiers (termed persistent URLs, or PURLs) for classifying the data. Links to standardized data sets shared using our proposed format along with a tutorial and links to templates can be found at http://snrnasm.bio.unc.edu.

Rocca-Serra, Philippe; Bellaousov, Stanislav; Birmingham, Amanda; Chen, Chunxia; Cordero, Pablo; Das, Rhiju; Davis-Neulander, Lauren; Duncan, Caia D.S.; Halvorsen, Matthew; Knight, Rob; Leontis, Neocles B.; Mathews, David H.; Ritz, Justin; Stombaugh, Jesse; Weeks, Kevin M.; Zirbel, Craig L.; Laederach, Alain

2011-01-01

185

Nucleic Acid Conjugated Nanomaterials for Enhanced Molecular Recognition  

PubMed Central

Nucleic acids, whether designed or selected in vitro, play important roles in biosensing, medical diagnostics and therapy. Specifically, the conjugation of functional nucleic acid-based probe molecules and nanomaterials has resulted in an unprecedented improvement in the field of molecular recognition. With their unique physical and chemical properties, nanomaterials facilitate the sensing process and amplify the signal of recognition events. Thus, the coupling of nucleic acids with various nanomaterials opens up a promising future for molecular recognition. The literature offers a broad spectrum of recent advances in biosensing by employing different nano-platforms with designed nucleic acids, especially gold nanoparticles, carbon nanotubes, silica nanoparticles and quantum dots. The advantages of these novel combinations are discussed from the perspective of molecular recognition in chemistry, biology and medicine, along with the problems confronting future applications.

Wang, Hao; Yang, Ronghua; Yang, Liu; Tan, Weihong

2009-01-01

186

Binary malachite green aptamer for fluorescent detection of nucleic acids.  

PubMed

A new probe that can fluorescently report the presence of specific nucleic acids in solution with extremely high selectivity was developed. The probe consists of malachite green-a triphenylmethane dye-and two short RNA strands, each of which comprises a fragment complementary to an analyte molecule and a fragment of a malachite green aptamer (MGA). The two RNA strands form MGA upon hybridization to the adjacent positions of the nucleic acid analyte. MGA is able to bind malachite green and enhance the fluorescence of the dye, thus monitoring the presence of the nucleic acid in solution. The probe reliably discriminates against 41 out of 42 possible single nucleotide substitutions in 14-mer DNA analyte at room temperature in physiological buffer. Consisting of unmodified RNA strands, which can be expressed in living cells, binary MGA probe represents a promising instrument for real-time nucleic acid monitoring in vivo. PMID:16144363

Kolpashchikov, Dmitry M

2005-09-14

187

Nucleic Acid Duplexes Incorporating a Dissociable Covalent Base Pair  

NASA Astrophysics Data System (ADS)

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.

Gao, Kui; Orgel, Leslie E.

1999-12-01

188

Nucleic acids encoding hyperactive PiggyBac transposases  

US Patent & Trademark Office Database

The present invention provides PiggyBac transposase proteins, nucleic acids encoding the same, compositions comprising the same, kits comprising the same, non-human transgenic animals comprising the same, and methods of using the same.

2013-03-19

189

Formulation of a Peptide Nucleic Acid Based Nucleic Acid Delivery Construct  

PubMed Central

Gene delivery biomaterials need to be designed to efficiently achieve nuclear delivery of plasmid DNA. Polycations have been used to package DNA and other nucleic acids within sub-micron sized particles, offering protection from shear-induced or enzymatic degradation. However, cytotoxicity issues coupled with limited in vivo transfection efficiencies minimize the effectiveness of this approach. In an effort to improve upon existing technologies aimed at delivering nucleic acids, an alternative approach to DNA packaging was explored. Peptide nucleic acids (PNAs) were used to directly functionalize DNA with poly(ethylene glycol) (PEG) chains that provide a steric layer and inhibit multimolecular aggregation during complexation. DNA prePEGylation by this strategy was predicted to enable the formation of more homogeneous and efficiently packaged polyplexes. In this work, DNA-PNA-peptide-PEG (DP3) conjugates were synthesized and self-assembled with 25 kDa poly(ethylenimine) (PEI). Complexes with small standard deviations and average diameters ranging from 30 – 50 nm were created, with minimal dependence of complex size on N:P ratio (PEI amines to DNA phosphates). Furthermore, PEI-DNA interactions were altered by the derivitization strategy, resulting in tighter compaction of the PEI-DP3 complexes in comparison with PEI-DNA complexes. Transfection experiments in Chinese Hamster Ovary (CHO) cells revealed comparable transfection efficiencies but reduced cytotoxicities of the PEI-DP3 complexes relative to PEI-DNA complexes. The enhanced cellular activities of the PEI-DP3 complexes were maintained following the removal of free PEI from the PEI-DP3 formulations, whereas the cellular activity of the conventional PEI-DNA formulations was reduced by free PEI removal. These findings suggest that DNA prePEGylation by the PNA-based strategy might provide a way to circumvent cytotoxicity and formulation issues related to the use of PEI for in vivo gene delivery.

Millili, Peter G.; Yin, Daniel H.; Fan, Haihong; Naik, Ulhas P.; Sullivan, Millicent O.

2010-01-01

190

Electrochemical Molecular Analysis Without Nucleic Acid Amplification  

PubMed Central

Electrochemical biosensors have revolutionized glucose monitoring but have not yet fulfilled their promise of a low cost, direct detection replacement for genetic amplification tests such as PCR [K. Kerman, M. Kobayashi, E. Tamiya, Recent trends in electro-chemical DNA biosensor technology, Meas. Sci. Technol. 15 (2004) R1-R11; A. Chaubey, B.D. Malhotra, Mediated biosensors. Biosens. Bioelectron. 17 (6-7) (2002) 441-456]. It has been anticipated that the integration of nanoscale chemical structures such as self-assembled monolayers with electrochemical biosensors would increase sensitivity by decreasing inherent system noise. We have designed a novel biosensing approach incorporating such integration and achieved rapid, ultra-low concentration sensitivities without target amplification. Raw samples are mixed with lysis buffer to allow hybridization of nucleic acid targets with anchor and signal probes before immobilizing a signaling enzyme proximate to the biosensor surface. A bias potential is subsequently applied and the secondary byproduct of a cyclic peroxidase reaction measured. Further studies have demonstrated the application of our approach in protein, clinical chemistry, and ionic assays.

Gau, Vincent; Ma, Shu-Ching; Wang, Hua; Tsukuda, Joni; Kibler, John; Haake, David A.

2006-01-01

191

Nucleic acid modifications with epigenetic significance.  

PubMed

Epigenetic modifications influence gene expression without alterations to the underlying nucleic acid sequence. In addition to the well-known 5-methylcytosine (5mC), 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxycytosine (5caC) have recently been discovered in genomic DNA, which all result from iterative oxidation of 5mC by the TET (Ten-Eleven-Translocate) family of enzymes. Recent studies have proposed the roles of these oxidized cytosines in mediating active demethylation of 5mC. Through affinity-based genome-wide sequencing and oxidation-assisted base-resolution sequencing methods, 5hmC is found to be dynamically regulated during development, and is enriched mainly in distal regulatory elements in human and mouse embryonic cells. Among RNA modifications, N(6)-methyladenosine (m(6)A) is a widespread yet poorly studied base modification in mRNA and non-coding RNA. The recent discovery that m(6)A in RNA is the major substrate of the fat mass and obesity associated (FTO) protein draws attention to the potential regulatory functions of reversible RNA methylations, which can be dynamic, and could be important in many fundamental cellular functions. PMID:23092881

Fu, Ye; He, Chuan

2012-10-22

192

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

PubMed Central

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.

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

2012-01-01

193

Fluorogenic, catalytic, photochemical reaction for amplified detection of nucleic acids.  

PubMed

Photochemical, nucleic acid-induced reactions, which are controlled by nontoxic red light, are well-suited for detection of nucleic acids in live cells, since they do not require any additives and can be spatially and temporally regulated. We have recently described the first reaction of this type, in which a phenylselenyl derivative of thymidine (5'-PhSeT-ODNa) is cleaved in the presence of singlet oxygen (Fülöp, A., Peng, X., Greenberg, M. M., Mokhir, A. (2010) A nucleic acid directed, red light-induced chemical reaction. Chem. Commun. 46, 5659-5661). The latter reagent is produced upon exposure of a photosensitizer 3'-PS-ODNb (PS = Indium(III)-pyropheophorbide-a-chloride: InPPa) to >630 nm light. In 2012 we reported on a fluorogenic version of this reaction (Dutta, S., Flottmann, B., Heilemann, M., Mokhir, A. (2012) Hybridization and reaction-based, fluorogenic nucleic acid probes. Chem. Commun. 47, 9664-9666), which is potentially applicable for the detection of nucleic acids in cells. Unfortunately, its yield does not exceed 25% and no catalytic turnover could be observed in the presence of substrate excess. This problem occurs due to the efficient, competing oxidation of the substrate containing an electron rich carbon-carbon double bonds (SCH?CHS) in the presence of singlet oxygen with formation of a noncleavable product (SCH?CHSO). Herein we describe a related, but substantially improved photochemical, catalytic transformation of a fluorogenic, organic substrate, which consists of 9,10-dialkoxyanthracene linked to fluorescein, with formation of a bright fluorescent dye. In highly dilute solution this reaction occurs only in the presence of a nucleic acid template. We developed three types of such a reaction and demonstrated that they are high yielding and generate over 7.7 catalytic turnovers, are sensitive to single mismatches in nucleic acid targets, and can be applied for determination of both the amount of nucleic acids and potentially their localization. PMID:23964892

Dutta, Subrata; Fülöp, Annabelle; Mokhir, Andriy

2013-09-03

194

Nucleic acid-associated autoantigens: Pathogenic involvement and therapeutic potential  

Microsoft Academic Search

Autoimmunity to ubiquitously expressed macromolecular nucleic acid–protein complexes such as the nucleosome or the spliceosome is a characteristic feature of systemic autoimmune diseases. Disease-specificity and\\/or association with clinical features of some of these autoimmune responses suggest pathogenic involvement which, however, has been proven in only a few cases so far. Although the mechanisms leading to autoimmunity against nucleic acid-containing complexes

Markus H. Hoffmann; Sylvie Trembleau; Sylviane Muller; Günter Steiner

2010-01-01

195

Nucleic Acid Transport in Plant-Pathogen Interactions  

Microsoft Academic Search

\\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

Robert Lartey; Vitaly Citovsky

196

A library of IR bands of nucleic acids in solution  

Microsoft Academic Search

This review presents a compilation and discussion of infrared (IR) bands characteristic of nucleic acids in various conformations. The entire spectral range 1800–800 cm?1 relevant for DNA\\/RNA in aqueous solution has been subdivided into four sections. Each section contains descriptions of bands appearing from group specific parts of nucleic acid structure, such as nucleobase, base–sugar, sugar–phosphate and sugar moiety. The

Martina Banyay; Munna Sarkar; Astrid Gräslund

2003-01-01

197

NUCLEIC ACID RECOGNITION BY OB-FOLD PROTEINS  

Microsoft Academic Search

? Abstract The OB-fold domain is a compact structural motif frequently used for nucleic acid recognition. Structural comparison of all OB-fold\\/nucleic acid complexes solved to date confirms the low degree of sequence similarity among members of this family while highlighting several structural sequence determinants common to most of these OB-folds. Loops connecting the secondary structural elements in the OB-fold core

Douglas L. Theobald; Rachel M. Mitton-Fry; Deborah S. Wuttke

2003-01-01

198

Stereochemistry of 2?,5? Nucleic Acids and Their Constituents  

Microsoft Academic Search

Shape and dimension of the preferred nucleotide repeats in nucleic acids are found to depend on whether the sugar-phosphate linkage is of 2?,5? or 3?,5? type. It is shown that a nucleotide which is “compact” in 3?,5? nucleic acids is rendered “extended” and vice versa for a given sugar pucker. It is interesting that this feature is accompanied by a

B. J. Premraj; N. Yathindra

1998-01-01

199

Metal complex derivatives of peptide nucleic acids (PNA).  

PubMed

Peptide nucleic acid (PNA) is a non-cyclic pseudopeptide-nucleic acid structural mimic with promising applications within diagnostics and drug discovery. This review focuses on metal complex derivatives of PNA. Metal ions and their complexes display unique physical and chemical properties and offer the opportunity to introduce new labels and probes for bioanalytical and diagnostic applications of PNA, but also to modulate or to introduce new (for example catalytic) functions and biological activities. PMID:22210345

Krämer, Roland; Mokhir, Andriy

2012-01-01

200

Structural probes in quadruplex nucleic acid structure determination by NMR.  

PubMed

Traditionally, isotope-labelled DNA and RNA have been fundamental to nucleic acid structural studies by NMR. Four-stranded nucleic acid architectures studies increasingly benefit from a plethora of nucleotide conjugates for resonance assignments, the identification of hydrogen bond alignments, and improving the population of preferred species within equilibria. In this paper, we review their use for these purposes. Most importantly we identify reasons for the failure of some modifications to result in quadruplex formation. PMID:23128087

Karsisiotis, Andreas Ioannis; Webba da Silva, Mateus

2012-11-05

201

Encapsulation of Nucleic Acids and Opportunities for Cancer Treatment  

Microsoft Academic Search

The development of nucleic acid drugs for the treatment of various cancers has shown great promise in recent years. However,\\u000a efficient delivery of these drugs to target cells remains a significant challenge towards the successful development of such\\u000a therapies. This review provides a comprehensive overview of encapsulation technologies being developed for the delivery of\\u000a nucleic acid-based anti-cancer agents. Both micro

Lisa Brannon-Peppas; Bilal Ghosn; Krishnendu Roy; Kenneth Cornetta

2007-01-01

202

Condensation of nucleic acids by intercalating aromatic cations.  

PubMed

Certain intercalating aromatic cations, such as the fluorochrome acridine orange or the antitumor drug Mitoxantrone, induce condensation of nucleic acids in solutions. The appearance of the condensed form during titration of nucleic acids with these intercalating ligands can be quantitatively monitored by light scatter measurements. The resulting highly reproducible light scatter transition curves are typical of the cooperative processes, and the transitions occur at different critical concentrations of the ligands depending upon both the ligand itself and the primary structure (base and sugar composition) and the secondary structure (single- or double-stranded) of the nucleic acids. The mechanism of condensation of nucleic acids by intercalating cationic ligands is discussed in light of the model of interactions occurring between certain intercalators and single-stranded nucleic acids and compared with the condensation induced by polyvalent "simple" cations such as Co3+ or spermine4+. The described phenomenon can have an application in analytical and preparative biochemistry for characterization of the primary and secondary structure of nucleic acids and for separation of the compounds. The possibility that the condensation plays a role in mutagenic and pharmacological effects of aromatic cations is considered. PMID:6209715

Kapuscinski, J; Darzynkiewicz, Z

1984-12-01

203

Nucleic acid in-situ hybridization detection of infectious agents  

NASA Astrophysics Data System (ADS)

Limitations of traditional culture methods and newer polymerase chain reaction (PCR)-based methods for detection and speciation of infectious agents demonstrate the need for more rapid and better diagnostics. Nucleic acid hybridization is a detection technology that has gained wide acceptance in cancer and prenatal cytogenetics. Using a modification of the nucleic acid hybridization technique known as fluorescence in-situ hybridization, infectious agents can be detected in a variety of specimens with high sensitivity and specificity. The specimens derive from all types of human and animal sources including body fluids, tissue aspirates and biopsy material. Nucleic acid hybridization can be performed in less than one hour. The result can be interpreted either using traditional fluorescence microscopy or automated platforms such as micro arrays. This paper demonstrates proof of concept for nucleic acid hybridization detection of different infectious agents. Interpretation within a cytologic and histologic context is possible with fluorescence microscopic analysis, thereby providing confirmatory evidence of hybridization. With careful probe selection, nucleic acid hybridization promises to be a highly sensitive and specific practical diagnostic alternative to culture, traditional staining methods, immunohistochemistry and complicated nucleic acid amplification tests.

Thompson, Curtis T.

2000-04-01

204

Single-stranded nucleic acids promote SAMHD1 complex formation.  

PubMed

SAM domain and HD domain-containing protein 1 (SAMHD1) is a dGTP-dependent triphosphohydrolase that degrades deoxyribonucleoside triphosphates (dNTPs) thereby limiting the intracellular dNTP pool. Mutations in SAMHD1 cause Aicardi-Goutières syndrome (AGS), an inflammatory encephalopathy that mimics congenital viral infection and that phenotypically overlaps with the autoimmune disease systemic lupus erythematosus. Both disorders are characterized by activation of the antiviral cytokine interferon-? initiated by immune recognition of self nucleic acids. Here we provide first direct evidence that SAMHD1 associates with endogenous nucleic acids in situ. Using fluorescence cross-correlation spectroscopy, we demonstrate that SAMHD1 specifically interacts with ssRNA and ssDNA and establish that nucleic acid-binding and formation of SAMHD1 complexes are mutually dependent. Interaction with nucleic acids and complex formation do not require the SAM domain, but are dependent on the HD domain and the C-terminal region of SAMHD1. We finally demonstrate that mutations associated with AGS exhibit both impaired nucleic acid-binding and complex formation implicating that interaction with nucleic acids is an integral aspect of SAMHD1 function. PMID:23371319

Tüngler, Victoria; Staroske, Wolfgang; Kind, Barbara; Dobrick, Manuela; Kretschmer, Stefanie; Schmidt, Franziska; Krug, Claudia; Lorenz, Mike; Chara, Osvaldo; Schwille, Petra; Lee-Kirsch, Min Ae

2013-01-31

205

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

Microsoft Academic Search

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

JianHua Gan; Jia Sheng; Zhen Huang

2011-01-01

206

Interactions of porphyrins with nucleic acids.  

PubMed

The interactions of tetrakis(4-N-methylpyridyl)-porphine (H2TMpyP-4) and its copper(II), nickel(II), zinc(II), cobalt(III), iron(III), and manganese(III) derivatives with several nucleic acids have been investigated. Spectrophotometric titrations of H2TMpyP-4 and Cu(II)TMpyP-4 with the synthetic polymer poly(dG-dC) could be analyzed by a nearest-neighbor exclusion model leading to n approximately equal to two base pairs and equilibrium constants of 7.7 X 10(5) M-1 and 8.0 X 10(5) M-1, respectively. The other metal derivatives [except for the nickel(II) porphyrin] do not provide sufficiently large color changes with poly(dG-dC) to allow analysis. In contrast, all of these porphyrins interact with poly(dA-dT) and DNA. For those porphyrins investigated, the binding profiles are not adequately fit by a nearest-neighbor exclusion model but have profiles suggesting that cooperativity effects are important. Spectral and circular dichroic experiments both suggest base specificity. With calf thymus DNA, the copper(II) and nickel(II) derivatives show prominent negative circular dichroism (CD) features and large red shifts and hypochromicity of the Soret absorption band characteristic of GC specificity, as demonstrated with the synthetic polymer. The other metal derivatives show prominent positive induced visible CD features with small red shifts and hypochromicity of the absorption bands in the Soret region characteristic of AT specificity. Only the metal-free derivative has a conservative CD spectrum suggesting distribution among GC and AT sites. PMID:6860636

Pasternack, R F; Gibbs, E J; Villafranca, J J

1983-05-10

207

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

Microsoft Academic Search

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

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

2006-01-01

208

Nucleic acid sequences and expression system relating to Enterococcus faecium for diagnostics and therapeutics  

US Patent & Trademark Office Database

The invention provides isolated polypeptide and nucleic acid sequences derived Enterococcus faecium that are useful in diagnosis and therapy of pathological conditions; antibodies against the polypeptides; and methods for the production of the polypeptides. The invention also provides methods for the detection, prevention and treatment of pathological conditions resulting from bacterial infection.

2003-06-24

209

Effect of temperature on the protein and nucleic acid content of thermotolerant yeasts  

Microsoft Academic Search

The effect of growth at 30°, 35° and 40° on the biomass yield and on the nucleic acid and protein content of twelve isolates of yeast has been studied. Although yields of 41.6% and a true protein content of 34% were obtained, each of the strains exhibited a lower yield and protein content at 40° than at the lower temperatures.

E. T. A. Shaikh Idris; D. R. Berry

1980-01-01

210

Two-dimensional condensation of nucleic acid components and oligonucleotides  

Microsoft Academic Search

DNA adsorption at the electrode surfaces is of fundamental interest for the development of DNA-based biosensors (1). Purine and pyrimidine derivatives currently occuring in nucleic acids posses an extraordinary high ability of self-association at the electrode surface and can form there by a two-dimensional (2-D) condensation a monomolecular layer (self-assembled monolayer - SAM) (2,3). By this high condensation ability nucleic

Vladimír Vetterl

211

Synthesis and Properties of Hyaluronic Acid Conjugated Nucleic Acid Analogs—1: Synthesis of Deacetylhyaluronan and Introduction of Nucleic Acid Bases  

Microsoft Academic Search

The conjugation of nucleic acid base with hyaluronan was achieved by using the activated ester of pentachlorophenyl trichloroacetate. The conditions of de-N-acetylation of sodium hyaluronic acid were studied. In low concentrations of NaOH, the degree of deacetylation was 26%, while in 7.4N NaOH, the degree of deacetylation was 76% and the viscosity was 1.12 dL\\/g. Thymine and 5-fluorouracil bases were

Takehiko Wada; Suwabun Chirachanchai; Naoto Izawa; Yoshiaki Inaki; Kchi Takemoto

1994-01-01

212

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

PubMed

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

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

213

Recent Progress in Nucleic Acid Aptamer-Based Biosensors and Bioassays  

PubMed Central

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.

Mok, Wendy; Li, Yingfu

2008-01-01

214

Theoretical study of the influence of ribose on the proton transfer phenomenon of nucleic acid bases  

NASA Astrophysics Data System (ADS)

The first comprehensive theoretical study of ribose's effects on the behavior of proton transfer of nucleic acid base is presented. The specific hydrogen bonding of the ribose hydroxyls plays a very important role in the stabilization of the structure of ribonucleoside. Nine stable uridine conformations have been reported. The intermolecular proton transfer of the isolated, monohydrated uridine complexes in three different regions were extensively explored on the basis of density functional theory at the B3LYP/6-31+G ? level. With the introduction of the ribose, not only the structural parameters of the nucleic acid bases changed, but also the energy barriers of the proton transfer process changed. Furthermore, changes of the electron distributions of the molecular orbital of the nucleic acid bases were also analyzed by NBO analysis. Consideration of the ribose's influence represents a much more real situation in the RNA.

Zhang, Liqun; Li, Haoran; Hu, Xingbang; Jalbout, Abraham F.

2007-08-01

215

Structural Requirements for the Procoagulant Activity of Nucleic Acids  

PubMed Central

Nucleic acids, especially extracellular RNA, are exposed following tissue- or vessel damage and have previously been shown to activate the intrinsic blood coagulation pathway in vitro and in vivo. Yet, no information on structural requirements for the procoagulant activity of nucleic acids is available. A comparison of linear and hairpin-forming RNA- and DNA-oligomers revealed that all tested oligomers forming a stable hairpin structure were protected from degradation in human plasma. In contrast to linear nucleic acids, hairpin forming compounds demonstrated highest procoagulant activities based on the analysis of clotting time in human plasma and in a prekallikrein activation assay. Moreover, the procoagulant activities of the DNA-oligomers correlated well with their binding affinity to high molecular weight kininogen, whereas the binding affinity of all tested oligomers to prekallikrein was low. Furthermore, four DNA-aptamers directed against thrombin, activated protein C, vascular endothelial growth factor and nucleolin as well as the naturally occurring small nucleolar RNA U6snRNA were identified as effective cofactors for prekallikrein auto-activation. Together, we conclude that hairpin-forming nucleic acids are most effective in promoting procoagulant activities, largely mediated by their specific binding to kininogen. Thus, in vivo application of therapeutic nucleic acids like aptamers might have undesired prothrombotic or proinflammatory side effects.

Gansler, Julia; Jaax, Miriam; Leiting, Silke; Appel, Bettina; Greinacher, Andreas; Fischer, Silvia; Preissner, Klaus T.

2012-01-01

216

Nucleic acid detection and quantification in the developing world.  

PubMed

Techniques using nucleic acid amplification have not had the same amount of impact on research and clinical diagnosis in the developing world as that observed in the West. This is unsurprising when the costs and infrastructure required to perform nucleic acid amplification are considered. Despite this, nucleic acid amplification is being increasingly used in both research and diagnosis in countries such as Zambia and Tanzania. Scientific research in the developing world is made possible through the support and development of the necessary laboratory infrastructure and the establishment of special transport for the reagents and samples. This has enabled world-leading country-relevant research to be performed by local scientists on subjects ranging from rapid diagnosis of infectious diseases to measuring the RNA gene expression in an immune response. Concomitantly, the challenge presented by the need for tests that are more appropriate for a resource-poor setting has led to a number of newer methodologies for nucleic acid detection, which can be tailored to be performed in the field without the need for training in molecular biology. As nucleic acid amplification techniques become both simpler and cheaper, their impact is likely to play an increasingly crucial role in research and diagnosis in the developing world. PMID:19290873

Huggett, Jim; Green, Clare; Zumla, Alimuddin

2009-04-01

217

Nucleic acid-based nanoengineering: novel structures for biomedical applications  

PubMed Central

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine.

Li, Hanying; LaBean, Thomas H.; Leong, Kam W.

2011-01-01

218

Characterization of alpha helices interacting with nucleic acids.  

PubMed

Protein-nucleic acid interactions play a vital role in most genetic processes. An enhanced insight into such interactions can be obtained from the structure database of these complexes. Here, we report an overall survey on the geometry of alpha helices which interact with nucleic acids through hydrogen bonds and/or non-bonded interactions. Using the program RADIL based on an algorithm developed from this laboratory, 161 alpha helices in 70 non-redundant nucleic acid binding protein chains solved using X-ray crystallography are analysed. The helical geometry has been characterized as bent, canonical, terminally or completely distorted. The analysis reveals that approximately 70% of the alpha helices possess distortions of any one kind, viz., bend, terminal distortion or complete distortion. Nearly one-third of the total helices possess bends, with a majority of the bending occurring in 5-15 degrees range. In addition, a majority of the bent helices approach the nucleic acid helix in a perpendicular direction. The program RADIL has been useful in characterizing the nucleic acid-induced structural variations in alpha helices, however small they may be. PMID:18667362

Sreekanth, R; Pattabhi, Vasantha; Rajan, S S

2008-07-01

219

BGL4 Beta-Glucosidase and Nucleic Acids Encoding the Same.  

National Technical Information Service (NTIS)

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 BGL...

F. Goedegebuur J. Yao M. Ward N. Dunn-Coleman

2005-01-01

220

High-Volume Extraction of Nucleic Acids by Magnetic Bead Technology for Ultrasensitive Detection of Bacteria in Blood Components  

Microsoft Academic Search

Background: Nucleic acid isolation, the most techni- cally demanding and laborious procedure performed in molecular diagnostics, harbors the potential for im- provements in automation. A recent development is the use of magnetic beads covered with nucleic acid-bind- ing matrices. We adapted this technology with a broad- range 23S rRNA real-time reverse transcription (RT)- PCR assay for fast and sensitive detection

Melanie Stormer; Knut Kleesiek; Jens Dreier

221

TOPICAL REVIEW: Nanopore sensors for nucleic acid analysis  

Microsoft Academic Search

In the past decade, nanometre-scale pores have been explored as the basis for technologies to analyse and sequence single nucleic acid molecules. Most approaches involve using such a pore to localize single macromolecules and interact with them to garner some information on their composition. Though nanopore sensors cannot yet claim success at deoxyribonucleic acid (DNA) sequencing, nanopore-based technologies offer one

Jonathan J. Nakane; Mark Akeson; Andre Marziali

2003-01-01

222

Enhanced Graphic Matrix Analysis of Nucleic Acid and Protein Sequences  

Microsoft Academic Search

The enhanced graphic matrix procedure analyzes nucleic acid and amino acid sequences for features of possible biological interest and reveals the spatial patterns of such features. When a sequence is compared to itself the technique shows regions of self-complementarity, direct repeats, and palindromic subsequences. Comparison of two different sequences, exemplified by immunoglobulin kappa light chain genes, by using colored graphic

Jacob V. Maizel; Robert P. Lenk

1981-01-01

223

Multiple sequence alignments of partially coding nucleic acid sequences  

Microsoft Academic Search

Background: High quality sequence alignments of RNA and DNA sequences are an important prerequisite for the comparative analysis of genomic sequence data. Nucleic acid sequences, however, exhibit a much larger sequence heterogeneity compared to their encoded protein sequences due to the redundancy of the genetic code. It is desirable, therefore, to make use of the amino acid sequence when aligning

Roman R. Stocsits; Ivo L. Hofacker; Claudia Fried; Peter F. Stadler

2005-01-01

224

Methods for the covalent attachment of nucleic acids and their derivatives to proteins  

NASA Astrophysics Data System (ADS)

The methods for the affinity modification of proteins, specific to nucleic acids, by activated nucleic acid analogues and their components, are considered. The active groups introduced into proteins or nucleic acids and the symmetrical cross-linking agents used to obtain covalent protein-nucleic acid complexes are listed. The methods for the analysis of covalently linked protein-nucleic acid adducts as well as procedures for the identification of the aminoacids in the protein participating in the formation of bonds with nucleic acids are surveyed. The bibliography includes 112 references.

Sheflyan, Galina Ya; Kubareva, Elena A.; Gromova, Elizaveta S.

1996-08-01

225

Nature and magnitude of aromatic stacking of nucleic acid bases.  

PubMed

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 base-stacking 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 base-stacking 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. PMID:18464974

Sponer, Jirí; Riley, Kevin E; Hobza, Pavel

2008-04-07

226

Nature and Magnitude of Aromatic Stacking of Nucleic Acid Bases  

SciTech Connect

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.

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

2008-04-07

227

Pyrophosphate-condensing activity linked to nucleic acid synthesis.  

PubMed Central

In some preparations of DNA dependent RNA polymerase a new enzymatic activity has been found which catalyzes the condensation of two pyrophosphate molecules, liberated in the process of RNA synthesis, to one molecule of orthophosphate and one molecule of Mg (or Mn) - chelate complex with trimetaphosphate. This activity can also cooperate with DNA-polymerase, on condition that both enzymes originate from the same cells. These results point to two general conclusions. First, energy is conserved in the overall process of nucleic acid synthesis and turnover, so that the process does not require an energy influx from the cell's general resources. Second, the synthesis of nucleic acids is catalyzed by a complex enzyme system which contains at least two separate enzymes, one responsible for nucleic acid polymerization and the other for energy conservation via pyrophosphate condensation. Images

Volloch, V Z; Rits, S; Tumerman, L

1979-01-01

228

RNA: the new revolution in nucleic acid vaccines.  

PubMed

Nucleic acid vaccines have the potential to address issues of safety and effectiveness sometimes associated with vaccines based on live attenuated viruses and recombinant viral vectors. In addition, methods to manufacture nucleic acid vaccines are suitable as generic platforms and for rapid response, both of which will be very important for addressing newly emerging pathogens in a timely fashion. Plasmid DNA is the more widely studied form of nucleic acid vaccine and proof of principle in humans has been demonstrated, although no licensed human products have yet emerged. The RNA vaccine approach, based on mRNA and engineered RNA replicons derived from certain RNA viruses, is gaining increased attention and several vaccines are under investigation for infectious diseases, cancer and allergy. Human clinical trials are underway and the prospects for success are bright. PMID:23735226

Geall, Andrew J; Mandl, Christian W; Ulmer, Jeffrey B

2013-06-02

229

Nucleic acid structure analysis: Local, mathematically rigorous, comparable  

SciTech Connect

A more sophisticated mathematical treatments for analyzing nucleic acid coordinate data is presented. The methodology is both rigorous and comparable for parameterizing nucleic acids in terms of the local structural morphology of complementary and neighboring base pairs. Chapter 1 clearly defines the problems of nucleic acid structure parameterization by examining the consequences of the EMBO workshop guidelines published in 1989. Chapter 2 defines mathematics to rigorously and comparably calculate all of the parameters for nucleic acid structure from a local viewpoint. The mathematics satisfies all EMBO guidelines for local structural parameters. One of the main features making this program flexible is that any base pair relationship can be rigorously analyzed. This is because the meaning of zero for the complementary base parameters is clearly definable for any base pairing relationship. Chapter 3 analyses and explains why certain pairwise parameter correlations were observed between rotational and translational parameters. It was observed that the method of calculating the rotational parameters greatly affected the calculated translational parameters. As a result of our analysis, we determined the optimum location about which rotations should be performed in order to reduce and/or eliminate the correlations which are artifacts of the mathematics employed and do not reflect true structural properties of nucleic acids. Chapter 4 presents an analysis of the available nucleic acid X-ray crystallographic structural data, showing that the experimental base pairs do not generally have the ideal Watson-Crick structure. By utilizing a hybrid between helical and Cartesian parameterization methods, the relative distribution of the complementary base parameters was examined as a function of the nearest neighboring base pairs. The final chapter includes a review article explaining each of the available methods in plain English as well as giving the mathematics.

Babcock, M.S.

1993-01-01

230

Kit for detecting nucleic acid sequences using competitive hybridization probes  

DOEpatents

A kit is provided for detecting a target nucleic acid sequence in a sample, the kit comprising: a first hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the first hybridization probe including a first complexing agent for forming a binding pair with a second complexing agent; and a second hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the first hybridization probe does not selectively hybridize, the second hybridization probe including a detectable marker; a third hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a first portion of the target sequence, the third hybridization probe including the same detectable marker as the second hybridization probe; and a fourth hybridization probe which includes a nucleic acid sequence that is sufficiently complementary to selectively hybridize to a second portion of the target sequence to which the third hybridization probe does not selectively hybridize, the fourth hybridization probe including the first complexing agent for forming a binding pair with the second complexing agent; wherein the first and second hybridization probes are capable of simultaneously hybridizing to the target sequence and the third and fourth hybridization probes are capable of simultaneously hybridizing to the target sequence, the detectable marker is not present on the first or fourth hybridization probes and the first, second, third, and fourth hybridization probes each include a competitive nucleic acid sequence which is sufficiently complementary to a third portion of the target sequence that the competitive sequences of the first, second, third, and fourth hybridization probes compete with each other to hybridize to the third portion of the target sequence.

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

2001-01-01

231

Recent Advances in Chemical Modification of Peptide Nucleic Acids  

PubMed Central

Peptide nucleic acid (PNA) has become an extremely powerful tool in chemistry and biology. Although PNA recognizes single-stranded nucleic acids with exceptionally high affinity and sequence selectivity, there is considerable ongoing effort to further improve properties of PNA for both fundamental science and practical applications. The present paper discusses selected recent studies that improve on cellular uptake and binding of PNA to double-stranded DNA and RNA. The focus is on chemical modifications of PNA's backbone and heterocyclic nucleobases. The paper selects representative recent studies and does not attempt to provide comprehensive coverage of the broad and vibrant field of PNA modification.

Rozners, Eriks

2012-01-01

232

Analysis of single nucleic acid molecules with protein nanopores  

PubMed Central

We describe the methods used in our laboratory for the analysis of single nucleic acid molecules with protein nanopores. The technical section is preceded by a review of the variety of experiments that can be done with protein nanopores. The end goal of much of this work is single-molecule DNA sequencing, although sequencing is not discussed explicitly here. The technical section covers the equipment required for nucleic acid analysis, the preparation and storage of the necessary materials, and aspects of signal processing and data analysis.

Maglia, Giovanni; Heron, Andrew J.; Stoddart, David; Japrung, Deanpen; Bayley, Hagan

2011-01-01

233

Towards Improved Accuracy of Bordetella pertussis Nucleic Acid Amplification Tests  

PubMed Central

In many clinical microbiology laboratories, nucleic acid amplification tests such as PCR have become the routine methods for the diagnosis of pertussis. While PCR has greatly increased the ability of laboratories to detect Bordetella pertussis infections, it has also been associated with false-positive results that can, given the tendency of B. pertussis to cause outbreaks, result in unnecessary and costly control measures. The species specificity of Bordetella gene targets and their number of copies per genome greatly impact the performance characteristics of nucleic acid amplification tests for B. pertussis. It is crucial that laboratorians recognize these characteristics, to limit false-positive test results and prevent pseudo-outbreaks.

2012-01-01

234

Biomimetic high density lipoprotein nanoparticles for nucleic acid delivery.  

PubMed

We report a gold nanoparticle-templated high density lipoprotein (HDL AuNP) platform for gene therapy that combines lipid-based nucleic acid transfection strategies with HDL biomimicry. For proof-of-concept, HDL AuNPs are shown to adsorb antisense cholesterylated DNA. The conjugates are internalized by human cells, can be tracked within cells using transmission electron microscopy, and regulate target gene expression. Overall, the ability to directly image the AuNP core within cells, the chemical tailorability of the HDL AuNP platform, and the potential for cell-specific targeting afforded by HDL biomimicry make this platform appealing for nucleic acid delivery. PMID:21319839

McMahon, Kaylin M; Mutharasan, R Kannan; Tripathy, Sushant; Veliceasa, Dorina; Bobeica, Mariana; Shumaker, Dale K; Luthi, Andrea J; Helfand, Brian T; Ardehali, Hossein; Mirkin, Chad A; Volpert, Olga; Thaxton, C Shad

2011-02-14

235

Conformational Flexibility of Pyrimidine Ring in Nucleic Acid Bases  

NASA Astrophysics Data System (ADS)

Nucleic acid bases (NABs) have been considered for many years to be planar and conformationally rigid. However, recently, two possible sources of nucleobases nonplanarity have been found. Ab initio quantum-chemical calculations using large basis sets augmented by inclusion of electron correlation and recent experimental studies revealed that amino groups in isolated cytosine, guanine, and adenine adopt a nonplanar trigonal-pyramidal configuration. Since the values of amino group inversion barriers do not exceed approximately 1 kcal mol-1, this group possesses rather flexible geometry. A different source of nonplanarity of nucleobases originates from the high deformability of the pyrimidine ring. Transition of such a ring in uracil, thymine, cytosine, and guanine molecules from a planar equilibrium conformation to a sofa configuration characterized by a relevant torsion angle of ±20° entails an increase of energy by less than 1.5 kcal mol-1. Therefore, at room temperature, certain fraction of isolated DNA bases should possess nonplanar structure of the heterocyclic ring. This review summarizes recent theoretical studies on the flexibility of the NABs.

Shishkin, Oleg V.; Gorb, Leonid; Leszczynski, Jerzy

236

Modeling nucleic acid structure in the presence of single-stranded binding proteins  

NASA Astrophysics Data System (ADS)

There are many important proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV, the RecA DNA repair protein in bacteria, and all proteins involved in mRNA splicing and translation. We extend the Vienna Package for quantitatively modeling the secondary structure of nucleic acids to include proteins which bind to unpaired portions of the nucleic acid. All parameters needed to model nucleic acid secondary structures in the absence of proteins have been previously measured. This leaves the footprint and sequence dependent binding affinity of the protein as adjustable parameters of our model. Using this model we are able to predict the probability of the protein binding at any position in the nucleic acid sequence, the impact of the protein on nucleic acid base pairing, the end-to-end distance distribution for the nucleic acid, and FRET distributions for fluorophores attached to the nucleic acid.

Forties, Robert; Bundschuh, Ralf

2009-03-01

237

"Clickable" LNA/DNA probes for fluorescence sensing of nucleic acids and autoimmune antibodies.  

PubMed

Herein we describe fluorescent oligonucleotides prepared by click chemistry between novel alkyne-modified locked nucleic acid (LNA) strands and a series of fluorescent azides for homogeneous (all-in-solution) detection of nucleic acids and autoimmune antibodies. PMID:24107917

Jørgensen, Anna S; Gupta, Pankaj; Wengel, Jesper; Astakhova, I Kira

2013-10-22

238

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

SciTech Connect

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.

Nasarabadi, Shanavaz (Livermore, CA)

2011-01-11

239

Interactive Fluorophore and Quencher Pairs for Labeling Fluorescent Nucleic Acid Hybridization Probes  

Microsoft Academic Search

The use of fluorescent nucleic acid hybridization probes that generate a fluorescence signal only when they bind to their\\u000a target enables real-time monitoring of nucleic acid amplification assays. Real-time nucleic acid amplification assays markedly\\u000a improves the ability to obtain qualitative and quantitative results. Furthermore, these assays can be carried out in sealed\\u000a tubes, eliminating carryover contamination. Fluorescent nucleic acid hybridization

Salvatore A. E. Marras

2008-01-01

240

Feature Selection for Classication of Nucleic Acid Sequences  

Microsoft Academic Search

Abstract: To summarize, this work studied the effect of feature selection techniques for classifying nucleic acid sequences. The scientific contribution of this study comprises several aspects. The first aspect concerns the algorithmical part of the work, where we made advances in the field of pattern recognition, developing new methods for feature selection, feature ranking and feature weighting. A second aspect

Yvan Saeys

2004-01-01

241

Inhibition of miRNA Maturation by Peptide Nucleic Acids.  

PubMed

Molecules able to interfere in miRNA genesis and function are potent tools to unravel maturation and processing pathways. Antisense oligonucleotides or analogs are actually employed for the inhibition of miRNA function. Here we illustrate how Peptide Nucleic Acids oligomers targeting pre-miRNA are exploited to inhibit miRNA maturation. PMID:24166311

Avitabile, Concetta; Fabbri, Enrica; Bianchi, Nicoletta; Gambari, Roberto; Romanelli, Alessandra

2014-01-01

242

A CODE RELATING SEQUENCE TO STRUCTURE IN NUCLEIC ACIDS  

Microsoft Academic Search

Nucleic acids are elucidated in configuration space. An algorithm relating sequence to stability in A and B helical secondary structures, is stated to incorporate NMR conformational and optical melting data. This made possible a classification of elementary sequences in terms of configuration forces driving between A and B states, a finding useful in prediction of structural behavior of different sequences

Mieczys?aw Remin

2001-01-01

243

Nucleic acid probes in diagnosis of viral diseases of man  

Microsoft Academic Search

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

J. K. Kulski; Mary Norval

1985-01-01

244

InnovationsPrenatal diagnosis: progress through plasma nucleic acids  

Microsoft Academic Search

Over the past 40 years, much effort has been spent on developing non-invasive prenatal diagnostic methods. Since 1997, the progress of this field has been accelerated by the unexpected finding of extracellular fetal nucleic acids in maternal plasma. These developments have been translated into many novel genetic, epigenetic and gene-expression markers, and are expected to have a fundamental impact on

Rossa W. K. Chiu; Y. M. Dennis Lo

2006-01-01

245

Electrochemical microfluidic biosensor for nucleic acid detection with integrated minipotentiostat  

Microsoft Academic Search

An electrochemical microfluidic biosensor with an integrated minipotentiostat for the quantification of RNA was developed based on nucleic acid hybridization and liposome signal amplification. Specificity of the biosensor was ensured by short DNA probes that hybridize with the target RNA or DNA sequence. The reporter probe was coupled to liposomes entrapping the electrochemically active redox couple potassium ferri\\/ferrohexacyanide. The capture

Sylvia Kwakye; Vasily N. Goral; Antje J. Baeumner

2006-01-01

246

Nucleic acid encoding TGF-. beta. and its uses  

SciTech Connect

This patent describes a method. It comprises: constructing a vector which includes nucleic acid encoding biologically active TGF-{beta}, transforming a host eukaryotic cell with the vector, culturing the transformed cell and recovering mature TGF-{beta} from the culture medium.

Derynck, R.M.A.; Goeddel, D.V.

1989-12-12

247

Targeting DNA G-Quadruplex Structures with Peptide Nucleic Acids  

PubMed Central

Regulation of genetic functions based on targeting DNA or RNA sequences with complementary oligonucleotides is especially attractive in the post-genome era. Oligonucleotides can be rationally designed to bind their targets based on simple nucleic acid base pairing rules. However, the use of natural DNA and RNA oligonucleotides as targeting probes can cause numerous off-target effects. In addition, natural nucleic acids are prone to degradation in vivo by various nucleases. To address these problems, nucleic acid mimics such as peptide nucleic acids (PNA) have been developed. They are more stable, show less off-target effects, and, in general, have better binding affinity to their targets. However, their high affinity to DNA can reduce their sequence-specificity. The formation of alternative DNA secondary structures, such as the G-quadruplex, provides an extra level of specificity as targets for PNA oligomers. PNA probes can target the loops of G-quadruplex, invade the core by forming PNA-DNA guanine-tetrads, or bind to the open bases on the complementary cytosine-rich strand. Not only could the development of such G-quadruplex-specific probes allow regulation of gene expression, but it will also provide a means to clarify the biological roles G-quadruplex structures may possess.

Panyutin, Igor G.; Onyshchenko, Mykola I.; Englund, Ethan A.; Appella, Daniel H.; Neumann, Ronald D.

2012-01-01

248

Thermodynamic database for protein-nucleic acid interactions (ProNIT)  

Microsoft Academic Search

Motivation: Protein-nucleic acid interactions are funda- mental to the regulation of gene expression. In order to elucidate the molecular mechanism of protein-nucleic acid recognition and analyze the gene regulation network, not only structural data but also quantitative binding data are necessary. Although there are structural databases for proteins and nucleic acids, there exists no database for their experimental binding data.

Ponraj Prabakaran; Jianghong An; M. Michael Gromiha; Samuel Selvaraj; Hatsuho Uedaira; Hidetoshi Kono; Akinori Sarai

2001-01-01

249

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

Microsoft Academic Search

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

Bavykin; Sergei

2011-01-01

250

PROTEIN NUCLEIC ACID INTERACTIONS; GRANT # DE-FG02-96ER62166; ; FINAL REPORT  

Microsoft Academic Search

The overall goal of this collaborative project is to develop methods for analyzing protein-nucleic acid interactions. Nucleic acid-binding proteins have a central role in all aspects of genetic activity within an organism, such as transcription, replication, and repair. Thus, it is extremely important to examine the nature of complexes that are formed between proteins and nucleic acids, as they form

Helen M. Berman; Janet Thornton

2005-01-01

251

Search for a Putative Scrapie Genome in Purified Prion Fractions Reveals a Paucity of Nucleic Acids  

Microsoft Academic Search

Scrapie can be transmitted by novel infectious patho- gens termed prions. No evidence for a scrapie-specific nucleic acid has been detected to date. To investigate amounts, types and sizes of nucleic acid molecules associated with prions in purified preparations, ali- quots were deproteinized, and the nucleic acids ana- lysed by PAGE and silver staining. Digestion with nucleases and exposure to

Norbert Meyer; Voiker Rosenbaum; Bettina Schmidt; Kay Gilles; Carol Mirenda; Darlene Groth; Detlev Riesner

1991-01-01

252

Retroviral Nucleocapsid Proteins Display Nonequivalent Levels of Nucleic Acid Chaperone Activity  

Microsoft Academic Search

Human immunodeficiency virus type 1 (HIV-1) nucleocapsid protein (NC) is a nucleic acid chaperone that facilitates the remodeling of nucleic acids during various steps of the viral life cycle. Two main features of NC's chaperone activity are its abilities to aggregate and to destabilize nucleic acids. These functions are associated with NC's highly basic character and with its zinc finger

Kristen M. Stewart-Maynard; Margareta Cruceanu; Fei Wang; My-Nuong Vo; Robert J. Gorelick; Mark C. Williams; Ioulia Rouzina; Karin Musier-Forsyth

2008-01-01

253

Process for labeling single-stranded nucleic acids and hybridization probes  

SciTech Connect

A process is described for labeling a single-stranded nucleic acid which comprises the steps of: contacting the nucleic acid with one or more labeling compositions containing an alkylating moiety, a divalent organic moiety, and a monovalent label moiety; and activating the complex so as to induce the alkylating moiety to bond covalently to the nucleic acid.

Watson, R.M.; Sheldon, E.L. III; Snead, R.M.

1989-04-18

254

Regulatory mechanisms of nucleic acid-mediated innate immune responses in the tumor microenvironment  

PubMed Central

We identified novel mechanisms whereby TIM-3 suppresses innate immunity as induced by nucleic acids. Interaction of TIM-3 with HMGB1 inhibits the recruitment of nucleic acids to the endosomal compartment of dendritic cells, impairing the transduction of innate immune signals. Thus, TIM-3 is an effective target for enhancing the immunogenicity of nucleic acids in the context of cancer therapy.

Jinushi, Masahisa

2012-01-01

255

Bacterial Viability and Antibiotic Susceptibility Testing with SYTOX Green Nucleic Acid Stain  

Microsoft Academic Search

A fluorescent nucleic acid stain that does not penetrate living cells was used to assess the integrity of the plasma membranes of bacteria. SYTOX Green nucleic acid stain is an unsymmetrical cyanine dye with three positive charges that is completely excluded from live eukaryotic and prokaryotic cells. Binding of SYTOX Green stain to nucleic acids resulted in a >500-fold enhancement

BRUCE L. ROTH; MARTIN POOT; STEPHEN T. YUE; PAUL J. MILLARD

1997-01-01

256

Methods and compositions for linking binding domains in nucleic acid binding proteins  

US Patent & Trademark Office Database

We describe a method of producing a modified nucleic acid binding polypeptide, the method comprising the steps of: (a) providing a nucleic acid binding polypeptide comprising a plurality of nucleic acid binding modules; (b) selecting a first binding domain consisting of one or two contiguous nucleic acid binding modules; (c) selecting a second binding domain consisting of one or two contiguous nucleic acid binding modules; and (d) introducing a flexible linker sequence to link the first and second binding domains, the flexible linker sequence comprising five or more amino acid residues. Use of structured linkers, alone or in combination with flexible linkers, is also disclosed.

2010-12-14

257

A novel sample preparation method that enables nucleic acid analysis from ultrathin sections.  

PubMed

The ability to isolate and perform nucleic acid analyses of individual cells is critical to studying the development of various cell types and structures. We present a novel biological sample preparation method developed for laser capture microdissection-assisted nucleic acid analysis of ultrathin cell/tissue sections. We used cells of the mitotic bed of the tadpole teeth of Lithobates sphenocephalus (Southern Leopard Frog). Cells from the mitotic beds at the base of the developing teeth series were isolated and embedded in the methacrylate resin, Technovit® 9100®. Intact cells of the mitotic beds were thin sectioned and examined by bright-field and transmission electron microscopy. The cytological and ultrastructural anatomy of the immature and progressively more mature tooth primordia appeared well preserved and intact. A developmental series of tooth primordia were isolated by laser capture microdissection (LCM). Processing of these cells for RNA showed that intact RNA could be isolated. The study demonstrates that Technovit® 9100® can be used as an embedding medium for extremely small tissues and from individual cells, a prerequisite step to LCM and nucleic acid analyses. A relatively small amount of sample material was needed for the analysis, which makes this technique ideal for cell-specific analyses when the desired cells are limited in quantity. PMID:23518143

Klink, Vincent P; Thibaudeau, Giselle; Altig, Ronald

2013-03-21

258

Novel nucleic acid architectures involving locked nucleic acid (LNA) and pyrene residues: Results from an Indo-Danish collaboration  

Microsoft Academic Search

We report herein our results for locked nucleic acid (LNA)-type oligonucleotides containing pyrene residues. Pyrene has a large hydrophobic and planar surface area and is therefore a potential intercalating unit; furthermore, it is interesting as a fluorescent tag when covalently bound to DNA. Synthesis and hybridization of conformationally locked universal base surrogates are described together with efficient interstrand communication as

B. Ravindra Babu; Mads D. Sørensen; Patrick J. Hrdlicka; Smriti Trikha; Ashok K. Prasad; Virinder S. Parmar; Jesper Wengel

2005-01-01

259

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

NASA Astrophysics Data System (ADS)

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.

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

2004-07-01

260

NAFlex: a web server for the study of nucleic acid flexibility.  

PubMed

We present NAFlex, a new web tool to study the flexibility of nucleic acids, either isolated or bound to other molecules. The server allows the user to incorporate structures from protein data banks, completing gaps and removing structural inconsistencies. It is also possible to define canonical (average or sequence-adapted) nucleic acid structures using a variety of predefined internal libraries, as well to create specific nucleic acid conformations from the sequence. The server offers a variety of methods to explore nucleic acid flexibility, such as a colorless wormlike-chain model, a base-pair resolution mesoscopic model and atomistic molecular dynamics simulations with a wide variety of protocols and force fields. The trajectories obtained by simulations, or imported externally, can be visualized and analyzed using a large number of tools, including standard Cartesian analysis, essential dynamics, helical analysis, local and global stiffness, energy decomposition, principal components and in silico NMR spectra. The server is accessible free of charge from the mmb.irbbarcelona.org/NAFlex webpage. PMID:23685436

Hospital, Adam; Faustino, Ignacio; Collepardo-Guevara, Rosana; González, Carlos; Gelpí, Josep Lluis; Orozco, Modesto

2013-05-17

261

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

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

Min Wang; Jinghe Yang; Xia Wu; Fang Huang

2000-01-01

262

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

NASA Astrophysics Data System (ADS)

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.

Tsugita, Akira

263

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

Microsoft Academic Search

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

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

2004-01-01

264

High affinity nucleic acid aptamers for streptavidin incorporated into bi-specific capture ligands  

Microsoft Academic Search

We have isolated 2'-Fluoro-substituted RNA aptamers that bind to streptavidin (SA) with an affinity around 7 ± 1.8 nM, comparable with that of recently described peptide aptamers. Binding to SA was not prevented by prior saturation with biotin, enabling nucleic acid aptamers to form useful ternary complexes. Muta- genesis, secondary structure analysis, ribonuclease footprinting and deletion analysis provided evidence for

Abdessamad Tahiri-Alaoui; Laura Frigotto; Nick Manville; Jamal Ibrahim; Pascale Romby; William James

2002-01-01

265

Nucleic Acids Packaging Processes: Effects of Adenine Tracts and Sequence-Dependent Curvature  

Microsoft Academic Search

The effects of short runs of adenines (A-tracts) upon nucleic acids packaging processes and the properties of the resulting condensates were investigated by using random DNA sequences isolated from natural sources, as well as synthetic segments obtained by an extensive ligation of specific oligomers. Reiteration of short A-tracts (AN where N<3) within the DNA molecules is found to be compatible

Ziv Reich; Rodolfo Ghirlando; Abraham Minsky

1992-01-01

266

One-step purification of nucleic acid for gene expression analysis via Immiscible Filtration Assisted by Surface Tension (IFAST)†  

PubMed Central

The extraction and purification of nucleic acids from complex samples (e.g. blood, biopsied tissue, cultured cells, food) is an essential prerequisite for many applications in biology including genotyping, transcriptional analysis, systems biology, epigenetic analysis, and virus/bacterial detection. In this report, we describe a new process of nucleic acid extraction that utilizes “pinned” aqueous/organic liquid interfaces in microchannels to streamline the extraction mechanism, replacing all washing steps with a single traverse of an immiscible fluid barrier, termed Immiscible Filtration Assisted by Surface Tension (IFAST). Nucleic acids in biological samples are bound to paramagnetic particles and then drawn across the IFAST device (or array of IFAST devices) using a magnet. While the strength of the IFAST barrier is suitable for separation of nucleic acids from lysate in its current embodiment, its permeability can be selectively adapted by adjusting the surface tensions/energies associated with the cell lysate, the immiscible phase, and the device surface, enabling future expansion to other non-nucleic acid applications. Importantly, processing time is reduced from 15–45 minutes to less than 5 minutes while maintaining purity, yield, and scalability equal to or better than prevailing methods. Operation is extremely simple and no additional lab infrastructure is required. The IFAST technology thus significantly enhances researchers’ abilities to isolate and analyze nucleic acids, a process which is critical and ubiquitous in an extensive array of scientific fields.

Berry, Scott M.; Alarid, Elaine T.; Beebe, David J.

2011-01-01

267

A partition function algorithm for interacting nucleic acid strands  

PubMed Central

Recent interests, such as RNA interference and antisense RNA regulation, strongly motivate the problem of predicting whether two nucleic acid strands interact. Motivation: Regulatory non-coding RNAs (ncRNAs) such as microRNAs play an important role in gene regulation. Studies on both prokaryotic and eukaryotic cells show that such ncRNAs usually bind to their target mRNA to regulate the translation of corresponding genes. The specificity of these interactions depends on the stability of intermolecular and intramolecular base pairing. While methods like deep sequencing allow to discover an ever increasing set of ncRNAs, there are no high-throughput methods available to detect their associated targets. Hence, there is an increasing need for precise computational target prediction. In order to predict base-pairing probability of any two bases in interacting nucleic acids, it is necessary to compute the interaction partition function over the whole ensemble. The partition function is a scalar value from which various thermodynamic quantities can be derived. For example, the equilibrium concentration of each complex nucleic acid species and also the melting temperature of interacting nucleic acids can be calculated based on the partition function of the complex. Results: We present a model for analyzing the thermodynamics of two interacting nucleic acid strands considering the most general type of interactions studied in the literature. We also present a corresponding dynamic programming algorithm that computes the partition function over (almost) all physically possible joint secondary structures formed by two interacting nucleic acids in O(n6) time. We verify the predictive power of our algorithm by computing (i) the melting temperature for interacting RNA pairs studied in the literature and (ii) the equilibrium concentration for several variants of the OxyS–fhlA complex. In both experiments, our algorithm shows high accuracy and outperforms competitors. Availability: Software and web server is available at http://compbio.cs.sfu.ca/taverna/pirna/ Contact: cenk@cs.sfu.ca; backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are avaliable at Bioinformatics online.

Chitsaz, Hamidreza; Salari, Raheleh; Sahinalp, S. Cenk; Backofen, Rolf

2009-01-01

268

Nucleic acid-based approaches to STAT inhibition  

PubMed Central

Silencing of abnormally activated genes can be accomplished in a highly specific manner using nucleic acid based approaches. The focus of this review includes the different nucleic acid based inhibition strategies such as antisense oligodeoxynucleotides, small interfering RNA (siRNA), dominant-negative constructs, G-quartet oligonucleotides and decoy oligonucleotides, their mechanism of action and the effectiveness of these approaches to targeting the STAT (signal transducer and activator of transcription) proteins in cancer. Among the STAT proteins, especially STAT3, followed by STAT5, are the most frequently activated oncogenic STATs, which have emerged as plausible therapeutic cancer targets. Both STAT3 and STAT5 have been shown to regulate numerous oncogenic signaling pathways including proliferation, survival, angiogenesis and migration/invasion.

Sen, Malabika; Grandis, Jennifer R.

2012-01-01

269

Detection of nucleic acid hybrids by prolonged chemiluminescence  

SciTech Connect

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.

Dattagupta, N.; Clemens, A.H.

1988-12-27

270

Ultrasensitive nucleic acid sequence detection by single-molecule electrophoresis  

SciTech Connect

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.

Castro, A; Shera, E.B.

1996-09-01

271

7-Azidomethoxy Coumarins as Profluorophores for Templated Nucleic Acid Detection  

PubMed Central

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.

Franzini, Raphael M.

2012-01-01

272

Physical chemistry of nucleic acids and their complexes.  

PubMed

Studies of the physical properties of nucleic acids began almost immediately following the discovery of the DNA structure. Early investigations focused on the stability and specificity of multi-strand polynucleotide complexes, then gradually on their interaction with other molecules, particularly proteins. As molecular and structural biology expanded to provide detailed information about biochemical mechanisms, physical studies eventually acquired the additional constraint that they should be relevant to functioning biological systems. We describe work in our laboratory that began with investigations of relatively simple questions about the role of electrostatic interactions in the stabilization of multi-strand nucleic acid structures, and evolved to studies of chromatin structure in vitro and within the nucleus. Published 2013 Wiley Periodicals, Inc*. Biopolymers 99: 910-915, 2013. PMID:23765314

Ghirlando, Rodolfo; Felsenfeld, Gary

2013-12-01

273

Efficient Nucleic Acid Detection by Templated Reductive Quencher Release  

PubMed Central

RNA-templated fluorescence activation is a nucleic acid detection strategy that offers the possibility of direct visual detection of genetic information in living cells. Here we describe a new reaction strategy for fluorescence activation, in which a phosphine on one DNA probe reduces an azide group in a linker on a second probe, resulting in linker cleavage and release of a fluorescence quenching group. These “Q-STAR” probes are shown to yield a strong fluorescence turn-on signal in ca. 20 min, with very low background and substantial amplification by turnover on the template. A green/red pair of such probes allowed the discrimination of two bacterial species by a single nucleotide difference in their 16S rRNA. The beneficial properties of the reductive quencher release design makes these probes promising candidates for widespread applications in the detection of nucleic acids in vitro and in cells.

Franzini, Raphael M.; Kool, Eric T.

2009-01-01

274

Ring current shielding effects in nucleic acid double helices.  

PubMed

Values of ring current shielding in parts-per-million have been calculated for double helical nucleic acids in the A-RNA (RNA-11), A' -RNA (RNA-12) and B-DNA geometries. Atomic coordinates determined previously from x-ray diffraction of fibers were used to calculate the positions of protons relative to both nearest and second nearest neighboring bases, including those on the complementary strand. The magnitude of the diamagnetic shielding was then calculated for each aromatic ring. From these calculations tables were constructed for use in determining the shielding expected for carbon-bound and ring nitrogen-bound protons of any double helical nucleic acid sequence. The results are compared with available experimental data for several oligonucleotides and with previous ring current shielding calculations where differences of up to 0.4 ppm are found. PMID:958893

Arter, D B; Schmidt, P G

1976-06-01

275

IN VITRO SELECTION OF FUNCTIONAL NUCLEIC ACIDS  

Microsoft Academic Search

? 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

David S. Wilson; Jack W. Szostak

1999-01-01

276

Reactions between Singlet Oxygen and the Constituents of Nucleic Acids  

PubMed Central

Bases, nucleosides, nucleotides, and polynucleotides were exposed to chemically generated singlet oxygen to determine whether the species oxidized paralleled those oxidized in photodynamic reactions. In neutral or basic aqueous solution guanine, guanosine, deoxyguanosine, guanylic acid, deoxyguanylic acid, thymine, and uracil reacted with singlet oxygen. Since these compounds are oxidized in photodynamic processes, this study provides further evidence that singlet oxygen is the active intermediate in the photodynamic oxidation of nucleic acid constituents. Dienophilic attack by singlet oxygen is considered to be a plausible mechanism in these reactions.

Hallett, F. R.; Hallett, B. P.; Snipes, W.

1970-01-01

277

Polymerization of murine recombinant prion protein in nucleic acid solution  

Microsoft Academic Search

Summary.  ?Recombinant prion protein has been used earlier to understand the structural properties of cellular prion protein PrPC and to understand conformational change of PrPC to its isoform, PrPSc which is believed to be responsible for the prion disease. Here we report that murine recombinant prion protein, MoPrPC polymerizes in the presence of nucleic acid. The aggregation process and the properties

P. K. Nandi; E. Leclerc

1999-01-01

278

A partition function algorithm for interacting nucleic acid strands  

Microsoft Academic Search

Recent interests, such as RNA interference and antisense RNA regulation, strongly motivate the problem of predicting whether two nucleic acid strands interact. Motivation: Regulatory non-coding RNAs (ncRNAs) such as microRNAs play an important role in gene regulation. Studies on both prokaryotic and eukaryotic cells show that such ncRNAs usually bind to their target mRNA to regulate the translation of corresponding

Hamidreza Chitsaz; Raheleh Salari; Süleyman Cenk Sahinalp; Rolf Backofen

2009-01-01

279

Immune Recognition of Nucleic Acids and Their Metabolites  

Microsoft Academic Search

\\u000a Recent research suggests that nucleic acids are active modulators of the immune system. RNA and DNA can be detected by specific\\u000a receptors – the so-called Toll-like receptors, RIG-I-like receptors, and NOD-like receptors. Resultant intra- and intercellular\\u000a activations of the innate immune system are pivotal in both protective and pathological immune responses during infection\\u000a and other immunological disorders. Moreover, our immune

Shohei Koyama; Shizuo Akira; Ken J. Ishii

280

Translating Nucleic Acid Aptamers to Antithrombotic Drugs in Cardiovascular Medicine  

Microsoft Academic Search

Nucleic acid aptamers offer several distinct advantages for the selective inhibition of protein targets within the coagulation\\u000a cascade. A highly attractive feature of aptamers as antithrombotics is their ability to encode for complementary “controlling\\u000a agents” which selectively bind to and neutralize their active counterparts via Watson–Crick base pairing or, in a less selective\\u000a and clinically characterized manner, cationic polymers that

Thomas J. Povsic; Bruce A. Sullenger; Steven L. Zelenkofske; Christopher P. Rusconi; Richard C. Becker

2010-01-01

281

Recognition schemes for protein-nucleic acid interactions  

Microsoft Academic Search

The molecular forces involved in protein-nucleic acid interaction are electrostatic, stacking and hydrogen-bonding. These\\u000a interactions have a certain amount of specificity due to the directional nature of such interactions and the spatial contributions\\u000a of the steric effects of different substituent groups. Quantum chemical calculations on these interactions have been reported\\u000a which clearly bring out such features.\\u000a \\u000a While the binding energies

Girjesh Govil; N. Y. Kumar; M. Ravi Kumar; R. V. Hosur; Kunal B. Roy; H. Todd Miles

1985-01-01

282

Developing nucleic acid-based electrical detection systems  

PubMed Central

Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and requirements for an ideal detector suitable for nucleic acid analysis include high sensitivity and high specificity protocol that can be completed in a relatively short time offering at the same time low detection limit. Moreover, systems that can be miniaturized and automated present a significant advantage over conventional technology, especially if detection is needed in the field. Electrical system technology for nucleic acid-based detection is an enabling mode for making miniaturized to micro- and nanometer scale bio-monitoring devices via the fusion of modern micro- and nanofabrication technology and molecular biotechnology. The electrical biosensors that rely on the conversion of the Watson-Crick base-pair recognition event into a useful electrical signal are advancing rapidly, and recently are receiving much attention as a valuable tool for microbial pathogen detection. Pathogens may pose a serious threat to humans, animal and plants, thus their detection and analysis is a significant element of public health. Although different conventional methods for detection of pathogenic microorganisms and their toxins exist and are currently being applied, improvements of molecular-based detection methodologies have changed these traditional detection techniques and introduced a new era of rapid, miniaturized and automated electrical chip detection technologies into pathogen identification sector. In this review some developments and current directions in nucleic acid-based electrical detection are discussed.

Gabig-Ciminska, Magdalena

2006-01-01

283

Current and Future Developments in Nucleic Acid-Based Diagnostics  

Microsoft Academic Search

The detection and characterization of specific nucleic acids of medico-veterinary pathogens have proven invaluable for diagnostic\\u000a purposes. Apart from hybridization and sequencing techniques, polymerase chain reaction (PCR) and numerous other methods have\\u000a contributed significantly to this process. The integration of amplification and signal detection systems, including on-line\\u000a real-time devices, have increased speed and sensitivity and greatly facilitated the quantification of

Gerrit J. Viljoen; Marco Romito; Pravesh D. Kara

284

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

PubMed Central

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.

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

2009-01-01

285

System for portable nucleic acid testing in low resource settings  

NASA Astrophysics Data System (ADS)

Our overall goal is to enable timely diagnosis of infectious diseases through nucleic acid testing at the point-of-care and in low resource settings, via a compact system that integrates nucleic acid sample preparation, isothermal DNA amplification, and nucleic acid lateral flow (NALF) detection. We herein present an interim milestone, the design of the amplification and detection subsystem, and the characterization of thermal and fluidic control and assay execution within this system. Using an earlier prototype of the amplification and detection unit, comprised of a disposable cartridge containing flexible pouches, passive valves, and electrolysis-driven pumps, in conjunction with a small heater, we have demonstrated successful execution of an established and clinically validated isothermal loop-mediated amplification (LAMP) reaction targeting Mycobacterium tuberculosis (M.tb) DNA, coupled to NALF detection. The refined design presented herein incorporates miniaturized and integrated electrolytic pumps, novel passive valves, overall design changes to facilitate integration with an upstream sample preparation unit, and a refined instrument design that automates pumping, heating, and timing. Nucleic acid amplification occurs in a two-layer pouch that facilitates fluid handling and appropriate thermal control. The disposable cartridge is manufactured using low-cost and scalable techniques and forms a closed system to prevent workplace contamination by amplicons. In a parallel effort, we are developing a sample preparation unit based on similar design principles, which performs mechanical lysis of mycobacteria and DNA extraction from liquefied and disinfected sputum. Our next step is to combine sample preparation, amplification, and detection in a final integrated cartridge and device, to enable fully automated sample-in to answer-out diagnosis of active tuberculosis in primary care facilities of low-resource and high-burden countries.

Lu, Hsiang-Wei; Roskos, Kristina; Hickerson, Anna I.; Carey, Thomas; Niemz, Angelika

2013-03-01

286

Application of living free radical polymerization for nucleic acid delivery.  

PubMed

Therapeutic gene delivery can alter protein function either through the replacement of nonfunctional genes to restore cellular health or through RNA interference (RNAi) to mask mutated and harmful genes. Researchers have investigated a range of nucleic acid-based therapeutics as potential treatments for hereditary, acquired, and infectious diseases. Candidate drugs include plasmids that induce gene expression and small, interfering RNAs (siRNAs) that silence target genes. Because of their self-assembly with nucleic acids into virus-sized nanoparticles and high transfection efficiency in vitro, cationic polymers have been extensively studied for nucleic acid delivery applications, but toxicity and particle stability have limited the clinical applications of these systems. The advent of living free radical polymerization has improved the quality, control, and reproducibility of these synthesized materials. This process yields well-defined, narrowly disperse materials with designed architectures and molecular weights. As a result, researchers can study the effects of polymer architecture and molecular weight on transfection efficiency and cytotoxicity, which will improve the design of next-generation vectors. In this Account, we review findings from structure-function studies that have elucidated key design motifs necessary for the development of effective nucleic acid vectors. Researchers have used robust methods such as atom transfer radical polymerization (ATRP), reverse addition-fragmentation chain transfer polymerization (RAFT), and ring-opening metastasis polymerization (ROMP) to engineer materials that enhance extracellular stability and cellular specificity and decrease toxicity. In addition, we discuss polymers that are biodegradable, form supramolecular structures, target specific cells, or facilitate endosomal release. Finally, we describe promising materials with a range of in vivo applications from pulmonary gene delivery to DNA vaccines. PMID:22242774

Chu, David S H; Schellinger, Joan G; Shi, Julie; Convertine, Anthony J; Stayton, Patrick S; Pun, Suzie H

2012-01-13

287

Strategies for signal amplification in nucleic acid detection  

Microsoft Academic Search

Many aspects of molecular genetics necessitate the detection of nucleic acid sequences. Current approaches involving target\\u000a amplification (in situ PCR, Primed in situ Labeling, Self-Sustained Sequence Replication, Strand Displacement Amplification), probe amplification (Ligase Chain Reaction,\\u000a Padlock Probes, Rolling Circle Amplification) and signal amplification (Tyramide Signal Amplification, Branched DNA Amplification)\\u000a are summarized in the present review, together with their advantages and

S. Calin Andras; J. Brian Power; Edward C. Cocking; Michael R. Davey

2001-01-01

288

Potent and nontoxic antisense oligonucleotides containing locked nucleic acids  

Microsoft Academic Search

Insufficient efficacy and\\/or specificity of antisense oligonucleotides limit their in vivo usefulness. We demonstrate here that a high-affinity DNA analog, locked nucleic acid (LNA), confers several desired properties to antisense agents. Unlike DNA, LNA\\/DNA copolymers were not degraded readily in blood serum and cell extracts. However, like DNA, the LNA\\/DNA copolymers were capable of activating RNase H, an important antisense

Claes Wahlestedt; Peter Salmi; Liam Good; Johanna Kela; Thomas Johnsson; Tomas Hökfelt; Christian Broberger; Frank Porreca; Josephine Lai; Kunkun Ren; Michael Ossipov; Alexei Koshkin; Nana Jakobsen; Jan Skouv; Henrik Oerum; Mogens Havsteen Jacobsen; Jesper Wengel

2000-01-01

289

Design of antisense oligonucleotides stabilized by locked nucleic acids  

Microsoft Academic Search

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

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

2002-01-01

290

NMR solution structures of LNA (locked nucleic acid) modified quadruplexes  

Microsoft Academic Search

We have determined the NMR solution structures of the quadruplexes formed by d(TGLGLT) and d(TL4T), where L denotes LNA (locked nucleic acid) modified G-residues. Both structures are tetrameric, parallel and right-handed and the native global fold of the corresponding DNA quadruplex is retained upon introduction of the LNA nucleotides. However, local structural alterations are observed owing to the locked LNA

Jakob T. Nielsen; Khalil Arar; Michael Petersen

2006-01-01

291

CANADA: designing nucleic acid sequences for nanobiotechnology applications.  

PubMed

The design of nucleic acid sequences for a highly specific and efficient hybridization is a crucial step in DNA computing and DNA-based nanotechnology applications. The CANADA package contains software tools for designing DNA sequences that meet these and other requirements, as well as for analyzing and handling sequences. CANADA is freely available, including a detailed manual and example input files, at http://ls11-www.cs.uni-dortmund.de/molcomp/downloads. PMID:19530109

Feldkamp, Udo

2010-02-01

292

Excited-state properties of nucleic acid components  

NASA Astrophysics Data System (ADS)

Measurements were made of the fluorescence and phosphorescence spectra and lifetimes, and also of the absorption spectra, lifetimes, extinction coefficients, and quantum yields of the T1 lower triplet states of thymine, uracil, their N, N'-dimethyl derivatives, thymidine, thymidine monophosphate, uridine, and uridine monophosphate in various solvents at 300 °K. The influence of the solvent on the quantum yield of the T1 state of nucleic acid components is discussed.

Salet, C.; Bensasson, R. V.; Becker, R. S.

1981-12-01

293

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

Microsoft Academic Search

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

E. L. Madsen

2000-01-01

294

Nucleic acid scavengers inhibit thrombosis without increasing bleeding.  

PubMed

Development of effective, yet safe, antithrombotic agents has been challenging because such agents increase the propensity of patients to bleed. Recently, naturally occurring polyphosphates such as extracellular DNA, RNA, and inorganic polyphosphates have been shown to activate blood coagulation. In this report, we evaluate the anticoagulant and antithrombotic activity of nucleic acid-binding polymers in vitro and in vivo. Such polymers bind to DNA, RNA, and inorganic polyphosphate molecules with high affinity and inhibit RNA- and polyphosphate-induced clotting and the activation of the intrinsic pathway of coagulation in vitro. Moreover, [NH(2)(CH(2))(2)NH(2)](G = 3);dendri PAMAM(NH(2))(32) (PAMAM G-3) prevents thrombosis following carotid artery injury and pulmonary thromboembolism in mice without significantly increasing blood loss from surgically challenged animals. These studies indicate that nucleic acid-binding polymers are able to scavenge effectively prothrombotic nucleic acids and other polyphosphates in vivo and represent a new and potentially safer class of antithrombotic agents. PMID:22837404

Jain, Shashank; Pitoc, George A; Holl, Eda K; Zhang, Ying; Borst, Luke; Leong, Kam W; Lee, Jaewoo; Sullenger, Bruce A

2012-07-25

295

Translating nucleic acid aptamers to antithrombotic drugs in cardiovascular medicine.  

PubMed

Nucleic acid aptamers offer several distinct advantages for the selective inhibition of protein targets within the coagulation cascade. A highly attractive feature of aptamers as antithrombotics is their ability to encode for complementary "controlling agents" which selectively bind to and neutralize their active counterparts via Watson-Crick base pairing or, in a less selective and clinically characterized manner, cationic polymers that can counteract the activity of an aptamer or free/protein-complexed nucleic acid. The former property allows aptamer-based antithrombotic therapies to be administered with a goal of selective, high intensity target inhibition, knowing that rapid drug reversal is readily available. In addition, by purposefully varying the ratio of active agent to a specific controlling agent administered, the intensity of antithrombotic therapy can be regulated with precision according to patient needs and the accompanying clinical conditions. REG1, currently undergoing phase 2B clinical investigation, consists of an RNA aptamer (RB006; pegnivacogin) which targets factor IXa and its complementary controlling agent (RB007; anivamersen). Aptamers directed against other serine coagulation proteases, some with and some without parallel controlling agents, have been designed. Aptamers directed against platelet surface membrane receptor targets are in preclinical development. The following review offers a contemporary summary of nucleic acid aptamers as a translatable platform for regulatable antithrombotic drugs expanding the paradigm of patient- and disease-specific treatment in clinical practice. PMID:21080135

Povsic, Thomas J; Sullenger, Bruce A; Zelenkofske, Steven L; Rusconi, Christopher P; Becker, Richard C

2010-11-16

296

Interactions of pyronin Y(G) with nucleic acids.  

PubMed

Spectral properties of pyronin Y(PY) alone or in complexes with natural and synthetic nucleic acids of various base compositions have been studied in aqueous solution containing 10 or 150 mM NaCl and 5 mM Hepes at pH 7.0. The dimerization constant (KD = 6.27 X 10(3), M-1) and the absorption spectra of the dye in monomeric and dimeric form were established. The complexes of PY with single-stranded (ss) nucleic acids show a hypsochromic shift in absorption, and their fluorescence is quenched by over 90% compared to free dye. In contrast, complexes with double-stranded (ds) RNA or DNA (binding by intercalation) exhibit a bathochromic shift in their absorption (excitation) spectrum, and their fluorescence is correlated with the base composition of the binding site. Namely, guanine quenches fluorescence of PY by up to 90%, whereas A, C, I, T, and U bases exert a rather minor effect on the fluorescence quantum yield of the dye. The intrinsic association constant of the dye to ds RNA (Ki = 6.96 X 10(4), M-1) and to ds DNA (Ki = 1.74 X 10(4), M-1) was measured in 150 mM NaCl; the binding site size was 2-3 base pair for both polymers. Implications of these findings for qualitative and quantitative cytochemistry of nucleic acids are discussed. PMID:3582061

Kapuscinski, J; Darzynkiewicz, Z

1987-03-01

297

Nucleic acid-induced antiviral immunity in shrimp.  

PubMed

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

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

2013-06-15

298

Carbon nanotubes and nucleic acids: tools and targets  

NASA Astrophysics Data System (ADS)

Nucleic acids are playing an important role in the rapid development of nanotechnologies. Our Editor's Choice [1] discusses the use of nucleic acids to disperse and sort single walled carbon nanotubes (SWNTs). The cover picture shows a two-dimensional photoluminescence (PL) spectrum of highly purified (6,5) SWNT:DNA hybrids. The fine resolution of the PL peaks displays photo-excited intermediates in a range of energies between ES22 and ES11 transitions revealing for the first time specific phonon-assisted optical absorption and energy relaxation mechanisms.The first author, Bibiana Onoa, has been working on carbon nanotubes and nucleic acids in the molecular electronics group of Dupont Central Research and Development. Her current research focuses on the development of nanotechnologies that allow fast and economical detection of pathogens.This special issue of physica status solidi (a) presents representative contributions and main topics on Trends in Nanotechnology from the TNT2005 International Conference in Oviedo (Spain).

Onoa, Bibiana; Zheng, Ming; Dresselhaus, Mildred S.; Diner, Bruce A.

2006-05-01

299

Nucleic Acid sample preparation using spontaneous biphasic plug flow.  

PubMed

Nucleic acid (NA) extraction and purification has become a common technique in both research and clinical laboratories. Current methods require repetitive wash steps with a pipet that are laborious and time-consuming, making the procedure inefficient for clinical settings. We present here a simple technique that relies on spontaneous biphasic plug flow inside a capillary to achieve sample preparation. By filling the sample with oil, aqueous contaminants were displaced from the captured NA without pipetting wash buffers or use of external force and equipment. mRNA from mammalian cell culture was purified, and polymerase chain reaction (PCR) amplification showed similar threshold cycle values as those obtained from a commercially available kit. Human immunodeficiency virus (HIV) viral-like particles were spiked into serum and a 5-fold increase in viral RNA extraction yield was achieved compared to the conventional wash method. In addition, viral RNA was successfully purified from human whole blood, and a limit of detection of approximately 14 copies of RNA extracted per sample was determined. The results demonstrate the utility of the current technique for nucleic acid purification for clinical purposes, and the overall approach provides a potential method to implement nucleic acid testing in low-resource settings. PMID:23941230

Thomas, Peter C; Strotman, Lindsay N; Theberge, Ashleigh B; Berthier, Erwin; O'Connell, Rachel; Loeb, Jennifer M; Berry, Scott M; Beebe, David J

2013-09-04

300

Nucleic acid scavengers inhibit thrombosis without increasing bleeding  

PubMed Central

Development of effective, yet safe, antithrombotic agents has been challenging because such agents increase the propensity of patients to bleed. Recently, naturally occurring polyphosphates such as extracellular DNA, RNA, and inorganic polyphosphates have been shown to activate blood coagulation. In this report, we evaluate the anticoagulant and antithrombotic activity of nucleic acid-binding polymers in vitro and in vivo. Such polymers bind to DNA, RNA, and inorganic polyphosphate molecules with high affinity and inhibit RNA- and polyphosphate-induced clotting and the activation of the intrinsic pathway of coagulation in vitro. Moreover, [NH2(CH2)2NH2]?(G = 3);dendri PAMAM(NH2)32 (PAMAM G-3) prevents thrombosis following carotid artery injury and pulmonary thromboembolism in mice without significantly increasing blood loss from surgically challenged animals. These studies indicate that nucleic acid-binding polymers are able to scavenge effectively prothrombotic nucleic acids and other polyphosphates in vivo and represent a new and potentially safer class of antithrombotic agents.

Jain, Shashank; Pitoc, George A.; Holl, Eda K.; Zhang, Ying; Borst, Luke; Leong, Kam W.; Lee, Jaewoo; Sullenger, Bruce A.

2012-01-01

301

Delivery of nucleic acid into aquatic animals  

US Patent & Trademark Office Database

Disclosed are methods for delivering a preselected polypeptide into an aquatic animal by contacting the aquatic animal with an aqueous medium containing an isolated non-infectious, non-integrating polynucleotide encoding an immunogen, wherein the polynucleotide is operably linked to a promoter that controls the expression of the polynucleotide in the aquatic animal, and wherein expression of the polypeptide stimulates a detectable biological response in the animal. Also disclosed are methods for delivering a desired polynucleotide into an aquatic animal comprising contacting the aquatic animal with an aquatic medium containing an isolated non-infectious, non-integrating polynucleotide, wherein the polynucleotide is substantially complementary to all or a portion of a messenger RNA (mRNA) encoding a preselected polypeptide, and wherein expression of the polypeptide stimulates or represses a detectable biological response in the animal. Methods are further disclosed for delivering a preselected polynucleotide into an aquatic animal comprising contacting the aquatic animal with an aqueous medium containing an isolated non-infectious, non-integrating polynucleotide that is not in contact with a liposome or lipid carrier, wherein the polynucleotide stimulates a detectable biological response in the animal.

2002-10-08

302

A theoretical analysis of specificity of nucleic acid interactions with oligonucleotides and peptide nucleic acids (PNAs) 1 1 Edited by I. Tinoco  

Microsoft Academic Search

We treat theoretically the problem of the specificity of interaction between nucleic acid and an oligonucleotide, its analog or its mimic (such as peptide nucleic acid, or PNA). We consider simplest models with only essential details using numerical solutions of kinetic equations and the kinetic Monte Carlo method. In our first model, describing the formation of complementary duplex, we demonstrate

Aleksey Lomakin; Maxim D Frank-Kamenetskii

1998-01-01

303

Proteins and nucleic acids encoding same  

US Patent & Trademark Office Database

The present invention provides novel isolated polynucleotides and small molecule target polypeptides encoded by the polynucleotides. Antibodies that immunospecifically bind to a novel small molecule target polypeptide or any derivative, variant, mutant or fragment of that polypeptide, polynucleotide or antibody are disclosed, as are methods in which the small molecule target polypeptide, polynucleotide and antibody are utilized in the detection and treatment of a broad range of pathological states. More specifically, the present invention discloses methods of using recombinantly expressed and/or endogenously expressed proteins in various screening procedures for the purpose of identifying therapeutic antibodies and therapeutic small molecules associated with diseases.

Patturajan; Meera (Branford, CT)

2006-04-25

304

Easily denaturing nucleic acids derived from intercalating nucleic acids: thermal stability studies, dual duplex invasion and inhibition of transcription start  

Microsoft Academic Search

The bulged insertions of (R )-1-O-(pyren-1-ylmethyl)- glycerol (monomer P) in two complementary 8mer DNA strands (intercalating nucleic acids) opposite to each other resulted in the formation of an easily denaturing duplex, which had lower thermal stability (21.0? C) than the wild-type double-stranded DNA (dsDNA, 26.0? C), but both modified oligodeoxy- nucleotides had increased binding affinity toward complementary single-stranded DNA (ssDNA)

Vyacheslav V. Filichev; Birte Vester; Lykke H. Hansen; Erik B. Pedersen

2005-01-01

305

Nucleic acid hybridization in the diagnosis of viral infections.  

PubMed

Recombinant DNA technology, including molecular cloning and nucleic acid hybridization, is now being applied to problems in clinical virology. Although viral isolation in cell culture remains the most sensitive and specific diagnostic test for many viruses, for some viruses, isolation in cell culture is lengthy or difficult or has not yet been achieved. Utilization of hybridization techniques has already resulted in important new information concerning the pathogenesis of a number of viruses, such as Epstein-Barr virus, hepatitis B virus, and human papillomavirus. In addition, time to diagnosis for viruses such as cytomegalovirus, Epstein-Barr virus, and varicella-zoster virus can be significantly shortened to 36 to 48 hours, a great improvement over standard isolation with obvious importance for patient management. Hybridization techniques have also been applied to screening of antiviral agents. Although results of studies to date have been encouraging, significant problems remain to be solved before these techniques can be applied in a routine diagnostic laboratory. First, more sensitive assays must be developed. One approach is the generation of probes with higher specific activities. Synthesis of single-stranded probes using recombinant M13 bacteriophage as a template results in probes of higher specific activities that also cannot re-anneal to themselves because they are not complementary. Thus, more probe is available to anneal to sample DNA. Synthesis of cRNA probes that form more stable hybrids with DNA is another approach that is receiving attention. A second problem is reagent safety and stability. The most sensitive and commonly used label in the studies reviewed in this article has been 32P. With its half-life of 2 weeks, potential hazards to personnel, and disposal problems, it is probably not suitable for clinical laboratories. A major step in the development of nonradioactive, stable probes has been synthesis of biotinylated nucleotide analogues that can be efficiently incorporated into DNA or RNA. Biotinylated probes are stable for 1 to 2 years at -20 degrees C, and their use obviates the need for autoradiography, thus shortening reaction times. In addition, very high concentrations of probes can be used without the background problems encountered with radiolabels. To date, biotinylated probes have been significantly less sensitive than those labeled with 32P, but continued efforts to improve sensitivity have yielded promising results.(ABSTRACT TRUNCATED AT 400 WORDS) PMID:3899479

Landry, M L; Fong, C K

1985-09-01

306

Computational analysis of propensities of amino acids and nucleotides usage at protein-nucleic acid interfaces  

Microsoft Academic Search

n ot fou nd . Abstract—The mechanism of protein-nucleic acid interaction is still not very clear, especially that of protein-RNA interaction. Therefore, with the increasing of available protein-nucleic acid complex structures in the protein data bank database, we have collected all the structures and then analyzed the rules controlling the recognition of residues by nucleotides using classical statistical methods. The

Jiansheng Wu; Shancheng Yan; Lihua Tang; Dong Hu

2011-01-01

307

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

Microsoft Academic Search

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

Zhengping Li; Ke’an Li; Shenyang Tong

2000-01-01

308

Primate and Murine Type-C Viral Nucleic Acid Association Kinetics: Analysis of Model Systems and Natural Tissues  

PubMed Central

Hybridization studies employing single-stranded 3H-DNA transcripts of type-C viruses isolated from a woolly monkey or gibbon ape failed to detect nucleic acid sequences homologous to these viruses in the DNA from a variety of uninfected primate species. The possible significance of these results for the epidemiology of type-C viruses in primates is discussed.

Scolnick, E. M.; Parks, W.; Kawakami, T.; Kohne, Dave; Okabe, H.; Gilden, Ray; Hatanaka, M.

1974-01-01

309

The peptide nucleic acids as probes for chromosomal analysis: application to human oocytes, polar bodies and preimplantation embryos  

Microsoft Academic Search

Peptide nucleic acids (PNA) are synthetic DNA mimics based on an uncharged polyamide backbone, which hybridize with complementary DNA with high affinity and specificity. PNA have recently become recognized as efficient tools for in situ chromosomal identification. In the present study, this new approach has been tried on isolated human oocytes, polar bodies and blastomeres. Using centromeric PNA probes specific

P. Paulasova; B. Andreo; J. Diblik; M. Macek; F. Pellestor

2004-01-01

310

Electrophoretic Mobility Shift Assay (EMSA) for Detecting Protein-Nucleic Acid Interactions  

PubMed Central

The gel electrophoresis mobility shift assay (EMSA) is used to detect protein complexes with nucleic acids. It is the core technology underlying a wide range of qualitative and quantitative analyses for the characterization of interacting systems. In the classical assay, solutions of protein and nucleic acid are combined and the resulting mixtures are subjected to electrophoresis under native conditions through polyacrylamide or agarose gel. After electrophoresis, the distribution of species containing nucleic acid is determined, usually by autoradiography of 32P-labeled nucleic acid. In general, protein-nucleic acid complexes migrate more slowly than the corresponding free nucleic acid. In this article, we identify the most important factors that determine the stabilities and electrophoretic mobilities of complexes under assay conditions. A representative protocol is provided and commonly used variants are discussed. Expected outcomes are briefly described. References to extensions of the method and a troubleshooting guide are provided.

Hellman, Lance M.; Fried, Michael G.

2009-01-01

311

[Studies on rapid detection of food-borne pathogenic bacteria by nucleic acid testing and related technology].  

PubMed

The traditional methods of bacteria isolation, cultivation and identification are time-consuming, which can't meet the needs of the control and prevention of food-borne diseases. Recently, various kinds of rapid methods for food-borne pathogenic bacteria detection have emerged with the prompt development of nucleic acid testing technology. The application studies on polymerase chain reaction and the techniques derived from it, nucleic acid isothermal amplification, oligonucleotide microarray, immunomagnetic separation and DNA biosensing on food-borne pathogenic bacteria including Salmonella, Staphylococcus aureus and Enterohemorrhagic Escherchia coli, etc. were reviewed. PMID:18589620

Cao, Wei; Wang, Mingzhong; Wang, Xiaoying; Liu, Xiumei

2008-03-01

312

Modeling nucleic acid structure in the presence of single-stranded binding proteins  

Microsoft Academic Search

There are many important proteins which bind single-stranded nucleic acids, such as the nucleocapsid protein in HIV, the RecA DNA repair protein in bacteria, and all proteins involved in mRNA splicing and translation. We extend the Vienna Package for quantitatively modeling the secondary structure of nucleic acids to include proteins which bind to unpaired portions of the nucleic acid. All

Robert Forties; Ralf Bundschuh

2009-01-01

313

Cations as Mediators of the Adsorption of Nucleic Acids on Clay Surfaces in Prebiotic Environments  

Microsoft Academic Search

Monovalent ([Na+] > 10 mM) and divalent ([Ca2+], [Mg2+] > 1.0 mM) cations induced the precipitationof nucleic acid molecules. In the presence of clay minerals (montmorillonite and kaolinite), there was adsorption instead of precipitation. The cation concentration needed for adsorption depended on both the valence of the cations and the chemical nature of the nucleic acid molecules. Double-stranded nucleic acids

Marco Franchi; James P. Ferris; Enzo Gallori

2003-01-01

314

Murine recombinant prion protein induces ordered aggregation of linear nucleic acids to condensed globular structures  

Microsoft Academic Search

Summary.  ?Interaction between nucleic acid and recombinant murine prion protein, MoPrPC resulted in a time-dependent change in the nucleic acid morphology revealed by electron microscopy. After the addition of\\u000a the protein to DNA, association of small number of nucleic acid molecules (nucleo-protein complex) was followed by aggregation\\u000a of large number of them still retaining their initial linear morphology. With increase in

P. K. Nandi; P.-Y. Sizaret

2001-01-01

315

Extracellular Nucleic Acids of the Marine Phototrophic Bacterium Rhodovulum sulfidophilum and Related Bacteria: Physiology and Biotechnology  

Microsoft Academic Search

\\u000a Extracellular nucleic acids of high molecular weight are present ubiquitously throughout the environment, such as seawater\\u000a and soil. These nucleic acids were formerly thought to be derived from cells by cell death, but recent studies have shown\\u000a that they are at least partly derived from the active release of nucleic acids from some bacterial cells. Marine phototrophic\\u000a bacteria, Rhodovulum sulfidophilum

Yo Kikuchi

316

Nanopore Analysis of Nucleic Acids: Single-Molecule Studies of Molecular Dynamics, Structure, and Base Sequence  

Microsoft Academic Search

Nucleic acids are linear polynucleotides in which each base is covalently linked to a pentose sugar and a phosphate group\\u000a carrying a negative charge. If a pore having roughly the crosssectional diameter of a single-stranded nucleic acid is embedded\\u000a in a thin membrane and a voltage of 100 mV or more is applied, individual nucleic acids in solution can be

Felix Olasagasti; David W. Deamer

2009-01-01

317

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

Microsoft Academic Search

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,

Cheng Zhi Huang; Ke An Li; Shen Yang Tong

1997-01-01

318

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

Microsoft Academic Search

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

Cheng Zhi Huang; Yuan Fang Li; Shen Yang Tong

1997-01-01

319

Sensitive isothermal detection of nucleic-acid sequence by primer generation-rolling circle amplification  

Microsoft Academic Search

A simple isothermal nucleic-acid amplification reaction, primer generation-rolling circle amplifica- tion (PG-RCA), was developed to detect specific nucleic-acid sequences of sample DNA. This ampli- fication method is achievable at a constant tem- perature (e.g. 608C) simply by mixing circular single-stranded DNA probe, DNA polymerase and nicking enzyme. Unlike conventional nucleic-acid amplification reactions such as polymerase chain reaction (PCR), this reaction

Taku Murakami; Jun Sumaoka; Makoto Komiyama

2009-01-01

320

Polymerase-directed synthesis of C5-ethynyl locked nucleic acids  

Microsoft Academic Search

Modified nucleic acids have considerable potential in nanobiotechnology for the development of nanomedicines and new materials. Locked nucleic acid (LNA) is one of the most prominent nucleic acid analogues reported so far and we herein for the first time report the enzymatic incorporation of LNA-U and C5-ethynyl LNA-U nucleotides into oligonucleotides. Phusion High Fidelity and KOD DNA polymerases efficiently incorporated

Rakesh N. Veedu; Harsha V. Burri; Pawan Kumar; Pawan K. Sharma; Patrick J. Hrdlicka; Birte Vester; Jesper Wengel

2010-01-01

321

Semisynthetic nucleic acid–protein conjugates: applications in life sciences and nanobiotechnology  

Microsoft Academic Search

Semi-synthetic conjugates of nucleic acids and proteins can be generated by either covalent coupling chemistry, or else by non-covalent biomolecular recognition systems, such as receptor–ligands of complementary nucleic acids. These nucleic acid–protein conjugates are versatile molecular tools which can be applied, for instance, in the self-assembly of high-affinity reagents for immunological detection assays, the fabrication of laterally microstructured biochips containing

Christof M Niemeyer

2001-01-01

322

Evaluation of commercial kits for the extraction and purification of viral nucleic acids from environmental and fecal samples.  

PubMed

The extraction and purification of nucleic acids is a critical step in the molecular detection of enteric viruses from environmental or fecal samples. In the present study, the performance of three commercially available kits was assessed: the MO BIO PowerViral Environmental DNA/RNA Isolation kit, the Qiagen QIAamp Viral RNA Mini kit, and the Zymo ZR Virus DNA/RNA Extraction kit. Viral particles of adenovirus 2 (AdV), murine norovirus (MNV), and poliovirus type 1 (PV1) were spiked in molecular grade water and three different types of sample matrices (i.e., biosolids, feces, and surface water concentrates), extracted with the kits, and the yields of the nucleic acids were determined by quantitative PCR (qPCR). The MO BIO kit performed the best with the biosolids, which were considered to contain the highest level of inhibitors and provided the most consistent detection of spiked virus from all of the samples. A qPCR inhibition test using an internal control plasmid DNA and a nucleic acid purity test using an absorbance at 230 nm for the nucleic acid extracts demonstrated that the MO BIO kit was able to remove qPCR inhibitors more effectively than the Qiagen and Zymo kits. These results suggest that the MO BIO kit is appropriate for the extraction and purification of viral nucleic acids from environmental and clinical samples that contain high levels of inhibitors. PMID:23578704

Iker, Brandon C; Bright, Kelly R; Pepper, Ian L; Gerba, Charles P; Kitajima, Masaaki

2013-04-08

323

Use of carbonyl group addition--elimination reactions for synthesis of nucleic acid conjugates.  

PubMed

This review outlines the synthesis of covalent conjugates of oligonucleotides and their analogues that are obtained by reactions of carbonyl compounds with various nucleophiles such as primary amines, N-alkoxyamines, hydrazines, and hydrazides. The products linked by imino, oxime, hydrazone, or thiazolidine groups are shown to be useful intermediates for a wide range of chemical biology applications. Methods for their preparation, isolation, purification, and analysis are highlighted, and the comparative stabilities of the respective linkages are evaluated. The relative merits of incorporation of a carbonyl group, particularly an aldehyde group, into either the oligonucleotide or the ligand parts are considered. Examples of harnessing of aldehyde-nucleophile coupling for the labeling of nucleic acids are given, as well as their conjugation to various biomolecules (e.g. peptides and small molecule ligands), site-specific cross-linking of oligonucleotides to nucleic acid-binding proteins, assembly of multibranched supramolecular structures, and immobilization on functionalized surfaces. Future perspectives of bioconjugation and complex molecular engineering via carbonyl group addition-elimination reactions in nucleic acids chemistry are discussed. PMID:15898711

Zatsepin, Timofei S; Stetsenko, Dmitry A; Gait, Michael J; Oretskaya, Tatiana S

324

Development and performance evaluation of calf diarrhea pathogen nucleic acid purification and detection workflow.  

PubMed

Calf diarrhea (scours) is a primary cause of illness and death in young calves. Significant economic losses associated with this disease include morbidity, mortality, and direct cost of treatment. Multiple pathogens are responsible for infectious diarrhea, including, but not limited to, Bovine coronavirus (BCV), bovine Rotavirus A (BRV), and Cryptosporidium spp. Identification and isolation of carrier calves are essential for disease management. Texas Veterinary Medical Diagnostic Laboratory current methods for calf diarrhea pathogen identification include electron microscopy (EM) for BCV and BRV and a direct fluorescent antibody test (DFAT) for organism detection of Cryptosporidium spp. A workflow was developed consisting of an optimized fecal nucleic acid purification and multiplex reverse transcription quantitative polymerase chain reaction (RT-qPCR) for single tube concurrent detection of BCV, BRV, and Cryptosporidium spp., and an internal control to monitor nucleic acid purification efficacy and PCR reagent functionality. In "spike-in" experiments using serial dilutions of each pathogen, the analytical sensitivity was determined to be <10 TCID(50)/ml for BCV and BRV, and <20 oocysts for Cryptosporidium spp. Analytical specificity was confirmed using Canine and Feline coronavirus, Giardia spp., and noninfected bovine purified nucleic acid. Diagnostic sensitivity was ?98% for all pathogens when compared with respective traditional methods. The results demonstrate that the newly developed assay can purify and subsequently detect BCV, BRV, and Cryptosporidium spp. concurrently in a single PCR, enabling simplified and streamlined calf diarrhea pathogen identification. PMID:22914823

Schroeder, Megan E; Bounpheng, Mangkey A; Rodgers, Sandy; Baker, Rocky J; Black, Wendy; Naikare, Hemant; Velayudhan, Binu; Sneed, Loyd; Szonyi, Barbara; Clavijo, Alfonso

2012-09-01

325

Poly(alkylene oxide) Copolymers for Nucleic Acid Delivery  

PubMed Central

CONSPECTUS The advancement of gene-based therapeutics to the clinic is limited by the ability to deliver physiologically relevant doses of nucleic acids to target tissues safely and effectively. Polymer and lipid based nano-assemblies have been successfully employed over the last couple of decades for the delivery of nucleic acids to treat a variety of disease states. Results of phase I/II clinical studies to evaluate the efficacy and biosafety of these gene delivery vehicles have been encouraging, thus promoting the design of more efficient and biocompatible systems. Research has focused on designing carriers to achieve biocompatibility, stability in the circulatory system, biodistribution to target the disease site, and intracellular delivery, all of which enhance the resulting therapeutic effect. The family of poly(alkylene oxide) (PAO) includes random, block and branched polymers, among which the ABA type triblocks copolymers of ethylene oxide (EO) and propylene oxide (PO) (commercially known as Pluronic®) have received the greatest consideration. In this Account, we highlight examples of polycation-PAO conjugates, liposome-PAO formulations, and PAO micelles for nucleic acid delivery. Among the various polymer design consideration, which include molecular weight of polymer, molecular weight of blocks, and length of blocks, it has been found that the overall hydrophobic-lipophilic balance (HLB) is a critical parameter in defining the behavior of the polymer conjugates for gene delivery. The effects of varying this parameter are discussed in the context of improving gene delivery processes, such as serum-stability and association with cell membranes. Other innovative macromolecular modifications discussed in this category include the work done by our group to enhance the serum stability and efficiency of lipoplexes using PAO graft copolymers, development of a PAO gel-based carrier for sustained and stimuli responsive delivery, and biodegradable PAO-based amphiphilic block copolymers.

Mishra, Swati; Peddada, Lavanya Y.; Devore, David I.; Roth, Charles M.

2012-01-01

326

Polymerized spermine as a novel polycationic nucleic acid carrier system.  

PubMed

Spermine, an endogenous amino-group bearing monomer that condenses DNA in sperm, was used as the basic building block to form polycationic nucleic acid carriers via condensation with one of three linker molecules - bischloroformate, succinyl chloride, and glyoxal. The three cationic polymers, polyspermine carbamate (PSP-Carb), polyspermine amide (PSP-Amide) and polyspermine imine (PSP-Imine) were examined for their degradability, cytotoxicity, ability to condense nucleic acids to nanoparticles, and ability to transfect genes or siRNA to cells. PSP-Carb and PSP-Amide exhibited a half-life of more than 2 months when incubated in aqueous buffers at 37°C, while the half-life of PSP-Imine was 11h. Relative cytotoxicity of the polymers, as measured by COS-7 and HepG2 cell viability, was in the order of PSP-Carb>PSP-Amide>PSP-Imine. Each cationic polymer condensed the luciferase plasmid to nanoparticles of 150-200 nm diameters and with a zeta potential of +15-30 mV when the mass ratio of polymer-to-DNA was over 8/1. The three polycationic carriers showed similar luciferase transfection activity in COS-7 cells, while the transfection efficiency of PSP-Carb was significantly higher than that of the other two in HepG2 cells. PSP-Amide exhibited significantly higher gene silencing activity in COS-7 cells, suggesting the linkage structures play an important role in the activity of the polyspermine-based nucleic acid carriers. PMID:22683452

Du, Zixiu; Chen, Moying; He, Qianqian; Zhou, Yi; Jin, Tuo

2012-06-07

327

Poly(alkylene oxide) copolymers for nucleic acid delivery.  

PubMed

The advancement of gene-based therapeutics to the clinic is limited by the ability to deliver physiologically relevant doses of nucleic acids to target tissues safely and effectively. Over the last couple of decades, researchers have successfully employed polymer and lipid based nanoassemblies to deliver nucleic acids for the treatment of a variety of diseases. Results of phase I/II clinical studies to evaluate the efficacy and biosafety of these gene delivery vehicles have been encouraging, which has promoted the design of more efficient and biocompatible systems. Research has focused on designing carriers to achieve biocompatibility, stability in the circulatory system, biodistribution to target the disease site, and intracellular delivery, all of which enhance the resulting therapeutic effect. The family of poly(alkylene oxide) (PAO) polymers includes random, block, and branched structures, among which the ABA type triblocks copolymers of ethylene oxide (EO) and propylene oxide (PO) (commercially known as Pluronic) have received the greatest consideration. In this Account, we highlight examples of polycation-PAO conjugates, liposome-PAO formulations, and PAO micelles for nucleic acid delivery. Among the various polymer design considerations, which include molecular weight of polymer, molecular weight of blocks, and length of blocks, the overall hydrophobic-lipophilic balance (HLB) is a critical parameter in defining the behavior of the polymer conjugates for gene delivery. We discuss the effects of varying this parameter in the context of improving gene delivery processes, such as serum stability and association with cell membranes. Other innovative macromolecular modifications discussed in this category include our work to enhance the serum stability and efficiency of lipoplexes using PAO graft copolymers, the development of a PAO gel-based carrier for sustained and stimuli responsive delivery, and the development of biodegradable PAO-based amphiphilic block copolymers. PMID:22260518

Mishra, Swati; Peddada, Lavanya Y; Devore, David I; Roth, Charles M

2012-01-19

328

Conducting Polymer Based Nucleic Acid Sensor for Environment Monitoring  

NASA Astrophysics Data System (ADS)

Nucleic acid sensor based on polyaniline has been fabricated by covalently immobilizing double stranded calf thymus (dsCT) DNA onto perchlorate (ClO-4) doped polyaniline (PANI) film deposited onto indium-tin-oxide (ITO) glass plate using 1-(3-(dimethylamino) propyl)-3-ethylcarbodiimide hydrochloride (EDC)/N-hydroxyl succinimide (NHS) chemistry. These dsCT-DNA-PANI/ITO and PANI/ITO electrodes have been characterized using square wave voltammetry, electrochemical impedance, and Fourier-transform-infra-red (FTIR) measurements. This disposable dsCT-DNA-PANI/ITO bioelectrode is stable for about four months, can be used to detect arsenic trioxide (0.1ppm) in 30s.

Malhotra, Bansi Dhar; Prabhakar, Nirmal; Solanki, Pratima R.

329

Thermodynamic Profile of Interaction of Porphyrins with Nucleic Acids  

NASA Astrophysics Data System (ADS)

The binding of a number of novel water soluble porphyrins to nucleic acids (NA) were studied monitoring the changes in Soret region of absorbance spectra, fluorescence spectra and circular dichroism (CD) spectra of formed complexes. The binding modes for all complexes were dtermined. The binding isotherms were used to calculate the binding constant, Kb, and binding free energy, ?Gb = -RTlnKb. By performing these experiments as a function of temperature, we evaluated the van't Hoff binding enthalpies, ?Hb and the binding entropies, ?Sb. Generalization concerning the established correlation between the binding mode and thermodynamic profile was done.

Haroutiunian, Samvel; Dalyan, Yeva; Ghazaryan, Ara; Chalikian, Tigran

330

Enantioselective Properties of Nucleic Acid Aptamer Molecular Recognition Elements  

NASA Astrophysics Data System (ADS)

Target-specific chiral selectors, which are characterized by a predictable elution order depending on the target enantiomer employed for the selection of the chiral selector, have recently received much attention in the enantioselective analysis field. In this context, bioaffinity-based molecular recognition tools such as nucleic acid aptamers have notably demonstrated very attractive features for the chiral discrimination of active molecules. In this chapter, the enantioselective properties of aptamer chiral selectors and the major factors that control and modulate the liquid chromatography and capillary electrophoresis enantiomer separation are addressed.

Peyrin, Eric

331

Nucleic acid aptamers as antithrombotic agents: Opportunities in extracellular therapeutics.  

PubMed

Antithrombotic therapy for the acute management of thrombotic disorders has been stimulated and guided actively by our current understanding of platelet biology, coagulation proteases, and vascular science. A translatable platform for coagulation, based soundly on biochemistry, enzymology and cellular events on platelets and tissue factor-baring cells, introduces fundamental constructs, mechanistic clarity, and an unparalleled opportunity for accelerating the development and clinical investigation of both disease- and patient-specific therapies. In the current review, we build upon and expand substantially our observations surrounding nucleic acids as antithrombotic agents. PMID:20135076

Becker, Richard C; Povsic, Thomas; Cohen, Mauricio G; Rusconi, Christopher P; Sullenger, Bruce

2010-02-02

332

[Mass spectrometry of nucleic acids in molecular medicine].  

PubMed

A stable streamlining trend in the field of medical diagnostics by practical adoption of high-tech and knowledge-intensive analytical systems providing for molecular level studies has appeared during the last few decades. An illustrative example of such technologies is mass spectrometry methods for analyzing biomolecules. This review is intended to brief the potential of the state-of-the-art inventory of spectrometry equipment and illustrate the application of mass spectrometry of nucleic acids (DNA and RNA) for solving practical problems related to the analysis of human genomic DNA and clinically significant microorganisms of bacterial and viral natures. PMID:19537166

Il'ina, E N; Govorun, V M

333

Liquid Chromatography-Mass Spectrometry of Nucleic Acids  

Microsoft Academic Search

\\u000a By virtue of its high-resolving capability, short analysis time, and advanced instrumentation high-performance liquid chromatography\\u000a (HPLC) has become a versatile technique for the separation and characterization of nucleic acids. Among the various chromatographic\\u000a modes, which have been summarized in several reviews (1–6), ion-pair reversed-phase HPLC (IP-RPHPLC) represents the most popular chromatographic technique applicable to the separation\\u000a of single-and double-stranded DNA

Herbert Oberacher; Walther Parson

334

Antibody-linked Spherical Nucleic Acids for Cellular Targeting  

PubMed Central

Spherical nucleic acid (SNAs) constructs are promising new single entity gene regulation materials capable of both cellular transfection and gene knockdown, but thus far are promiscuous structures, exhibiting excellent genetic but little cellular selectivity. In this communication, we describe a strategy to impart targeting capabilities to these constructs through non-covalent functionalization with a complementary antibody-DNA conjugate. As a proof-of concept, we designed HER2-targeting SNAs and demonstrated that such structures exhibit cell type selectivity in terms of their uptake, and significantly greater gene knockdown in cells overexpressing the target antigen as compared to the analogous antibody-free and off-target materials.

Zhang, Ke; Hao, Liangliang; Hurst, Sarah J.; Mirkin, Chad A.

2012-01-01

335

BGL3 beta-glucosidase and nucleic acids encoding the same  

DOEpatents

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.

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

2008-04-01

336

BGL3 beta-glucosidase and nucleic acids encoding the same  

DOEpatents

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.

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

2007-09-25

337

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

DOEpatents

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.

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

2008-03-18

338

BGL4 beta-glucosidase and nucleic acids encoding the same  

DOEpatents

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.

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

2008-01-22

339

BGL3 beta-glucosidase and nucleic acids encoding the same  

DOEpatents

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.

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

2012-10-30

340

BGL6 .beta.-glucosidase and nucleic acids encoding the same  

DOEpatents

The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl6, and the corresponding BGL6 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL6, recombinant BGL6 proteins and methods for producing the same.

Dunn-Coleman, Nigel; Ward, Michael

2012-10-02

341

BGL7 beta-glucosidase and nucleic acids encoding the same  

DOEpatents

The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl7, and the corresponding BGL7 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL7, recombinant BGL7 proteins and methods for producing the same.

Dunn-Coleman, Nigel; Ward, Michael

2013-01-29

342

BGL3 beta-glucosidase and nucleic acids encoding the same  

DOEpatents

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.

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

2011-06-14

343

BGL4 beta-glucosidase and nucleic acids encoding the same  

DOEpatents

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.

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

2011-12-06

344

BGL6 beta-glucosidase and nucleic acids encoding the same  

DOEpatents

The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl6, and the corresponding BGL6 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL6, recombinant BGL6 proteins and methods for producing the same.

Dunn-Coleman, Nigel (Los Gatos, CA); Ward, Michael (San Francisco, CA)

2009-09-01

345

BGL7 beta-glucosidase and nucleic acids encoding the same  

DOEpatents

The present invention provides a novel .beta.-glucosidase nucleic acid sequence, designated bgl7, and the corresponding BGL7 amino acid sequence. The invention also provides expression vectors and host cells comprising a nucleic acid sequence encoding BGL7, recombinant BGL7 proteins and methods for producing the same.

Dunn-Coleman, Nigel (Los Gatos, CA); Ward, Michael (San Francisco, CA)

2008-08-05

346

Integrity and Amplification of Nucleic Acids From Snap-Frozen Prostate Tissues From Robotic-Assisted Laparoscopic and Open Prostatectomies  

PubMed Central

Context Recently, robotic-assisted laparoscopic prostatectomy has replaced open retropubic radical prostatectomy as the surgical procedure of choice. This less-invasive approach offers many advantages but exposes prostate tissue to longer periods of warm ischemia that may affect subsequent analysis of biomarkers. Objective To analyze the nucleic acid quality and quantity isolated from open versus laparoscopic prostatectomies. Design Nucleic acids were isolated from 10 open-obtained and 10 laparoscopic-obtained tissues stored in our prostate sample repository. Nucleic acid integrity was assessed via electrophoresis and polymerase chain reaction amplification of RNA and DNA targets ranging in size from 125 to 939 base pairs. Results The DNA yield, integrity, and polymerase chain reaction amplification were identical between samples obtained from both surgical approaches. The RNA integrity number and yield were similar, as was ?-2 microglobulin mRNA amplification up to 652 base pairs. However, 2 of 10 samples (20%) collected robotically showed decreased real-time reverse transcriptase-polymerase chain reaction amplification of prostate-specific antigen messenger RNA, especially with targets larger than 300 base pairs. Conclusions Generally, the quality and quantity of nucleic acids isolated from prostate tissue obtained via open or laparoscopic approaches are equivalent, suggesting that procurement of tissues is appropriate from either procedure. However, some loss of reverse transcriptase-polymerase chain reaction amplification of larger RNA targets was noted in the laparoscopic samples; appropriate design of assays to keep amplicon sizes small and the use of internal controls to assess RNA integrity is recommended.

Voss, Barbara L.; Santiano, Kristine; Milano, Mary; Mangold, Kathy A.; Kaul, Karen L.

2013-01-01

347

A method to find palindromes in nucleic acid sequences  

PubMed Central

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.

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

2013-01-01

348

Analyzing and Building Nucleic Acid Structures with 3DNA  

PubMed Central

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 sites.

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

2013-01-01

349

Detection of strains of potato virus S by nucleic acid spot hybridization (NASH)  

Microsoft Academic Search

Summary  Two complementary DNA (cDNA) clones (0.9 kb and 1.6 kb) reacting to the ordinary strain of potato virus S (PVS) were compared\\u000a with single-stranded randomly primed cDNA (prepared to total genomic RNA) as probes for various strains of PVS, using the\\u000a technique of nucleic acid spot hybridization (NASH). The cDNA clones detected 11 PVS isolates well, including both Andean\\u000a and

Gary D. Foster; Peter R. Mills

1990-01-01

350

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

NASA Astrophysics Data System (ADS)

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.

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

1996-10-01

351

Molecular cytogenetics by polymerase catalyzed amplification or in situ labelling of specific nucleic acid sequences  

SciTech Connect

The Polymerase Chain Reaction (PCR) can be performed on isolated cells or chromosomes and the product can be analyzed by DNA technology or by FISH to test metaphases. The authors have good experiences analyzing aberrant chromosomes by FACS sorting, PCR with degenerated primers and painting of test metaphases with the PCR product. They also utilize polymerases for PRimed IN Situ labelling (PRINS) of specific nucleic acid sequences. In PRINS oligonucleotides are hybridized to their target sequences and labeled nucleotides are incorporated at the site of hybridization with the oligonucleotide as primer. PRINS may eventually allow the study of individual genes, gene expression and even somatic mutations (in mRNA) in single cells.

Bolund, L.; Brandt, C.; Hindkjaer, J.; Koch, J.; Koelvraa, S.; Pedersen, S. (Univ. of Aarhus (Denmark))

1993-01-01

352

Compatible solute influence on nucleic acids: Many questions but few answers  

PubMed Central

Compatible solutes are small organic osmolytes including but not limited to sugars, polyols, amino acids, and their derivatives. They are compatible with cell metabolism even at molar concentrations. A variety of organisms synthesize or take up compatible solutes for adaptation to extreme environments. In addition to their protective action on whole cells, compatible solutes display significant effects on biomolecules in vitro. These include stabilization of native protein and nucleic acid structures. They are used as additives in polymerase chain reactions to increase product yield and specificity, but also in other nucleic acid and protein applications. Interactions of compatible solutes with nucleic acids and protein-nucleic acid complexes are much less understood than the corresponding interactions of compatible solutes with proteins. Although we may begin to understand solute/nucleic acid interactions there are only few answers to the many questions we have. I summarize here the current state of knowledge and discuss possible molecular mechanisms and thermodynamics.

Kurz, Matthias

2008-01-01

353

Methods of combined bioprocessing and related microorganisms, thermophilic and/or acidophilic enzymes, and nucleic acids encoding said enzymes  

DOEpatents

A genetically modified organism comprising: at least one nucleic acid sequence and/or at least one recombinant nucleic acid isolated from Alicyclobacillus acidocaldarius and encoding a polypeptide involved in at least partially degrading, cleaving, transporting, metabolizing, or removing polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, xylan-, glucan-, galactan-, or mannan-decorating groups; and at least one nucleic acid sequence and/or at least one recombinant nucleic acid encoding a polypeptide involved in fermenting sugar molecules to a product. Additionally, enzymatic and/or proteinaceous extracts may be isolated from one or more genetically modified organisms. The extracts are utilized to convert biomass into a product. Further provided are methods of converting biomass into products comprising: placing the genetically modified organism and/or enzymatic extracts thereof in fluid contact with polysaccharides, cellulose, lignocellulose, hemicellulose, lignin, starch, sugars, sugar oligomers, carbohydrates, complex carbohydrates, chitin, heteroxylans, glycosides, and/or xylan-, glucan-, galactan-, or mannan-decorating groups.

Thompson, David N; Apel, William A; Thompson, Vicki S; Ward, Thomas E

2013-07-23

354

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

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

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

1999-01-01

355

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

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

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

1998-01-01

356

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

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

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

357

Bifunctional mesoporous zirconium phosphonates for delivery of nucleic acids.  

PubMed

The bifunctional mesoporous zirconium phosphonates (ZrBFs) were synthesized through surfactant-assisted co-condensation of ZrCl(4) with two different phosphonic acids, both 1-phosphomethylproline (H(3)PMP) and 1,4-bis(phosphomethyl)piperazine (BPMP), in a one-pot procedure. The L-proline group of H(3)PMP and piperazine group of BPMP in the frameworks endow ZrBFs with pH-controllable release function and high cell penetration capability, which was derived from the reversible protonation-deprotonation of L-proline groups and piperazine groups on the mesoporous walls under different pH values (pH sensitivity) as well as further functionalization with biological modifiers via the carboxyls in L-proline groups on the outer surface (functionalizability), respectively. ZrBFs, possessing cationic frameworks once formed, exhibit high payload for salmon sperm DNA as model nucleic acid owing to strong electrostatic attraction between them. On the basis of pH-sensitive ZrBFs carriers and assisted by lag-time films coating, the time- and pH-controlled oral colon-targeted nucleic acid delivery systems have been developed, which can carry most of the loaded salmon sperm DNA to the colon under dual control, time control and pH value control. Furthermore, salmon sperm DNA can remain intact during delivery, as evidenced by the fact that the released salmon sperm DNA in the pH transition release experiment still retain its structural integrity and native conformation. Also, fluorescence spectra demonstrate that ZrBFs can be further functionalized with a cell-penetrating peptide of octaarginine (R8) via the carboxyls in L-proline groups of H(3)PMP on the outer surface using a coupling agent, which will enhance the penetration capability of ZrBFs through biomembranes. ZrBFs have a potential application as a new kind of carrier in oral delivery of nucleic acids targeting the colon for gene therapy of colon-related diseases due to their unique bifunctionality. PMID:23347141

Tang, Yan; Ren, Yubao; Shi, Xin

2013-01-24

358

Studies on nucleic acid metachromasy. II. Metachromatic and orthochromatic staining by toluidine blue of nucleic acids in tissue sections.  

PubMed

Acrolein-fixed, polyester wax-embedded tissue sections showed excellent preservation of light microscopic architecture and, when stained with toluidine blue, intense color contrast between DNA, which stained orthochromatically, and RNA, which stained metachromatically. This method has practical value for differentiating DNA from RNA in the same section. The color contrast was impaired by substituting formaldehyde for acrolein or paraffin for polyester wax, and was negligible in tissues fixed in formaldehyde or Carnoy's fluid and embedded in paraffin. Quality of structural preservation paralleled degree of color contrast. Metachromatic staining can be analysed, by the quantitative parameters of Bradley and colleagues, to provide inferences regarding the conformation of biopolymers in tissue sections. Comparison of the nucleic acid color contrasts in toluidine blue-stained sections with titrations of fixative-treated nucleic acids against toluidine blue in solution indicated a greater difference in conformation between DNA- and RNA-protein in acrolein-polyester sections than between acrolein-treated free DNA and RNA in solution. This is supported by recent evidence that the conformation of ribosomal RNA is quite different in whole ribosomes from that assumed by the same RNA free in solution. The acrolein-polyester method may enhance color contrast by providing superior preservation of ordered nucleoprotein conformations. PMID:4160917

Feder, N; Wolf, M K

1965-11-01

359

Method for Sequencing Nucleic Acid Molecules. (PAT-APPL-11-015 138).  

National Technical Information Service (NTIS)

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....

H. G. Craighead J. Korlach M. Levene M. Webb S. Turner

2004-01-01

360

Method for Sequencing Nucleic Acid Molecules. (PAT-APPL-11-014 015).  

National Technical Information Service (NTIS)

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....

H. G. Craighead J. Korlach M. Levine S. Turner W. W. Webb

2004-01-01

361

Selection of Fluorophore and Quencher Pairs for Fluorescent Nucleic Acid Hybridization Probes  

Microsoft Academic Search

Summary With the introduction of simple and relatively inexpensive methods for labeling nucleic acids with non-radioactive labels, doors have been opened that enable nucleic acid hybridization probes to be used for research and development, as well as for clinical diagnostic applications. The use of fluorescent hybridization probes that generate a fluorescence signal only when they bind to their target enables

Salvatore A. E. Marras

362

Nucleic acid probes as a diagnostic method for tickborne hemoparasites of veterinary importance  

Microsoft Academic Search

An increased number of articles on the use of nucleic acid-based hybridization techniques for diagnostic purposes have been recently published. This article reviews nucleic acid-based hybridization as an assay to detect hemoparasite infections of economic relevance in veterinary medicine. By using recombinant DNA techniques, selected clones containing inserts of Anaplasma, Babesia, Cowdria or Theileria genomic DNA sequences have been obtained,

J. V. Figueroa; G. M. Buening

1995-01-01

363

Real-time investigation of nucleic acids phosphorylation process using molecular beacons  

Microsoft Academic Search

Phosphorylation of nucleic acids is an indispensable process to repair strand interruption of nucleic acids. We have studied the process of phosphoryla- tion using molecular beacon (MB) DNA probes in real-time and with high selectivity. The MB employed in this method is devised to sense the product of a 'phosphorylation-ligation' coupled enzyme reaction. Compared with the current assays, this novel

Zhiwen Tang; Kemin Wang; Weihong Tan; Changbei Ma; Jun Li; Lingfeng Liu; Qiuping Guo; Xiangxian Meng

2005-01-01

364

Structural Studies on Nucleic Acids: From Nucleotides to the Double Helix  

Microsoft Academic Search

In the field of nucleic acids the nucleoside and nucleotide units represent the lowest level of structural sophistication. Since they play a role in a number of metablic processes as regulators and as coenzymes, their structural properties are as important as those of the polymeric nucleic acids which form single, double, triple and quadruple he1 ices, depending on their nucleotide

Wolfram Saenger

1990-01-01

365

Chemical physics of solid-state nucleic acids: new intriguing horizons  

Microsoft Academic Search

A critical comprehensive review on the chemical physics of biologically important polyanions, nucleic acids is presented. A careful survey of the available experimental data on nucleic acid condensed samples definitely reveals the effect of (a) intramolecular dynamics and (b) intra- and intermolecular interactions on the physical properties of these biopolymers. The intramolecular dynamics ought to embrace all the possible degrees

E. B Starikov

1997-01-01

366

Adsorption of Nucleic Acid Components on Rutile (TiO2) Surfaces  

Microsoft Academic Search

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

H. James Cleaves; Caroline M. Jonsson; Christopher L. Jonsson; Dimitri A. Sverjensky; Robert M. Hazen

2010-01-01

367

Superior structure stability and selectivity of hairpin nucleic acid probes with an L-DNA stem  

Microsoft Academic Search

Hairpin nucleic acid probes have been highly useful in many areas, especially for intracellular and in vitro nucleic acid detection. The success of these probes can be attributed to the ease with which their conformational change upon target binding can be coupled to a variety of signal transduction mechan- isms. However, false-positive signals arise from the opening of the hairpin

Youngmi Kim; Chaoyong James Yang; Weihong Tan

2007-01-01

368

Electrophoretic mobility shift assay (EMSA) for detecting protein–nucleic acid interactions  

Microsoft Academic Search

The gel electrophoresis mobility shift assay (EMSA) is used to detect protein complexes with nucleic acids. It is the core technology underlying a wide range of qualitative and quantitative analyses for the characterization of interacting systems. In the classical assay, solutions of protein and nucleic acid are combined and the resulting mixtures are subjected to electrophoresis under native conditions through

Lance M Hellman; Michael G Fried

2007-01-01

369

Sequence and structural-selective nucleic acid binding revealed by the melting of mixtures  

Microsoft Academic Search

A simple method for the detection of sequence- and structural-selective ligand binding to nucleic acids is described. The method is based on the commonly used thermal denaturation method in which ligand binding is registered as an elevation in the nucleic acid melting temperature (Tm). The method can be extended to yield a new, higher -throughput, assay by the simple expediency

Xiaochun Shi; Jonathan B. Chaires

2006-01-01

370

Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009  

Microsoft Academic Search

The current issue of Nucleic Acids Research includes descriptions of 179 databases, of which 95 are new. These databases (along with several molecular biology databases described in other journals) have been included in the Nucleic Acids Research online Molecular Biology Database Collection, bringing the total number of databases in the collection to 1170. In this introductory com- ment, we briefly

Michael Y. Galperin; Guy Cochrane

2009-01-01

371

Continuum Solvent Models to Study the Structure and Dynamics of Nucleic Acids and Complexes with Ligands  

Microsoft Academic Search

T he aqueous environment has an important influence on the structure and function of nucleic acids. The explicit inclusion of many solvent molecules and ions during simulation studies on nucleic acids can lead to prohibitively expensive computational demands and limits the maximum simulation time. Many applications such as systematic conformational searches and ligand- receptor docking approaches used for example in

Martin Zacharias

372

The significance of changes in nucleic acid metabolism for the relations between host and obligate parasites  

Microsoft Academic Search

Several basic questions are discussed concerning the interpretation of changes in nucleic acid metabolism of plants after infection with obligate parasites. The contribution of both host and parasite to the increased nucleic acid concentration in infected plants has been shown by cytological and chemical methods. Whereas a higher synthesis of ribosomal RNA is evident in rust-infected wheat, no such evidence

R. Heitefuss

1968-01-01

373

Sequence Dependence of Low-Frequency Raman-Active Modes in Nucleic Acids.  

National Technical Information Service (NTIS)

Vibrational modes of nucleic acids with frequencies less than about 300 cm are characterized by in phase motion extending over many nucleotides. These phonons are commonly referred to as long-wavelength or low- frequency modes of nucleic acids. Recent inf...

G. Edwards C. Liu

1990-01-01

374

Optical absorption assay for strand-exchange reactions in unlabeled nucleic acids  

Microsoft Academic Search

The nucleic acid exchange reaction is a common feature for genetic recombination, DNA replication and transcription. Due to the fact that in the strand- exchange reactions the reactant and product mole- cules have similar or identical nucleotide sequences, the reaction is undetectable. As a rule, the nucleic acids with radioactive or fluorescence labels are used in such studies. Besides the

Besik I. Kankia

2004-01-01

375

Velocity and processivity of helicase unwinding of double-stranded nucleic acids  

Microsoft Academic Search

Helicases are molecular motors which unwind double-stranded nucleic acids (dsNA) in cells. Many helicases move with directional bias on single- stranded (ss) nucleic acids, and couple their directional translocation to strand separation. A model of the coupling between translocation and unwinding uses an interaction potential to represent passive and active helicase mechanisms. A passive helicase must wait for thermal fluctuations

376

Metal complexes as structure-selective binding agents for nucleic acids  

Microsoft Academic Search

Concomitant with our increasing knowledge of the structure and biological role of nucleic acids is the interest in the development of small molecules that can regulate DNA and RNA function. While considerable effort has been devoted to synthesising compounds that can target specific DNA and RNA sequences, there is growing interest in developing agents that can recognise nucleic acid structural

F. Richard Keene; Jayden A. Smith; J. Grant Collins

2009-01-01

377

Increased interstitial pressure improves nucleic acid delivery to skin enabling a comparative analysis of constitutive promoters  

Microsoft Academic Search

Nucleic acid-based therapies hold great promise for treatment of skin disorders if delivery challenges can be overcome. To investigate one mechanism of nucleic acid delivery to keratinocytes, a fixed mass of expression plasmid was intradermally injected into mouse footpads in different volumes, and reporter expression was monitored by intravital imaging or skin sectioning. Reporter gene expression increased with higher delivery

E González-González; H Ra; R Spitler; R P Hickerson; C H Contag; R L Kaspar

2010-01-01

378

A novel environment-sensitive biodegradable polydisulfide with protonatable pendants for nucleic acid delivery  

Microsoft Academic Search

Clinical application of nucleic acid-based therapies is limited by the lack of safe and efficient delivery systems. The purpose of this study is to design and evaluate novel biodegradable polymeric carriers sensitive to environmental changes for efficient delivery of nucleic acids, including plasmid DNA and siRNA. A novel polydisulfide with protonatable pendants was synthesized by the oxidative polymerization of a

Xu-Li Wang; Randy Jensen; Zheng-Rong Lu

2007-01-01

379

An uncommon nucleotide conformation shown by molecular structure of deoxyuridine-5'-phosphate and nucleic acid stereochemistry  

Microsoft Academic Search

CRYSTAL structure determinations of nucleic acid fragments have shown that several of the conformational features found in the monomeric building blocks are also manifested at the nucleic acid level. Stereochemical variations between thymine and uracil nucleotides are therefore of interest as they can provide a structural basis for some of the differences between the conformations of DNA and RNA. X-ray

M. A. Viswamitra; T. P. Seshadri

1975-01-01

380

Artificial Functional Nucleic Acids: Aptamers, Ribozymes, and Deoxyribozymes Identified by In Vitro Selection  

Microsoft Academic Search

The discovery of natural RNA catalysts (ribozymes) inspired the use of in vitro selection methodology to develop artificial functional nucleic acids (FNAs). In vitro selection is the experimental process by which large random-sequence pools of RNA or DNA are used as the starting point to identify particular nucleic acid sequences that have desired functions. When this function is binding of

Scott K. Silverman

2009-01-01

381

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

Microsoft Academic Search

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

Richard Lavery; Heinz Sklenar

1988-01-01

382

The measurement and distribution of dissolved nucleic acids in aquatic environments  

Microsoft Academic Search

Nucleic acids (DNA and RNA) are ubiquitous components of the dissolved organic matter (DOM) pool of all oceanic, neritic, estuarine, and freshwater habitats studied to date. A new method for the quantitative determination ofdissolved nucleic acids (DNA and RNA) in water and scdimcnt samples was developed, evaluated, and utilized in a study of various marine and freshwater ecosystems. Under appropriate

DAVID M. KARL; MEGAN D. BAILIFF

1989-01-01

383

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

Code of Federal Regulations, 2013 CFR

...nucleic acids extracted from human respiratory specimens or viral culture. The detection and identification of a specific viral...Influenza A Virus Subtypes Using Multiplex Nucleic Acid Assays.â See § 866.1(e) for the availability of these guidance...

2013-04-01

384

Effects of Locked Nucleic Acid Substitutions on the Stability of Oligonucleotide Hairpins  

Microsoft Academic Search

An understanding of the stability of nucleic acid folding is critical for applications involving RNA viruses, small molecule–RNA binding, and therapeutics, for example. To explore factors that affect this stability, hairpins made from oligonucleotides containing both a GAAA tetraloop and three to five complements in the stem have been used as models where locked nucleic acids (LNAs) have been substituted

Chelsea Hull; Corinne Szewcyk; Pamela M. St. John

2012-01-01

385

Instrument-free nucleic acid amplification assays for global health settings  

Microsoft Academic Search

Many infectious diseases that affect global health are most accurately diagnosed through nucleic acid amplification and detection. However, existing nucleic acid amplification tests are too expensive and complex for most low-resource settings. The small numbers of centralized laboratories that exist in developing countries tend to be in urban areas and primarily cater to the affluent. In contrast, rural area health

Paul Labarre; David Boyle; Kenneth Hawkins; Bernhard Weigl

2011-01-01

386

Quantitative Reverse Transcription Strand Displacement Amplification: Quantitation of Nucleic Acids Using an Isothermal Amplification Technique  

Microsoft Academic Search

Recent advances in nucleic acid amplification techniques have allowed for quantitation of viral nucleic acid levels in clinical specimens. The most prevalent testing is carried out for HIV viral load. Strand displacement amplification (SDA) is an isothermal DNA amplification system utilizing a restriction enzyme and a DNA polymerase with strand displacement properties. SDA was adapted for quantitative RNA amplification (QRT-SDA)

Colleen M. Nycz; Cheryl H. Dean; Perry D. Haaland; Catherine A. Spargo; G. Terrance Walker

1998-01-01

387

Real-time assays with molecular beacons and other fluorescent nucleic acid hybridization probes  

Microsoft Academic Search

Background: A number of formats for nucleic acid hybridization have been developed to identify DNA and RNA sequences that are involved in cellular processes and that aid in the diagnosis of genetic and infectious diseases. Methods: The introduction of hybridization probes with interactive fluorophore pairs has enabled the development of homogeneous hybridization assays for the direct identification of nucleic acids.

Salvatore A. E. Marras; Sanjay Tyagi; Fred Russell Kramer

2006-01-01

388

Unexpected detection of DNA by nucleic acid sequence-based amplification technique  

Microsoft Academic Search

Nucleic acid sequence-based amplification (NASBA) is a technique that has been previously shown to selectively mediate the detection of RNA in microbial cells. In a series of tests, nucleic acids were extracted from Salmonella enterica serotype Typhimurium and Mycobacterium avium subsp. paratuberculosis, and subjected to four enzymatic treatments prior to NASBA. These enzymatic treatments were DNase, RNase, S1 nuclease, and

David Rodr??guez-Làzaro; Joy Lloyd; John Ikonomopoulos; Maria Pla; Nigel Cook

2004-01-01

389

[Determination of the nucleic acids in pig embryonic kidney cells by magnetic cytaphoresis].  

PubMed

Gallocyanine-chrome alum-stained pig embryonic kidney cells have paramagnetic properties. They move under the influence of gradient magnetic field (magnetophoresis). The velocity of magnetophoresis is proportional to the content of nucleic acids in cells. This allows to estimate the content of nucleic acids per cell dry weight by magnetophoresis and analytical centrifugation. PMID:2473104

Chikov, V M; Maksimova, E V

390

Final Report Nucleic Acid System: Hybird PCR and Multiplex Assay Project Phase II.  

National Technical Information Service (NTIS)

This report covers phase 2 (year 2) of the Nucleic Acid System - Hybrid PCR and Multiplex Assay project. The objective of the project is to reduce to practice the detection and identification of biological warfare pathogens by the nucleic acid recognition...

R. P. Koopman R. G. Langlois S. Nasarabadi W. J. Benett B. W. Colston D. C. Johnson S. B. Brown P. L. Stratton F. P. Milanovich

2002-01-01

391

Calibrating nucleic acids torsional energetics in force-field: insights from model compounds  

Microsoft Academic Search

The development of force fields that accurately describe both the structure and the dynamics of nucleic acids in condensed phase is an ongoing effort. The development of the latest versions of the CHARMM and AMBER nucleic acids relied on ab initio as well as on experimental target data for the parametrization. Here we compare the two latest versions of the

D Bosch; N Foloppe; N Pastor; L Pardo; M Campillo

2001-01-01

392

Cells labeled with multiple fluorophores bound to a nucleic acid carrier  

SciTech Connect

In passing labeled cells through a cell sorter, the improvement which comprises employing a labeled cell comprising a cell, an antibody specific to and bound to such cell, a nucleic acid fragment joined to the antibody, and a plurality of labels on the nucleic acid fragment. Because of the presence of multiple labels, the sensitivity of the separation of labeled cells in increased.

Dattagupta, N.; Kamarch, M.E.

1989-04-25

393

Potential in vivo roles of nucleic acid triple-helices  

PubMed Central

The ability of double-stranded DNA to form a triple-helical structure by hydrogen bonding with a third strand is well established, but the biological functions of these structures remain largely unknown. There is considerable albeit circumstantial evidence for the existence of nucleic triplexes in vivo and their potential participation in a variety of biological processes including chromatin organization, DNA repair, transcriptional regulation and RNA processing has been investigated in a number of studies to date. There is also a range of possible mechanisms to regulate triplex formation through differential expression of triplex-forming RNAs, alteration of chromatin accessibility, sequence unwinding and nucleotide modifications. With the advent of next generation sequencing technology combined with targeted approaches to isolate triplexes, it is now possible to survey triplex formation with respect to their genomic context, abundance and dynamical changes during differentiation and development, which may open up new vistas in understanding genome biology and gene regulation.

Buske, Fabian A

2011-01-01

394

A facile method for attaching nitroxide spin labels at the 5? terminus of nucleic acids  

PubMed Central

In site-directed spin labeling (SDSL), a nitroxide moiety containing a stable, unpaired electron is covalently attached to a specific site within a macromolecule, and structural and dynamic information at the labeling site is obtained via electron paramagnetic resonance (EPR) spectroscopy. Successful SDSL requires efficient site-specific incorporation of nitroxides. Work reported here presents a new method for facile nitroxide labeling at the 5? terminus of nucleic acids of arbitrary sizes. T4-polynucleotide kinase was used to enzymatically substitute a phosphorothioate group at the 5? terminus of a nucleic acid, and the resulting phosphorothioate was then reacted with an iodomethyl derivative of a nitroxide. The method was successfully demonstrated on both chemically synthesized and naturally occurring nucleic acids. The attached nitroxides reported duplex formation as well as tertiary folding of nucleic acids, indicating that they serve as a valid probe in nucleic acid studies.

Qin, Peter Z.

2007-01-01

395

Nucleic Acids Research annual Database Issue and the NAR online Molecular Biology Database Collection in 2009  

PubMed Central

The current issue of Nucleic Acids Research includes descriptions of 179 databases, of which 95 are new. These databases (along with several molecular biology databases described in other journals) have been included in the Nucleic Acids Research online Molecular Biology Database Collection, bringing the total number of databases in the collection to 1170. In this introductory comment, we briefly describe some of these new databases and review the principles guiding the selection of databases for inclusion in the Nucleic Acids Research annual Database Issue and the Nucleic Acids Research online Molecular Biology Database Collection. The complete database list and summaries are available online at the Nucleic Acids Research web site (http://nar.oxfordjournals.org/).

Galperin, Michael Y.; Cochrane, Guy R.

2009-01-01

396

Spherical Nucleic Acids: A New Form of DNA  

NASA Astrophysics Data System (ADS)

Spherical Nucleic Acids (SNAs) are a new class of nucleic acid-based nanomaterials that exhibit unique properties currently being explored in the contexts of gene-based cancer therapies and in the design of programmable nanoparticle-based materials. The properties of SNAs differ from canonical, linear nucleic acids by virtue of their dense packing into an oriented 3-dimensional array. SNAs can be synthesized from a number of useful nanoparticle templates, such as plasmonic gold and silver, magnetic oxides, luminescent semi-conductor quantum dots, and silica. In addition, by crosslinking the oligonucleotides and dissolving the core, they can be made in a hollow form as well. This dissertation describes the evolution of SNAs from initial studies of inorganic nanoparticle-based materials densely functionalized with oligonucleotides to the proving of a hypothesis that their unique properties can be observed in a core-less structure if the nucleic acids are densely packed and highly oriented. Chapter two describes the synthesis of densely functionalized polyvalent oligonucleotide superparamagnetic iron oxide nanoparticles using the copper-catalyzed azide-alkyne cycloaddition reaction. These particles are shown to exhibit cooperative binding in a density- and salt concentration-dependent fashion, with nearly identical behaviors to those of SNA-functionalized gold nanoparticles. Importantly, these particles are the first non-gold particles shown to be capable of entering cells in high numbers via the SNA-mediated cellular uptake pathway, and provided the first evidence that SNA-mediated cellular uptake is core-independent. In the third chapter, a gold nanoparticle catalyzed alkyne cross-linking reaction is described that is capable of forming hollow organic nanoparticles using polymers with alkyne-functionalized backbones. With this method, the alkyne-modified polymers adsorb to the particle surfaces, cross-link on the surface, allowing the gold nanoparticle to be subsequently dissolved oxidatively with KCN or Iodine. The reaction pathway is analyzed through characterization of the reaction progression and resulting products, and a mechanistic pathway is proposed. This is the first report of a gold nanoparticle catalyzed reaction involving the conversion of propargyl ethers to terminal alcohols, which can subsequently cross-link if densely arranged on a gold nanoparticle surface. Importantly, these structures can be synthesized using gold nanoparticles of a range of sizes, thereby providing control over the size and properties of the resulting crosslinked particle. Chapter four returns to the topic of SNAs and builds upon the chemistry of chapter three culminating in the synthesis of cross-linked hollow SNA nanoparticles. These structures are formed by the cross-linking of synthetically modified alkyne-bearing oligonucleotides through the pathway described in chapter three. When the gold core is dissolved, the resulting hollow SNAs exhibit nearly identical binding, nuclease resistance, cellular uptake, and gene regulation properties of SNA-gold nanoparticle conjugates. Indeed, this chapter demonstrates that the unique properties of SNA-nanoparticle conjugates are core-independent and stem solely from the dense ensemble of oligonucleotides arranged on their surfaces. The fifth chapter further asserts the synthetic achievements made in chapter four by showing how hollow SNAs can be substituted for SNA-gold nanoparticles in the context of DNA-programmable assembly. In this case, they can be used as building blocks within binary synthetic schemes to synthesize unique nanoparticle superlattices. It bolsters the design rules of DNA-programmable assembly by showing that the predicted structures form based on the behavior of SNA hybridization, and are universal for any SNA-functionalized nanoparticle.

Cutler, Joshua Isaac

397

Diastereomer characterizations of nitroxide-labeled nucleic acids  

SciTech Connect

Site-directed spin labeling (SDSL) obtains structural and dynamic information of a macromolecule using a site-specifically attached stable nitroxide radical. SDSL studies of arbitrary DNA and RNA sequences can be achieved using an efficient phosphorothioate labeling scheme, where a nitroxide is attached to a phosphorothioate substituted at a target site during chemical synthesis. The chemically introduced phosphorothioate contains two diastereomers (Rp and Sp), and nitroxides attached to each diastereomer may experience different local environments. Here, we report work on using anion-exchange HPLC to separate and characterize diastereomers in three DNA oligonucleotides and one RNA oligonucleotide. In all oligonucleotides studied, the Rp diastereomer was found to elute earlier than the Sp in the unlabeled oligonucleotides, while a reversal in the elution order (Sp earlier than Rp) was observed for nitroxide-labeled oligonucleotides. The results enable a one-step purification procedure for preparing diastereomerically pure nitroxide-labeled oligonucleotides. This expands the score of nucleic acids SDSL.

Grant, Gian Paola G.; Popova, Anna [Department of Chemistry, University of Southern California, LJS-251, 840 Downey Way, Los Angeles, CA 90089-0744 (United States); Qin, Peter Z. [Department of Chemistry, University of Southern California, LJS-251, 840 Downey Way, Los Angeles, CA 90089-0744 (United States)], E-mail: pzq@usc.edu

2008-07-04

398

Nucleic Acid-Based Therapy Approaches for Huntington's Disease  

PubMed Central

Huntington's disease (HD) is caused by a dominant mutation that results in an unstable expansion of a CAG repeat in the huntingtin gene leading to a toxic gain of function in huntingtin protein which causes massive neurodegeneration mainly in the striatum and clinical symptoms associated with the disease. Since the mutation has multiple effects in the cell and the precise mechanism of the disease remains to be elucidated, gene therapy approaches have been developed that intervene in different aspects of the condition. These approaches include increasing expression of growth factors, decreasing levels of mutant huntingtin, and restoring cell metabolism and transcriptional balance. The aim of this paper is to outline the nucleic acid-based therapeutic strategies that have been tested to date.

Vagner, Tatyana; Young, Deborah; Mouravlev, Alexandre

2012-01-01

399

Imaging of nucleic acids with atomic force microscopy.  

PubMed

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

Lyubchenko, Yuri L; Shlyakhtenko, Luda S; Ando, Toshio

2011-02-16

400

2011 Rita Schaffer Lecture: Nanoparticles for Intracellular Nucleic Acid Delivery  

PubMed Central

Nanoparticles are a promising technology for delivery of new types of therapeutics. A polymer library approach has allowed engineering of polymeric particles that are particularly effective for the delivery of DNA and siRNA to human cells. Certain chemical structural motifs, degradable linkages, hydrophobicity, and biophysical properties are key for successful intracellular delivery. Small differences to biomaterial structure, and especially the type of degradable linkage in the polymers, can be critical for successful delivery of siRNA vs. DNA. Furthermore, subtle changes to biomaterial structure can facilitate cell-type gene delivery specificity between human brain cancer cells and healthy cells as well as between human retinal endothelial cells and epithelial cells. These polymeric nanoparticles are effective for nucleic acid delivery in a broad range of human cell types and have applications to regenerative medicine, ophthalmology, and cancer among many other biomedical research areas.

Green, Jordan J.

2012-01-01

401

2011 Rita Schaffer lecture: nanoparticles for intracellular nucleic acid delivery.  

PubMed

Nanoparticles are a promising technology for delivery of new types of therapeutics. A polymer library approach has allowed engineering of polymeric particles that are particularly effective for the delivery of DNA and siRNA to human cells. Certain chemical structural motifs, degradable linkages, hydrophobicity, and biophysical properties are key for successful intracellular delivery. Small differences to biomaterial structure, and especially the type of degradable linkage in the polymers, can be critical for successful delivery of siRNA vs. DNA. Furthermore, subtle changes to biomaterial structure can facilitate cell-type gene delivery specificity between human brain cancer cells and healthy cells as well as between human retinal endothelial cells and epithelial cells. These polymeric nanoparticles are effective for nucleic acid delivery in a broad range of human cell types and have applications to regenerative medicine, ophthalmology, and cancer among many other biomedical research areas. PMID:22451256

Green, Jordan J

2012-03-27

402

Imaging of nucleic acids with atomic force microscopy  

PubMed Central

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.

Lyubchenko, Yuri L.; Shlyakhtenko, Luda S.; Ando, Toshio

2011-01-01

403

Method for increasing the sensitivity of nucleic acid hybridization assays  

SciTech Connect

A hybridization assay method is described for detecting a specific polynucleotide target sequence wherein a nucleic acid containing target sample in single stranded form is affixed to a support. It is contacted thereon under hybridizing conditions with a non-radioactive reporter group labeled single-stranded polynucleotide probe having a sequence complementary to the target sequence, the probe being bound to the affixed sample when the target is present. The probe hybridizer with the target sequence, then the unbound portion of the probe is removed from the support, and the presence of the probe is detected by means of its reporter group, wherein the sensitivity of the assay is increased by employing the additional steps comprising: (a) after removal of the unbound portion of the probe, dehybridizing the bound portion; (b) concentrating the dehybridized separated probe onto a solid support; and (c) detecting the presence of the probe on the solid support by means of the non-radioactive reporter group.

Heller, M.J.

1989-04-25

404

Backbone modification of nucleic acids: synthesis, structure and therapeutic applications.  

PubMed

Nucleic acids have been extensively modified by replacing the phosphodiester group or the whole sugar phosphodiester with alternative anionic, neutral and cationic structures. Several of these modified oligonucleotides exhibit improved properties including enhanced recognition and binding to RNA, duplex DNA and proteins. This has resulted in the development of new and more potent antisense and antigene agents, as well as aptamers. Furthermore, backbone modified oligonucleotides have also been used in the development of several alternative strategies, which rely on altogether different mechanisms of action and show significant promise for therapeutic intervention. In this review the latest advances in the synthesis and evaluation of the most promising backbone modified oligos will be discussed, with a view to their future as novel pharmaceuticals. PMID:11472234

Micklefield, J

2001-08-01

405

Drug delivery systems based on nucleic acid nanostructures.  

PubMed

The field of DNA nanotechnology has progressed rapidly in recent years and hence a large variety of 1D-, 2D- and 3D DNA nanostructures with various sizes, geometries and shapes is readily accessible. DNA-based nanoobjects are fabricated by straight forward design and self-assembly processes allowing the exact positioning of functional moieties and the integration of other materials. At the same time some of these nanosystems are characterized by a low toxicity profile. As a consequence, the use of these architectures in a biomedical context has been explored. In this review the progress and possibilities of pristine nucleic acid nanostructures and DNA hybrid materials for drug delivery will be discussed. For the latter class of structures, a distinction is made between carriers with an inorganic core composed of gold or silica and amphiphilic DNA block copolymers that exhibit a soft hydrophobic interior. PMID:23742878

de Vries, Jan Willem; Zhang, Feng; Herrmann, Andreas

2013-06-03

406

Increased nucleic Acid receptor expression in chronic periodontitis.  

PubMed

Background: Nucleic acid sensing has emerged as one of the important components of the immune system triggering inflammation. The aim of this study is to determine the expression of bacterial DNA sensors, including Toll-like receptor 9 (TLR-9), DNA-dependent activator of interferon-regulatory factors (DAI), and absent in melanoma 2 (AIM2) in chronic periodontitis (CP versus healthy) (H) tissues. Methods: Thirty-five CP and 27 H gingival biopsies were included. Real-time quantitative polymerase chain reaction was performed to determine mRNA levels of AIM2, DAI, and TLRs (TLR-1 through TLR-9). The difference in gene expression for each sensor between CP and H tissues was calculated using analysis of covariance. The Spearman test was used to determine correlations among innate receptors. The expression of TLR-9, AIM2, and DAI in gingival tissues was further confirmed using immunohistochemistry. Results: The present results reveal statistically significant upregulation of TLR-9 (P <0.006), DAI (P <0.001), and TLR-8 (P <0.01) in CP tissues compared to H sites. Although mRNA expression was not changed significantly between groups for other receptors, the present results reveal significant correlations between receptors (P <0.05), suggesting that cooperation between multiple components of the host immune system may influence the overall response. Immunohistochemistry further confirmed expression of TLR-9, AIM2, and DAI in gingival tissues. Conclusions: This study highlights a possible role for nucleic acid receptors in periodontal inflammation. Future investigations will determine whether cytoplasmic receptors and their ligands can be targeted to improve clinical outcomes in periodontitis. PMID:23646855

Sahingur, S Esra; Xia, Xia-Juan; Voth, Stephanie C; Yeudall, W Andrew; Gunsolley, John C

2013-05-07

407

5' Unlocked Nucleic Acid Modification Improves siRNA Targeting.  

PubMed

Optimization of small interfering RNAs (siRNAs) is important in RNA interference (RNAi)-based therapeutic development. Some specific chemical modifications can control which siRNA strand is selected by the RNA-induced silencing complex (RISC) for gene silencing. Intended strand selection will increase potency and reduce off-target effects from the unintended strand. Sometimes, blocking RISC loading of the unintended strand leads to improved intended strand-silencing potency, but the generality of this phenomenon is unclear. Specifically, unlocked nucleic acid (UNA) modification of the 5' end of canonical (i.e., 19+2) siRNAs abrogates gene silencing of the modified strand, but the fate and potency of the unmodified strand has not been investigated. Here, we show that 5' UNA-modified siRNAs show improved silencing potency of the unmodified strand. We harness this advantageous property in a therapeutic context, where a limited target region in a conserved HIV 5' long terminal repeat U5 region would otherwise yield siRNAs with undesired strand selection properties and poor silencing. Applying 5' UNA modification to the unintended sense (S) strand of these otherwise poorly targeted siRNAs dramatically improves on-target silencing by the intended antisense (AS) strand in pNL4-3.luciferase studies. This study highlights the utility of 5' UNA siRNA modification in therapeutic contexts where siRNA sequence selection is constrained.Molecular Therapy-Nucleic Acids (2013) 2, e103; doi:10.1038/mtna.2013.36; published online 2 July 2013. PMID:23820891

Snead, Nicholas M; Escamilla-Powers, Julie R; Rossi, John J; McCaffrey, Anton P

2013-07-02

408

A simple nucleic acid hybridization\\/latex agglutination assay for the rapid detection of polymerase chain reaction amplicons  

Microsoft Academic Search

We have developed a new method for the detection of nucleic acid hybridization, based on a simple latex agglutination test that can be evaluated by the unaided eye. Nucleic acid, e.g., a polymerase chain reaction (PCR) product, is denatured and incubated with polystyrene beads carrying covalently bound complementary oligonucleotide sequences. Hybridization of the nucleic acids leads to aggregation of the

Sabine Vollenhofer-Schrumpf; Ronald Buresch; Manfred Schinkinger

2007-01-01

409

Probing Structure and Function with Alternative Nucleic Acids Bearing 2?,5?Linked, Zwitterionic, and Isocytosine·Isoguanine Components  

Microsoft Academic Search

The incorporation of alternative functional components into nucleic acids can provide insight into what molecular features are necessary for an informational macromolecule to be successful. It can also provide a means to improve particular physical characteristics of nucleic acids for diagnostic and therapeutic purposes, or probe mechanisms. By testing the fitness of nucleic acid-like molecules derived by structural permutations of

Christopher Switzer; John C. Chaput

2001-01-01

410

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

Microsoft Academic Search

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

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

2005-01-01

411

Lateral flow microarrays: a novel platform for rapid nucleic acid detection based on miniaturized lateral flow chromatography  

Microsoft Academic Search

Widely used nucleic acid assays are poorly suited for field deployment where access to laboratory instrumentation is limited or unavailable. The need for field deployable nucleic acid detection demands inexpensive, facile systems without sacrificing information capacity or sensitivity. Here we describe a novel microarray platform capable of rapid, sensitive nucleic acid detection without specialized instrumentation. The approach is based on

Darren J. Carter; R. Bruce Cary

2007-01-01

412

Seasonal changes in nucleic acids, amino acids and protein content in juvenile Norway lobster ( Nephrops norvegicus )  

Microsoft Academic Search

The objective of this study was to describe the seasonal variations in nucleic acid contents and amino acid profiles in the muscle of juvenile Nephrops norvegicus. RNA and protein contents, and RNA:protein and RNA:DNA ratios varied significantly between seasons, being highest in spring and lowest in autumn\\/winter ( PPP=0.05). In respect to protein-bound amino acid content (BAA), a significant increase

R. Rosa; M. L. Nunes

2003-01-01

413

Decomposition of nucleic acids and some of their degradation products by microorganisms  

Microsoft Academic Search

A study was made of the decomposition of nucleic acids, uric acid and urea by different groups of soil microorganisms including\\u000a bacilli, non-coryneform rods, corynebacteria (arthrobacters and non-arthrobacters), streptomycetes, fungi and yeasts. Hydrolysis\\u000a of nucleic acids was found to be a common phenomenon. The decomposition of uric acid was readily carried out by arthrobacters\\u000a and streptomycetes. Most bacilli, however, lacked

J. Antheunisse

1972-01-01

414

Complete nucleic acid sequence of Penaeus monodon densovirus (PmDNV) from India.  

PubMed

The complete nucleic acid sequence of the Penaeus monodon densovirus (PmDNV) from India was characterized. Analysis of the whole genome, consisting of 6310 bp revealed the presence of three open reading frames (ORFs), comprising 1281 bp, 1734 bp and 2460 bp, respectively. The complete genome and amino acid sequences of three proteins viz., NS1, NS2 and VP were compared with PmDNV from Thailand, PmergDNV from Australia and other partial sequences in GenBank, respectively. Highest nucleotide similarity was observed with the Thai strain (88%), while 33, 32 and 91 amino acid substitutions were observed in the NS2, NS1 and VP, respectively. Phylogenetic analysis of shrimp, insect and vertebrate parvovirus sequences revealed that the Indian PmDNV is more closely related to Thai isolates than all other parvoviruses reported so far. PMID:20156496

Safeena, Muhammed P; Tyagi, Anuj; Rai, Praveen; Karunasagar, Iddya; Karunasagar, Indrani

2010-02-13

415

Nucleic Acid Sensors and Type I Interferon Production in Systemic Lupus Erythematosus  

PubMed Central

The characteristic serologic feature of systemic lupus erythematosus (SLE) is autoantibodies against one’s own nucleic acid or nucleic acid-binding proteins – DNA and RNA-binding nuclear proteins. Circulating autoantibodies can deposit in the tissue, causing inflammation and production of cytokines such as type 1 interferon (IFN). Investigations in human patients and animal models have implicated environmental as well as genetic factors in the biology of the SLE autoimmune response. Viral/Bacterial nucleic acid is a potent stimulant of innate immunity by both toll-like receptor (TLR) and non-TLR signaling cascades. Additionally, foreign DNA may act as an immunogen to drive an antigen-specific antibody response. Self nucleic acid is normally restricted to the nucleus or the mitochondria, away from the DNA/RNA sensors, and mechanisms exist to differentiate between foreign and self nucleic acid. In normal immunity, a diverse range of DNA and RNA sensors in different cell types form a dynamic and integrated molecular network to prevent viral infection. In SLE, pathologic activation of these sensors occurs via immune complexes consisting of autoantibodies bound to DNA or to nucleic acid-protein complexes. In this review, we will discuss recent studies outlining how mismanaged nucleic acid sensing networks promote autoimmunity and result in the over-production of type I IFN. This information is critical for improving therapeutic strategies for SLE disease.

Shrivastav, Meena; Niewold, Timothy B.

2013-01-01

416

Effects of Phosfon-S on Nucleic Acid Metabolism in Pisum sativum Alaska  

PubMed Central

Phosfon-S, a substance which inhibits stem elongation, alters nucleic acid metabolism in Pisum sativum Alaska. Methylated albumin kieselguhr (MAK) columns were used to fractionate 32P-labeled nucleic acids. Phosfon-S treatment of the plants resulted in a decrease in soluble RNA and an increase in ribosomal RNA. Specific activities of the various nucleic acid fractions were lower as a result of treatment. The nucleic acids from treated tissues were more resistant to RNase degradation, and endogenous RNase activity was lower in treated tissues. When RNase treated nucleic acids were fractionated on MAK columns, the DNA-RNA fractions from treated plants had a higher specific activity than that of the control, which was not true before nuclease treatment. Spectrophotometric examination of this fraction revealed a difference in absorption spectra, possibly indicating a Phosfon-S nucleic acid complex. It is suggested that these alterations in nucleic acid metabolism could in turn alter a wide variety of metabolic processes, resulting in retarded growth.

Brook, Judith; West, S. H.; Anthony, D. S.

1967-01-01

417

Nucleic acids and endosomal pattern recognition: how to tell friend from foe?  

PubMed Central

The innate immune system has evolved endosomal and cytoplasmic receptors for the detection of viral nucleic acids as sensors for virus infection. Some of these pattern recognition receptors (PRR) detect features of viral nucleic acids that are not found in the host such as long stretches of double-stranded RNA (dsRNA) and uncapped single-stranded RNA (ssRNA) in case of Toll-like receptor (TLR) 3 and RIG-I, respectively. In contrast, TLR7/8 and TLR9 are unable to distinguish between viral and self-nucleic acids on the grounds of distinct molecular patterns. The ability of these endosomal TLR to act as PRR for viral nucleic acids seems to rely solely on the mode of access to the endolysosomal compartment in which recognition takes place. The current dogma states that self-nucleic acids do not enter the TLR-sensing compartment under normal physiological conditions. However, it is still poorly understood how dendritic cells (DC) evade activation by self-nucleic acids, in particular with regard to specific DC subsets, which are specialized in taking up material from dying cells for cross-presentation of cell-associated antigens. In this review we discuss the current understanding of how the immune system distinguishes between foreign and self-nucleic acids and point out some of the key aspects that still require further research and clarification.

Brencicova, Eva; Diebold, Sandra S.

2013-01-01

418

The importance of nucleic acid and carbohydrate metabolism in cell division  

Microsoft Academic Search

Disturbance of the process of phosphorylation by 2, 4-dinitrophenol, exclusion of desoxyribonuclease by adenine, derangement of the synthesis of nucleic acids by tripaflavine cause pronounced decrease of mitotic activity in the corneal, intestinal and tongue epithelium. Nucleic metabolism of a cell is one of the fundamental metabolic processes which is connected with cell division. Changes of the carbohydrate metabolism (experiments

L. M. Ermolenko

1957-01-01

419

The Practical and Pedagogical Advantages of an Ambigraphic Nucleic Acid Notation  

Microsoft Academic Search

The universally applied IUPAC notation for nucleic acids was adopted primarily to facilitate the mental association of G, A, T, C, and the related ambiguity characters with the bases they represent. However, it is possible to create a notation that offers greater support for the basic manipulations and analyses to which genetic sequences frequently are subjected. By designing a nucleic

David A. Rozak

2006-01-01

420

Onset of nucleic acid synthesis during germination of Pisum sativum L  

Microsoft Academic Search

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

Nigel E. Robinson; John A. Bryant

1975-01-01

421

Detection of Human Enteric Viruses in Oysters by In Vivo and In Vitro Amplification of Nucleic Acids  

Microsoft Academic Search

ThisstudydescribesthedetectionofenterovirusesandhepatitisAvirusin31naturallycontaminatedoyster specimens by nucleic acid amplification and oligonucleotide probing. Viruses were extracted by adsorption- elution-precipitation from 50-g oyster samples harvested from an area receiving sewage effluent discharge. Ninety percent of each extract was inoculated into primate kidney cell cultures for virus isolation and infectivity assay. Viruses in the remaining 10% of oyster extract that was not inoculated into cell cultures

HYENMI CHUNG; LEE-ANN JAYKUS; ANDMARK D. SOBSEY

1996-01-01

422

Detection of Salmonella invA by isothermal and chimeric primer-initiated amplification of nucleic acids (ICAN) in Zambia  

Microsoft Academic Search

The isothermal and chimeric primer-initiated amplification of nucleic acids (ICAN) is a new isothermal DNA amplification method composed of exo Bca DNA polymerase, RNaseH and DNA–RNA chimeric primers. We detected invA of Salmonella from chicken carcasses, egg yolk and cattle fecal samples. Fifty-three of 59 isolates were invA-positive in ICAN-chromatostrip detection. The result was consistent with those obtained by standard

Emiko Isogai; Chitwambi Makungu; John Yabe; Patson Sinkala; Andrew Nambota; Hiroshi Isogai; Hideto Fukushi; Manda Silungwe; Charles Mubita; Michelo Syakalima; Bernard Mudenda Hang'ombe; Shunji Kozaki; Jun Yasuda

2005-01-01

423

Synthesis and properties of carbohydrate-phosphate backbone-modified oligonucleotide analogues and nucleic acid mimetics  

NASA Astrophysics Data System (ADS)

Advances in the synthesis of oligo(deoxy)ribonucleotide analogues and nucleic acid mimetics made in the last decade are summarized. Attention is focused on new methods for the synthesis of derivatives with a modified ribose-phosphate backbone (phosphorothioate, boranophosphate, and nucleoside phosphonate derivatives) and derivatives devoid of the phosphate group. Among nucleic acid mimetics, conformationally restricted modified peptide nucleic acids, including those bearing a negative or positive charge, and morpholino oligomers are considered. Advantages and drawbacks of the main types of analogues as regards the complexity of the synthesis and the possibility of their application as antisense agents or reagents for hybridization analysis are compared.

Abramova, Tatyana V.; Silnikov, Vladimir N.

2011-05-01

424

Carbon composite micro- and nano-tubes-based electrodes for detection of nucleic acids  

NASA Astrophysics Data System (ADS)

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.

Prasek, Jan; Huska, Dalibor; Jasek, Ondrej; Zajickova, Lenka; Trnkova, Libuse; Adam, Vojtech; Kizek, Rene; Hubalek, Jaromir

2011-05-01

425

Are isolated anti-HBc blood donors in high risk group? The detection of HBV DNA in isolated anti-HBc cases with nucleic acid amplification test (NAT) based on transcription-mediated amplification (TMA) and HBV discrimination  

Microsoft Academic Search

AimHepatitis B virus (HBV) can be transmitted by blood transfusions even so using serological tests having high sensitivity and specificity. We aimed to detect HBV DNA in isolated Anti-HBc donors and show if they have transfusion risk or not.

Hüsnü Altunay; Erdogan Kosan; Ilhan Birinci; Armagan Aksoy; Kaan Kirali; Suat Saribas; Mustafa Aslan; Pelin Yuksel; Esra Alan; Osman Sadi Yenen; Bekir Kocazeybek

2010-01-01

426

Synthesis and characterization of peptide nucleic acid platinum nanoclusters  

NASA Astrophysics Data System (ADS)

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.

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

2006-03-01

427

Adsorption of amino acids and nucleic acid bases onto minerals: a few suggestions for prebiotic chemistry experiments  

NASA Astrophysics Data System (ADS)

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.

Zaia, Dimas A. M.

2012-10-01

428

Does the High Nucleic Acid Content of Individual Bacterial Cells Allow Us To Discriminate between Active Cells and Inactive Cells in Aquatic Systems?  

Microsoft Academic Search

The nucleic acid contents of individual bacterial cells as determined with three different nucleic acid-specific fluorescent dyes (SYBR I, SYBR II, and SYTO 13) and flow cytometry were compared for different seawater samples. Similar fluorescence patterns were observed, and bacteria with high apparent nucleic acid contents (HNA) could be discriminated from bacteria with low nucleic acid contents (LNA). The best

PHILIPPE LEBARON; PIERRE SERVAIS; HELENE AGOGUE; CLAUDE COURTIES; FABIEN JOUX

2001-01-01

429

Rare-earth-cation-induced change in the cholesteric twisting of neighboring nucleic acid molecules  

SciTech Connect

Certain physicochemical characteristics of particles of the cholesteric liquid-crystal dispersions of complexes of double-stranded nucleic acids with rare earth elements have been determined. It is shown for the first time that the binding of the rare earth cations to linear nucleic acid molecules ordered in the structure of particles of the cholesteric liquid crystal dispersions is accompanied not only by amplification of the abnormal band in the circular dichroism spectrum, but also by the disappearance of the characteristic maximum on the X-ray scattering curves for small angles. The (cholesteric 1-cholesteric 2) transition induced by rare earth cations is an example of the operation of a microscopic machine consisting of spatially ordered nucleic acid molecules. Particles of the cholesteric liquid crystal dispersions of nucleic acid complexes with rare earth elements hold the abnormal optical properties for a long time.

Yevdokimov, Yu. M., E-mail: yevdokim@eimb.ru; Salyanov, V. I.; Kondrashina, O. V. [Russian Academy of Sciences, Engelhardt Institute of Molecular Biology (Russian Federation); Gasanov, A. A. [Giredmet Research and Design Institute (Russian Federation); Shtykova, E. V.; Dembo, K. A. [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2007-03-15

430

Branched and Multi-Chain Nucleic Acid Switches for Sensing and Screening.  

National Technical Information Service (NTIS)

Embodiments of the invention relate to a branched or multichain nucleic acid switch adapted to switch from a first conformation to a second conformation upon ligand binding. The switch includes a probe strand, P, which includes the ligand binding domain; ...

B. S. Hudson P. N. Borer

2005-01-01

431

Fluorescent imaging and quantitation of solid support-bound nucleic acids  

NASA Astrophysics Data System (ADS)

Recent advances in molecular biology have enabled the deposition of nucleic acids on solid phases to form arrays of oligonucleotides. Such arrays are being applied in milli to nanoscale molecular and biochemical analysis such as genetic mutation detection, gene expression quantitation and DNA sequencing using so-called DNA chip arrays. A major obstacle to continue use of such arrays is detection and analysis of the arrayed nucleic acids, nucleic acids, nucleic acids' targets that bind via hybridization to the arrays and the products of array-based biochemical reactions. We report here on the design and utility of our experimental set-up for analysis of surface bound, arrayed oligonucleotides, and our experience in detection and quantitation of multiple fluorescent labels bound to the surface through attachment, hybridization, and arrayed primer extension.

Bogdanov, Valery L.; Rogers, Yu-Hui; Boyce-Jacino, Michael

1997-05-01

432

Therapeutic and Diagnostic Methods and Compositions Based on Notch Proteins and Nucleic Acids  

National Technical Information Service (NTIS)

The present invention relates to therapeutic and diagnostic methods and compositions based on Notch proteins and nucleic acids. The invention provides for treatment of disorders of cell fate or differentiation by administration of a therapeutic compound o...

C. M. Blaumueller P. Zagouras R. G. Fehon S. Artavanis-Tsakonas

2004-01-01

433

Protection against Malaria by Immunization with a Plasmodium Yoelii Circumsporozoite Protein Nucleic Acid Vaccine.  

National Technical Information Service (NTIS)

Nucleic acid vaccines provide an exciting new alternative approach to developing the multiantigen vaccines designed to induce protective antibody and T-cell responses against Plasmodium proteins that many experts believe will be required for effective pro...

S. L. Hoffman M. Sedegah R. C. Hedstrom

1994-01-01

434

Method for detection of polymorphic restriction sites and nucleic acid sequences  

SciTech Connect

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.

Saiki, R.K.; Erlich, H.A.

1987-07-28

435

Nucleic Acid Probes for Detection of Phytopathogenic Bacteria. Phase 1 Final Report.  

National Technical Information Service (NTIS)

The study examined the feasibility of developing a diagnostic procedure for bacterial diseases in crop plants based on nucleic acid hybridization technologies. Erwinia carotovora var. atroseptica (ECa) was chosen as the test organism for the study. A libr...

G. King

1984-01-01

436

Monitoring Gene Expression In Vivo with Nucleic Acid Molecular Switches  

SciTech Connect

The overall objectives of this project were (1) to develop allosteric ribozymes capable of acting as molecular switches for monitoring the levels of both wild-type and mutant mRNA species in living cells and whole animals and (2) to develop highly efficient reagents to deliver nucleic acid molecular switches into living cells, tissues and animals with the ultimate goal of expression profiling specific mRNAs of diagnostic or prognostic value within tumors in animals. During the past year, we have moved our laboratory to Nevada and in the moving process we have lost electronic and paper copies of prior progress reports concerning the construction and biological properties of the molecular switches. Since there was minimal progress during the last year on molecular switches, we are relying on past project reports to provide a summary of our data on this facet of the grant. Here we are summarizing the work done on the delivery reagents and their application to inducing mutations in living cells, which will include work done during the no cost extension.

David C. Ward; Patricia Bray-Ward

2005-01-26

437

Membrane Protected Apoptotic Trophoblast Microparticles Contain Nucleic Acids  

PubMed Central

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.

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

438

Phospholipid conjugate for intracellular delivery of peptide nucleic acids  

PubMed Central

Peptide nucleic acids (PNAs) have a number of attractive features that have made them an ideal choice for antisense and antigene-based tools, probes and drugs, but their poor membrane permeability has limited their application as therapeutic or diagnostic agents. Herein we report a general method for the synthesis of phospholipid-PNAs (LP-PNAs), and compare the effect of non-cleavable lipids and bioreductively cleavable lipids (L and LSS) and phospholipid (LP) on the splice-correcting bioactivity of a PNA bearing the cell penetrating Arg9 group (PNA-R9). While the three constructs show similar and increasing bioactivity at 1–3 ?M, the activity of LP-PNA-R9 continues to increase from 4–6 ?M while the activity of L-PNA-R9 remains constant and LSS-PNA-R9 decreases rapidly in parallel with their relative cytotoxicity. The activity of both LP-PNA-R9 and L-PNA-R9 were found to dramatically increase with chloroquine, as expected for an endocytotic entry mechanism. Both constructs were also found to have CMC values of 1.0 and 4.5 ?M in 150 mM NaCl, pH 7 water, suggesting that micelle formation may play a hitherto unrecognized role in modulating toxicity and/or facilitating endocytosis.

Shen, Gang; Fang, Huafeng; Song, Yinyin; Bielska, Agata A.; Wang, Zhenghui; Taylor, John-Stephen A.

2009-01-01

439

G-quadruplex nucleic acids and human disease  

PubMed Central

Alternate DNA structures that deviate from B-form double-stranded DNA such as G-quadruplex (G4) DNA can be formed by sequences that are widely distributed throughout the human genome. G-quadruplex secondary structures, formed by the stacking of planar quartets composed of four guanines that interact by Hoogsteen hydrogen bonding, can affect cellular DNA replication and transcription, and influence genomic stability. The unique metabolism of G-rich chromosomal regions that potentially form quadruplexes may influence a number of biological processes including immunoglobulin gene rearrangements, promoter activation and telomere maintenance. A number of human diseases are characterized by telomere defects, and it is proposed that G-quadruplex structures which form at telomere ends play an important role in telomere stability. Evidence from cellular studies and model organisms suggests that diseases with known defects in G4 DNA helicases are likely to be perturbed in telomere maintenance and cellular DNA replication. In this minireview, we discuss the connections of G-quadruplex nucleic acids to human genetic diseases and cancer based on the recent literature.

Wu, Yuliang; Brosh, Robert M.

2010-01-01

440

Improved assay-dependent searching of nucleic acid sequence databases  

PubMed Central

Nucleic acid-based biochemical assays are crucial to modern biology. Key applications, such as detection of bacterial, viral and fungal pathogens, require detailed knowledge of assay sensitivity and specificity to obtain reliable results. Improved methods to predict assay performance are needed for exploiting the exponentially growing amount of DNA sequence data and for reducing the experimental effort required to develop robust detection assays. Toward this goal, we present an algorithm for the calculation of sequence similarity based on DNA thermodynamics. In our approach, search queries consist of one to three oligonucleotide sequences representing either a hybridization probe, a pair of Padlock probes or a pair of PCR primers with an optional TaqMan™ probe (i.e. in silico or ‘virtual’ PCR). Matches are reported if the query and target satisfy both the thermodynamics of the assay (binding at a specified hybridization temperature and/or change in free energy) and the relevant biological constraints (assay sequences binding to the correct target duplex strands in the required orientations). The sensitivity and specificity of our method is evaluated by comparing predicted to known sequence tagged sites in the human genome. Free energy is shown to be a more sensitive and specific match criterion than hybridization temperature.

Gans, Jason D.

2008-01-01

441

Pyrene excimer signaling molecular beacons for probing nucleic acids.  

PubMed

Molecular beacon DNA probes, containing 1-4 pyrene monomers on the 5' end and the quencher DABCYL on the 3' end, were engineered and employed for real-time probing of DNA sequences. In the absence of a target sequence, the multiple-pyrene labeled molecular beacons (MBs) assumed a stem-closed conformation resulting in quenching of the pyrene excimer fluorescence. In the presence of target, the beacons switched to a stem-open conformation, which separated the pyrene label from the quencher molecule and generated an excimer emission signal proportional to the target concentration. Steady-state fluorescence assays resulted in a subnanomolar limit of detection in buffer, whereas time-resolved signaling enabled low-nanomolar target detection in cell-growth media. It was found that the excimer emission intensity could be scaled by increasing the number of pyrene monomers conjugated to the 5' terminal. Each additional pyrene monomer resulted in substantial increases in the excimer emission intensities, quantum yields, and excited-state lifetimes of the hybridized MBs. The long fluorescence lifetime ( approximately 40 ns), large Stokes shift (130 nm), and tunable intensity of the excimer make this multiple-pyrene moiety a useful alternative to traditional fluorophore labeling in nucleic acid probes. PMID:18078339

Conlon, Patrick; Yang, Chaoyong James; Wu, Yanrong; Chen, Yan; Martinez, Karen; Kim, Youngmi; Stevens, Nathan; Marti, Angel A; Jockusch, Steffen; Turro, Nicholas J; Tan, Weihong

2007-12-14

442

Flavin conjugates for delivery of peptide nucleic acids.  

PubMed

Oligonucleotides and their analogues, such as peptide nucleic acids (PNAs), can be used in chemical strategies to artificially control gene expression. Inefficient cellular uptake and inappropriate cellular localization still remain obstacles in biological applications, however, especially for PNAs. Here we demonstrate that conjugation of PNAs to flavin resulted in efficient internalization into cells through an endocytic pathway. The flavin-PNAs exhibited antisense activity in the sub-micromolar range, in the context of a treatment facilitating endosomal escape. Increased endosomal release of flavin conjugates into the cytoplasm and/or nucleus was shown by chloroquine treatment and also--when the flavin-PNA was conjugated to rhodamine, a mild photosensitizer--upon light irradiation. In conclusion, an isoalloxazine moiety can be used as a carrier and attached to a cargo biomolecule, here a PNA, for internalization and functional cytoplasmic/nuclear delivery. Our findings could be useful for further design of PNAs and other oligonucleotide analogues as potent antisense agents. PMID:23129496

Marlin, Fanny; Simon, Philippe; Bonneau, Stéphanie; Alberti, Patrizia; Cordier, Céline; Boix, Charlotte; Perrouault, Loïc; Fossey, Aurélie; Saison-Behmoaras, Tula; Fontecave, Marc; Giovannangeli, Carine

2012-11-05

443

A novel nucleic acid analogue shows strong angiogenic activity.  

PubMed

A novel nucleic acid analogue (2Cl-C.OXT-A) significantly stimulated tube formation of human umbilical endothelial cells (HUVEC). Its maximum potency at 100muM 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. PMID:20691660

Tsukamoto, Ikuko; Sakakibara, Norikazu; Maruyama, Tokumi; Igarashi, Junsuke; Kosaka, Hiroaki; Kubota, Yasuo; Tokuda, Masaaki; Ashino, Hiromi; Hattori, Kenichi; Tanaka, Shinji; Kawata, Mitsuhiro; Konishi, Ryoji

2010-08-05

444

Linear and nonlinear optical properties of nucleic acid bases  

NASA Astrophysics Data System (ADS)

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.

Alparone, Andrea

2013-01-01

445

Functional nucleic acid entrapment in sol-gel derived materials.  

PubMed

Functional nucleic acids (FNAs) are single-stranded DNA or RNA molecules, typically generated through in vitro selection, that have the ability to act as receptors for target molecules (aptamers) or perform catalysis of a chemical reaction (deoxyribozymes and ribozymes). Fluorescence-signaling aptamers and deoxyribozymes have recently emerged as promising biological recognition and signaling elements, although little has been done to evaluate their potential for solid-phase assays, particularly with species made of RNA due to their lack of chemical stability and susceptibility to nuclease attack. Herein, we present a detailed overview of the methods utilized for solid-phase immobilization of FNAs using a sol-gel entrapment method that can provide protection from nuclease degradation and impart long-term chemical stability to the FNA reporter systems, while maintaining their signaling capabilities. This article will also provide a brief review of the results of such entrapment studies involving fluorescence-signaling versions of a DNA aptamer, selected RNA-cleaving deoxyribozymes, and two different RNA aptamers in a series of sol-gel derived composites, ranging from highly polar silica to hydrophobic methylsilsesquioxane-based materials. Given the ability to produce sol-gel derived materials in a variety of configurations, particularly as thin film coatings on electrodes, optical fibers, and other devices, this entrapment method should provide a useful platform for numerous solid-phase FNA-based biosensing applications. PMID:24025165

Carrasquilla, Carmen; Brennan, John D

2013-09-08

446

Binding of hen egg white lysozyme fibrils with nucleic acids.  

PubMed

Non proteinaceous substances are found to be associated with toxic protein aggregates commonly known as fibrils. Hen egg white lysozyme (HEWL) is able to form fibrillar species under various conditions. Here for the first time we report concentration dependent binding affinities of preformed HEWL fibrils towards DNA and RNA at physiological pH (pH 7.4). We have found that HEWL fibrils bind with DNA and RNA that is distinctly different when compared to native HEWL. The association constant (Ka) of native HEWL and ct-DNA at pH 7.4 is 6.8×10(5)M(-1). We have also investigated the conformational alterations of DNA that occur on binding with HEWL fibrils. Our study has demonstrated dominant electrostatic interactions between oppositely charged polyelectrolytes which accounts for the binding of nucleic acids with fibrils. The affinity between the moieties could lead to disruption in the functions of cellular components that might be attributed to the toxicity of the aggregates formed in vivo. PMID:23933246

Ghosh, Sudeshna; Pandey, Nitin K; Sen, Sambuddha; Tripathy, Debi Ranjan; Dasgupta, Swagata

2013-07-20

447

Improved nucleic acid descriptors for siRNA efficacy prediction  

PubMed Central

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.

Sciabola, Simone; Cao, Qing; Orozco, Modesto; Faustino, Ignacio; Stanton, Robert V.

2013-01-01

448

Universal fluorescent labeling of amplification products using locked nucleic acids.  

PubMed

Amplification/hybridization-based genetic analyses using primers containing locked nucleic acids (LNAs) present many benefits. Here, we developed a novel design for universal fluorescent PCR using LNAs. Universal fluorescent PCR generates intermediate nonlabeled fragments and final fluorescent fragments in a two-step amplification process that uses locus-specific primers with universal tails and universal fluorescent primers. In this study, a few standard nucleotides were replaced with LNAs only in the fluorescent universal primers. The sequence of the fluorescent universal primer significantly affected the amplification efficiency. For primers with three LNAs, the fluorescent primers with stable M13(-47) sequences provided the most efficient signal (approximately tenfold higher than the primers with M13(-21) sequences at lower Tm values). Moreover, AT-rich LNA substitutions in the fluorescent primers produced much lower amplification efficiencies than GC-rich substitutions. GC-rich LNAs produced greater differences in Tm values among primers, and resulted in the preferential production of fluorescently labeled amplicons. The specificity and sensitivity of LNA-containing fluorescent primers were assessed by genotyping eight STRs in Japanese individuals, and full STR profiles could be generated using as little as 0.25 ng of genomic DNA. The method permitted clear discrimination of alleles and represents sensitive STR genotyping at a reduced cost. PMID:23161600

Asari, Masaru; Oka, Kumiko; Omura, Tomohiro; Maseda, Chikatoshi; Tasaki, Yoshikazu; Shiono, Hiroshi; Matsubara, Kazuo; Matsuda, Mitsuyoshi; Shimizu, Keiko

2013-01-14

449

Effect of trifluralin on growth, morphology, and nucleic Acid synthesis.  

PubMed

Roots and shoots of corn seedlings (Zea mays L. var. Dixie 18) germinated in trifluralin (alpha,alpha,alpha-trifluoro-2,6-dinitro-N,N-dipropyl-p-toluidine) solutions are characterized by radial enlargement of the cortical cells and by multinucleate cells in the meristematic regions. Trifluralin inhibits elongation of Avena coleoptile sections at concentrations of 0.1 mum to 10 mum. Synthesis of DNA, RNA, and protein is suppressed in the root tips while no significant effect is noticeable in the shoots of corn germinated in trifluralin. A (32)P time-course study of 48, 72, and 96 hours utilizing phenol extraction and MAK column separation of corn root and shoot nucleic acids showed suppression of (32)P incorporation in the treated roots; however, the 72 and 96 hour treated shoots incorporated a much greater amount than the control with most of the increased incorporation found in the sRNA and DNA fractions. The increased activity in the DNA may be due to a high G-C type DNA. No selective suppression or enhancement of any particular RNA species was noticed in the treated plants. PMID:16656762

Schultz, D P; Funderburk, H H; Negi, N S

1968-02-01

450

Oxidatively Modified Nucleic Acids in Preclinical Alzheimer's Disease (PCAD) Brain  

PubMed Central

Previous studies show increased oxidative DNA and RNA damage and diminished 8-oxoguanine glycosylase (OGG1) mediated base excision repair in vulnerable brain regions of mild cognitive impairment and late-stage Alzheimer’s disease (LAD) subjects compared to normal control (NC) subjects. Recently, a preclinical stage of AD (PCAD) has been described in which subjects show no overt clinical manifestations of AD but demonstrate significant AD pathology at autopsy. To determine if DNA or RNA oxidation are significantly elevated in PCAD brain we quantified 8-OHG in sections of hippocampus/parahippocamapal gyri in PCAD and NC subjects using immunohistochemistry and confocal microscopy and in superior and middle temporal gyri (SMTG) using gas chromatography/mass spectrometry. To determine if increased DNA oxidation is associated with altered repair capacity, levels of OGG1 protein in HPG were measured by immunohistochemistry and levels of OGG1 mRNA were measured in SMTG using quantitative PCR. Results show significantly increased (p < 0.05) 8-OHG immunostaining in DNA and RNA of PCAD HPG and significantly increased 8-OHG in PCAD SMTG. Quantification of OGG1 showed significantly elevated mRNA in PCAD SMTG and a trend toward elevated immunostaining in PCAD HPG. Overall, the data suggest oxidative damage to nucleic acids and a compensatory increase in OGG1 expression occur early in the pathogenesis of AD.

Lovell, Mark A.; Soman, Sony; Bradley, Melissa A.

2011-01-01

451

JAWS: just add water system - a device for detection of nucleic acids in Martian ice caps  

Microsoft Academic Search

The design of a device for nucleic acid detection in the Martian ice caps is presented; the Just Add Water System (JAWS). It is based on fiber-optic PNA (peptide nucleic acid) light up probe random microsphere universal array technology. JAWS is designed to be part of a larger system with a regulation of pH and salt concentrations e.g. the MOD

Anders J. Hansen; Eske Willerslev; Søren Mørk; Mads M. Hedegaard; Regin Rønn; Daniel C. Jeffares

2002-01-01

452

Inhibition of Nucleic Acid Synthesis Caused by X-Irradiation of the Nucleolus  

Microsoft Academic Search

Living cells grown in tissue culture have been irradiated with a narrow beam of soft X-rays of effective diameter 2\\\\cdot 5 mu . The method has been used in conjunction with quantitative ultra-violet photomicrography to investigate the role of the nucleolus in nucleic acid synthesis. The results show that X-irradiation of the nucleolus reduces the amount of nucleic acid synthesized

J. Seed

1960-01-01

453

Molecular dissection of the reovirus ?1 protein nucleic acids binding site  

Microsoft Academic Search

A recent study has shown that the reovirus ?1 protein can unwind double-stranded nucleic acid molecules, a process energetically coupled to the hydrolysis of nucleoside 5?-triphosphates. In the present study, it was demonstrated that ?1, expressed as a fusion protein with the Escherichia coli maltose-binding protein (MBP), posseses a non-specific affinity for various nucleic acids. The study also showed that

M Bisaillon; G Lemay

1997-01-01

454

Nucleic Acid Model Building: The Multiple Backbone Solutions Associated with a Given Base Morphology  

Microsoft Academic Search

A constrained model building procedure is used to generate nucleic acid structures of the familiar A-, B-, and Z-DNA duplexes. Attention is focused upon the multiple structural solutions associated with the arrangements of nucleic acid base pairs rather than the optimum sugar-phosphate structure. The glycosyl (?) and sugar torsions (both the ring puckering and the exocyclic C5?-C4? (?) torsion) are

A. R. Srinivasan; Wilma K. Olson

1987-01-01

455

Probing the structure of nucleic acids with Ni(II) complexes  

Microsoft Academic Search

The structure of nucleic acids determines their biological function. Interest in the development of novel probes from structures of nucleic acid has led to the discovery of conformation-specific oxidation of guanine sites in DNA and RNA using Ni(II) complexes. The reaction is highly dependent upon the nature of Ni(II) complexes with the most important feature of a strong in-plane ligand

1992-01-01

456

Nucleic Acid Binding Proteins in Highly Purified Creutzfeldt-Jakob Disease Preparations  

Microsoft Academic Search

The nature of the infectious agent causing human Creutzfeldt-Jakob disease (CJD), a slowly progressive dementia, is controversial. As in scrapie, no agent-specific proteins or nucleic acids have been identified. However, biological features of exponential replication and agent strain variation, as well as physical size and density data, are most consistent with a viral structure-i.e., a nucleic acid-protein complex. It is

T. Sklaviadis; A. Akowitz; E. E. Manuelidis; L. Manuelidis

1993-01-01

457

Determination for micro amounts of nucleic acids by a resonance light scattering technique with dequalinium chloride  

Microsoft Academic Search

Based on the strong enhancement effect of nucleic acids on resonance light scattering of dequalinium chloride, the determination method for micro amounts of nucleic acids has been developed. Under the experimental conditions (5.0×10?5 mol l?1 dequalinium, pH 7.0, at room temperature) the linear range of this assay is 0.04–10.0 ?g ml?1 for calf thymus DNA and fish sperm DNA, and

Zheng-Ping Li; Ke-An Li; Shen-Yang Tong

2001-01-01

458

Plasmacytoid dendritic cells: sensing nucleic acids in viral infection and autoimmune diseases  

Microsoft Academic Search

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

Michel Gilliet; Wei Cao; Yong-Jun Liu

2008-01-01

459

2'-bis-pyrene modified oligonucleotides: sensitive fluorescent probes of nucleic acids structure.  

PubMed

A new type of fluorescent nucleic acid probes, 2-bis-pyrene-modified oligonucleotides, is described. Preparation of these conjugates involves attachment of two pyrene moieties to the 2'-phosphate group introduced into any position within a sequence by solid-phase phosphoramidite synthesis. Good hybridization properties of the 2'-bis-pyrene probes, their nuclease resistance and sensitivity of fluorescence to the type of complementary nucleic acid have been demonstrated. PMID:16248025

Novopashina, D S; Stetsenko, D A; Totskaya, O S; Repkova, M N; Venyaminova, A G

2005-01-01

460

Detection of Mycoplasma pneumoniae by Real-Time Nucleic Acid Sequence-Based Amplification  

Microsoft Academic Search

Real-time isothermal nucleic acid sequence-based amplification (RT-NASBA) was applied to the detection of Mycoplasma pneumoniae. In vitro-generated M. pneumoniae RNA was used to assess the sensitivity of the assay. The 95% hit rate was 148 molecules of M. pneumoniae RNA in the amplification and 104 molecules of in vitro-generated RNA after nucleic acid extraction. The sensitivity of the RT-NASBA and

K. Loens; M. Ieven; D. Ursi; T. Beck; M. Overdijk; P. Sillekens; H. Goossens

2003-01-01