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1

Nucleic acid isolation process  

DOEpatents

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

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

1990-01-01

2

Method for nucleic acid isolation using supercritical fluids  

DOEpatents

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

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

1999-07-13

3

Method for nucleic acid isolation using supercritical fluids  

DOEpatents

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

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

1999-01-01

4

Isolated menthone reductase and nucleic acid molecules encoding same  

DOEpatents

The present invention provides isolated menthone reductase proteins, isolated nucleic acid molecules encoding menthone reductase proteins, methods for expressing and isolating menthone reductase proteins, and transgenic plants expressing elevated levels of menthone reductase protein.

Croteau, Rodney B; Davis, Edward M; Ringer, Kerry L

2013-04-23

5

Isolation of nucleic acid binding proteins: an approach for isolation of cell surface, nucleic acid binding proteins.  

PubMed

An approach for isolation of cell surface, nucleic acid binding proteins is described. This approach relies on affinity modification of the proteins of living cells with reactive oligonucleotides bearing a haptenic group. Covalently modified proteins were isolated by hapten-specific affinity chromatography with subsequent SDS-PAGE. Isolated 68-kDa proteins responsible for the binding of oligonucleotides were MS/MS sequenced and identified as keratin K1, keratin K10, keratin K2e, and albumin. PMID:15251967

Chelobanov, Boris P; Laktionov, Pavel P; Kharkova, Maria V; Rykova, Elena Y; Vlassov, Valentin V

2004-06-01

6

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. PMID:23874571

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

2013-01-01

7

Isolation and Analysis of the Nucleic Acids and Polysaccharides from Clostridium welchii  

PubMed Central

A method previously described for the use of bentonite in the isolation of the nucleic acids from two gram-positive organisms was applied to the isolation of the nucleic acids from two strains of Clostridium welchii. The nucleic acids were separated from polysaccharides by the fractional precipitation of their cetyltrimethyl-ammonium salts from sodium chloride solution, and the base composition of the nucleic acids was determined. One strain of C. welchii investigated (NCTC 10578) was shown to produce considerable quantities of an acidic and also a weakly acidic or neutral polysaccharide; the other strain (ATCC 10543) gave very small quantities of the latter but none of the former polysaccharide. The monosaccharide composition of these polysaccharides was determined and the acidic polysaccharide was shown to resemble dermatan sulfate. PMID:5423367

Darby, G. K.; Jones, A. S.; Kennedy, J. F.; Walker, R. T.

1970-01-01

8

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

9

Simple and rapid procedure suitable for quantitative isolation of low and high molecular weight extracellular nucleic acids.  

PubMed

The procedure based on binding of nucleic acids with glass surface in presence of chaotropic salts was adapted for efficient isolation of 100-10000 b.p. DNA fragments and 50-10,000 b. RNA fragments. The method provide 90% and 85% efficacy of isolation of 100 b.p. DNA and 100 b. RNA fragments respectively. High molecular weight nucleic acids are isolated with 98% efficacy. Isolated nucleic acids are free from contaminations, influencing nucleic acids modifying enzymes and fluorochromes. The method is rapid, simple and cost-effective. PMID:15560075

Tamkovich, Svetlana N; Laktionov, Pavel P; Rykova, Elena Yu; Vlassov, Valentin V

2004-10-01

10

Automation of Nucleic Acid Isolation on KingFisher Magnetic Particle Processors  

Microsoft Academic Search

We describe automated nucleic acid (NA) isolation from diverse sample types using MagMAX kits (Ambion, Inc.) on KingFisher Magnetic Particle Processors (Thermo Scientific). The MagMAX-96 Blood RNA Isolation Kit is designed for total RNA isolation from whole blood from several species, without white blood cell fractionation, in about 45 min (including genomic DNA removal). The MagMAX-96 Total RNA Isolation Kit

Xingwang Fang; Roy C. Willis; Angela Burrell; Kurt Evans; Quoc Hoang; Weiwei Xu; Mangkey Bounpheng

2007-01-01

11

Microfluidic Devices for Nucleic Acid (NA) Isolation, Isothermal NA Amplification, and Real-Time Detection.  

PubMed

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

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

2015-01-01

12

An integrated, self-contained microfluidic cassette for isolation, amplification, and detection of nucleic acids  

PubMed Central

A self-contained, integrated, disposable, sample-to-answer, polycarbonate microfluidic cassette for nucleic acid—based detection of pathogens at the point of care was designed, constructed, and tested. The cassette comprises on-chip sample lysis, nucleic acid isolation, enzymatic amplification (polymerase chain reaction and, when needed, reverse transcription), amplicon labeling, and detection. On-chip pouches and valves facilitate fluid flow control. All the liquids and dry reagents needed for the various reactions are pre-stored in the cassette. The liquid reagents are stored in flexible pouches formed on the chip surface. Dry (RT-)PCR reagents are pre-stored in the thermal cycling, reaction chamber. The process operations include sample introduction; lysis of cells and viruses; solid-phase extraction, concentration, and purification of nucleic acids from the lysate; elution of the nucleic acids into a thermal cycling chamber and mixing with pre-stored (RT-)PCR dry reagents; thermal cycling; and detection. The PCR amplicons are labeled with digoxigenin and biotin and transmitted onto a lateral flow strip, where the target analytes bind to a test line consisting of immobilized avidin-D. The immobilized nucleic acids are labeled with up-converting phosphor (UCP) reporter particles. The operation of the cassette is automatically controlled by an analyzer that provides pouch and valve actuation with electrical motors and heating for the thermal cycling. The functionality of the device is demonstrated by detecting the presence of bacterial B.Cereus, viral armored RNA HIV, and HIV I virus in saliva samples. The cassette and actuator described here can be used to detect other diseases as well as the presence of bacterial and viral pathogens in the water supply and other fluids. PMID:20401537

Chen, Dafeng; Mauk, Michael; Qiu, Xianbo; Liu, Changchun; Kim, Jitae; Ramprasad, Sudhir; Ongagna, Serge; Abrams, William R.; Malamud, Daniel; Corstjens, Paul L. A. M.

2010-01-01

13

Nucleic acid detection compositions  

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.

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

2008-08-05

14

Cleavage of nucleic acids  

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.

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

2010-11-09

15

Cleavage of nucleic acids  

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.

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

2007-12-11

16

Cleavage of nucleic acids  

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.

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

2000-01-01

17

Nucleic Acid Isolation and Enrichment on a Microchip  

PubMed Central

This paper presents a microchip that isolates and enriches target-binding single-stranded DNA (ssDNA) from a randomized DNA mixture using a combination of solid-phase extraction and electrophoresis. Strands of ssDNA in a randomized mixture are captured via specific binding onto target-functionalized microbeads in a microchamber. The strands are further separated from impurities and enriched on-chip via electrophoresis. The microchip consists of two microchambers that are connected by a channel filled with agarose gel. In the isolation chamber, beads functionalized with human immunoglobulin E (IgE) are retained by a weir structure. An integrated heater elevates the temperature in the chamber to elute desired ssDNA from the beads, and electrophoretic transport of the DNA through the gel to the second chamber is accomplished by applying an electric potential difference between the two chambers. Experimental results show that ssDNA expressing binding affinity to IgE was captured and enriched from a sample of ssDNA with random sequences, demonstrating the potential of the microchip to enhance the sensitivity of ssDNA detection methods in dilute and complex biological samples. PMID:24729660

Kim, Jinho; Hilton, John P.; Yang, Kyung A.; Pei, Renjun; Stojanovic, Milan; Lin, Qiao

2014-01-01

18

Microfluidic platform for isolating nucleic acid targets using sequence specific hybridization  

PubMed Central

The separation of target nucleic acid sequences from biological samples has emerged as a significant process in today's diagnostics and detection strategies. In addition to the possible clinical applications, the fundamental understanding of target and sequence specific hybridization on surface modified magnetic beads is of high value. In this paper, we describe a novel microfluidic platform that utilizes a mobile magnetic field in static microfluidic channels, where single stranded DNA (ssDNA) molecules are isolated via nucleic acid hybridization. We first established efficient isolation of biotinylated capture probe (BP) using streptavidin-coated magnetic beads. Subsequently, we investigated the hybridization of target ssDNA with BP bound to beads and explained these hybridization kinetics using a dual-species kinetic model. The number of hybridized target ssDNA molecules was determined to be about 6.5 times less than that of BP on the bead surface, due to steric hindrance effects. The hybridization of target ssDNA with non-complementary BP bound to bead was also examined, and non-specific hybridization was found to be insignificant. Finally, we demonstrated highly efficient capture and isolation of target ssDNA in the presence of non-target ssDNA, where as low as 1% target ssDNA can be detected from mixture. The microfluidic method described in this paper is significantly relevant and is broadly applicable, especially towards point-of-care biological diagnostic platforms that require binding and separation of known target biomolecules, such as RNA, ssDNA, or protein. PMID:24404041

Wang, Jingjing; Morabito, Kenneth; Tang, Jay X.; Tripathi, Anubhav

2013-01-01

19

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

20

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

21

Nucleic Acids Molecular Biology Tools  

E-print Network

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

Qiu, Weigang

22

Isolation and comparative study of cell-free nucleic acids from human urine.  

PubMed

Cell-free nucleic acids (NA) from human urine were investigated. Concentrations of DNA and RNA in the urine of healthy people were independent of gender and were in the range of 6 ng/mL to 50 ng/mL and 24 ng/mL to 140 ng/mL, respectively. DNA fragments of 150-400 bp represent the main part of cell-free DNA, along with DNA fragments up to 1,300 bp, which were found in male urine, and DNA fragments up to 19 kbp, which were found in female urine. Analysis of circulating DNA, isolated from blood of breast cancer patients and cell-free DNA isolated from their urine by methylation-specific PCR, demonstrates that the presence of methylated promoters of RASSF1A and RARbeta2 genes in plasma was accompanied by the detection of the same methylated markers in urine. The data obtained demonstrate applicability of cell-free urine DNA in cancer diagnostics. PMID:17108229

Bryzgunova, Olga E; Skvortsova, Tatyana E; Kolesnikova, Elena V; Starikov, Andrey V; Rykova, Elena Yu; Vlassov, Valentin V; Laktionov, Pavel P

2006-09-01

23

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

PubMed

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

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

2015-02-01

24

Extracellular nucleic acids.  

PubMed

Extracellular nucleic acids are found in different biological fluids in the organism and in the environment: DNA is a ubiquitous component of the organic matter pool in the soil and in all marine and freshwater habitats. Data from recent studies strongly suggest that extracellular DNA and RNA play important biological roles in microbial communities and in higher organisms. DNA is an important component of bacterial biofilms and is involved in horizontal gene transfer. In recent years, the circulating extracellular nucleic acids were shown to be associated with some diseases. Attempts are being made to develop noninvasive methods of early tumor diagnostics based on analysis of circulating DNA and RNA. Recent observations demonstrated the possibility of nucleic acids exchange between eukaryotic cells and extracellular space suggesting their participation in so far unidentified biological processes. PMID:17563084

Vlassov, Valentin V; Laktionov, Pavel P; Rykova, Elena Y

2007-07-01

25

Liposomal spherical nucleic acids.  

PubMed

A novel class of metal-free spherical nucleic acid nanostructures was synthesized from readily available starting components. These particles consist of 30 nm liposomal cores, composed of an FDA-approved 1,2-dioleoyl-sn-glycero-3-phosphocholine (DOPC) lipid monomer. The surface of the liposomes was functionalized with DNA strands modified with a tocopherol tail that intercalates into the phospholipid layer of the liposomal core via hydrophobic interactions. The spherical nucleic acid architecture not only stabilizes these constructs but also facilitates cellular internalization and gene regulation in SKOV-3 cells. PMID:24983505

Banga, Resham J; Chernyak, Natalia; Narayan, Suguna P; Nguyen, SonBinh T; Mirkin, Chad A

2014-07-16

26

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

27

Invasive cleavage of nucleic acids  

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.

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

1999-01-01

28

Invasive cleavage of nucleic acids  

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.

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

2002-01-01

29

Chip-based sequencing nucleic acids  

DOEpatents

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

Beer, Neil Reginald

2014-08-26

30

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. PMID:22586108

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

2012-01-01

31

Nucleic Acid Chaperone Activity of HIV1  

E-print Network

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

Levin, Judith G.

32

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

33

Original article Comparison of nucleic and amino acid sequences and  

E-print Network

Original article Comparison of nucleic and amino acid sequences and phylogenetic analysis of open was investigated. Nucleic and deduced amino acid sequences from seven different EAV isolates (one European, one reference strain. ORF 3 nucleotide and amino acid sequence identities between these isolates (including

Boyer, Edmond

34

A Simpler Nucleic Acid  

NASA Technical Reports Server (NTRS)

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

Orgel, Leslie

2000-01-01

35

An ultrasensitive photoelectrochemical nucleic acid biosensor  

Microsoft Academic Search

A simple and ultrasensitive procedure for non- labeling detection of nucleic acids is described in this study. It is based on the photoelectrochemical detection of target nucleic acids by forming a nucleic acid\\/photoreporter adduct layer on an ITO electrode. The target nucleic acids were hybridized with immob- ilized oligonucleotide capture probes on the ITO elec- trode. A subsequent binding of

Zhiqiang Gao; Natalia C. Tansil

2005-01-01

36

Direct Isolation of Purines and Pyrimidines from Nucleic Acids Using Sublimation  

NASA Technical Reports Server (NTRS)

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

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

2003-01-01

37

High speed 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. Each type of labeled nucleotide comprises an acceptor fluorophore attached to a phosphate portion of the nucleotide such that the fluorophore is removed upon incorporation into a growing strand. Fluorescent signal is emitted via fluorescent resonance energy transfer between the donor fluorophore and the acceptor fluorophore as each nucleotide is incorporated into the growing strand. The sequence is deduced by identifying which base is being incorporated into the growing strand.

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)

2011-05-17

38

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

E-print Network

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

Wang, Wei Hua

39

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

E-print Network

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

Waterman, Michael S.

40

Optimizing the specificity of nucleic acid hybridization  

E-print Network

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

Zhang, David Yu

41

Characterization of Nucleic Acids by Nanopore Analysis  

E-print Network

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

42

Rapid hybridization of nucleic acids using isotachophoresis  

E-print Network

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

Santiago, Juan G.

43

Nucleic acid compositions and the encoding proteins  

SciTech Connect

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.; Chow, Virginia; Nong, Guang; Rice, John D.; St. John, Franz J.

2014-09-02

44

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

E-print Network

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

45

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

46

Prebiotically plausible mechanisms increase compositional diversity of nucleic acid sequences  

E-print Network

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

Nowak, Martin A.

47

Parsing nucleic acid pseudoknotted secondary structure: algorithm and applications  

E-print Network

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

Condon, Anne

48

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

49

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

50

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

51

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

52

Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same  

DOEpatents

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

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

2012-10-16

53

Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same  

DOEpatents

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

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

2014-09-30

54

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

PubMed

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

Majumder, S; Baranwal, V K

2011-06-01

55

Real-Time Nucleic Acid Sequence-Based Amplification Assay for Rapid Detection and Quantification of agr Functionality in Clinical Staphylococcus aureus Isolates  

PubMed Central

Staphylococcus aureus infections are a significant cause of morbidity and mortality in health care settings. S. aureus clinical isolates vary in the function of the accessory gene regulator (agr), which governs the expression of virulence determinants, including surface and exoproteins, while agr activity has been correlated with patient outcome and treatment efficiency. Here we describe a duplex real-time nucleic acid sequence-based amplification (NASBA) detection and quantification platform for rapid determination of agr functionality in clinical isolates. Using the effector of agr response, RNAIII, as the assay target, and expression of the gyrase gene (gyrB) as a normalizer, we were able to accurately discriminate agr functionality in a single reaction. Time to positivity (TTP) ratios between gyrB and RNAIII showed very good correlation with the ratios of RNAIII versus gyrB RNA standard inputs and were therefore used as a simple readout to evaluate agr functionality. We validated the assay by characterizing 106 clinical S. aureus isolates, including strains with genetically characterized agr mutations. All isolates with dysfunctional agr activity exhibited a TTP ratio (TTPgyrB/TTPRNAIII) lower than 1.10, whereas agr-positive isolates had a TTP ratio higher than this value. The results showed that the assay was capable of determining target RNA ratios over 8 logs (10?3 to 104) with high sensitivity and specificity, suggesting the duplex NASBA assay may be useful for rapid determination of agr phenotypes and virulence potential in S. aureus clinical isolates. PMID:22219302

Chen, Liang; Shopsin, Bo; Zhao, Yanan; Smyth, Davida; Wasserman, Gregory A.; Fang, Christina; Liu, Lisa

2012-01-01

56

Dendrimers as Nanovectors for Nucleic Acid Delivery  

NASA Astrophysics Data System (ADS)

Nucleic acid based gene therapy holds great promise in the treatment of various diseases. However, the success of both DNA- and siRNAbased gene therapies depends critically on safe and efficient nucleic acid delivery systems. Owing to their well-defined structure and multivalent cooperativity, dendrimers have attracted particular attention as ideal nanocarriers for nucleic acid delivery. The present chapter highlights the current status of dendrimers as non-viral nanovectors for both DNA and siRNA delivery, focusing on the different dendrimers investigated for their delivery efficiency with respect to structural alterations in the view to developing safe and efficient nanovectors for gene therapy application.

Liu, Xiaoxuan; Wang, Qi; Peng, Ling

2013-09-01

57

Probing Interactions Between Plant Virus Movement Proteins and Nucleic Acids  

E-print Network

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

Citovsky, Vitaly

58

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

E-print Network

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

Foster, Mark P.

59

Methods for analyzing nucleic acid sequences  

DOEpatents

The present invention is directed to a method of sequencing a target nucleic acid. The method provides a complex comprising a polymerase enzyme, a target nucleic acid molecule, and a primer, wherein the complex is immobilized on a support Fluorescent label is attached to a terminal phosphate group of the nucleotide or nucleotide analog. The growing nucleic acid strand is extended by using the polymerase to add a nucleotide analog to the nucleic acid strand. The nucleotide analog added to the oligonucleotide primer as a result of the polymerizing step is identified. The time duration of the signal from labeled nucleotides or nucleotide analogs that become incorporated is distinguished from freely diffusing labels by a longer retention in the observation volume for the nucleotides or nucleotide analogs that become incorporated than for the freely diffusing labels.

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)

2011-05-17

60

Replica amplification of nucleic acid arrays  

DOEpatents

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

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

2010-08-31

61

NMR studies of nucleic acid dynamics  

NASA Astrophysics Data System (ADS)

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

Al-Hashimi, Hashim M.

2013-12-01

62

NMR studies of nucleic acid dynamics  

PubMed Central

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

Al-Hashimi, Hashim M.

2014-01-01

63

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

64

In vitro evolution of nucleic acids  

NASA Technical Reports Server (NTRS)

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

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

1994-01-01

65

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

66

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

67

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

68

Nucleic acids, proteins, and chirality  

NASA Technical Reports Server (NTRS)

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

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

1984-01-01

69

Understanding nucleic acid-ion interactions.  

PubMed

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

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

2014-01-01

70

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

E-print Network

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

Weiblen, George D

71

Nucleic Acid Aptamers for Living Cell Analysis  

NASA Astrophysics Data System (ADS)

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

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

2014-06-01

72

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

73

21 CFR 866.3225 - Enterovirus nucleic acid assay.  

Code of Federal Regulations, 2011 CFR

...Identification . An enterovirus nucleic acid assay is a device that consists...detection of enterovirus ribonucleic acid (RNA) in cerebrospinal...The special control is FDA's guidance document entitled...Controls Guidance Document: Nucleic Acid Amplification Assay for the...

2011-04-01

74

21 CFR 866.3225 - Enterovirus nucleic acid assay.  

Code of Federal Regulations, 2013 CFR

...Identification . An enterovirus nucleic acid assay is a device that consists...detection of enterovirus ribonucleic acid (RNA) in cerebrospinal...The special control is FDA's guidance document entitled...Controls Guidance Document: Nucleic Acid Amplification Assay for the...

2013-04-01

75

21 CFR 866.3225 - Enterovirus nucleic acid assay.  

...Identification. An enterovirus nucleic acid assay is a device that consists...detection of enterovirus ribonucleic acid (RNA) in cerebrospinal...The special control is FDA's guidance document entitled...Controls Guidance Document: Nucleic Acid Amplification Assay for the...

2014-04-01

76

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{prime} 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, M.A.D.; Hall, J.S.G.; Lyamichev, V.; Olive, D.M.; Prudent, J.R.

1999-12-14

77

Detection of nucleic acid sequences by invader-directed cleavage  

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 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

78

Adaptive Recognition by Nucleic Acid Aptamers  

NSDL National Science Digital Library

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

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

2000-02-04

79

7-9/99 Neuman Chapter 23 Nucleic Acids  

E-print Network

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

Reed, Christopher A.

80

Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences  

E-print Network

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

Stadler, Peter F.

81

Multiple Sequence Alignments of Partially Coding Nucleic Acid Sequences  

E-print Network

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

Stadler, Peter F.

82

Enlarged similarity of nucleic acid sequences.  

PubMed

The concept of nucleic acid sequence base alternations is presented. The number of base alterations for the sequences of different length is established. The definition of "enlarged similarity" of nucleic acids sequences on the basis of sequence base alterations is introduced. Mutual information between sequences is used as a quantitative measure of enlarged similarity for two compared sequences. The method of mutual information calculation is developed considering the correlation of bases in compared sequences. The definitions of correlated similarity and evolution similarity between compared sequences are given. Results of the use of enlarged similarity approach for DNA sequences analysis are discussed. PMID:8905233

Korotkov, E V; Korotkova, M A

1996-06-30

83

Method for identifying and quantifying nucleic acid sequence aberrations  

DOEpatents

A method is disclosed 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. 11 figs.

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

1998-07-21

84

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

E-print Network

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

Herschlag, Dan

85

Paradigms for Computational Nucleic Acid Design Robert M. Dirks  

E-print Network

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

Winfree, Erik

86

Purification of Nucleic Acids from Whole Blood Using Isotachophoresis  

E-print Network

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

Santiago, Juan G.

87

Interaction of Nucleic Acids with the Glycocalyx Michael J. Palte  

E-print Network

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

Raines, Ronald T.

88

Volume 14 Number 1 1986 Nucleic Acids Research Sequence landscapes  

E-print Network

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

McConnell, Ross

89

Synthesis of Neomycin-DNA/ Peptide Nucleic Acid  

E-print Network

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

Stuart, Steven J.

90

Complexes of Nucleic Acids with Group I and II Cations  

E-print Network

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

Williams, Loren

91

Topological constraints in nucleic acid hybridization kinetics  

E-print Network

Topological constraints in nucleic acid hybridization kinetics Justin S. Bois, Suvir Venkataraman1 that the topological constraint of zero linking number between the loops effectively prevents conversion to the minimum constraints that govern the metastability of kissing complementary loops. This topological viewpoint suggests

Straight, Aaron

92

Topological constraints in nucleic acid hybridization kinetics  

Microsoft Academic Search

A theoretical examination of kinetic mechanisms for forming knots and links in nucleic acid structures sug- gests that molecules involving base pairs between loops are likely to become topologically trapped in persistent frustrated states through the mechan- ism of 'helix-driven wrapping'. Augmentation of the state space to include both secondary structure and topology in describing the free energy landscape illustrates

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

2005-01-01

93

Nucleic acid-coupled colorimetric analyte detectors  

DOEpatents

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.

Charych, Deborah H. (Albany, CA); Jonas, Ulrich (Mainz, DE)

2001-01-01

94

Miniaturized isothermal nucleic acid amplification, a review.  

PubMed

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

Asiello, Peter J; Baeumner, Antje J

2011-04-21

95

Chemical Etiology of Nucleic Acid Structure  

NSDL National Science Digital Library

Systematic chemical studies indicate that the capability of Watson-Crick base-pairing is widespread among potentially natural nucleic acid alternatives taken from RNA's close structural neighborhood. A comparison of RNA and such alternatives with regard to chemical properties that are fundamental to the biological function of RNA provides chemical facts that may contain clues to RNA's origin.

Albert Eschenmoser (The Scripps Research Institute ;)

1999-06-25

96

Enhanced fluorescence of the terbium–gadolinium–nucleic acids system and the determination of nucleic acids  

Microsoft Academic Search

It is first found that the fluorescence of Tb–nucleic acids (fish sperm DNA (fsDNA) and yeast RNA (yRNA)) can be increased by Sc3+, Y3+, La3+, Gd3+ and Lu3+, among which Gd3+ and Lu3+ have the greatest enhancement. This is a new co-luminescence system. This system is studied in detail and is applied to determine nucleic acids. The experiments indicated that

Cunguo Lin; Jinghe Yang; Xia Wu; Guiling Zhang; Rutao Liu; Xihui Cao; Rongjiang Han

2000-01-01

97

Nucleic acid analysis using terminal-phosphate-labeled nucleotides  

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)

2008-04-22

98

In vitro selection of functional nucleic acids  

NASA Technical Reports Server (NTRS)

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

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

1999-01-01

99

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

100

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

101

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

2013-02-15

102

Technical Notes Purification of Nucleic Acids from Whole Blood  

E-print Network

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

Santiago, Juan G.

103

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

104

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; Lyamichev, Victor I; Mast, Andrea L; Brow, Mary Ann D

2012-10-16

105

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

106

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

DOEpatents

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

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

2002-01-01

107

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. PMID:22029446

Kono, Dwight H.; Beutler, Bruce

2011-01-01

108

[Circulating nucleic acids and in vitro fertilization].  

PubMed

During the last years, the use of circulating nucleic acids (microRNAs and cell-free DNA) as diagnostic and/or prognostic tools in cancerology was widely documented. Likewise, in obstetrics and gynecology, the development of non-invasive prenatal testing based on the assessment of these biomarkers confirmed their growing interest in this speciality. In human reproduction, several studies were interested in the microRNAs, small non-coding RNA sequences, present in the ovarian follicle and their implication in folliculogenesis. Some of these microRNAs, as well as the vesicles which transport them, are easily detectable in the bloodstream and could be used as reliable biomarkers of interest in infertility care. Cell-free DNA level varies according to physiopathology and reflect the proportion of apoptotic and/or necrotic events occurring in the body. As a result, its quantification could give an additional help to the practitioners for ovarian functional status evaluation. Furthermore, these circulating nucleic acids could also constitute new predictive biomarkers of oocyte and/or embryo quality and represent a promising perspective for the prevention of in vitro fertilization implantation failures. In conclusion, these circulating nucleic acids open the way to the development of new diagnostic and/or prognostic innovative tests in order to improve in vitro fertilization outcomes. PMID:25155829

Scalici, E; Traver, S; Mullet, T; Ferrières, A; Monforte, M; Vintejoux, E; Hamamah, S

2014-10-01

109

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

DOE Data Explorer

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

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

110

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. PMID:21822475

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

2011-01-01

111

Mesoscopic modeling for nucleic acid chain dynamics  

NASA Astrophysics Data System (ADS)

To gain a deeper insight into cellular processes such as transcription and translation, one needs to uncover the mechanisms controlling the configurational changes of nucleic acids. As a step toward this aim, we present here a mesoscopic-level computational model that provides a new window into nucleic acid dynamics. We model a single-stranded nucleic as a polymer chain whose monomers are the nucleosides. Each monomer comprises a bead representing the sugar molecule and a pin representing the base. The bead-pin complex can rotate about the backbone of the chain. We consider pairwise stacking and hydrogen-bonding interactions. We use a modified Monte Carlo dynamics that splits the dynamics into translational bead motion and rotational pin motion. By performing a number of tests, we first show that our model is physically sound. We then focus on a study of the kinetics of a DNA hairpin—a single-stranded molecule comprising two complementary segments joined by a noncomplementary loop—studied experimentally. We find that results from our simulations agree with experimental observations, demonstrating that our model is a suitable tool for the investigation of the hybridization of single strands.

Sales-Pardo, M.; Guimerà, R.; Moreira, A. A.; Widom, J.; Amaral, L. A. N.

2005-05-01

112

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

113

SnapShot: Nucleic Acid Immune Sensors, Part 2.  

PubMed

The innate immune system has evolved sensors that can detect specific molecular fingerprints of non-self RNA or DNA. At the same time, some receptors respond to nucleic acids of both exogenous and endogenous origin, yet they are spatially segregated from endogenous nucleic acids. This SnapShot schematizes families and individual members of nucleic acid sensors with a focus on their ligands and the signaling pathways they employ. PMID:25526315

Hornung, Veit

2014-12-18

114

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

115

Determination of Three-Bond 1 P Couplings in Nucleic Acids  

E-print Network

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

Clore, G. Marius

116

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

2014-02-25

117

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)

2010-10-12

118

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

2012-02-14

119

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

120

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

121

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

2008-11-11

122

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

123

Nucleic acid probes in diagnostic medicine  

NASA Technical Reports Server (NTRS)

The need for improved diagnostic procedures is outlined and variations in probe technology are briefly reviewed. A discussion of the application of probe technology to the diagnosis of disease in animals and humans is presented. A comparison of probe versus nonprobe diagnostics and isotopic versus nonisotopic probes is made and the current state of sequence amplification is described. The current market status of nucleic acid probes is reviewed with respect to their diagnostic application in human and veterinary medicine. Representative product examples are described and information on probes being developed that offer promise as future products is discussed.

Oberry, Phillip A.

1991-01-01

124

Nucleic acid amplification using modular branched primers  

DOEpatents

Methods and compositions expand the options for making primers for use in amplifying nucleic acid segments. The invention eliminates the step of custom synthesis of primers for Polymerase Chain Reactions (PCR). Instead of being custom-synthesized, a primer is replaced by a combination of several oligonucleotide modules selected from a pre-synthesized library. A modular combination of just a few oligonucleotides essentially mimics the performance of a conventional, custom-made primer by matching the sequence of the priming site in the template. Each oligonucleotide module has a segment that matches one of the stretches within the priming site.

Ulanovsky, Levy (Westmont, IL)

2001-01-01

125

Bioluminescence regenerative cycle (BRC) system: Theoretical considerations for nucleic acid quantification assays  

E-print Network

Bioluminescence regenerative cycle (BRC) system: Theoretical considerations for nucleic acid Abstract A novel application of bioluminescence for nucleic acid quantification, the bioluminescence: Chemiluminescence; Bioluminescence; Gene expression; Nucleic acid; Polymerization; Enzyme kinetics; Positive

Hassibi, Arjang

126

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

Code of Federal Regulations, 2012 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...

2012-04-01

127

Nucleic Acids Research doi:10.1093/nar/gkf586  

E-print Network

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

Paris-Sud XI, Université de

128

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

129

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

Code of Federal Regulations, 2010 CFR

...control material for cystic fibrosis nucleic acid assays. 866.5910 Section...control material for cystic fibrosis nucleic acid assays. (a) Identification...control material for cystic fibrosis nucleic acid assays. A quality control...

2010-04-01

130

78 FR 36698 - Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for Mycobacterium tuberculosis  

Federal Register 2010, 2011, 2012, 2013

...Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for Mycobacterium...FDA) is proposing to reclassify nucleic acid-based in vitro diagnostic devices...II Special Controls Guideline: Nucleic Acid-Based In Vitro Diagnostic...

2013-06-19

131

Nucleic Acids Research doi:10.1093/nar/gki514  

E-print Network

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

Paris-Sud XI, Université de

132

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

E-print Network

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

Santiago, Juan G.

133

Nucleic Acids Research doi:10.1093/nar/gki1012  

E-print Network

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

Paris-Sud XI, Université de

134

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

...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...

2014-04-01

135

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

Code of Federal Regulations, 2011 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...

2011-04-01

136

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

...control material for cystic fibrosis nucleic acid assays. 866.5910 Section...control material for cystic fibrosis nucleic acid assays. (a) Identification...control material for cystic fibrosis nucleic acid assays. A quality control...

2014-04-01

137

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

Code of Federal Regulations, 2013 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...

2013-04-01

138

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

Code of Federal Regulations, 2011 CFR

...control material for cystic fibrosis nucleic acid assays. 866.5910 Section...control material for cystic fibrosis nucleic acid assays. (a) Identification...control material for cystic fibrosis nucleic acid assays. A quality control...

2011-04-01

139

77 FR 16126 - Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for Mycobacterium tuberculosis  

Federal Register 2010, 2011, 2012, 2013

...Microbiology Devices; Reclassification of Nucleic Acid-Based Systems for Mycobacterium...FDA) is proposing to reclassify nucleic acid-based in vitro diagnostic devices...Regulatory Background of the Device Nucleic acid-based in vitro diagnostic...

2012-03-19

140

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

Code of Federal Regulations, 2012 CFR

...control material for cystic fibrosis nucleic acid assays. 866.5910 Section...control material for cystic fibrosis nucleic acid assays. (a) Identification...control material for cystic fibrosis nucleic acid assays. A quality control...

2012-04-01

141

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

142

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

143

Detecting Microbial Nucleic Acids within Nematode Bodies: A Photo Essay  

Technology Transfer Automated Retrieval System (TEKTRAN)

We developed a taxa-specific, fluorescence in situ hybridization (FISH) technique to localize microbial nucleic acids within nematode bodies. This technique involves hybridization of a nucleic acid probe to target microbial sequences. Hybridization is detected microscopically, as the probes have f...

144

Release of nucleic acids by eukaryotic cells in tissue culture.  

PubMed

Extracellular nucleic acids in cultures of A431 and HeLa cells were investigated. The data obtained demonstrate the presence of high weight DNA and RNA in the extracellular medium. Temporal changes of extracellular nucleic acids levels in growth medium were investigated. PMID:15560083

Morozkin, Evgeniy S; Laktionov, Pavel P; Rykova, Elena Y; Bryzgunova, Olga E; Vlassov, Valentin V

2004-10-01

145

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

146

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

147

Nucleic acids encoding metal uptake transporters and their uses  

DOEpatents

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

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

1999-01-01

148

Solid phase sequencing of double-stranded nucleic acids  

DOEpatents

This invention relates to methods for detecting and sequencing of target double-stranded nucleic acid sequences, to nucleic acid probes and arrays of probes useful in these methods, and to kits and systems which contain these probes. Useful methods involve hybridizing the nucleic acids or nucleic acids which represent complementary or homologous sequences of the target to an array of nucleic acid probes. These probe comprise a single-stranded portion, an optional double-stranded portion and a variable sequence within the single-stranded portion. The molecular weights of the hybridized nucleic acids of the set can be determined by mass spectroscopy, and the sequence of the target determined from the molecular weights of the fragments. Nucleic acids whose sequences can be determined include nucleic acids in biological samples such as patient biopsies and environmental samples. Probes may be fixed to a solid support such as a hybridization chip to facilitate automated determination of molecular weights and identification of the target sequence.

Fu, Dong-Jing (Waltham, MA); Cantor, Charles R. (Boston, MA); Koster, Hubert (Concord, MA); Smith, Cassandra L. (Boston, MA)

2002-01-01

149

Simultaneous purification and fractionation of nucleic acids and proteins from complex  

E-print Network

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

Santiago, Juan G.

150

Applications of synchrotron-based spectroscopic techniques in studying nucleic acids and nucleic Acid-functionalized nanomaterials.  

PubMed

In this review, we summarize recent progress in the application of synchrotron-based spectroscopic techniques for nucleic acid research that takes advantage of high-flux and high-brilliance electromagnetic radiation from synchrotron sources. The first section of the review focuses on the characterization of the structure and folding processes of nucleic acids using different types of synchrotron-based spectroscopies, such as X-ray absorption spectroscopy, X-ray emission spectroscopy, X-ray photoelectron spectroscopy, synchrotron radiation circular dichroism, X-ray footprinting and small-angle X-ray scattering. In the second section, the characterization of nucleic acid-based nanostructures, nucleic acid-functionalized nanomaterials and nucleic acid-lipid interactions using these spectroscopic techniques is summarized. Insights gained from these studies are described and future directions of this field are also discussed. PMID:25205057

Wu, Peiwen; Yu, Yang; McGhee, Claire E; Tan, Li Huey; Lu, Yi

2014-12-01

151

Mechanism of helicase translocation along nucleic acid  

E-print Network

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

Zhang, Yunxin

2012-01-01

152

Overview of nucleic acid analysis programs.  

PubMed

We outline the mathematical distinctions among seven of the most popular computer programs currently used to analyze the spatial arrangements of bases and base pairs in nucleic acid helical structures. The schemes fall into three basic categories on the basis of their definitions of rotational parameters: matrix-based, projection-based, and combined matrix- and projection-based. The approaches also define and construct base and base-pair coordinate frames in a variety of ways. Despite these mathematical distinctions, the computed parameters from some programs are strongly correlated and directly comparable. By contrast, other programs which use identical methodologies sometimes yield very different results. The choice of reference frame rather than the mathematical formulation has the greater effect on calculated parameters. Any factor which influences the reference frame, such as fitting or not fitting standard bases to the experimentally derived coordinates, will have a noticeable effect on both complementary base pair and dimer step parameters. PMID:10217453

Lu, X J; Babcock, M S; Olson, W K

1999-02-01

153

Excess counterion accumulation around branched nucleic acids.  

PubMed

Many nucleic acids of biological importance possess elements of tertiary structure in which the regional phosphate charge density dramatically exceeds that of linear duplex DNA, as in the inter-helix junctions found in tRNAs, ribosomal RNAs, and Holliday intermediates in general recombination. However, despite a long-standing awareness that such structures have special counterion requirements for stability few studies have focused on their level of counterion association. In order to gauge the influence of high regional phosphate charge density on the extent of counterion association, we have defined the degree of "excess counterion association" for a four-branch DNA junction as the number of additional counterions (over the relevant linear DNA value) that are associated with the junction in a Donnan equilibrium dialysis experiment. Grand canonical Monte Carlo computations were used to determine the Donnan distribution (preferential interaction) coefficients, employing a "primitive model" description of the nucleic acid and the 1:1 electrolyte. We have determined that at least 24 excess counterions are associated with the junction in the long branch limit. The subsequent release of a portion of these additional counterions during the process of ligand binding is therefore likely to provide a strong directional influence on the binding of proteins and cationic ligands, with preferred binding near or on the junction vertex or near other elements of tertiary structure (e.g. pseudo-knots or triplexes) even if the ligands do not directly recognize the structural elements themselves. Moreover, excess counterion association is expected to play a significant role in determining the relative stabilities of alternative tertiary structures. PMID:7525974

Olmsted, M C; Hagerman, P J

1994-11-11

154

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

155

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

E-print Network

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

Sherrill, David

156

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. PMID:21844380

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

2011-01-01

157

Nucleic Acid Charge Transfer: Black, White and Gray  

PubMed Central

Theoretical studies of charge transport in deoxyribonucleic acid (DNA) and peptide nucleic acid (PNA) indicate that structure and dynamics modulate the charge transfer rates, and that different members of a structural ensemble support different charge transport mechanisms. Here, we review the influences of nucleobase geometry, electronic structure, solvent environment, and thermal conformational fluctuations on the charge transfer mechanism. We describe an emerging framework for understanding the diversity of charge transport mechanisms seen in nucleic acids. PMID:21528017

Venkatramani, Ravindra; Keinan, Shahar; Balaeff, Alexander; Beratan, David N.

2011-01-01

158

ATR-IR spectroscopy as applied to nucleic acid films  

NASA Astrophysics Data System (ADS)

For the first time the ATR technique was applied to obtain IR absorption spectra of DNA and RNA dry films. There was worked out procedure of the nucleic acid removal from germanium plate, which obviously was a main obstacle to application of ATR-IR spectroscopy to nucleic acids. This technique of IR spectroscopy was applied to confirmation of RNA tropism of aurin tricarboxylic acid observed by molecular biological methods.

Stepanyugin, Andriy V.; Samijlenko, Svitlana P.; Martynenko, Olena I.; Hovorun, Dmytro M.

2005-07-01

159

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

160

Oligonucleoside alkyl or arylphosphonate derivatives capable of crosslinking with or cleaving nucleic acids  

DOEpatents

A composition for inactivating a target nucleic acid which comprises an oligonucleoside alkyl or arylphosphonate analogue which is complementary to the sequence of the target nucleic acid is provided. It includes a functional group which reacts with the target nucleic acid to render the target nucleic acid inactive or nonfunctional. 16 figs.

Miller, P.S.; Ts'o, P.O.P.

1999-06-15

161

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

E-print Network

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

Gopalan, Venkat

162

Oligonucleoside alkyl or arylphosphonate derivatives capable of crosslinking with or cleaving nucleic acids  

DOEpatents

A composition for inactivating a target nucleic acid which comprises an oligonucleoside alkyl or arylphosphonate analogue which is complementary to the sequence of the target nucleic acid and includes a functional group which reacts with the target nucleic acid to render the target nucleic acid inactive or nonfunctional.

Miller, Paul S. (Baltimore, MD); Ts'o, Paul O.P. (Lutherville, MD)

1999-06-15

163

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

E-print Network

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

Levin, Judith G.

164

Nucleic Acids Research doi:10.1093/nar/gkn315  

E-print Network

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

Minnesota, University of

165

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

E-print Network

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

Stuart, Steven J.

166

NUCLEIC ACID DETECTION USING BIOLUMINESCENCE REGENERATIVE CYCLE AND STATISTICAL SIGNAL PROCESSING  

E-print Network

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

Hassibi, Arjang

167

Nucleic Acids Research doi:10.1093/nar/gkn295  

E-print Network

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

Paris-Sud XI, Université de

168

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

E-print Network

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

Levin, Judith G.

169

21 CFR 866.3225 - Enterovirus nucleic acid assay.  

Code of Federal Regulations, 2012 CFR

... Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3225 Enterovirus nucleic acid assay. (a)...

2012-04-01

170

21 CFR 866.3225 - Enterovirus nucleic acid assay.  

Code of Federal Regulations, 2010 CFR

... Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3225 Enterovirus nucleic acid assay. (a)...

2010-04-01

171

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. PMID:19658387

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

2009-01-01

172

Photolabile polyethylenimines for light-activated nucleic acid delivery.  

E-print Network

?? Two light-sensitive, cross-linkable polyethylenimines, P25M and B-PC-PEI, were synthesized for the capture and controlled release of nucleic acids. P25M consists of a polyethylenimine (PEI)… (more)

Handwerger, Rachel Gail

2007-01-01

173

Nucleic acid duplexes incorporating a dissociable covalent base pair  

NASA Technical Reports Server (NTRS)

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

1999-01-01

174

Functional nucleic acids as substrate for information processing.  

E-print Network

??Information processing applications driven by self-assembly and conformation dynamics of nucleic acids are possible. These underlying paradigms (self-assembly and conformation dynamics) are essential for natural… (more)

Ramlan, Effirul I.

2009-01-01

175

Definitions and nomenclature of nucleic acid structure components.  

PubMed

We report here recommendations for the definitions and nomenclature of nucleic acid structure parameters. These recommendations result from discussions at an EMBO Workshop on DNA Curvature and Bending held at Churchill College, Cambridge, in September 1988. PMID:2928107

Dickerson, R E

1989-03-11

176

Sharing and archiving nucleic acid structure mapping data.  

PubMed

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. PMID:21610212

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

2011-07-01

177

Molecular Modeling of Nucleic Acid Structure: Energy and Sampling  

PubMed Central

An overview of computer simulation techniques as applied to nucleic acid systems is presented. This unit discusses methods used to treat the energy and to sample representative configurations. Emphasis is placed on molecular mechanics and empirical force fields. PMID:18428876

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

2013-01-01

178

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

2013-09-18

179

Changes of nucleic acids of wheat seedlings under spaceflight conditions  

NASA Technical Reports Server (NTRS)

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

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

1983-01-01

180

Electric chips for rapid detection and quantification of nucleic acids  

Microsoft Academic Search

A silicon chip-based electric detector coupled to bead-based sandwich hybridization (BBSH) is presented as an approach to perform rapid analysis of specific nucleic acids. A microfluidic platform incorporating paramagnetic beads with immobilized capture probes is used for the biorecognition steps. The protocol involves simultaneous sandwich hybridization of a single-stranded nucleic acid target with the capture probe on the beads and

M Gabig-Ciminska; A Holmgren; H Andresen; K Bundvig Barken; M Wümpelmann; J Albers; R Hintsche; A Breitenstein; P Neubauer; M Los; A Czyz; G Wegrzyn; G Silfversparre; B Jürgen; T Schweder; S.-O Enfors

2004-01-01

181

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. PMID:23150809

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

2012-01-01

182

Nucleic acid immunization: a prophylactic gene therapy?  

PubMed

Nucleic acid (NA) vaccines may offer the safety of subunit or inactivated vaccines and, at the same time, provide the advantages of live recombinant vaccines, such as induction of a protective cellular immune response. In Germany, the so-called 'Gene Law' regulates the genetic modification of organisms such as prokaryotic or eukaryotic cells for the construction of recombinant NAs intended for use as NA vaccines. Neither NAs nor human beings treated with NAs are subject to Gene Law regulations but preclinical laboratory experiments are regulated by the Gene Law. Gene therapy, as defined in a recent draft of a European guideline for the production of gene therapeutics, includes the genetic modification of human somatic cells via transfer of NAs and thus includes NA vaccines. The guideline provides recommendations for the production of NA vaccines for human use and for preclinical safety testing. NA vaccines are products derived by biotechnological processes, as defined in part A of the annex of Council Regulation (EEC) No. 2309/93 of 22 July 1993. Applications for marketing authorization in Member States of the European Union will thus be reviewed by the European Agency for the Evaluation of Medicinal Products starting from 1 January 1995. Inoculation of NAs encompassing a full-length but int/nef-defective simian immunodeficiency provirus allowing limited replication of viruses released is being investigated at the Paul-Ehrlich-Institute as a model for a NA vaccine against AIDS.(ABSTRACT TRUNCATED AT 250 WORDS) PMID:7879417

Cichutek, K

1994-12-01

183

A self-replicating peptide nucleic acid.  

PubMed

While the non-enzymatic ligation and template-directed synthesis of peptide nucleic acids (PNA) have been reported since 1995, a case of self-replication of PNA has not been achieved yet. Here, we present evidence for autocatalytic feedback in a template directed synthesis of a self-complementary hexa-PNA from two trimeric building blocks. The course of the reaction was monitored in the presence of increasing initial concentrations of the product by RP-HPLC. Kinetic modeling with the SimFit program revealed parabolic growth characteristics. The observed template effect, as well as the rate of ligation, was significantly influenced by nucleophilic catalysts, pH value, and uncharged co-solvents. Systematic optimization of the reaction conditions allowed us to increase the autocatalytic efficiency of the system by two orders of magnitude. Our findings contribute to the hypothesis that PNA may have served as a primordial genetic molecule and was involved in a potential precursor of a RNA world. PMID:25065957

Plöger, Tobias A; von Kiedrowski, Günter

2014-09-21

184

Selenium Derivatization of Nucleic Acids for Crystallography  

SciTech Connect

The high-resolution structure of the DNA (5'-GTGTACA-C-3') with the selenium derivatization at the 2'-position of T2 was determined via MAD and SAD phasing. The selenium-derivatized structure (1.28 {angstrom} resolution) with the 2'-Se modification in the minor groove is isomorphorous to the native structure (2.0 {angstrom}). To directly compare with the conventional bromine derivatization, we incorporated bromine into the 5-postion of T4, determined the bromine-derivatized DNA structure at 1.5 {angstrom} resolution, and found that the local backbone torsion angles and solvent hydration patterns were altered in the structure with the Br incorporation in the major groove. Furthermore, while the native and Br-derivatized DNAs needed over a week to form reasonable-size crystals, we observed that the Se-derivatized DNAs grew crystals overnight with high-diffraction quality, suggesting that the Se derivatization facilitated the crystal formation. In addition, the Se-derivatized DNA sequences crystallized under a broader range of buffer conditions, and generally had a faster crystal growth rate. Our experimental results indicate that the selenium derivatization of DNAs may facilitate the determination of nucleic acid X-ray crystal structures in phasing and high-quality crystal growth. In addition, our results suggest that the Se derivatization can be an alternative to the conventional Br derivatization.

Jiang,J.; Sheng, J.; Carrasco, N.; Huang, Z.

2007-01-01

185

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

186

Bioanalytical applications of isothermal nucleic acid amplification techniques.  

PubMed

The most popular in vitro nucleic acid amplification techniques like polymerase chain reaction (PCR) including real-time PCR are costly and require thermocycling, rendering them unsuitable for uses at point-of-care. Highly efficient in vitro nucleic acid amplification techniques using simple, portable and low-cost instruments are crucial in disease diagnosis, mutation detection and biodefense. Toward this goal, isothermal amplification techniques that represent a group of attractive in vitro nucleic acid amplification techniques for bioanalysis have been developed. Unlike PCR where polymerases are easily deactivated by thermally labile constituents in a sample, some of the isothermal nucleic acid amplification techniques, such as helicase-dependent amplification and nucleic acid sequence-based amplification, enable the detection of bioanalytes with much simplified protocols and with minimal sample preparations since the entire amplification processes are performed isothermally. This review focuses on the isothermal nucleic acid amplification techniques and their applications in bioanalytical chemistry. Starting off from their amplification mechanisms and significant properties, the adoption of isothermal amplification techniques in bioanalytical chemistry and their future perspectives are discussed. Representative examples illustrating the performance and advantages of each isothermal amplification technique are discussed along with some discussion on the advantages and disadvantages of each technique. PMID:25467448

Deng, Huimin; Gao, Zhiqiang

2015-01-01

187

Nucleic Acids Research doi:10.1093/nar/gkn305  

E-print Network

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

Lin, Guohui

188

Method for nucleic acid hybridization using single-stranded DNA binding protein  

DOEpatents

Method of nucleic acid hybridization for detecting the presence of a specific nucleic acid sequence in a population of different nucleic acid sequences using a nucleic acid probe. The nucleic acid probe hybridizes with the specific nucleic acid sequence but not with other nucleic acid sequences in the population. The method includes contacting a sample (potentially including the nucleic acid sequence) with the nucleic acid probe under hybridizing conditions in the presence of a single-stranded DNA binding protein provided in an amount which stimulates renaturation of a dilute solution (i.e., one in which the t.sub.1/2 of renaturation is longer than 3 weeks) of single-stranded DNA greater than 500 fold (i.e., to a t.sub.1/2 less than 60 min, preferably less than 5 min, and most preferably about 1 min.) in the absence of nucleotide triphosphates.

Tabor, Stanley (Cambridge, MA); Richardson, Charles C. (Chestnut Hill, MA)

1996-01-01

189

Thermodynamics of Nucleic Acid ‘Shape Readout’ by an Aminosugar†  

PubMed Central

Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions. In addition to the direct readout mechanisms of nucleic acids such as H-bonding, shape recognition of nucleic acids is being increasingly recognized to play an equally important role in DNA recognition. Competition Dialysis, UV, Flourescent Intercalator displacement (FID), Computational Docking, and calorimetry studies were conducted to study the interaction of neomycin with a variety of nucleic acid conformations (shapes). At pH 5.5, these results suggest: (1) Neomycin binds three RNA structures (16S A site rRNA, poly(rA)•poly(rA), and poly(rA)•poly(rU)) with high affinities, Ka~107M?1. (2) The binding of neomycin to A-form GC-rich oligomer d(A2G15C15T2)2 has comparable affinity to RNA structures. (3) The binding of neomycin to DNA•RNA hybrids shows a three-fold variance attributable to their structural differences (poly(dA) •poly(rU), Ka=9.4×106M?1 and poly(rA)•poly(dT), Ka=3.1×106M?1). (4) The interaction of neomycin with DNA triplex poly(dA)•2poly(dT) yields a binding affinity of Ka=2.4×105M?1. (5) Poly(dA-dT)2 showed the lowest association constant for all nucleic acids studied (Ka=<105). (6) Neomycin binds to G-quadruplexes with Ka~104-105M?1. (7) Computational studies show that the decrease in major groove width in the B to A transition correlates with increasing neomycin affinity. Neomycin’s affinity for various nucleic acid structures can be ranked as follows, RNAs and GC-rich d(A2G15C15T2)2 structures > poly(dA)•poly(rU) > poly(rA)•poly(dT) > T•A-T triplex , G-quadruplexes, B-form AT-rich or GC-rich DNA sequences. The results illustrate the first example of a small molecule based ‘shape readout’ of different nucleic acid conformations. PMID:21863895

Xi, Hongjuan; Davis, Erik; Ranjan, Nihar; Xue, Liang; Hyde-Volpe, David; Arya, Dev P.

2012-01-01

190

Conformational transitions in human translin enable nucleic acid binding  

PubMed Central

Translin is a highly conserved RNA- and DNA-binding protein that plays essential roles in eukaryotic cells. Human translin functions as an octamer, but in the octameric crystallographic structure, the residues responsible for nucleic acid binding are not accessible. Moreover, electron microscopy data reveal very different octameric configurations. Consequently, the functional assembly and the mechanism of nucleic acid binding by the protein remain unclear. Here, we present an integrative study combining small-angle X-ray scattering (SAXS), site-directed mutagenesis, biochemical analysis and computational techniques to address these questions. Our data indicate a significant conformational heterogeneity for translin in solution, formed by a lesser-populated compact octameric state resembling the previously solved X-ray structure, and a highly populated open octameric state that had not been previously identified. On the other hand, our SAXS data and computational analyses of translin in complex with the RNA oligonucleotide (GU)12 show that the internal cavity found in the octameric assemblies can accommodate different nucleic acid conformations. According to this model, the nucleic acid binding residues become accessible for binding, which facilitates the entrance of the nucleic acids into the cavity. Our data thus provide a structural basis for the functions that translin performs in RNA metabolism and transport. PMID:23980029

Pérez-Cano, Laura; Eliahoo, Elad; Lasker, Keren; Wolfson, Haim J.; Glaser, Fabian; Manor, Haim; Bernadó, Pau; Fernández-Recio, Juan

2013-01-01

191

Stability of Pyrimidine Nucleic Acid Bases with Respect to Intra- and Intermolecular Proton Transfer Reactions Induced by Excess Electrons  

Microsoft Academic Search

Chemically transformed nucleic acid bases are considered as sources of point mutations in genetic material. Our computational results and photoelectron spectra provide information about chemical transformations of pyrimidine bases induced by excess electrons. The isolated pyrimidine bases as well as their complexes with X (X= amino acid, carboxylic acid, or alcohol) have been studied with the B3LYP and MPW1K density

Iwona Dabkowska; Maciej Haranczyk; Janusz Rak; Maciej Gutowski; Shoujun Xu; J. Michael Nilles; Dunja Radisic; Kit H. Bowen

2003-01-01

192

Synthesis and characterization of peptide nucleic acid platinum nanoclusters  

Microsoft Academic Search

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

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

2006-01-01

193

Molecular properties and medical applications of peptide nucleic acids.  

PubMed

Peptide Nucleic Acids (PNAs) are molecules combining structural features of proteins and nucleic acid. They resemble DNA or RNA by forming helical polyamides containing nitrogen bases attached to the backbone consisting of N-(2-aminoethyl)-glycine monomers, which mimics the alternating ribose-phosphodiester-backbone of a nucleic acid. Because PNAs bind exceptionally strong to complementary DNA or RNA sequences obeying Watson-Crick base paring, they became attractive candidates for antisense and antigen therapies. PNAs are also being tested as novel antibiotics, gene-activating agents, and as molecular probes for FISH and imaging or biosensors used in diagnostics. Although PNAs offer many exiting medical applications, improving their cellular uptake and developing specific delivery strategies is crucial for a successful entry in the clinic in the near future. PMID:24766383

Malcher, Jakub; Weso?y, Joanna; Bluyssen, Hans A R

2014-05-01

194

Encapsulation of nucleic acids and opportunities for cancer treatment.  

PubMed

The development of nucleic acid drugs for the treatment of various cancers has shown great promise in recent years. However, efficient delivery of these drugs to target cells remains a significant challenge towards the successful development of such therapies. This review provides a comprehensive overview of encapsulation technologies being developed for the delivery of nucleic acid-based anti-cancer agents. Both micro and nanoparticles systems are discussed along with their use in delivering plasmid DNA as well as oligonucleotides. The majority of the systems discussed have used DNA immunotherapy as the potential mode of anticancer therapy, which requires targeting to antigen presenting cells. Other applications, including those with oligonucleotides, focus on targeting tumor cells directly. The results obtained so far show the excellent promise of encapsulation as an efficient means of delivering therapeutic nucleic acids. PMID:17372693

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

2007-04-01

195

Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes.  

PubMed

NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3-0.6 ppm and correlation coefficients (r(2)) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization. PMID:25404135

Victora, Andrea; Möller, Heiko M; Exner, Thomas E

2014-12-16

196

Accurate ab initio prediction of NMR chemical shifts of nucleic acids and nucleic acids/protein complexes  

PubMed Central

NMR chemical shift predictions based on empirical methods are nowadays indispensable tools during resonance assignment and 3D structure calculation of proteins. However, owing to the very limited statistical data basis, such methods are still in their infancy in the field of nucleic acids, especially when non-canonical structures and nucleic acid complexes are considered. Here, we present an ab initio approach for predicting proton chemical shifts of arbitrary nucleic acid structures based on state-of-the-art fragment-based quantum chemical calculations. We tested our prediction method on a diverse set of nucleic acid structures including double-stranded DNA, hairpins, DNA/protein complexes and chemically-modified DNA. Overall, our quantum chemical calculations yield highly/very accurate predictions with mean absolute deviations of 0.3–0.6 ppm and correlation coefficients (r2) usually above 0.9. This will allow for identifying misassignments and validating 3D structures. Furthermore, our calculations reveal that chemical shifts of protons involved in hydrogen bonding are predicted significantly less accurately. This is in part caused by insufficient inclusion of solvation effects. However, it also points toward shortcomings of current force fields used for structure determination of nucleic acids. Our quantum chemical calculations could therefore provide input for force field optimization. PMID:25404135

Victora, Andrea; Möller, Heiko M.; Exner, Thomas E.

2014-01-01

197

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

2011-03-01

198

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. PMID:20627172

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

2011-01-01

199

Nanopores and nucleic acids: prospects for ultrarapid sequencing  

NASA Technical Reports Server (NTRS)

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

Deamer, D. W.; Akeson, M.

2000-01-01

200

Biomimetic High Density Lipoprotein Nanoparticles For Nucleic Acid Delivery  

PubMed Central

We report a gold nanoparticle-templated high density lipoprotein (HDL AuNP) platform for gene therapy which 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 (TEM), 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

2014-01-01

201

Evidence for novel viruses by analysis of nucleic acids in virus-like particle fractions from Ambrosia psilostachya.  

PubMed

To test the hypothesis that many viruses remain to be discovered in plants, a procedure was developed to sequence nucleic acids cloned randomly from virus-like particle fractions of plant homogenates. As a test of the efficiency of the procedure we targeted Ambrosia psilostachya, western ragweed, plants growing at the Tallgrass Prairie Preserve of northeastern Oklahoma. Amplifiable nucleic acid was found in the fractions from six of twelve specimens and sequences were characterized from four of them. Evidence was obtained for the presence of viruses belonging to two families (Caulimoviridae, Flexiviridae). Multiple viral species were found in two of the four specimens and their level within the isolated nucleic acid population varied from less than 1-37%. None of the sequences were derived from reported sequences of known viruses. Thus, the analysis of nucleic acid from virus-like particles is a useful tool to expand our knowledge of the universe of viruses to non-cultivated species. PMID:18590770

Melcher, Ulrich; Muthukumar, Vijay; Wiley, Graham B; Min, Byoung Eun; Palmer, Michael W; Verchot-Lubicz, Jeanmarie; Ali, Akhtar; Nelson, Richard S; Roe, Bruce A; Thapa, Vaskar; Pierce, Margaret L

2008-09-01

202

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

E-print Network

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

Lee, Jeong-Bong

203

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

DOEpatents

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

204

Multicenter Evaluation of the Verigene Clostridium difficile Nucleic Acid Assay  

PubMed Central

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

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

2013-01-01

205

Multicenter evaluation of the Verigene Clostridium difficile nucleic acid assay.  

PubMed

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

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

2013-12-01

206

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

E-print Network

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

Heller, Eric

207

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

208

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

E-print Network

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

Luther, Douglas S.

209

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

E-print Network

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

Bong, Dennis

210

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

E-print Network

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

Pierce, Niles A.

211

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

E-print Network

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

Winfree, Erik

212

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

E-print Network

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

Santiago, Juan G.

213

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

E-print Network

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

Kenis, Paul J. A.

214

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

E-print Network

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

Pierce, Niles A.

215

Nucleic Acids Research doi:10.1093/nar/gkn148  

E-print Network

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

Paris-Sud XI, Université de

216

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

E-print Network

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

Turro, Nicholas J.

217

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

E-print Network

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

Hassibi, Arjang

218

Nucleic Acids Research doi:10.1093/nar/gkn031  

E-print Network

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

Paris-Sud XI, Université de

219

Adsorption of Nucleic Acid Components on Rutile (TiO2) Surfaces  

E-print Network

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

Sverjensky, Dimitri A.

220

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

E-print Network

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

Das, Rhiju

221

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

E-print Network

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

Tullius, Thomas D.

222

A HANDHELD MAGNETIC SENSING PLATFORM FOR ANTIGEN AND NUCLEIC ACID DETECTION  

E-print Network

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

Weinreb, Sander

223

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

E-print Network

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

Dietz, Hendrik

224

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

E-print Network

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

Widom, Michael

225

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

E-print Network

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

Tullius, Thomas D.

226

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

E-print Network

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

Rohs, Remo

227

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

E-print Network

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

Beebe, David J.

228

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

E-print Network

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

Santiago, Juan G.

229

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

E-print Network

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

Williams, Loren

230

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

E-print Network

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

Paris-Sud XI, Université de

231

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

E-print Network

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

Heller, Eric

232

Nucleic Acids Research doi:10.1093/nar/gkn472  

E-print Network

Nucleic Acids Research doi:10.1093/nar/gkn472 36:4902-4912, 2008. First published 24 Jul 2008;Nucleic Acids Res. Marie-Cécile Didiot, Zhaoxia Tian, Céline Schaeffer, Murugan Subramanian, Jean://nar.oxfordjournals.org Additional information about Nucleic Acids Research, including how to subscribe can be found at Published

Boyer, Edmond

233

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

E-print Network

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

Paris-Sud XI, Université de

234

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

E-print Network

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

Turro, Claudia

235

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

E-print Network

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

Schlegel, H. Bernhard

236

Quantitative and Comprehensive Decomposition of the Ion Atmosphere around Nucleic Acids  

E-print Network

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

Herschlag, Dan

237

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

E-print Network

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

Bong, Dennis

238

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

E-print Network

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

Herschlag, Dan

239

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

E-print Network

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

Gottgens, Hans

240

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

241

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

E-print Network

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

Bansal, Manju

242

Chitosans for delivery of nucleic acids Michael D. Buschmann, Abderrazzak Merzouki, Marc Lavertu, Marc  

E-print Network

Ã?Ã? Ã? Ã?Ã?Ã? Ã? Ã?Ã? Chitosans for delivery of nucleic acids Michael D. Buschmann, Abderrazzak Merzouki Thibault, Myriam Jean, Vincent Darras, Chitosans for delivery of nucleic acids, Advanced Drug Delivery MANUSCRIPT ACCEPTED MANUSCRIPT 1 Title: Chitosans for Delivery of Nucleic Acids Michael D. Buschmann

Buschmann, Michael

243

Data mining of molecular dynamics trajectories of nucleic acids.  

PubMed

Analysis, storage, and transfer of molecular dynamic trajectories are becoming the bottleneck of computer simulations. In this paper we discuss different approaches for data mining and data processing of huge trajectory files generated from molecular dynamic simulations of nucleic acids. PMID:16363879

Noy, Agnes; Meyer, Tim; Rueda, Manuel; Ferrer, Carles; Valencia, Antonion; Pérez, Alberto; de la Cruz, Xavier; López-Bes, J M; Pouplana, R; Fernandez-Recio, J; Luque, F Javier; Orozco, Modesto

2006-02-01

244

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

PubMed

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

Tateishi-Karimata, Hisae; Sugimoto, Naoki

2014-08-01

245

Arrays of nucleic acid probes on biological chips  

DOEpatents

DNA chips containing arrays of oligonucleotide probes can be used to determine whether a target nucleic acid has a nucleotide sequence identical to or different from a specific reference sequence. The array of probes comprises probes exactly complementary to the reference sequence, as well as probes that differ by one or more bases from the exactly complementary probes.

Chee, Mark (Palo Alto, CA); Cronin, Maureen T. (Los Altos, CA); Fodor, Stephen P. A. (Palo Alto, CA); Huang, Xiaohua X. (Mt. View, CA); Hubbell, Earl A. (Mt. View, CA); Lipshutz, Robert J. (Palo Alto, CA); Lobban, Peter E. (Palo Alto, CA); Morris, MacDonald S. (San Jose, CA); Sheldon, Edward L. (Menlo Park, CA)

1998-11-17

246

Mfold web server for nucleic acid folding and hybridization prediction  

Microsoft Academic Search

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

Michael Zuker

2003-01-01

247

A DNA origami nanorobot controlled by nucleic acid hybridization.  

PubMed

A prototype for a DNA origami nanorobot is designed, produced, and tested. The cylindrical nanorobot (diameter of 14 nm and length of 48 nm) with a switchable flap, is able to respond to an external stimulus and reacts by a physical switch from a disarmed to an armed configuration able to deliver a cellular compatible message. In the tested design the robot weapon is a nucleic acid fully contained in the inner of the tube and linked to a single point of the internal face of the flap. Upon actuation the nanorobot moves the flap extracting the nucleic acid that assembles into a hemin/G-quadruplex horseradish peroxidase mimicking DNAzyme catalyzing a colorimetric reaction or chemiluminescence generation. The actuation switch is triggered by an external nucleic acid (target) that interacts with a complementary nucleic acid that is beard externally by the nanorobot (probe). Hybridization of probe and target produces a localized structural change that results in flap opening. The flap movement is studied on a two-dimensional prototype origami using Förster resonance energy transfer and is shown to be triggered by a variety of targets, including natural RNAs. The nanorobot has potential for in vivo biosensing and intelligent delivery of biological activators. PMID:24648163

Torelli, Emanuela; Marini, Monica; Palmano, Sabrina; Piantanida, Luca; Polano, Cesare; Scarpellini, Alice; Lazzarino, Marco; Firrao, Giuseppe

2014-07-01

248

Nanopores and nucleic acids: prospects for ultrarapid sequencing  

Microsoft Academic Search

DNA and RNA molecules can be detected as they are driven through a nanopore by an applied electric field at rates ranging from several hundred microseconds to a few milliseconds per molecule. The nanopore can rapidly discriminate between pyrimidine and purine segments along a single-stranded nucleic acid molecule. Nanopore detection and characterization of single molecules represents a new method for

David W Deamer; Mark Akeson

2000-01-01

249

Concepts and terms at electrochemical nucleic acid-based biosensors  

Microsoft Academic Search

An evaluation of concepts, terms and methodology used at electrochemical nucleic acids-based biosensors is given together with the demonstration of effectiveness of the application of selected nanomaterials at the construction of carbon paste-based disposable electrochemical NA biosensors.

Jan Labuda

2009-01-01

250

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

PubMed

This thesis establishes oligonucleotide design rules and applications of a novel group of DNA stabilizing molecules collectively called Twisted Intercalating Nucleic Acid - TINA. Three peer-reviewed publications form the basis for the thesis. One publication describes an improved and rapid method for determination of DNA melting points and two publications describe the effects of positioning TINA molecules in parallel triplex helix and antiparallel duplex helix forming DNA structures. The third publication establishes that TINA molecules containing oligonucleotides improve an antiparallel duplex hybridization based capture assay's analytical sensitivity compared to conventionel DNA oligonucleotides. Clinical microbiology is traditionally based on pathogenic microorganisms' culture and serological tests. The introduction of DNA target amplification methods like PCR has improved the analytical sensitivity and total turn around time involved in clinical diagnostics of infections. Due to the relatively weak hybridization between the two strands of double stranded DNA, a number of nucleic acid stabilizing molecules have been developed to improve the sensitivity of DNA based diagnostics through superior binding properties. A short introduction is given to Watson-Crick and Hoogsteen based DNA binding and the derived DNA structures. A number of other nucleic acid stabilizing molecules are described. The stabilizing effect of TINA molecules on different DNA structures is discussed and considered in relation to other nucleic acid stabilizing molecules and in relation to future use of TINA containing oligonucleotides in clinical diagnostics and therapy. In conclusion, design of TINA modified oligonucleotides for antiparallel duplex helixes and parallel triplex helixes follows simple purpose dependent rules. TINA molecules are well suited for improving multiplex PCR assays and can be used as part of novel technologies. Future research should test whether combinations of TINA molecules and other nucleic acid stabilizing molecules can increase analytical sensitivity whilst maintaining nucleobase mismatch discrimination in triplex helix based diagnostic assays. PMID:22239845

Schneider, Uffe Vest

2012-01-01

251

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

DOEpatents

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

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

2014-01-14

252

Nucleic Acids Research doi:10.1093/nar/gkn325  

E-print Network

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

253

Method for promoting specific alignment of short oligonucleotides on nucleic acids  

DOEpatents

Disclosed is a method for promoting specific alignment of short oligonucleotides on a nucleic acid polymer. The nucleic acid polymer is incubated in a solution containing a single-stranded DNA-binding protein and a plurality of oligonucleotides which are perfectly complementary to distinct but adjacent regions of a predetermined contiguous nucleotide sequence in the nucleic acid polymer. The plurality of oligonucleotides anneal to the nucleic acid polymer to form a contiguous region of double stranded nucleic acid. Specific application of the methods disclosed include priming DNA synthesis and template-directed ligation.

Studier, F. William (Stony Brook, NY); Kieleczawa, Jan (Coram, NY); Dunn, John J. (Bellport, NY)

1996-01-01

254

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

E-print Network

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

Shaqfeh, Eric

255

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

E-print Network

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

Luther, Douglas S.

256

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

257

Electroporation-enhanced delivery of nucleic acid vaccines.  

PubMed

The naked delivery of nucleic acid vaccines is notoriously inefficient, and an enabling delivery technology is required to direct efficiently these constructs intracellularly. A delivery technology capable of enhancing nucleic acid uptake in both cells in tissues and in culture is electroporation (EP). EP is a physical delivery mechanism that increases the permeability of mammalian cell membranes and allows the trafficking of large macromolecules into the cell. EP has now been used extensively in the clinic and been shown to be an effective method to increase both the uptake of the construct and the breadth and magnitude of the resulting immune responses. Excitingly, 2014 saw the announcement of the first EP-enhanced DNA vaccine Phase II trial demonstrating clinical efficacy. This review seeks to introduce the reader to EP as a technology to enhance the delivery of DNA and RNA vaccines and highlight several published clinical trials using this delivery modality. PMID:25487734

Broderick, Kate E; Humeau, Laurent M

2014-12-01

258

A quantitative measure of chirality inside nucleic acid databank.  

PubMed

We show the capability of a chirality index (Pietropaolo et al., Proteins 2008;70:667-677) to investigate nucleic acid structures because of its high sensitivity to helical conformations. By analyzing selected structures of DNA and RNA, we have found that sequences rich in cytosine and guanine have a tendency to left-handed chirality, in contrast to regions rich in adenine or thymine which show strong negative, right-handed, chirality values. We also analyze RNA structures, where specific loops and hairpin motifs are characterized by a well-defined chirality value. We find that in nucleosome the chirality is exalted, whereas in ribosome it is reduced. Our results illustrate the sensitivity of this descriptor for nucleic acid conformations. PMID:21618614

Pietropaolo, Adriana; Parrinello, Michele

2011-08-01

259

A rapid multiplex assay for nucleic acid-based diagnostics.  

PubMed

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

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

2010-02-01

260

Nucleic Acid Aptamers: Research Tools in Disease Diagnostics and Therapeutics  

PubMed Central

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

Yadava, Pramod K.

2014-01-01

261

Synthesis of modified peptide nucleic acids.  

E-print Network

??Les Acides Peptido-nucléiques (PNA) sont des analogues synthétiques d’oligonucleotides naturels, ils sont constitués d’une répétition d’unités N-(2-aminoethyl)-glycine reliées par une liaison peptidique. Leur stabilité chimique… (more)

Chouikhi, Dalila

2013-01-01

262

Method and apparatus for staining immobilized nucleic acids  

DOEpatents

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

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

2000-01-01

263

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

264

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

265

Bioluminescence regenerative cycle (BRC) system for nucleic acid quantification assays  

NASA Astrophysics Data System (ADS)

A new label-free methodology for nucleic acid quantification has been developed where the number of pyrophosphate molecules (PPi) released during polymerization of the target nucleic acid is counted and correlated to DNA copy number. The technique uses the enzymatic complex of ATP-sulfurylase and firefly luciferase to generate photons from PPi. An enzymatic unity gain positive feedback is also implemented to regenerate the photon generation process and compensate any decay in light intensity by self regulation. Due to this positive feedback, the total number of photons generated by the bioluminescence regenerative cycle (BRC) can potentially be orders of magnitude higher than typical chemiluminescent processes. A system level kinetic model that incorporates the effects of contaminations and detector noise was used to show that the photon generation process is in fact steady and also proportional to the nucleic acid quantity. Here we show that BRC is capable of detecting quantities of DNA as low as 1 amol (10-18 mole) in 40?lit aqueous solutions, and this enzymatic assay has a controllable dynamic range of 5 orders of magnitude. The sensitivity of this technology, due to the excess number of photons generated by the regenerative cycle, is not constrained by detector performance, but rather by possible PPi or ATP (adenosine triphosphate) contamination, or background bioluminescence of the enzymatic complex.

Hassibi, Arjang; Lee, Thomas H.; Davis, Ronald W.; Pourmand, Nader

2003-07-01

266

Molecular assembly for high-performance bivalent nucleic acid inhibitor  

PubMed Central

It is theorized that multivalent interaction can result in better affinity and selectivity than monovalent interaction in the design of high-performance ligands. Accordingly, biomolecular engineers are increasingly taking advantage of multivalent interactions to fabricate novel molecular assemblies, resulting in new functions for ligands or enhanced performance of existing ligands. Substantial efforts have been expended in using small molecules or epitopes of antibodies for designing multifunctional or better-performing ligands. However, few attempts to use nucleic acid aptamers as functional domains have been reported. In this study, we explore the design of bivalent nucleic acid ligands by using thrombin and its aptamers as the model by which to evaluate its functions. By assembling two thrombin-binding aptamers with optimized design parameters, this assembly has resulted in the successful development of a nucleic acid-based high-performance bivalent protein inhibitor. Our experimentation proved (i) that the simultaneous binding of two aptamers after linkage achieved 16.6-fold better inhibition efficiency than binding of the monovalent ligand and (ii) that such an improvement originated from changes in the kinetics of the binding interactions, with a koff rate ?1/50 as fast. In addition, the newly generated aptamer assembly is an excellent anticoagulant reagent when tested with different samples. Because this optimized ligand design offers a simple and noninvasive means of accomplishing higher performance from known functional aptamers, it holds promise as a potent antithrombin agent in the treatment of various diseases related to abnormal thrombin activities. PMID:18398007

Kim, Youngmi; Cao, Zehui; Tan, Weihong

2008-01-01

267

The role of immunostimulatory nucleic acids in septic shock  

PubMed Central

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

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

2012-01-01

268

Molecular Modeling of Nucleic Acid Structure: Electrostatics and Solvation  

PubMed Central

This unit presents an overview of computer simulation techniques as applied to nucleic acid systems, ranging from simple in vacuo molecular modeling techniques to more complete all-atom molecular dynamics treatments that include an explicit representation of the environment. The third in a series of four units, this unit focuses on critical issues in solvation and the treatment of electrostatics. UNITS 7.5 & 7.8 introduced the modeling of nucleic acid structure at the molecular level. This included a discussion of how to generate an initial model, how to evaluate the utility or reliability of a given model, and ultimately how to manipulate this model to better understand the structure, dynamics, and interactions. Subject to an appropriate representation of the energy, such as a specifically parameterized empirical force field, the techniques of minimization and Monte Carlo simulation, as well as molecular dynamics (MD) methods, were introduced as means to sample conformational space for a better understanding of the relevance of a given model. From this discussion, the major limitations with modeling, in general, were highlighted. These are the difficult issues in sampling conformational space effectively—the multiple minima or conformational sampling problems—and accurately representing the underlying energy of interaction. In order to provide a realistic model of the underlying energetics for nucleic acids in their native environments, it is crucial to include some representation of solvation (by water) and also to properly treat the electrostatic interactions. These are discussed in detail in this unit. PMID:18428877

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

2014-01-01

269

DNA Polymorphism: A Comparison of Force Fields for Nucleic Acids  

PubMed Central

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 latter two is the primary focus of this paper. The performance of each force field is evaluated first on its ability to reproduce the B-DNA decamer d(CGATTAATCG)2 in solution with simulations in which the long-range electrostatics were treated by the particle mesh Ewald method; the crystal structure determined by Quintana et al. (1992) is used as the starting point for all simulations. A detailed analysis of the structural and solvation properties shows how well the different force fields can reproduce sequence-specific features. The results are compared with data from experimental and previous theoretical studies. PMID:12609851

Reddy, Swarnalatha Y.; Leclerc, Fabrice; Karplus, Martin

2003-01-01

270

Deep Ultraviolet Mapping of Intracellular Protein and Nucleic Acid in Femtograms per Pixel  

PubMed Central

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

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

2011-01-01

271

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

NASA Astrophysics Data System (ADS)

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

Szeto, Kylan; Craighead, Harold G.

2014-09-01

272

Differential fluorescence quenching of fluorescent nucleic acid base analogues by native nucleic acid monophosphates.  

PubMed

Fluorescent nucleic acid base analogues (FBAs) are used widely as probes of DNA and RNA structure and dynamics. Of increasing utility are the pteridone adenosine analogues (6MAP, DMAP) and pteridine guanosine analogues (3MI, 6MI). These FBAs (collectively referred to as PTERs) are useful, in part, because their fluorescence quantum yields, Phi(f), are modulated by base stacking with native bases (NBs), making them sensitive reporters of DNA structure. The quenching mechanism has been hypothesized to be photoinduced electron transfer following selective excitation of the FBA, but hard evidence for this has been lacking. The degree of quenching shows some dependence on the neighboring bases, but there has been no real determination as to whether FBA*:NB complexes satisfy the basic thermodynamic requirement for spontaneous PET: a negative free energy for the electron transfer reaction. Indeed, quenching may result from entirely different mechanisms. To address these questions, Stern-Volmer (S-V) experiments were performed using the native-base monophosphate nucleotides (NMPs) GMP, AMP, CMP, and dTMP in aqueous solutions as quenchers to obtain quenching rate constants, k(q). Cyclic voltammetry (CV) and optical absorption and emission data of the PTERS were obtained in aprotic organic solvents. These data were used to obtain excited-state redox potentials from which electron transfer free energies were derived using the Rehm-Weller equation. The reorganization energies for PET were obtained using the Scandola-Balzani equation, taking into account the free energy contribution due to water. 6MAP*, DMAP*, and 3MI* gave negative free energies between -0.1 and -0.2 eV and reorganization energies of about 0.13 eV. They all displayed ET activation energies below the accessible thermal energy (0.038 eV = 3/2k(B)T, where k(B) is Boltzmann's constant) for all NMPs with the exception of CMP, whose activation barrier was only about 35% higher (approximately 0.05 eV). Thus, we conclude that these PTERs act as electron acceptors and promote NMP oxidation. However, 6MI* had positive ET free energies for all NMPs with the exception of GMP (and then only for nucleobase oxidation). The magnitudes of these free energies (> or = 0.45 eV for AMP, CMP, and dTMP) suggest that 6MI* may not quenched by PET. PMID:20387838

Narayanan, Madhavan; Kodali, Goutham; Singh, Vijay; Xing, Yangjun; Hawkins, Mary E; Stanley, Robert J

2010-05-01

273

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

E-print Network

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

Wong, Pak Kin

274

Enhanced anti-HIV-1 activity of G-quadruplexes comprising locked nucleic acids and intercalating nucleic acids  

PubMed Central

Two G-quadruplex forming sequences, 5?-TGGGAG and the 17-mer sequence T30177, which exhibit anti-HIV-1 activity on cell lines, were modified using either locked nucleic acids (LNA) or via insertions of (R)-1-O-(pyren-1-ylmethyl)glycerol (intercalating nucleic acid, INA) or (R)-1-O-[4-(1-pyrenylethynyl)phenylmethyl]glycerol (twisted intercalating nucleic acid, TINA). Incorporation of LNA or INA/TINA monomers provide as much as 8-fold improvement of anti-HIV-1 activity. We demonstrate for the first time a detailed analysis of the effect the incorporation of INA/TINA monomers in quadruplex forming oligonucleotides (QFOs) and the effect of LNA monomers in the context of biologically active QFOs. In addition, recent literature reports and our own studies on the gel retardation of the phosphodiester analogue of T30177 led to the conclusion that this sequence forms a parallel, dimeric G-quadruplex. Introduction of the 5?-phosphate inhibits dimerisation of this G-quadruplex as a result of negative charge–charge repulsion. Contrary to that, we found that attachment of the 5?-O-DMT-group produced a more active 17-mer sequence that showed signs of aggregation—forming multimeric G-quadruplex species in solution. Many of the antiviral QFOs in the present study formed more thermally stable G-quadruplexes and also high-order G-quadruplex structures which might be responsible for the increased antiviral activity observed. PMID:21062811

Pedersen, Erik B.; Nielsen, Jakob T.; Nielsen, Claus; Filichev, Vyacheslav V.

2011-01-01

275

THE NUCLEIC ACIDS OF SOME INSECT VIRUSES  

PubMed Central

Purine and pyrimidine bases have been estimated from the desoxyribonucleic acids of eleven insect viruses. Their proportions vary in the different species in a balanced way so that the molar ratios adenine:thymine and guanine:cytosine are constant and close to unity, whereas adenine + thymine:guanine + cytosine ranges from 0.71 to 1.87. This ratio is identical for some biologically dissimilar viruses, and no general parallelism is evident between DNA composition and biological relationship. Two different viruses from one host have distinct DNA's. PMID:13011277

Wyatt, G. R.

1952-01-01

276

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

2013-07-01

277

Introduction of structural affinity handles as a tool in selective nucleic acid separations  

NASA Technical Reports Server (NTRS)

The method is used for separating nucleic acids and other similar constructs. It involves selective introduction, enhancement, or stabilization of affinity handles such as single-strandedness in the undesired (or desired) nucleic acids as compared to the usual structure (e.g., double-strandedness) of the desired (or undesired) nucleic acids. The undesired (or desired) nucleic acids are separated from the desired (or undesired) nucleic acids due to capture by methods including but not limited to immobilized metal affinity chromatography, immobilized single-stranded DNA binding (SSB) protein, and immobilized oligonucleotides. The invention is useful to: remove contaminating genomic DNA from plasmid DNA; remove genomic DNA from plasmids, BACs, and similar constructs; selectively separate oligonucleotides and similar DNA fragments from their partner strands; purification of aptamers, (deoxy)-ribozymes and other highly structured nucleic acids; Separation of restriction fragments without using agarose gels; manufacture recombinant Taq polymerase or similar products that are sensitive to host genomic DNA contamination; and other applications.

Willson, III, Richard Coale (Inventor); Cano, Luis Antonio (Inventor)

2011-01-01

278

Exogenous nucleic acids aggregate in non-P-body cytoplasmic granules when transfected into cultured cells  

Microsoft Academic Search

To modulate gene expression in research studies or in potential clinical therapies, transfection of exogenous nucleic acids\\u000a including plasmid DNA and small interference RNA (siRNA) are generally performed. However, the cellular processing and the\\u000a fate of these nucleic acids remain elusive. By investigating the cellular behavior of transfected nucleic acids using confocal\\u000a imaging, here we show that when siRNA was

Huang Huang; Na Wei; Yingfei Xiong; Feng Yang; Huaqiang Fang; Wenjun Xie; Zhuan Zhou; Heping Cheng; Zicai Liang; Quan Du

2010-01-01

279

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

E-print Network

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

Stadler, Peter F.

280

Origin of Overstretching Transitions in Single-Stranded Nucleic Acids  

NASA Astrophysics Data System (ADS)

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

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

2013-11-01

281

Non-Enzymatic Depurination of Nucleic Acids: Factors and Mechanisms  

PubMed Central

Depurination has attracted considerable attention since a long time for it is closely related to the damage and repair of nucleic acids. In the present study, depurination using a pool of 30-nt short DNA pieces with various sequences at diverse pH values was analyzed by High Performance Liquid Chromatography (HPLC). Kinetic analysis results showed that non-enzymatic depurination of oligodeoxynucleotides exhibited typical first-order kinetics, and its temperature dependence obeyed Arrhenius’ law very well. Our results also clearly showed that the linear relationship between the logarithms of rate constants and pH values had a salient point around pH 2.5. Interestingly and unexpectedly, depurination depended greatly on the DNA sequences. The depurination of poly (dA) was found to be extremely slow, and thymine rich sequences depurinated faster than other sequences. These results could be explained to some extent by the protonation of nucleotide bases. Moreover, two equations were obtained based on our data for predicting the rate of depurination under various conditions. These results provide basic data for gene mutagenesis and nucleic acids metabolism in acidic gastric juice and some acidic organelles, and may also help to rectify some misconceptions about depurination. PMID:25546310

An, Ran; Jia, Yu; Wan, Baihui; Zhang, Yanfang; Dong, Ping; Li, Jing; Liang, Xingguo

2014-01-01

282

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

2014-03-04

283

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

284

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

2014-03-25

285

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

286

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

287

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

288

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

289

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

290

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

291

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

2008-01-22

292

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

293

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

294

Nucleic acid binding activity of pns6 encoded by genome segment 6 of rice ragged stunt oryzavirus.  

PubMed

The ORF of genome segment 6 (S6) of rice ragged stunt oryzavirus (RRSV) Philippines isolate was cloned and sequenced based on the S6 sequence of the Thailand isolate. Pns6, the 71 kD product of S6 expressed in E. coli, was demonstrated to be a viral non-structural protein of RRSV by Western blotting. The gel mobility shift assays showed that Pns6 had nucleic acid binding activity. Pns6 could interact with single- and double-stranded forms of DNA and RNA, showing a preference for single-stranded nucleic acid and a slight preference for RRSV ssRNA over the rice ssRNA, as demonstrated by both competition and displacement assays. The binding of Pns6 to nucleic acids is strong and sequence non-specific. By using five truncated derivatives of Pns6, it was found that the basic region from amino acid 201 to 273 of Pns6 was the unique nucleic acid binding domain. Subcellular fractionation of leaf tissues of RRSV-infected rice plants and subsequent Western blotting had shown that Pns6 accumulated predominately in the cytoplasmic membrane fraction. The possible role of RRSV Pns6 in virus replication and assembly is discussed. PMID:15248020

Shao, Chao-Gang; Lü, Hui-Juan; Wu, Jian-Hua; Gong, Zu-Xun

2004-07-01

295

Nonenzymatic catalytic signal amplification for nucleic acid hybridization assays  

NASA Technical Reports Server (NTRS)

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

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

2006-01-01

296

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.

297

Phosphoryl guanidines: a new type of nucleic Acid analogues.  

PubMed

A new type of nucleic acid analogues with a phosphoryl guanidine group is described. Oxidation of polymer-supported dinucleoside 2-cyanoethyl phosphite by iodine in the presence of 1,1,3,3-tetramethyl guanidine yields a dinucleotide with an internucleoside tetramethyl phosphoryl guanidine (Tmg) group as the main product. The Tmg group is stable under conditions of solid-phase DNA synthesis and subsequent cleavage and deprotection with ammonia. Oligonucleotides with one or more Tmg groups bind their complementary DNA or RNA with affinity similar to that of natural oligodeoxyribonucleotides. PMID:25558402

Kupryushkin, M S; Pyshnyi, D V; Stetsenko, D A

2014-10-01

298

Phosphoryl Guanidines: A New Type of Nucleic Acid Analogues  

PubMed Central

A new type of nucleic acid analogues with a phosphoryl guanidine group is described. Oxidation of polymer-supported dinucleoside 2-cyanoethyl phosphite by iodine in the presence of 1,1,3,3-tetramethyl guanidine yields a dinucleotide with an internucleoside tetramethyl phosphoryl guanidine (Tmg) group as the main product. The Tmg group is stable under conditions of solid-phase DNA synthesis and subsequent cleavage and deprotection with ammonia. Oligonucleotides with one or more Tmg groups bind their complementary DNA or RNA with affinity similar to that of natural oligodeoxyribonucleotides. PMID:25558402

Kupryushkin, M. S.; Pyshnyi, D. V.; Stetsenko, D. A.

2014-01-01

299

Application of carboxyphenylboronic acid-functionalized magnetic nanoparticles for extracting nucleic acid from seeds.  

PubMed

Magnetic iron oxide nanoparticles functionalized with 4-carboxyphenylboronic acid (CPBA-MNPs) were developed for extracting genomic DNA, total RNA and nucleic acids from seeds. The seed samples were genetically-modified maize seeds and unmodified soybean seeds infected by bean pod mottle virus and tobacco ringspot virus. The total nucleic acids, genomic DNA, and RNA could be separately extracted from these seeds with high qualities using CPBA-MNPs under different conditions. Furthermore, the results of real-time quantitative qPCR and real-time reverse transcription (RT)-PCR indicated that the nucleic acids extracted from these seeds using CPBA-MNPs were suitable for the detection of genetically-modified seeds and seed-borne viruses. PMID:25214223

Sun, Ning; Deng, Congliang; Ge, Guanglu; Xia, Qiang

2015-01-01

300

Rapid identification of Stenotrophomonas maltophilia by peptide nucleic acid fluorescence in situ hybridization  

PubMed Central

The objective of this study was to develop a novel peptide nucleic acid (PNA) probe for Stenotrophomonas maltophilia identification by fluorescence in situ hybridization (FISH). The probe was evaluated using 33 human and veterinary clinical S. maltophilia isolates and 45 reference strains representing common bacterial species in the respiratory tract. The probe displayed 100% sensitivity and 100% specificity on pure cultures and allowed detection in sputum from cystic fibrosis patients. The detection limit was 104 CFU/mL in spiked tracheal aspirate and bronchoalveolar lavage from healthy horses. Altogether the study shows that this species-specific PNA FISH probe facilitates rapid detection of S. maltophilia in biological specimens. PMID:25356348

Hansen, N; Rasmussen, A K I; Fiandaca, M J; Kragh, K N; Bjarnsholt, T; Høiby, N; Stender, H; Guardabassi, L

2014-01-01

301

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

2014-04-08

302

DINAMelt web server for nucleic acid melting prediction  

PubMed Central

The DINAMelt web server simulates the melting of one or two single-stranded nucleic acids in solution. The goal is to predict not just a melting temperature for a hybridized pair of nucleic acids, but entire equilibrium melting profiles as a function of temperature. The two molecules are not required to be complementary, nor must the two strand concentrations be equal. Competition among different molecular species is automatically taken into account. Calculations consider not only the heterodimer, but also the two possible homodimers, as well as the folding of each single-stranded molecule. For each of these five molecular species, free energies are computed by summing Boltzmann factors over every possible hybridized or folded state. For temperatures within a user-specified range, calculations predict species mole fractions together with the free energy, enthalpy, entropy and heat capacity of the ensemble. Ultraviolet (UV) absorbance at 260 nm is simulated using published extinction coefficients and computed base pair probabilities. All results are available as text files and plots are provided for species concentrations, heat capacity and UV absorbance versus temperature. This server is connected to an active research program and should evolve as new theory and software are developed. The server URL is . PMID:15980540

Markham, Nicholas R.; Zuker, Michael

2005-01-01

303

Nucleic acid sequence detection using multiplexed oligonucleotide PCR  

DOEpatents

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

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

2006-12-26

304

Analyzing and building nucleic acid structures with 3DNA.  

PubMed

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

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

2013-01-01

305

Mechanism for the endocytosis of spherical nucleic acid nanoparticle conjugates  

PubMed Central

Intracellular delivery of nucleic acids as gene regulation agents typically requires the use of cationic carriers or viral vectors, yet issues related to cellular toxicity or immune responses hamper their attractiveness as therapeutic candidates. The discovery that spherical nucleic acids (SNAs), polyanionic structures comprised of densely packed, highly oriented oligonucleotides covalently attached to the surface of nanoparticles, can effectively enter more than 50 different cell types presents a potential strategy for overcoming the limitations of conventional transfection agents. Unfortunately, little is known about the mechanism of endocytosis of SNAs, including the pathway of entry and specific proteins involved. Here, we demonstrate that the rapid cellular uptake kinetics and intracellular transport of SNAs stem from the arrangement of oligonucleotides into a 3D architecture, which supports their targeting of class A scavenger receptors and endocytosis via a lipid-raft–dependent, caveolae-mediated pathway. These results reinforce the notion that SNAs can serve as therapeutic payloads and targeting structures to engage biological pathways not readily accessible with linear oligonucleotides. PMID:23613589

Choi, Chung Hang J.; Hao, Liangliang; Narayan, Suguna P.; Auyeung, Evelyn; Mirkin, Chad A.

2013-01-01

306

Mechanism for the endocytosis of spherical nucleic acid nanoparticle conjugates.  

PubMed

Intracellular delivery of nucleic acids as gene regulation agents typically requires the use of cationic carriers or viral vectors, yet issues related to cellular toxicity or immune responses hamper their attractiveness as therapeutic candidates. The discovery that spherical nucleic acids (SNAs), polyanionic structures comprised of densely packed, highly oriented oligonucleotides covalently attached to the surface of nanoparticles, can effectively enter more than 50 different cell types presents a potential strategy for overcoming the limitations of conventional transfection agents. Unfortunately, little is known about the mechanism of endocytosis of SNAs, including the pathway of entry and specific proteins involved. Here, we demonstrate that the rapid cellular uptake kinetics and intracellular transport of SNAs stem from the arrangement of oligonucleotides into a 3D architecture, which supports their targeting of class A scavenger receptors and endocytosis via a lipid-raft-dependent, caveolae-mediated pathway. These results reinforce the notion that SNAs can serve as therapeutic payloads and targeting structures to engage biological pathways not readily accessible with linear oligonucleotides. PMID:23613589

Choi, Chung Hang J; Hao, Liangliang; Narayan, Suguna P; Auyeung, Evelyn; Mirkin, Chad A

2013-05-01

307

UNAFold: software for nucleic acid folding and hybridization.  

PubMed

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

Markham, Nicholas R; Zuker, Michael

2008-01-01

308

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. PMID:18522725

Kurz, Matthias

2008-01-01

309

Nucleic acid delivery: the missing pieces of the puzzle?  

PubMed Central

Conspectus The ability of gene or RNA interference (RNAi) delivery to increase or decrease virtually any protein in a cell opens the path for cures to most diseases that afflict humans. However, their high molecular weight, anionic nature, and instability in the presence of enzymes, pose major obstacles to nucleic acid delivery and frustrates their use as human therapies. This Account describes current ideas on the mechanisms in non-viral nucleic acid delivery and how lipidic and polymeric carriers overcome some of the critical barriers to delivery. A multitude of polymeric and lipidic vectors have been developed over the last 20 years, only a small fraction of them have progressed into clinical trials. Given that none of these vectors has received FDA approval, indicates that the current vectors do not yet have suitable properties for effective in vivo nucleic acid delivery. Nucleic acid delivery is a multistep process and inefficiencies at any stage result in a dramatic decrease in gene delivery or gene silencing. Despite this, the majority of studies investigating synthetic vectors focus solely on optimization of endosomal escape. A small number of studies address how to improve uptake via targeted delivery. A smaller fraction examine the intracellular fate of the delivery systems and nucleic acid cargo. The internalization of genes into the cell nucleus remains an inefficient and mysterious process. In the case of DNA delivery, strategies to increase and accelerate the migration of DNA through the cytoplasm and transport it through the nuclear membrane are required. The barriers to siRNA delivery are fewer: siRNA is more readily released from the carrier, siRNA is more resistant to enzymatic degradation and the target is in the cytoplasm; hence, siRNA delivery systems are becoming a clinical reality. With regard to siRNA therapy, the exact cytoplasmic location of RISC formation and activity is unknown. This makes specific targeting of the RISC for more efficient siRNA delivery difficult. Furthermore, identifying the factors favoring the binding of siRNA to Ago-2 and understanding how the half-life of siRNA and Ago-2/siRNA complex in the cytoplasm can be modulated without interfering with RISC functions that are essential for normal cell activity could increase siRNA delivery efficiency. In this manuscript we concisely review the current synthetic vectors and for a few of these, propose alternative strategies. We suggest how certain cellular mechanisms might be exploited to improve gene transfection and silencing. Finally, we raise the question if some carriers are delivering the siRNA to cells capable of repackaging the siRNA into exosomes. The exosomes would then transport the siRNA into a subsequent population of cells where the siRNA effect is manifest. This piggy-back mechanism may be responsible for reported deep tissue siRNA effects using certain carriers. PMID:22428908

Nguyen, Juliane; Szoka, Francis C.

2012-01-01

310

Aminoglycoside-Nucleic Acid Interactions: Remarkable Stabilization of DNA and RNA Triple Helices by Neomycin  

E-print Network

Aminoglycoside-Nucleic Acid Interactions: Remarkable Stabilization of DNA and RNA Triple Helices by Neomycin Dev P. Arya,* R. Lane Coffee, Jr., Bert Willis, and Anna I. Abramovitch Contribution from. H. Prog. Nucleic Acid Res. Mol. Biol.. 1998, 59, 55-94. (7) Thuong, N. T.; Helene, C. Angew. Chem

Stuart, Steven J.

311

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

E-print Network

Evolution of functional nucleic acids in the presence of nonheritable backbone heterogeneity Simon that the early evolution of life was dominated by RNA, which can both transfer information from generation of heterogeneous nucleic acid molecules could evolve reproducible function. For such evolution to be possible

Heller, Eric

312

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

PubMed Central

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

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

2014-01-01

313

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

Microsoft Academic Search

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

JOHN L. JOHNSON

1973-01-01

314

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

E-print Network

Honey, I Shrunk the DNA: DNA Length as a Probe for Nucleic-Acid Enzyme Activity Antoine M. van movies'' of enzymes at the single-molecule level, and thus remove averaging over large numbers to manipulate individual DNA molecules17 have allowed a large number of nucleic-acid enzymes to be charac

315

Do Electrostatic Interactions Destabilize ProteinNucleic Acid Binding? Sanbo Qin,1  

E-print Network

Do Electrostatic Interactions Destabilize Protein­Nucleic Acid Binding? Sanbo Qin,1 Huan-Xiang Zhou to be enriched in posi- tively charged residues.1,2 However, many calcula- tions have found that electrostatic interaction energies between proteins and nucleic acids are positive, meaning that electrostatic interactions

Weston, Ken

316

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

317

Structure and function of circadian clock proteins and deuterium isotope effects in nucleic acid hydrogen bonds  

E-print Network

-terminal domain. Hydrogen bonds are of paramount importance in nucleic acid structure and function. Here we show that changes in the width and anharmonicity of vibrational potential energy wells of hydrogen bonded groups can be measured in nucleic acids and can...

Vakonakis, Ioannis

2005-08-29

318

Development and application of new nucleic acid-based technologies for microbial community analyses in foods  

Microsoft Academic Search

Several challenges still persist in the analysis of microorganisms in foods, particularly in studies of complex communities. Nucleic acid-based methods are promising tools in addressing new questions concerning microbial communities. We have developed several new methods in the field of nucleic acid-based microbial community analyses. These methods cover both sample preparation and detection approaches. The sample preparation method involves simplified

Knut Rudi; Hege K Nogva; Birgitte Moen; Hilde Nissen; Sylvia Bredholt; Trond Møretrø; Kristine Naterstad; Askild Holck

2002-01-01

319

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

E-print Network

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

Chen, Wei

320

Lipophilic nucleic acids--a flexible construction kit for organization and functionalization of surfaces.  

PubMed

Lipophilic nucleic acids have become a versatile tool for structuring and functionalization of lipid bilayers and biological membranes as well as cargo vehicles to transport and deliver bioactive compounds, like interference RNA, into cells by taking advantage of reversible hybridization with complementary strands. This contribution reviews the different types of conjugates of lipophilic nucleic acids, and their physicochemical and self-assembly properties. Strategies for choosing a nucleic acid, lipophilic modification, and linker are discussed. Interaction with lipid membranes and its stability, dynamic structure and assembly of lipophilic nucleic acids upon embedding into biological membranes are specific points of the review. A large diversity of conjugates including lipophilic peptide nucleic acid and siRNA provides tailored solutions for specific applications in bio- and nanotechnology as well as in cell biology and medicine, as illustrated through some selected examples. PMID:24650567

Schade, Matthias; Berti, Debora; Huster, Daniel; Herrmann, Andreas; Arbuzova, Anna

2014-06-01

321

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

PubMed Central

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

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

2013-01-01

322

Nucleic Acid Encoding A Lectin-Derived Progenitor Cell Preservation Factor  

DOEpatents

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

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

2001-10-30

323

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

E-print Network

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

Liu, David R.

324

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

E-print Network

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

Lohman, Timothy M.

325

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

E-print Network

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

Bansal, Manju

326

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

E-print Network

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

Sankoff, David

327

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

E-print Network

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

Boxer, Steven G.

328

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

E-print Network

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

Stuart, Steven J.

329

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

E-print Network

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

Levin, Judith G.

330

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

E-print Network

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

Levin, Judith G.

331

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

E-print Network

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

332

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

E-print Network

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

Chen, Irene

333

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

E-print Network

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

Heller, Eric

334

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

335

Interaction of keratin K1 with nucleic acids on the cell surface.  

PubMed

The interaction of surface proteins from A431 cells and cellular extracts with nucleic acids was investigated using affinity modification with 32P-labeled reactive oligonucleotide derivatives. Proteins with molecular weights of 68, 46, 38, and 28 kD as well as several low molecular weight proteins capable of binding to nucleic acids were found on the surface of intact cells. It was demonstrated that a protein with molecular weight of 68 kD is exposed at the cell surface, since the treatment of cells with trypsin results in the cleavage of this protein. Disruption of the integrity of the cell membrane (scrapping, treatment with trypsin, or permeabilization of the cell membrane with streptolysin O or saponin) disrupts the interaction of the reactive oligonucleotides with the cell surface proteins. Affinity modification of the cytosolic and membrane-cytosolic cell fractions with labeled oligonucleotides results in the modification of a large number of proteins, where proteins with molecular weights of 68, 46, 38, and 28 kD can be found as minor components. Surface oligonucleotide-binding proteins with molecular weight of ~68 kD were isolated by affinity chromatography after the modification of intact A431 cells with a reactive oligonucleotide derivative. The isolated surface oligonucleotide-binding proteins from A431 cells were sequenced, and one of the proteins was identified as keratin K1. PMID:14640967

Chelobanov, B P; Laktionov, P P; Kharkova, M V; Rykova, E Yu; Pyshnyi, D V; Pyshnaya, I A; Marcus, K; Meyer, H E; Vlassov, V V

2003-11-01

336

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. PMID:21310240

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

2011-01-01

337

Clinical applications of nucleic acid aptamers in cancer  

PubMed Central

Nucleic acid aptamers are small single-stranded DNA or RNA oligonucleotide segments, which bind to their targets with high affinity and specificity via unique three-dimensional structures. Aptamers are generated by an iterative in vitro selection process, termed as systematic evolution of ligands by exponential enrichment. Owing to their specificity, non-immunogenicity, non-toxicity, easily modified chemical structure and wide range of targets, aptamers appear to be ideal candidates for various clinical applications (diagnosis or treatment), such as cell detection, target diagnosis, molecular imaging and drug delivery. Several aptamers have entered the clinical pipeline for applications in diseases such as macular degeneration, coronary artery bypass graft surgery and various types of cancer. The aim of this review was to summarize and highlight the clinical applications of aptamers in cancer diagnosis and treatment. PMID:24772298

PEI, XIAOYU; ZHANG, JUN; LIU, JIE

2014-01-01

338

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

339

Nucleic acid detection using G-quadruplex amplification methodologies.  

PubMed

In the last decade, there has been an explosion in the use of G-quadruplex labels to detect various analytes, including DNA/RNA, proteins, metals and other metabolites. In this review, we focus on strategies for the detection of nucleic acids, using G-quadruplexes as detection labels or as enzyme labels that amplify detection signals. Methods to detect other analytes are briefly mentioned. We highlight various strategies, including split G-quadruplex, hemin-G-quadruplex conjugates, molecular beacon G-quadruplex or inhibited G-quadruplex probes. The tandem use of G-quadruplex labels with various DNA-modifying enzymes, such as polymerases (used for rolling circle amplification), exonucleases and endonucleases, is also discussed. Some of the detection modalities that are discussed in this review include fluorescence, colorimetric, chemiluminescence, and electrochemical methods. PMID:24135042

Roembke, Benjamin T; Nakayama, Shizuka; Sintim, Herman O

2013-12-15

340

Nucleic acid-metal organic framework (MOF) nanoparticle conjugates.  

PubMed

Nanoparticles of a metal-organic framework (MOF), UiO-66-N3 (Zr6O4OH4(C8H3O4-N3)6), were synthesized. The surface of the MOF was covalently functionalized with oligonucleotides, utilizing a strain promoted click reaction between DNA appended with dibenzylcyclooctyne and azide-functionalized UiO-66-N3 to create the first MOF nanoparticle-nucleic acid conjugates. The structure of the framework was preserved throughout the chemical transformation, and the surface coverage of DNA was quantified. Due to the small pore sizes, the particles are only modified on their surfaces. When dispersed in aqueous NaCl, they exhibit increased stability and enhanced cellular uptake when compared with unfunctionalized MOF particles of comparable size. PMID:24818877

Morris, William; Briley, William E; Auyeung, Evelyn; Cabezas, Maria D; Mirkin, Chad A

2014-05-21

341

Advances in the Determination of Nucleic Acid Conformational Ensembles  

NASA Astrophysics Data System (ADS)

Conformational changes in nucleic acids play a key role in the way genetic information is stored, transferred, and processed in living cells. Here, we describe new approaches that employ a broad range of experimental data, including NMR-derived chemical shifts and residual dipolar couplings, small-angle X-ray scattering, and computational approaches such as molecular dynamics simulations to determine ensembles of DNA and RNA at atomic resolution. We review the complementary information that can be obtained from diverse sets of data and the various methods that have been developed to combine these data with computational methods to construct ensembles and assess their uncertainty. We conclude by surveying RNA and DNA ensembles determined using these methods, highlighting the unique physical and functional insights obtained so far.

Salmon, Loïc; Yang, Shan; Al-Hashimi, Hashim M.

2014-04-01

342

Efficient algorithms for folding and comparing nucleic acid sequences.  

PubMed Central

Fast algorithms for analysing sequence data are presented. An algorithm for strict homologies finds all common subsequences of length greater than or equal to 6 in two given sequences. With it, nucleic acid pieces five thousand nucleotides long can be compared in five seconds on CDC 6600. Secondary structure algorithms generate the N most stable secondary structures of an RNA molecule, taking into account all loop contributions, and the formation of all possible base-pairs in stems, including odd pairs (G.G., C.U., etc.). They allow a typical 100-nucleotide sequence to be analysed in 10 seconds. The homology and secondary structure programs are respectively illustrated with a comparison of two phage genomes, and a discussion of Drosophila melanogaster 55 RNA folding. PMID:6174935

Dumas, J P; Ninio, J

1982-01-01

343

A novel nucleic acid analogue shows strong angiogenic activity  

SciTech Connect

Research highlights: {yields} A novel nucleic acid analogue (2Cl-C.OXT-A, m.w. 284) showed angiogenic potency. {yields} It stimulated the tube formation, proliferation and migration of HUVEC in vitro. {yields} 2Cl-C.OXT-A induced the activation of ERK1/2 and MEK in HUVEC. {yields} Angiogenic potency in vivo was confirmed in CAM assay and rabbit cornea assay. {yields} A synthesized small angiogenic agent would have great clinical therapeutic value. -- Abstract: A novel nucleic acid analogue (2Cl-C.OXT-A) significantly stimulated tube formation of human umbilical endothelial cells (HUVEC). Its maximum potency at 100 {mu}M was stronger than that of vascular endothelial growth factor (VEGF), a positive control. At this concentration, 2Cl-C.OXT-A moderately stimulated proliferation as well as migration of HUVEC. To gain mechanistic insights how 2Cl-C.OXT-A promotes angiogenic responses in HUVEC, we performed immunoblot analyses using phospho-specific antibodies as probes. 2Cl-C.OXT-A induced robust phosphorylation/activation of MAP kinase ERK1/2 and an upstream MAP kinase kinase MEK. Conversely, a MEK inhibitor PD98059 abolished ERK1/2 activation and tube formation both enhanced by 2Cl-C.OXT-A. In contrast, MAP kinase responses elicited by 2Cl-C.OXT-A were not inhibited by SU5416, a specific inhibitor of VEGF receptor tyrosine kinase. Collectively these results suggest that 2Cl-C.OXT-A-induces angiogenic responses in HUVEC mediated by a MAP kinase cascade comprising MEK and ERK1/2, but independently of VEGF receptor tyrosine kinase. In vivo assay using chicken chorioallantoic membrane (CAM) and rabbit cornea also suggested the angiogenic potency of 2Cl-C.OXT-A.

Tsukamoto, Ikuko, E-mail: tukamoto@med.kagawa-u.ac.jp [Department of Pharmaco-Bio-Informatics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)] [Department of Pharmaco-Bio-Informatics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan); Sakakibara, Norikazu; Maruyama, Tokumi [Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193 (Japan)] [Kagawa School of Pharmaceutical Sciences, Tokushima Bunri University, 1314-1 Shido, Sanuki, Kagawa 769-2193 (Japan); Igarashi, Junsuke; Kosaka, Hiroaki [Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)] [Department of Cardiovascular Physiology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan); Kubota, Yasuo [Department of Dermatology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)] [Department of Dermatology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan); Tokuda, Masaaki [Department of Cell Physiology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)] [Department of Cell Physiology, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan); Ashino, Hiromi [The Tokyo Metropolitan Institute of Medical Science, 1-6 Kamikitazawa2-chome, Setagaya-ku, Tokyo 156-8506 (Japan)] [The Tokyo Metropolitan Institute of Medical Science, 1-6 Kamikitazawa2-chome, Setagaya-ku, Tokyo 156-8506 (Japan); Hattori, Kenichi; Tanaka, Shinji; Kawata, Mitsuhiro [Teikoku Seiyaku Co., Ltd., Sanbonmatsu, Higashikagawa, Kagawa 769-2695 (Japan)] [Teikoku Seiyaku Co., Ltd., Sanbonmatsu, Higashikagawa, Kagawa 769-2695 (Japan); Konishi, Ryoji [Department of Pharmaco-Bio-Informatics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)] [Department of Pharmaco-Bio-Informatics, Faculty of Medicine, Kagawa University, 1750-1 Ikenobe, Miki, Kita, Kagawa 761-0793 (Japan)

2010-09-03

344

Electric chips for rapid detection and quantification of nucleic acids.  

PubMed

A silicon chip-based electric detector coupled to bead-based sandwich hybridization (BBSH) is presented as an approach to perform rapid analysis of specific nucleic acids. A microfluidic platform incorporating paramagnetic beads with immobilized capture probes is used for the bio-recognition steps. The protocol involves simultaneous sandwich hybridization of a single-stranded nucleic acid target with the capture probe on the beads and with a detection probe in the reaction solution, followed by enzyme labeling of the detection probe, enzymatic reaction, and finally, potentiometric measurement of the enzyme product at the chip surface. Anti-DIG-alkaline phosphatase conjugate was used for the enzyme labeling of the DIG-labeled detection probe. p-Aminophenol phosphate (pAPP) was used as a substrate. The enzyme reaction product, p-aminophenol (pAP), is oxidized at the anode of the chip to quinoneimine that is reduced back to pAP at the cathode. The cycling oxidation and reduction of these compounds result in a current producing a characteristic signal that can be related to the concentration of the analyte. The performance of the different steps in the assay was characterized using in vitro synthesized RNA oligonucleotides and then the instrument was used for analysis of 16S rRNA in Escherichia coli extract. The assay time depends on the sensitivity required. Artificial RNA target and 16S rRNA, in amounts ranging from 10(11) to 10(10) molecules, were assayed within 25 min and 4 h, respectively. PMID:14683637

Gabig-Ciminska, M; Holmgren, A; Andresen, H; Bundvig Barken, K; Wümpelmann, M; Albers, J; Hintsche, R; Breitenstein, A; Neubauer, P; Los, M; Czyz, A; Wegrzyn, G; Silfversparre, G; Jürgen, B; Schweder, T; Enfors, S-O

2004-01-15

345

DBBP: database of binding pairs in protein-nucleic acid interactions  

PubMed Central

Background Interaction of proteins with other molecules plays an important role in many biological activities. As many structures of protein-DNA complexes and protein-RNA complexes have been determined in the past years, several databases have been constructed to provide structure data of the complexes. However, the information on the binding sites between proteins and nucleic acids is not readily available from the structure data since the data consists mostly of the three-dimensional coordinates of the atoms in the complexes. Results We analyzed the huge amount of structure data for the hydrogen bonding interactions between proteins and nucleic acids and developed a database called DBBP (DataBase of Binding Pairs in protein-nucleic acid interactions, http://bclab.inha.ac.kr/dbbp). DBBP contains 44,955 hydrogen bonds (H-bonds) of protein-DNA interactions and 77,947 H-bonds of protein-RNA interactions. Conclusions Analysis of the huge amount of structure data of protein-nucleic acid complexes is labor-intensive, yet provides useful information for studying protein-nucleic acid interactions. DBBP provides the detailed information of hydrogen-bonding interactions between proteins and nucleic acids at various levels from the atomic level to the residue level. The binding information can be used as a valuable resource for developing a computational method aiming at predicting new binding sites in proteins or nucleic acids. PMID:25474259

2014-01-01

346

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE.  

PubMed

Both clinical and analytical metrics produced by microarray-based assay technology have recognized problems in reproducibility, reliability and analytical sensitivity. These issues are often attributed to poor understanding and control of nucleic acid behaviors and properties at solid-liquid interfaces. Nucleic acid hybridization, central to DNA and RNA microarray formats, depends on the properties and behaviors of single strand (ss) nucleic acids (e.g., probe oligomeric DNA) bound to surfaces. ssDNA's persistence length, radius of gyration, electrostatics, conformations on different surfaces and under various assay conditions, its chain flexibility and curvature, charging effects in ionic solutions, and fluorescent labeling all influence its physical chemistry and hybridization under assay conditions. Nucleic acid (e.g., both RNA and DNA) target interactions with immobilized ssDNA strands are highly impacted by these biophysical states. Furthermore, the kinetics, thermodynamics, and enthalpic and entropic contributions to DNA hybridization reflect global probe/target structures and interaction dynamics. Here we review several biophysical issues relevant to oligomeric nucleic acid molecular behaviors at surfaces and their influences on duplex formation that influence microarray assay performance. Correlation of biophysical aspects of single and double-stranded nucleic acids with their complexes in bulk solution is common. Such analysis at surfaces is not commonly reported, despite its importance to microarray assays. We seek to provide further insight into nucleic acid-surface challenges facing microarray diagnostic formats that have hindered their clinical adoption and compromise their research quality and value as genomics tools. PMID:24765522

Rao, Archana N; Grainger, David W

2014-04-01

347

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

PubMed Central

The Gag polyprotein of HIV-1 is essential for retroviral replication and packaging. The nucleocapsid (NC) protein is the primary region for the interaction of Gag with nucleic acids. In this study, we examine the interactions of Gag and its NC cleavage products (NCp15, NCp9 and NCp7) with nucleic acids using solution and single molecule experiments. The NC cleavage products bound DNA with comparable affinity and strongly destabilized the DNA duplex. In contrast, the binding constant of Gag to DNA was found to be ?10-fold higher than that of the NC proteins, and its destabilizing effect on dsDNA was negligible. These findings are consistent with the primary function of Gag as a nucleic acid binding and packaging protein and the primary function of the NC proteins as nucleic acid chaperones. Also, our results suggest that NCp7's capability for fast sequence-nonspecific nucleic acid duplex destabilization, as well as its ability to facilitate nucleic acid strand annealing by inducing electrostatic attraction between strands, likely optimize the fully processed NC protein to facilitate complex nucleic acid secondary structure rearrangements. In contrast, Gag's stronger DNA binding and aggregation capabilities likely make it an effective chaperone for processes that do not require significant duplex destabilization. PMID:16449201

Cruceanu, Margareta; Urbaneja, Maria A.; Hixson, Catherine V.; Johnson, Donald G.; Datta, Siddhartha A.; Fivash, Matthew J.; Stephen, Andrew G.; Fisher, Robert J.; Gorelick, Robert J.; Casas-Finet, Jose R.; Rein, Alan; Rouzina, Ioulia; Williams, Mark C.

2006-01-01

348

Single molecule DNA interaction kinetics of retroviral nucleic acid chaperone proteins  

NASA Astrophysics Data System (ADS)

Retroviral nucleocapsid (NC) proteins are essential for several viral replication processes including specific genomic RNA packaging and reverse transcription. The nucleic acid chaperone activity of NC facilitates the latter process. In this study, we use single molecule biophysical methods to quantify the DNA interactions of wild type and mutant human immunodeficiency virus type 1 (HIV-1) NC and Gag and human T-cell leukemia virus type 1 (HTLV-1) NC. We find that the nucleic acid interaction properties of these proteins differ significantly, with HIV-1 NC showing rapid protein binding kinetics, significant duplex destabilization, and strong DNA aggregation, all properties that are critical components of nucleic acid chaperone activity. In contrast, HTLV-1 NC exhibits significant destabilization activity but extremely slow DNA interaction kinetics and poor aggregating capability, which explains why HTLV-1 NC is a poor nucleic acid chaperone. To understand these results, we developed a new single molecule method for quantifying protein dissociation kinetics, and applied this method to probe the DNA interactions of wild type and mutant HIV-1 and HTLV-1 NC. We find that mutations to aromatic and charged residues strongly alter the proteins' nucleic acid interaction kinetics. Finally, in contrast to HIV-1 NC, HIV-1 Gag, the nucleic acid packaging protein that contains NC as a domain, exhibits relatively slow binding kinetics, which may negatively impact its ability to act as a nucleic acid chaperone.

Williams, Mark

2010-03-01

349

Observations on the nucleolar and total cell body nucleic acid of injured nerve cells  

PubMed Central

1. The nucleic acid content of neuronal nucleoli and the total cell body nucleic acid content of neurones of the hypoglossal nucleus were measured by ultraviolet absorption microspectrography. 2. After nerve injury both the nucleolar nucleic acid and the total cell body nucleic acid increased: nucleolar changes preceded those of the cell body. 3. The closer to the nerve cell body that the axon was injured the earlier was the onset and the decline of the nucleolar response. 4. Actinomycin D was given to prevent DNA-primed RNA synthesis, and the rate of `decay' of nucleolar RNA was measured. This rate varied after nerve injury and was closely related to the nucleolar nucleic acid content. 5. The apparent rate of transfer of labelled RNA from the neuronal nucleus into the cytoplasm changed after nerve injury in a manner closely related to the changes in nucleolar nucleic acid content. 6. It was demonstrated by making consecutive nerve injuries or by preventing or delaying nerve regeneration, that the nucleic acid changes were not induced by removal of contact between the neurone and its motor end-plate, and were not repressed by the restoration of such contact. 7. When regeneration was prevented the nucleolar nucleic acid content and the total cell body nucleic acid ultimately decreased to values less than normal: this decrease was greater when more of the axon was initially removed. 8. The results are discussed in relation to the factor responsible for derepression and repression of DNA cistrons for ribosome synthesis in injured nerve cells. ImagesABCAB PMID:5664236

Watson, W. E.

1968-01-01

350

Synthesis of phosphoramidites of isoGNA, an isomer of glycerol nucleic acid  

PubMed Central

Summary IsoGNA, an isomer of glycerol nucleic acid GNA, is a flexible (acyclic) nucleic acid with bases directly attached to its linear backbone. IsoGNA exhibits (limited) base-pairing properties which are unique compared to other known flexible nucleic acids. Herein, we report on the details of the preparation of isoGNA phosphoramidites and an alternative route for the synthesis of the adenine derivative. The synthetic improvements described here enable an easy access to isoGNA and allows for the further exploration of this structural unit in oligonucleotide chemistry thereby spurring investigations of its usefulness and applicability. PMID:25246971

Kim, Keunsoo; Punna, Venkateshwarlu; Karri, Phaneendrasai

2014-01-01

351

Nucleic acid biosynthesis in thymine-requiring strains of Salmonella typhimurium  

E-print Network

NUCLEIC ACID BIOSY?IRESIS IN TJJYKJIJE- REQUIRING STRAINS OF ~LLA TYPHIMURIUM A Thesis Submitted to the Graduate College of Texas A&M University in partial fulfillment of the requireJamt for the ~ of MASTER OF SCIENCE May 1977 Major Subject...: Biochemistry NUCLEIC ACID BIOS~IS IN THYMI5Z- RE@JIRING STRAINS OF SAI?3NELZA TYPHIKlRIUM A Thesis Approved as to style and oontent by: (phDxman 0 f Comittee) (Head of Departrrent) ( p May 1977 Nucleic acid biosynthesis in thymne- rrggfr' 9 9 'of g...

Harvey, Stephanie Ann

2012-06-07

352

Selenium derivatization of nucleic acids for X-ray crystal-structure and function studies.  

PubMed

It is estimated that over two thirds of all new crystal structures of proteins are determined via the protein selenium derivatization (selenomethionine (Se-Met) strategy). This selenium derivatization strategy via MAD (multi-wavelength anomalous dispersion) phasing has revolutionized protein X-ray crystallography. Through our pioneer research, similarly, Se has also been successfully incorporated into nucleic acids to facilitate the X-ray crystal-structure and function studies of nucleic acids. Currently, Se has been stably introduced into nucleic acids by replacing nucleotide O-atom at the positions 2', 4', 5', and in nucleobases and non-bridging phosphates. The Se derivatization of nucleic acids can be achieved through solid-phase chemical synthesis and enzymatic methods, and the Se-derivatized nucleic acids (SeNA) can be easily purified by HPLC, FPLC, and gel electrophoresis to obtain high purity. It has also been demonstrated that the Se derivatization of nucleic acids facilitates the phase determination via MAD phasing without significant perturbation. A growing number of structures of DNAs, RNAs, and protein-nucleic acid complexes have been determined by the Se derivatization and MAD phasing. Furthermore, it was observed that the Se derivatization can facilitate crystallization, especially when it is introduced to the 2'-position. In addition, this novel derivatization strategy has many advantages over the conventional halogen derivatization, such as more choices of the modification sites via the atom-specific substitution of the nucleotide O-atom, better stability under X-ray radiation, and structure isomorphism. Therefore, our Se-derivatization strategy has great potentials to provide rational solutions for both phase determination and high-quality crystal growth in nucleic-acid crystallography. Moreover, the Se derivatization generates the nucleic acids with many new properties and creates a new paradigm of nucleic acids. This review summarizes the recent developments of the atomic site-specific Se derivatization of nucleic acids for structure determination and function study. Several applications of this Se-derivatization strategy in nucleic acid and protein research are also described in this review. PMID:20397215

Sheng, Jia; Huang, Zhen

2010-04-01

353

a,b-D-Constrained Nucleic Acids Are Strong Terminators of Thermostable DNA Polymerases in Polymerase Chain  

E-print Network

a,b-D-Constrained Nucleic Acids Are Strong Terminators of Thermostable DNA Polymerases, RP) a,b-D- Constrained Nucleic Acids (CNA) are dinucleotide building blocks that can feature either B. Citation: Marti´nez O, Ecochard V, Mahe´o S, Gross G, Bodin P, et al. (2011) a,b-D-Constrained Nucleic

Paris-Sud XI, Université de

354

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

355

Nucleic Acid Aptamers as Potential Therapeutic and Diagnostic Agents for Lymphoma  

PubMed Central

Lymphomas are cancers that arise from white blood cells and usually present as solid tumors. Treatment of lymphoma often involves chemotherapy, and can also include radiotherapy and/or bone marrow transplantation. There is an un-questioned need for more effective therapies and diagnostic tool for lymphoma. Aptamers are single stranded DNA or RNA oligonucleotides whose three-dimensional structures are dictated by their sequences. The immense diversity in function and structure of nucleic acids enable numerous aptamers to be generated through an iterative in vitro selection technique known as Systematic Evolution of Ligands by EXponential enrichment (SELEX). Aptamers have several biochemical properties that make them attractive tools for use as potential diagnostic and pharmacologic agents. Isolated aptamers may directly inhibit the function of target proteins, or they can also be formulated for use as delivery agents for other therapeutic or imaging cargoes. More complex aptamer identification methods, using whole cancer cells (Cell-SELEX), may identify novel targets and aptamers to affect them. This review focuses on recent advances in the use of nucleic acid aptamers as diagnostic and therapeutic agents and as targeted delivery carriers that are relevant to lymphoma. Some representative examples are also discussed. PMID:25057429

Shum, Ka-To; Zhou, Jiehua; Rossi, John J.

2014-01-01

356

Intracellular Nucleic Acid Delivery by the Supercharged Dengue Virus Capsid Protein  

PubMed Central

Supercharged proteins are a recently identified class of proteins that have the ability to efficiently deliver functional macromolecules into mammalian cells. They were first developed as bioengineering products, but were later found in the human proteome. In this work, we show that this class of proteins with unusually high net positive charge is frequently found among viral structural proteins, more specifically among capsid proteins. In particular, the capsid proteins of viruses from the Flaviviridae family have all a very high net charge to molecular weight ratio (> +1.07/kDa), thus qualifying as supercharged proteins. This ubiquity raises the hypothesis that supercharged viral capsid proteins may have biological roles that arise from an intrinsic ability to penetrate cells. Dengue virus capsid protein was selected for a detailed experimental analysis. We showed that this protein is able to deliver functional nucleic acids into mammalian cells. The same result was obtained with two isolated domains of this protein, one of them being able to translocate lipid bilayers independently of endocytic routes. Nucleic acids such as siRNA and plasmids were delivered fully functional into cells. The results raise the possibility that the ability to penetrate cells is part of the native biological functions of some viral capsid proteins. PMID:24339931

Freire, João Miguel; Veiga, Ana Salomé; Conceição, Thaís M.; Kowalczyk, Wioleta; Mohana-Borges, Ronaldo; Andreu, David; Santos, Nuno C.; Da Poian, Andrea T.; Castanho, Miguel A. R. B.

2013-01-01

357

70967108 Nucleic Acids Research, 2007, Vol. 35, No. 21 Published online 16 October 2007 doi:10.1093/nar/gkm750  

E-print Network

7096­7108 Nucleic Acids Research, 2007, Vol. 35, No. 21 Published online 16 October 2007 doi:10 of Vif, displays cytidine deaminase and single- stranded (ss) nucleic acid binding activities. HIV-1 nucleocapsid protein (NC) also binds nucleic acids and has a unique property, nucleic acid chaperone activity

Levin, Judith G.

358

Cell-surface-bound nucleic acids: Free and cell-surface-bound nucleic acids in blood of healthy donors and breast cancer patients.  

PubMed

Concentrations of extracellular DNA and RNA in the blood of healthy donors and patients with malignant and nonmalignant breast tumors were investigated. Cell-surface-bound extracellular DNA and RNA were detached by PBS-EDTA treatment or mild trypsin treatment of erythrocytes and leukocytes. In healthy donors, almost all extracellular nucleic acids (98%) are bound at the surface of blood cells. In the blood of cancer patients, extracellular nucleic acids were found in plasma and not at the cell surface. In patients with nonmalignant breast tumors, extracellular nucleic acids were found both at the surface of blood cells and in plasma. In healthy donors, the cell-surface-bound DNA is represented by 20-kbp DNA fragments and smaller fragments that varied in amounts in different fractions. PMID:15251964

Laktionov, Pavel P; Tamkovich, Svetlana N; Rykova, Elena Yu; Bryzgunova, Olga E; Starikov, Andrey V; Kuznetsova, Nina P; Vlassov, Valentin V

2004-06-01

359

Plants having modified response to ethylene by transformation with an ETR nucleic acid  

DOEpatents

The invention includes transformed plants having at least one cell transformed with a modified ETR nucleic acid. Such plants have a phenotype characterized by a decrease in the response of at least one transformed plant cell to ethylene as compared to a plant not containing the transformed plant cell. Tissue and/or temporal specificity for expression of the modified ETR nucleic acid is controlled by selecting appropriate expression regulation sequences to target the location and/or time of expression of the transformed nucleic acid. The plants are made by transforming at least one plant cell with an appropriate modified ETR nucleic acid, regenerating plants from one or more of the transformed plant cells and selecting at least one plant having the desired phenotype.

Meyerowitz, Elliott M. (Pasadena, CA); Chang, Caren (Pasadena, CA); Bleecker, Anthony B. (Madison, WI)

2001-01-01

360

Extraction of total nucleic acids from ticks for the detection of bacterial and viral pathogens.  

PubMed

Ticks harbor numerous bacterial, protozoal, and viral pathogens that can cause serious infections in humans and domestic animals. Active surveillance of the tick vector can provide insight into the frequency and distribution of important pathogens in the environment. Nucleic-acid based detection of tick-borne bacterial, protozoan, and viral pathogens requires the extraction of both DNA and RNA (total nucleic acids) from ticks. Traditional methods for nucleic acid extraction are limited to extraction of either DNA or the RNA from a sample. Here we present a simple bead-beating based protocol for extraction of DNA and RNA from a single tick and show detection of Borrelia burgdorferi and Powassan virus from individual, infected Ixodes scapularis ticks. We determined expected yields for total nucleic acids by this protocol for a variety of adult tick species. The method is applicable to a variety of arthropod vectors, including fleas and mosquitoes, and was partially automated on a liquid handling robot. PMID:20180313

Crowder, Chris D; Rounds, Megan A; Phillipson, Curtis A; Picuri, John M; Matthews, Heather E; Halverson, Justina; Schutzer, Steven E; Ecker, David J; Eshoo, Mark W

2010-01-01

361

Understanding barriers to efficient nucleic acid delivery with bioresponsive block copolymers  

E-print Network

The delivery of nucleic acids has the potential to revolutionize medicine by allowing previously untreatable diseases to be clinically addressed. Viral delivery systems have been held back by immunogenicity and toxicity ...

Bonner, Daniel Kenneth

2012-01-01

362

Electrochemical control of reversible DNA hybridisation : for future use in nucleic acid amplification   

E-print Network

Denaturation and renaturation is indispensable for the biological function of nucleic acids in many cellular processes, such as for example transcription for the synthesis of RNA and DNA replication during cell division. ...

Syed, Shahida Nina

2014-06-28

363

Gene Therapy for Advanced Melanoma: Selective Targeting and Therapeutic Nucleic Acids  

PubMed Central

Despite recent advances, the treatment of malignant melanoma still results in the relapse of the disease, and second line treatment mostly fails due to the occurrence of resistance. A wide range of mutations are known to prevent effective treatment with chemotherapeutic drugs. Hence, approaches with biopharmaceuticals including proteins, like antibodies or cytokines, are applied. As an alternative, regimens with therapeutically active nucleic acids offer the possibility for highly selective cancer treatment whilst avoiding unwanted and toxic side effects. This paper gives a brief introduction into the mechanism of this devastating disease, discusses the shortcoming of current therapy approaches, and pinpoints anchor points which could be harnessed for therapeutic intervention with nucleic acids. We bring the delivery of nucleic acid nanopharmaceutics into perspective as a novel antimelanoma therapeutic approach and discuss the possibilities for melanoma specific targeting. The latest reports on preclinical and already clinical application of nucleic acids in melanoma are discussed. PMID:23634303

Viola, Joana R.; Rafael, Diana F.; Wagner, Ernst; Besch, Robert; Ogris, Manfred

2013-01-01

364

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

NASA Astrophysics Data System (ADS)

Based on the enhancement of the resonance light scattering (RLS) of Congo Red (CR) by nucleic acid, a new quantitative method for nucleic acid is developed. In the Tris-HCl buffer (pH 10.5), the weak light scattering of CR is greatly enhanced by addition of nucleic acid and CTMAB, the maximum peak is at 560 nm and the enhanced intensity of RLS is in proportion to the concentration of nucleic acid. The linear range is 1.0×10 -9 to 1.0×10 -6 g ml -1, 7.5×10 -8 to 1.0×10 -6 g ml -1 and 7.5×10 -8 to 2.5×10 -6 g ml -1 for herring sperm DNA, calf thymus DNA and yeast RNA, and the detection limits are 0.019, 0.89 and 1.2 ng ml -1 ( S/ N = 3), respectively. Actual biological samples were satisfactorily determined.

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

2005-01-01

365

On the Use of Nucleic Acid Sequences to Infer Early Branchings in the Tree of Life  

E-print Network

On the Use of Nucleic Acid Sequences to Infer Early Branchings in the Tree of Life Ziheng Yang *9 branchings in the tree of life involves as- sumptions made in various tree reconstruction methods, which

Yang, Ziheng

366

[Degradation of nucleic acids during generation of superoxide-anion in the presence of copper ions].  

PubMed

The efficiency of Escherichia coli nucleic acids samples: covalently closed circular DNA, linear chromosomal DNA, total RNA degradation mediated by the action of high oxygen pressure; hydrochloric hydroxylamine in alkaline conditions in the presence of cooper ions and in analogous conditions without cooper ions was studied. The nativity of nucleic acids was determined by means of fluorometric analysis of nucleic acids/ethidium bromide complexes. Experiments revealed, that the destructive effect of active oxygen species decreased in the following order: NH2OH.HCl in alkaline conditions in the presence of copper ions-NH2.HCl in alkaline conditions--high pressure of pure oxygen. The stability of nucleic acids decreased in the following order: covalently closed circular DNA-linear DNA-RNA. PMID:2451781

Vodolazkin, D I; Chistiakov, V A; Gus'kov, E P; Sherstnev, K B

1987-01-01

367

Development of polymer and lipid materials for enhanced delivery of nucleic acids and proteins  

E-print Network

The development of synthetic vectors enabling efficient intracellular delivery of macromolecular therapeutics such as nucleic acids and proteins could potentially catalyze the clinical translation of many gene and protein-based ...

Eltoukhy, Ahmed Atef

2013-01-01

368

In-silico design of computational nucleic acids for molecular information processing  

PubMed Central

Within recent years nucleic acids have become a focus of interest for prototype implementations of molecular computing concepts. During the same period the importance of ribonucleic acids as components of the regulatory networks within living cells has increasingly been revealed. Molecular computers are attractive due to their ability to function within a biological system; an application area extraneous to the present information technology paradigm. The existence of natural information processing architectures (predominately exemplified by protein) demonstrates that computing based on physical substrates that are radically different from silicon is feasible. Two key principles underlie molecular level information processing in organisms: conformational dynamics of macromolecules and self-assembly of macromolecules. Nucleic acids support both principles, and moreover computational design of these molecules is practicable. This study demonstrates the simplicity with which one can construct a set of nucleic acid computing units using a new computational protocol. With the new protocol, diverse classes of nucleic acids imitating the complete set of boolean logical operators were constructed. These nucleic acid classes display favourable thermodynamic properties and are significantly similar to the approximation of successful candidates implemented in the laboratory. This new protocol would enable the construction of a network of interconnecting nucleic acids (as a circuit) for molecular information processing. PMID:23647621

2013-01-01

369

5'to 3' nucleic acid synthesis using 3'-photoremovable protecting group  

DOEpatents

The present invention relates, in general, to a method of synthesizing a nucleic acid, and, in particular, to a method of effecting 5' to 3' nucleic acid synthesis. The method can be used to prepare arrays of oligomers bound to a support via their 5' end. The invention also relates to a method of effecting mutation analysis using such arrays. The invention further relates to compounds and compositions suitable for use in such methods.

Pirrung, Michael C. (Houston, TX); Shuey, Steven W. (Durham, NC); Bradley, Jean-Claude (Durham, NC)

1999-01-01

370

5[prime] to 3[prime] nucleic acid synthesis using 3[prime]-photoremovable protecting group  

DOEpatents

The present invention relates, in general, to a method of synthesizing a nucleic acid, and, in particular, to a method of effecting 5[prime] to 3[prime] nucleic acid synthesis. The method can be used to prepare arrays of oligomers bound to a support via their 5[prime] end. The invention also relates to a method of effecting mutation analysis using such arrays. The invention further relates to compounds and compositions suitable for use in such methods.

Pirrung, M.C.; Shuey, S.W.; Bradley, J.C.

1999-06-01

371

Cooperativity in the binding of the cationic biocide polyhexamethylene biguanide to nucleic acids  

Microsoft Academic Search

The interaction between the broad-spectrum antimicrobial agent, polyhexamethylene biguanide (PHMB), and various nucleic acids was investigated. Titration of either single- or double-stranded 100-bp DNA, or mixed-molecular weight marker DNA, or tRNA with PHMB caused precipitation of a complex between nucleic acid and PHMB in which the nucleotide\\/biguanide ratio was always close to unity. Binding of PHMB was highly cooperative, with

Michael J Allen; Andrew P Morby; Graham F White

2004-01-01

372

Mass spectral characterization of a protein-nucleic acid photocrosslink.  

PubMed Central

A photocrosslink between basic fibroblast growth factor (bFGF155) and a high affinity ssDNA oligonucleotide was characterized by positive ion electrospray ionization mass spectrometry (ESIMS). The DNA was a 61-mer oligonucleotide photoaptamer bearing seven bromodeoxyuridines, identified by in vitro selection. Specific photocrosslinking of the protein to the oligonucleotide was achieved by 308 nm XeCl excimer laser excitation. The cross-linked protein nucleic acid complex was proteolyzed with trypsin. The resulting peptide crosslink was purified by PAGE, eluted, and digested by snake venom phosphodiesterase/alkaline phosphatase. Comparison of the oligonucleotide vs. the degraded peptide crosslink by high performance liquid chromatography coupled to an electrospray ionization triple quadrupole mass spectrometer showed a single ion unique to the crosslinked material. Sequencing by collision induced dissociation (MS/MS) on a triple quadrupole mass spectrometer revealed that this ion was the nonapeptide TGQYKLGSK (residues 130-138) crosslinked to a dinucleotide at Tyr133. The MS/MS spectrum indicated sequential fragmentation of the oligonucleotide to uracil covalently attached to the nonapeptide followed by fragmentation of the peptide bonds. Tyr133 is located within the heparin binding pocket, suggesting that the in vitro selection targeted this negative ion binding region of bFGF155. PMID:10631998

Golden, M. C.; Resing, K. A.; Collins, B. D.; Willis, M. C.; Koch, T. H.

1999-01-01

373

Nucleic Acids for Ultra-Sensitive Protein Detection  

PubMed Central

Major advancements in molecular biology and clinical diagnostics cannot be brought about strictly through the use of genomics based methods. Improved methods for protein detection and proteomic screening are an absolute necessity to complement to wealth of information offered by novel, high-throughput sequencing technologies. Only then will it be possible to advance insights into clinical processes and to characterize the importance of specific protein biomarkers for disease detection or the realization of “personalized medicine”. Currently however, large-scale proteomic information is still not as easily obtained as its genomic counterpart, mainly because traditional antibody-based technologies struggle to meet the stringent sensitivity and throughput requirements that are required whereas mass-spectrometry based methods might be burdened by significant costs involved. However, recent years have seen the development of new biodetection strategies linking nucleic acids with existing antibody technology or replacing antibodies with oligonucleotide recognition elements altogether. These advancements have unlocked many new strategies to lower detection limits and dramatically increase throughput of protein detection assays. In this review, an overview of these new strategies will be given. PMID:23337338

Janssen, Kris P. F.; Knez, Karel; Spasic, Dragana; Lammertyn, Jeroen

2013-01-01

374

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

375

Method for producing labeled single-stranded nucleic acid probes  

DOEpatents

Disclosed is a method for the introduction of unidirectional deletions in a cloned DNA segment. More specifically, the method comprises providing a recombinant DNA construct comprising a DNA segment of interest inserted in a cloning vector, the cloning vector having an f1 endonuclease recognition sequence adjacent to the insertion site of the DNA segment of interest. The recombinant DNA construct is then contacted with the protein pII encoded by gene II of phage f1 thereby generating a single-stranded nick. The nicked DNA is then contacted with E. coli Exonuclease III thereby expanding the single-stranded nick into a single-stranded gap. The single-stranded gapped DNA is then contacted with a single-strand-specific endonuclease thereby producing a linearized DNA molecule containing a double-stranded deletion corresponding in size to the single-stranded gap. The DNA treated in this manner is then incubated with DNA ligase under conditions appropriate for ligation. Also disclosed is a method for producing single-stranded DNA probes. In this embodiment, single-stranded gapped DNA, produced as described above, is contacted with a DNA polymerase in the presence of labeled nucleotides to fill in the gap. This DNA is then linearized by digestion with a restriction enzyme which cuts outside the DNA segment of interest. The product of this digestion is then denatured to produce a labeled single-stranded nucleic acid probe.

Dunn, John J. (Bellport, NY); Quesada, Mark A. (Middle Island, NY); Randesi, Matthew (Upton, NY)

1999-10-19

376

Rapid genotyping using pyrene?perylene locked nucleic acid complexes  

PubMed Central

We have developed an assay for single strand DNA and RNA detection which is based on novel pyrene?perylene FRET pairs attached to short LNA/DNA probes. The assay is based on ratiometric emission upon binding of target DNA/RNA by three combinations of fluorescent LNA/DNA reporter strands. Specific geometry of the pyrene fluorophore attached to the 2?-amino group of 2?-amino-LNA in position 4 allows for the first time to efficiently utilize dipole?dipole orientation parameter for sensing of single-nucleotide polymorphisms (SNPs) in nucleic acid targets by FRET. Using novel probes, SNP detection is achieved with advantages of large Stokes shift (115 nm), high fluorescence quantum yields and low limit of target detection values (< 5 nM). Rapid and accurate genotyping of highly polymorphic HIV Pol cDNA and RNA fragments performed herein proves the possibility for broad application of the novel pyrene?perylene FRET pairs, e.g., in imaging and clinical diagnostics. PMID:24044052

Kumar, T. Santhosh; Myznikova, Anna; Samokhina, Evgeniya; Astakhova, Irina Kira

2013-01-01

377

Nucleic acid aptamers: clinical applications and promising new horizons.  

PubMed

Aptamers are a special class of nucleic acid molecules that are beginning to be investigated for clinical use. These small RNA/DNA molecules can form secondary and tertiary structures capable of specifically binding proteins or other cellular targets; they are essentially a chemical equivalent of antibodies. Aptamers have the advantage of being highly specific, relatively small in size, and non-immunogenic. Since the discovery of aptamers in the early 1990s, great efforts have been made to make them clinically relevant for diseases like cancer, HIV, and macular degeneration. In the last two decades, many aptamers have been clinically developed as inhibitors for targets such as vascular endothelial growth factor (VEGF) and thrombin. The first aptamer based therapeutic was FDA approved in 2004 for the treatment of age-related macular degeneration and several other aptamers are currently being evaluated in clinical trials. With advances in targeted-therapy, imaging, and nanotechnology, aptamers are readily considered as potential targeting ligands because of their chemical synthesis and ease of modification for conjugation. Preclinical studies using aptamer-siRNA chimeras and aptamer targeted nanoparticle therapeutics have been very successful in mouse models of cancer and HIV. In summary aptamers are in several stages of development, from pre-clinical studies to clinical trials and even as FDA approved therapeutics. In this review, we will discuss the current state of aptamers in clinical trials as well as some promising aptamers in pre-clinical development. PMID:21838685

Ni, X; Castanares, M; Mukherjee, A; Lupold, S E

2011-01-01

378

Locked nucleic acid oligomers as handles for single molecule manipulation  

PubMed Central

Single-molecule manipulation (SMM) techniques use applied force, and measured elastic response, to reveal microscopic physical parameters of individual biomolecules and details of biomolecular interactions. A major hurdle in the application of these techniques is the labeling method needed to immobilize biomolecules on solid supports. A simple, minimally-perturbative labeling strategy would significantly broaden the possible applications of SMM experiments, perhaps even allowing the study of native biomolecular structures. To accomplish this, we investigate the use of functionalized locked nucleic acid (LNA) oligomers as biomolecular handles that permit sequence-specific binding and immobilization of DNA. We find these probes form bonds with DNA with high specificity but with varied stability in response to the direction of applied mechanical force: when loaded in a shear orientation, the bound LNA oligomers were measured to be two orders of magnitude more stable than when loaded in a peeling, or unzipping, orientation. Our results show that LNA provides a simple, stable means to functionalize dsDNA for manipulation. We provide design rules that will facilitate their use in future experiments. PMID:25159617

Berezney, John P.; Saleh, Omar A.

2014-01-01

379

Solution influence on biomolecular equilibria - Nucleic acid base associations  

NASA Technical Reports Server (NTRS)

Various attempts to construct an understanding of the influence of solution environment on biomolecular equilibria at the molecular level using computer simulation are discussed. First, the application of the formal statistical thermodynamic program for investigating biomolecular equilibria in solution is presented, addressing modeling and conceptual simplications such as perturbative methods, long-range interaction approximations, surface thermodynamics, and hydration shell. Then, Monte Carlo calculations on the associations of nucleic acid bases in both polar and nonpolar solvents such as water and carbon tetrachloride are carried out. The solvent contribution to the enthalpy of base association is positive (destabilizing) in both polar and nonpolar solvents while negative enthalpies for stacked complexes are obtained only when the solute-solute in vacuo energy is added to the total energy. The release upon association of solvent molecules from the first hydration layer around a solute to the bulk is accompanied by an increase in solute-solvent energy and decrease in solvent-solvent energy. The techniques presented are expectd to displace less molecular and more heuristic modeling of biomolecular equilibria in solution.

Pohorille, A.; Pratt, L. R.; Burt, S. K.; Macelroy, R. D.

1984-01-01

380

Proposed Ancestors of Phage Nucleic Acid Packaging Motors (and Cells)  

PubMed Central

I present a hypothesis that begins with the proposal that abiotic ancestors of phage RNA and DNA packaging systems (and cells) include mobile shells with an internal, molecule-transporting cavity. The foundations of this hypothesis include the conjecture that current nucleic acid packaging systems have imprints from abiotic ancestors. The abiotic shells (1) initially imbibe and later also bind and transport organic molecules, thereby providing a means for producing molecular interactions that are links in the chain of events that produces ancestors to the first molecules that are both information carrying and enzymatically active, and (2) are subsequently scaffolds on which proteins assemble to form ancestors common to both shells of viral capsids and cell membranes. Emergence of cells occurs via aggregation and merger of shells and internal contents. The hypothesis continues by using proposed imprints of abiotic and biotic ancestors to deduce an ancestral thermal ratchet-based DNA packaging motor that subsequently evolves to integrate a DNA packaging ATPase that provides a power stroke. PMID:21994778

Serwer, Philip

2011-01-01

381

A microfluidic biosensor based on nucleic acid sequence recognition.  

PubMed

The development of a generic semi-disposable microfluidic biosensor for the highly sensitive detection of pathogens via their nucleic acid sequences is presented in this paper. Disposable microchannels with defined areas for capture and detection of target pathogen RNA sequence were created in polydimethylsiloxane (PDMS) and mounted onto a reusable polymethylmethacrylate (PMMA) stand. Two different DNA probes complementary to unique sequences on the target pathogen RNA serve as the biorecognition elements. For signal generation and amplification, one probe is coupled to dye encapsulated liposomes while the second probe is coupled to superparamagnetic beads for target immobilization. The probes hybridize to target RNA and the liposome-target-bead complex is subsequently captured on a magnet. The amount of liposomes captured correlates directly to the concentration of target sequence and is quantified using a fluorescence microscope. Dengue fever virus serotype 3 sequences and probes were used as a model analyte system to test the sensor. Probe binding and target capture conditions were optimized for sensitivity resulting in a detection limit of as little as 10 amol microL(-1) (10 pmol L(-1)). Future biosensors will be designed to incorporate a mixer and substitute the fluorescence detection with an electrochemical detection technique to provide a truly portable microbiosensor system. PMID:12830353

Kwakye, Sylvia; Baeumner, Antje

2003-08-01

382

Logic gates and antisense DNA devices operating on a translator nucleic Acid scaffold.  

PubMed

A series of logic gates, "AND", "OR", and "XOR", are designed using a DNA scaffold that includes four "footholds" on which the logic operations are activated. Two of the footholds represent input-recognition strands, and these are blocked by complementary nucleic acids, whereas the other two footholds are blocked by nucleic acids that include the horseradish peroxidase (HRP)-mimicking DNAzyme sequence. The logic gates are activated by either nucleic acid inputs that hybridize to the respective "footholds", or by low-molecular-weight inputs (adenosine monophosphate or cocaine) that yield the respective aptamer-substrate complexes. This results in the respective translocation of the blocking nucleic acids to the footholds carrying the HRP-mimicking DNAzyme sequence, and the concomitant release of the respective DNAzyme. The released product-strands then self-assemble into the hemin/G-quadruplex-HRP-mimicking DNAzyme that biocatalyzes the formation of a colored product and provides an output signal for the different logic gates. The principle of the logic operation is, then, implemented as a possible paradigm for future nanomedicine. The nucleic acid inputs that bind to the blocked footholds result in the translocation of the blocking nucleic acids to the respective footholds carrying the antithrombin aptamer. The released aptamer inhibits, then, the hydrolytic activity of thrombin. The system demonstrates the regulation of a biocatalytic reaction by a translator system activated on a DNA scaffold. PMID:19507821

Shlyahovsky, Bella; Li, Yang; Lioubashevski, Oleg; Elbaz, Johann; Willner, Itamar

2009-07-28

383

Stability of free and mineral-protected nucleic acids: Implications for the RNA world  

NASA Astrophysics Data System (ADS)

Using molecular dynamics simulations we study the structural stability of three different nucleic acids intercalated within a magnesium aluminium layered double hydroxide (LDH) mineral, at varying degrees of hydration, and free in aqueous solution. The nucleotides investigated are ribose nucleic acid (RNA), deoxyribose nucleic acid (DNA) and peptide nucleic acid (PNA), all in duplex form. Our simulations show that DNA has enhanced Watson-Crick hydrogen-bonding when intercalated within the LDH clay interlayers, compared with intercalated RNA and PNA, whilst the reverse trend is found for the nucleic acids in bulk water. The tendency for LDH to alter the stability of the three nucleic acids persists for higher temperature and pressure conditions. The uncharged protein backbone of PNA is found to have a detrimental effect on the overall stability of the duplex, as it experiences a greatly reduced electrostatic interaction with the charged LDH sheets compared to RNA and DNA. Assuming an RNA world, in which RNA preceded the DNA/protein world, at some point in time DNA must have taken over the role as the information storage molecule from RNA. These results suggest that a mineral based origin of life may have favoured DNA as the information-storage biomolecule over potentially competing RNA and PNA, providing a route to modern biology from the RNA world.

Swadling, Jacob B.; Coveney, Peter V.; Christopher Greenwell, H.

2012-04-01

384

Exosome encased spherical nucleic acid gold nanoparticle conjugates as potent microRNA regulation agents.  

PubMed

Exosomes are a class of naturally occurring nanomaterials that play crucial roles in the protection and transport of endogenous macromolecules, such as microRNA and mRNA, over long distances. Intense effort is underway to exploit the use of exosomes to deliver synthetic therapeutics. Herein, transmission electron microscopy is used to show that when spherical nucleic acid (SNA) constructs are endocytosed into PC-3 prostate cancer cells, a small fraction of them (<1%) can be naturally sorted into exosomes. The exosome-encased SNAs are secreted into the extracellular environment from which they can be isolated and selectively re-introduced into the cell type from which they were derived. In the context of anti-miR21 experiments, the exosome-encased SNAs knockdown miR-21 target by approximately 50%. Similar knockdown of miR-21 by free SNAs requires a ?3000-fold higher concentration. PMID:24106176

Alhasan, Ali H; Patel, Pinal C; Choi, Chung Hang J; Mirkin, Chad A

2014-01-15

385

Exosome Encased Spherical Nucleic Acid Gold Nanoparticle Conjugates As Potent MicroRNA Regulation Agents  

PubMed Central

Exosomes are a class of naturally occurring nanomaterials that play crucial roles in the protection and transport of endogenous macromolecules, such as microRNA and mRNA, over long distances. Intense effort is underway to exploit the use of exosomes to deliver synthetic therapeutics. Herein, we use transmission electron microscopy to show that when spherical nucleic acid (SNA) constructs are endocytosed into PC-3 prostate cancer cells, a small fraction of them (< 1%) can be naturally sorted into exosomes. The exosome-encased SNAs are secreted into the extracellular environment from which they can be isolated and selectively re-introduced into the cell type from which they were derived. In the context of anti-miR21 experiments, the exosome-encased SNAs knockdown miR-21 target by approximately 50%. Similar knockdown of miR-21 by free SNAs requires a ~3000-fold higher concentration. PMID:24106176

Alhasan, Ali H.; Patel, Pinal C.; Choi, Chung Hang J.

2013-01-01

386

A New Heat Shock Protein That Binds Nucleic Acids* (Received for publication, August 20, 1998, and in revised form, September 28, 1998)  

E-print Network

A New Heat Shock Protein That Binds Nucleic Acids* (Received for publication, August 20, 1998 describe the isolation of Hsp15, a new, very abun- dant heat shock protein that binds to DNA and RNA. Hsp15 category from that of many other heat shock proteins that act as mo- lecular chaperones or proteases

Bardwell, James

387

Simple Protocol for Secondary School Hands-On Activity: Electrophoresis of Pre-Stained Nucleic Acids on Agar-Agar Borate Gels  

ERIC Educational Resources Information Center

An extremely simple, inexpensive, and safe method is presented, which emulates nucleic acids isolation and electrophoretic analysis as performed in a research environment, in the context of a secondary school hands-on activity. The protocol is amenable to an interdisciplinary approach, taking into consideration the electrical and chemical…

Britos, Leticia; Goyenola, Guillermo; Orono, Silvia Umpierrez

2004-01-01

388

Peptide nucleic acid probe for protein affinity purification based on biotin-streptavidin interaction and peptide nucleic acid strand hybridization.  

PubMed

We describe a new method for protein affinity purification that capitalizes on the high affinity of streptavidin for biotin but does not require dissociation of the biotin-streptavidin complex for protein retrieval. Conventional reagents place both the selectively reacting group (the "warhead") and the biotin on the same molecule. We place the warhead and the biotin on separate molecules, each linked to a short strand of peptide nucleic acid (PNA), synthetic polymers that use the same bases as DNA but attached to a backbone that is resistant to attack by proteases and nucleases. As in DNA, PNA strands with complementary base sequences hybridize. In conditions that favor PNA duplex formation, the warhead strand (carrying the tagged protein) and the biotin strand form a complex that is held onto immobilized streptavidin. As in DNA, the PNA duplex dissociates at moderately elevated temperature; therefore, retrieval of the tagged protein is accomplished by a brief exposure to heat. Using iodoacetate as the warhead, 8-base PNA strands, biotin, and streptavidin-coated magnetic beads, we demonstrate retrieval of the cysteine protease papain. We were also able to use our iodoacetyl-PNA:PNA-biotin probe for retrieval and identification of a thiol reductase and a glutathione transferase from soybean seedling cotyledons. PMID:25447466

Tse, Jenny; Wang, Yuanyuan; Zengeya, Thomas; Rozners, Eriks; Tan-Wilson, Anna

2015-02-01

389

Nucleic Acids Research, 2007, 19 doi:10.1093/nar/gkm623  

E-print Network

Nucleic Acids Research, 2007, 1­9 doi:10.1093/nar/gkm623 A systematic strategy for large within the Tir1 QTL region. Subsequent re-sequencing in Daxx identified a deletion of an amino acid subsequently changes the primary amino acid structure of the gene. In other cases the polymorphism may lie

Steve Kemp

390

Integration of On-chip Isotachophoresis and Functionalized Hydrogels for Enhanced-Sensitivity Nucleic Acid Detection  

E-print Network

for Enhanced-Sensitivity Nucleic Acid Detection Giancarlo Garcia-Schwarz and Juan G. Santiago* Department% perchloric acid from Sigma-Aldrich (St. Louis, MO). We purchased the photoinitiator 2,2- azobis[2-methyl-N-(2-hydroxyethyl) propionamide] (VA-086) from Wako Chemicals (Richmond, VA). We also purchased hydrochloric acid

Santiago, Juan G.

391

Brnsted Acids The Strongest Isolable Acid**  

E-print Network

Brønsted Acids The Strongest Isolable Acid** Mark Juhasz, Stephan Hoffmann, Evgenii Stoyanov, Kee-Chan Kim, and Christopher A. Reed* Acids based on carborane anions as conjugate bases (Figure 1) are a new class of Brønsted (protic) acids, notable for their "strong yet gentle" qualities.[1] For example

Reed, Christopher A.

392

DimaSense™: A Novel Nucleic Acid Detection System  

SciTech Connect

Recently, we developed a suite of methods for the rational design and fabrication of well-defined nanoparticle architectures, including clusters using bio-encoded nanoscale building blocks and layer-by-layer stepwise assembly on a solid support. In particular, the Nano-Assembly platform using Encoded Solid Supports (NAESS) allows for controlled interactions, purification of side products, modularity of design, and the construction of complex nanoparticle architectures. This approach offers several advantages over the current art of designing nanoparticle clusters, which include the high-yield synthesis of desired architectures, a 'plug-and-play' design allowing for the introduction of a variety of sensing modalities, and ease of scalability in high-throughput and synthesis yield. As a utility proof of concept, we implemented our unique cluster fabrication platform to design gold nanoparticle dimers which are linked via a single-stranded DNA oligonucleotide recognition motif. The design of this motif is such that binding of complementary nucleic acids results in specific, selective and rapid dimer dissociation, which can be monitored by dynamic light scattering (DLS). We demonstrated single level mismatch selectivity using this approach. The limit of detection was determined to be 1011 molecules of synthetic target RNA or DNA within 30 minutes of incubation at 33 C. This detection limit is determined by the dimer's concentration which can be probed by currently used standard DLS instruments. We also demonstrated a specific detection of target RNA in a solution containing competing 1,000-fold excess of non-complementary DNA fragments, 10% BSA, and endonucleases. Molecular diagnostic companies, RNA-based technology developers, and personalized medicine companies have applications that could benefit from using DimaSense{trademark}. The technology represents a platform which enables the simple and reasonably inexpensive design and fabrication of highly selective genetic sensors. These sensors operate with very low concentrations of target, can utilize standard instrumentation, produce detection results rapidly, and are robust enough to function in the presence of many competing genetic targets. Many current genetic target detection products/approaches/technologies rely upon methods (such as qPCR) which are more complicated, cumbersome, and costly to perform, and are not well suited to point-of-care diagnostic applications. Several clinical diagnostic applications, particularly point-of-care (POC) diagnostics for infectious diseases, are possible and appear to be a good fit for the technology. In addition, the advent of personalized medicine will create opportunities for molecular diagnostic companies with the capabilities of rapidly and quantitatively detecting nucleic acid sequences. The global POC market was {approx}$7.7B in 2010, with a recent annual growth rate of {approx}7%. A specific disease or disease-class diagnostic would need to be identified before a more meaningful sub-market value could be stated. Additional validation of the technology to show that it displays appropriate performance parameters for a commercial application on 'real world' samples is required for true commercial readiness. In addition, optimization of sensor design parameters, to effect a 10-fold increase in sensitivity, may be required to produce a commercially ready sensor system. These validation and sensor design optimization are estimated to require 3-4 months and {approx}$75k. For an unregulated product to give this sensor system a distinct competitive advantage, 2-3 years of product development and $1.5-3M are likely required. For regulated markets, time to market (through clinic) and cost would depend upon the product.

Stadler, A.

2011-05-18

393

Remote Enantioselection Transmitted by an Achiral Peptide Nucleic Acid Backbone  

NASA Technical Reports Server (NTRS)

short homochiral segment of DNA into a PNA helix could have guaranteed that the next short segment of DNA to be incorporated would have the same handedness as the first. Once two segments of the same handedness were present, the probability that a third segment would have the same handedness would increase, and so on. Evolution could then slowly dilute out the PNA part. This scenario would ultimately allow the formation of a chiral oligonucleotide by processes that are largely resistant to enantiomeric crossinhibition. It is important to note that the ligation of homochiral dinucleotides on a nucleic acid template would probably be at least as enantiospecific as the reaction that we have studied. The disadvantage of using chiral monomers as components of a replicating system arises from the difficulty of generating a first long homochiral template from a racemic mixture of monomers, although results of experiments designed to overcome this difficulty by employing homochiral tetramers have been reported.l l The probability of obtaining a homochiral n-mer from achiral substrates is approximately 1P-I if the nontemplate-directed extension of the primer is not enantioselective. Hence, it would be very hard to get started with a homochiral 40-mer, for example. No such difficulty exists in a scenario that originates with an achiral genetic material and in which the incorporation of very few chiral monomers in this achiral background gradually progresses towards homochirality. It seems possible that some PNA sequences could act as catalysts, analogous to ribozymes, even though PNA lacks clear metal binding sites. Although such catalysts could not be enantioselective, the incorporation of as few as two chiral nucleotides could then impose chiral specificity on the system. Furthermore, such patch chimeras could help to bridge the gap in catalytic potential between PNA and RNA, while guaranteeing enantioselectivity.

Kozlov, Igor A.; Orgel, Leslie E.; Nielsen, Peter E.

2000-01-01

394

Physical methods of nucleic acid transfer: general concepts and applications  

PubMed Central

Physical methods of gene (and/or drug) transfer need to combine two effects to deliver the therapeutic material into cells. The physical methods must induce reversible alterations in the plasma membrane to allow the direct passage of the molecules of interest into the cell cytosol. They must also bring the nucleic acids in contact with the permeabilized plasma membrane or facilitate access to the inside of the cell. These two effects can be achieved in one or more steps, depending upon the methods employed. In this review, we describe and compare several physical methods: biolistics, jet injection, hydrodynamic injection, ultrasound, magnetic field and electric pulse mediated gene transfer. We describe the physical mechanisms underlying these approaches and discuss the advantages and limitations of each approach as well as its potential application in research or in preclinical and clinical trials. We also provide conclusions, comparisons, and projections for future developments. While some of these methods are already in use in man, some are still under development or are used only within clinical trials for gene transfer. The possibilities offered by these methods are, however, not restricted to the transfer of genes and the complementary uses of these technologies are also discussed. As these methods of gene transfer may bypass some of the side effects linked to viral or biochemical approaches, they may find their place in specific clinical applications in the future. This article is part of a themed section on Vector Design and Drug Delivery. For a list of all articles in this section see the end of this paper, or visit: http://www3.interscience.wiley.com/journal/121548564/issueyear?year=2009 PMID:19154421

Villemejane, Julien; Mir, Lluis M

2009-01-01

395

Base pairing and base mis-pairing in nucleic acids  

NASA Technical Reports Server (NTRS)

In recent years we have learned that DNA is conformationally active. It can exist in a number of different stable conformations including both right-handed and left-handed forms. Using single crystal X-ray diffraction analysis we are able to discover not only additional conformations of the nucleic acids but also different types of hydrogen bonded base-base interactions. Although Watson-Crick base pairings are the predominant type of interaction in double helical DNA, they are not the only types. Recently, we have been able to examine mismatching of guanine-thymine base pairs in left-handed Z-DNA at atomic resolution (1A). A minimum amount of distortion of the sugar phosphate backbone is found in the G x T pairing in which the bases are held together by two hydrogen bonds in the wobble pairing interaction. Because of the high resolution of the analysis we can visualize water molecules which fill in to accommodate the other hydrogen bonding positions in the bases which are not used in the base-base interactions. Studies on other DNA oligomers have revealed that other types of non-Watson-Crick hydrogen bonding interactions can occur. In the structure of a DNA octamer with the sequence d(GCGTACGC) complexed to an antibiotic triostin A, it was found that the two central AT base pairs are held together by Hoogsteen rather than Watson-Crick base pairs. Similarly, the G x C base pairs at the ends are also Hoogsteen rather than Watson-Crick pairing. Hoogsteen base pairs make a modified helix which is distinct from the Watson-Crick double helix.

Wang, A. H. J.; Rich, A.

1986-01-01

396

Chance and necessity in the selection of nucleic acid catalysts  

NASA Technical Reports Server (NTRS)

In Tom Stoppard's famous play [Rosencrantz and Guildenstern are Dead], the ill-fated heroes toss a coin 101 times. The first 100 times they do so the coin lands heads up. The chance of this happening is approximately 1 in 10(30), a sequence of events so rare that one might argue that it could only happen in such a delightful fiction. Similarly rare events, however, may underlie the origins of biological catalysis. What is the probability that an RNA, DNA, or protein molecule of a given random sequence will display a particular catalytic activity? The answer to this question determines whether a collection of such sequences, such as might result from prebiotic chemistry on the early earth, is extremely likely or unlikely to contain catalytically active molecules, and hence whether the origin of life itself is a virtually inevitable consequence of chemical laws or merely a bizarre fluke. The fact that a priori estimates of this probability, given by otherwise informed chemists and biologists, ranged from 10(-5) to 10(-50), inspired us to begin to address the question experimentally. As it turns out, the chance that a given random sequence RNA molecule will be able to catalyze an RNA polymerase-like phosphoryl transfer reaction is close to 1 in 10(13), rare enough, to be sure, but nevertheless in a range that is comfortably accessible by experiment. It is the purpose of this Account to describe the recent advances in combinatorial biochemistry that have made it possible for us to explore the abundance and diversity of catalysts existing in nucleic acid sequence space.

Lorsch, J. R.; Szostak, J. W.

1996-01-01

397

Intracellular fate of spherical nucleic acid nanoparticle conjugates.  

PubMed

Spherical nucleic acid (SNA) nanoparticle conjugates are a class of bionanomaterials that are extremely potent in many biomedical applications. Their unique ability to enter multiple mammalian cell types as single-entity agents arises from their novel three-dimensional architecture, which consists of a dense shell of highly oriented oligonucleotides chemically attached typically to a gold nanoparticle core. This architecture allows SNAs to engage certain cell surface receptors to facilitate entry. Here, we report studies aimed at determining the intracellular fate of SNAs and the trafficking events that occur inside C166 mouse endothelial cells after cellular entry. We show that SNAs traffic through the endocytic pathway into late endosomes and reside there for up to 24 h after incubation. Disassembly of oligonucleotides from the nanoparticle core is observed 16 h after cellular entry, most likely due to degradation by enzymes such as DNase II localized in late endosomes. Our observations point to these events being likely independent of core composition and treatment conditions, and they do not seem to be particularly dependent upon oligonucleotide sequence. Significantly and surprisingly, the SNAs do not enter the lysosomes under the conditions studied. To independently track the fate of the particle core and the fluorophore-labeled oligonucleotides that comprise its shell, we synthesized a novel class of quantum dot SNAs to determine that as the SNA structures are broken down over the 24 h time course of the experiment, the oligonucleotide fragments are recycled out of the cell while the nanoparticle core is not. This mechanistic insight points to the importance of designing and synthesizing next-generation SNAs that can bypass the degradation bottleneck imposed by their residency in late endosomes, and it also suggests that such structures might be extremely useful for endosomal signaling pathways by engaging receptors that are localized within the endosome. PMID:24841494

Wu, Xiaochen A; Choi, Chung Hang J; Zhang, Chuan; Hao, Liangliang; Mirkin, Chad A

2014-05-28

398

Intracellular Fate of Spherical Nucleic Acid Nanoparticle Conjugates  

PubMed Central

Spherical nucleic acid (SNA) nanoparticle conjugates are a class of bionanomaterials that are extremely potent in many biomedical applications. Their unique ability to enter multiple mammalian cell types as single-entity agents arises from their novel three-dimensional architecture, which consists of a dense shell of highly oriented oligonucleotides chemically attached typically to a gold nanoparticle core. This architecture allows SNAs to engage certain cell surface receptors to facilitate entry. Here, we report studies aimed at determining the intracellular fate of SNAs and the trafficking events that occur inside C166 mouse endothelial cells after cellular entry. We show that SNAs traffic through the endocytic pathway into late endosomes and reside there for up to 24 h after incubation. Disassembly of oligonucleotides from the nanoparticle core is observed 16 h after cellular entry, most likely due to degradation by enzymes such as DNase II localized in late endosomes. Our observations point to these events being likely independent of core composition and treatment conditions, and they do not seem to be particularly dependent upon oligonucleotide sequence. Significantly and surprisingly, the SNAs do not enter the lysosomes under the conditions studied. To independently track the fate of the particle core and the fluorophore-labeled oligonucleotides that comprise its shell, we synthesized a novel class of quantum dot SNAs to determine that as the SNA structures are broken down over the 24 h time course of the experiment, the oligonucleotide fragments are recycled out of the cell while the nanoparticle core is not. This mechanistic insight points to the importance of designing and synthesizing next-generation SNAs that can bypass the degradation bottleneck imposed by their residency in late endosomes, and it also suggests that such structures might be extremely useful for endosomal signaling pathways by engaging receptors that are localized within the endosome. PMID:24841494

Zhang, Chuan; Hao, Liangliang; Mirkin, Chad A.

2014-01-01

399

Multiplexed analysis of genes using nucleic acid-stabilized silver-nanocluster quantum dots.  

PubMed

Luminescent nucleic acid-stabilized Ag nanoclusters (Ag NCs) are applied for the optical detection of DNA and for the multiplexed analysis of genes. Two different sensing modules including Ag NCs as luminescence labels are described. One sensing module involves the assembly of a three-component sensing module composed of a nucleic acid-stabilized Ag NC and a quencher-modified nucleic acid hybridized with a nucleic acid scaffold that is complementary to the target DNA. The luminescence of the Ag NCs is quenched in the sensing module nanostructure. The strand displacement of the scaffold by the target DNA separates the nucleic acid-functionalized Ag NCs, leading to the turned-on luminescence of the NCs and to the optical readout of the sensing process. By implementing two different-sized Ag NC-modified sensing modules, the parallel multiplexed analysis of two genes (the Werner Syndrome gene and the HIV, human immunodeficiency, gene), using 615 and 560 nm luminescent Ag NCs, is demonstrated. The second sensing module includes the nucleic acid functionalized Ag NCs and the quencher-modified nucleic acid hybridized with a hairpin DNA scaffold. The luminescence of the Ag NCs is quenched in the sensing module. Opening of the hairpin by the target DNA triggers the luminescence of the Ag NCs, due to the spatial separation of the Ag NCs/quencher units. The system is applied for the optical detection of the BRAC1 gene. In addition, by implementing two-sized Ag NCs, the multiplexed analysis of two genes by the hairpin sensing module approach is demonstrated. PMID:25327411

Enkin, Natalie; Wang, Fuan; Sharon, Etery; Albada, H Bauke; Willner, Itamar

2014-11-25

400

Experimental characterization of the human non-sequence-specific nucleic acid interactome  

PubMed Central

Background The interactions between proteins and nucleic acids have a fundamental function in many biological processes, including gene transcription, RNA homeostasis, protein translation and pathogen sensing for innate immunity. While our knowledge of the ensemble of proteins that bind individual mRNAs in mammalian cells has been greatly augmented by recent surveys, no systematic study on the non-sequence-specific engagement of native human proteins with various types of nucleic acids has been reported. Results We designed an experimental approach to achieve broad coverage of the non-sequence-specific RNA and DNA binding space, including methylated cytosine, and tested for interaction potential with the human proteome. We used 25 rationally designed nucleic acid probes in an affinity purification mass spectrometry and bioinformatics workflow to identify proteins from whole cell extracts of three different human cell lines. The proteins were profiled for their binding preferences to the different general types of nucleic acids. The study identified 746 high-confidence direct binders, 139 of which were novel and 237 devoid of previous experimental evidence. We could assign specific affinities for sub-types of nucleic acid probes to 219 distinct proteins and individual domains. The evolutionarily conserved protein YB-1, previously associated with cancer and drug resistance, was shown to bind methylated cytosine preferentially, potentially conferring upon YB-1 an epigenetics-related function. Conclusions The dataset described here represents a rich resource of experimentally determined nucleic acid-binding proteins, and our methodology has great potential for further exploration of the interface between the protein and nucleic acid realms. PMID:23902751

2013-01-01

401

Optimizing Scoring Function of Protein-Nucleic Acid Interactions with Both Affinity and Specificity  

PubMed Central

Protein-nucleic acid (protein-DNA and protein-RNA) recognition is fundamental to the regulation of gene expression. Determination of the structures of the protein-nucleic acid recognition and insight into their interactions at molecular level are vital to understanding the regulation function. Recently, quantitative computational approach has been becoming an alternative of experimental technique for predicting the structures and interactions of biomolecular recognition. However, the progress of protein-nucleic acid structure prediction, especially protein-RNA, is far behind that of the protein-ligand and protein-protein structure predictions due to the lack of reliable and accurate scoring function for quantifying the protein-nucleic acid interactions. In this work, we developed an accurate scoring function (named as SPA-PN, SPecificity and Affinity of the Protein-Nucleic acid interactions) for protein-nucleic acid interactions by incorporating both the specificity and affinity into the optimization strategy. Specificity and affinity are two requirements of highly efficient and specific biomolecular recognition. Previous quantitative descriptions of the biomolecular interactions considered the affinity, but often ignored the specificity owing to the challenge of specificity quantification. We applied our concept of intrinsic specificity to connect the conventional specificity, which circumvents the challenge of specificity quantification. In addition to the affinity optimization, we incorporated the quantified intrinsic specificity into the optimization strategy of SPA-PN. The testing results and comparisons with other scoring functions validated that SPA-PN performs well on both the prediction of binding affinity and identification of native conformation. In terms of its performance, SPA-PN can be widely used to predict the protein-nucleic acid structures and quantify their interactions. PMID:24098651

Yan, Zhiqiang; Wang, Jin

2013-01-01

402

Comparison of methods in the recovery of nucleic acids from archival formalin-fixed paraffin-embedded autopsy tissues.  

PubMed

Archival formalin-fixed paraffin-embedded (FFPE) human tissue collections are typically in poor states of storage across the developing world. With advances in biomolecular techniques, these extraordinary and virtually untapped resources have become an essential part of retrospective epidemiological studies. To successfully use such tissues in genomic studies, scientists require high nucleic acid yields and purity. In spite of the increasing number of FFPE tissue kits available, few studies have analyzed their applicability in recovering high-quality nucleic acids from archived human autopsy samples. Here we provide a study involving 10 major extraction methods used to isolate total nucleic acid from FFPE tissues ranging in age from 3 to 13years. Although all 10 methods recovered quantifiable amounts of DNA, only 6 recovered quantifiable RNA, varying considerably and generally yielding lower DNA concentrations. Overall, we show quantitatively that TrimGen's WaxFree method and our in-house phenol-chloroform extraction method recovered the highest yields of amplifiable DNA, with considerable polymerase chain reaction (PCR) inhibition, whereas Ambion's RecoverAll method recovered the most amplifiable RNA. PMID:20079706

Okello, John B A; Zurek, Jaymi; Devault, Alison M; Kuch, Melanie; Okwi, Andrew L; Sewankambo, Nelson K; Bimenya, Gabriel S; Poinar, Debi; Poinar, Hendrik N

2010-05-01

403

[Genotoxic modification of nucleic acid bases and biological consequences of it. Review and prospects of experimental and computational investigations  

NASA Technical Reports Server (NTRS)

The review is presented of experimental and computational data on the influence of genotoxic modification of bases (deamination, alkylation, oxidation) on the structure and biological functioning of nucleic acids. Pathways are discussed for the influence of modification on coding properties of bases, on possible errors of nucleic acid biosynthesis, and on configurations of nucleotide mispairs. The atomic structure of nucleic acid fragments with modified bases and the role of base damages in mutagenesis and carcinogenesis are considered.

Poltev, V. I.; Bruskov, V. I.; Shuliupina, N. V.; Rein, R.; Shibata, M.; Ornstein, R.; Miller, J.

1993-01-01

404

Nucleic acid-induced antiviral immunity in invertebrates: an evolutionary perspective.  

PubMed

Nucleic acids derived from viral pathogens are typical pathogen associated molecular patterns (PAMPs). In mammals, the recognition of viral nucleic acids by pattern recognition receptors (PRRs), which include Toll-like receptors (TLRs) and retinoic acid-inducible gene (RIG)-I-like receptors (RLRs), induces the release of inflammatory cytokines and type I interferons (IFNs) through the activation of nuclear factor ?B (NF-?B) and interferon regulatory factor (IRF) 3/7 pathways, triggering the host antiviral state. However, whether nucleic acids can induce similar antiviral immunity in invertebrates remains ambiguous. Several studies have reported that nucleic acid mimics, especially dsRNA mimic poly(I:C), can strongly induce non-specific antiviral immune responses in insects, shrimp, and oyster. This behavior shows multiple similarities to the hallmarks of mammalian IFN responses. In this review, we highlight the current understanding of nucleic acid-induced antiviral immunity in invertebrates. We also discuss the potential recognition and regulatory mechanisms that confer non-specific antiviral immunity on invertebrate hosts. PMID:24685509

Wang, Pei-Hui; Weng, Shao-Ping; He, Jian-Guo

2015-02-01

405

Variables Influencing Extraction of Nucleic Acids from Microbial Plankton (Viruses, Bacteria, and Protists) Collected on Nanoporous Aluminum Oxide Filters  

PubMed Central

Anodic aluminum oxide (AAO) filters have high porosity and can be manufactured with a pore size that is small enough to quantitatively capture viruses. These properties make the filters potentially useful for harvesting total microbial communities from water samples for molecular analyses, but their performance for nucleic acid extraction has not been systematically or quantitatively evaluated. In this study, we characterized the flux of water through commercially produced nanoporous (0.02 ?m) AAO filters (Anotop; Whatman) and used isolates (a virus, a bacterium, and a protist) and natural seawater samples to test variables that we expected would influence the efficiency with which nucleic acids are recovered from the filters. Extraction chemistry had a significant effect on DNA yield, and back flushing the filters during extraction was found to improve yields of high-molecular-weight DNA. Using the back-flush protocol, the mass of DNA recovered from microorganisms collected on AAO filters was ?100% of that extracted from pellets of cells and viruses and 94% ± 9% of that obtained by direct extraction of a liquid bacterial culture. The latter is a minimum estimate of the relative recovery of microbial DNA, since liquid cultures include dissolved nucleic acids that are retained inefficiently by the filter. In conclusion, we demonstrate that nucleic acids can be extracted from microorganisms on AAO filters with an efficiency similar to that achievable by direct extraction of microbes in suspension or in pellets. These filters are therefore a convenient means by which to harvest total microbial communities from multiple aqueous samples in parallel for subsequent molecular analyses. PMID:24747903

Mueller, Jaclyn A.; Culley, Alexander I.

2014-01-01

406

Variables influencing extraction of nucleic acids from microbial plankton (viruses, bacteria, and protists) collected on nanoporous aluminum oxide filters.  

PubMed

Anodic aluminum oxide (AAO) filters have high porosity and can be manufactured with a pore size that is small enough to quantitatively capture viruses. These properties make the filters potentially useful for harvesting total microbial communities from water samples for molecular analyses, but their performance for nucleic acid extraction has not been systematically or quantitatively evaluated. In this study, we characterized the flux of water through commercially produced nanoporous (0.02 ?m) AAO filters (Anotop; Whatman) and used isolates (a virus, a bacterium, and a protist) and natural seawater samples to test variables that we expected would influence the efficiency with which nucleic acids are recovered from the filters. Extraction chemistry had a significant effect on DNA yield, and back flushing the filters during extraction was found to improve yields of high-molecular-weight DNA. Using the back-flush protocol, the mass of DNA recovered from microorganisms collected on AAO filters was ? 100% of that extracted from pellets of cells and viruses and 94% ± 9% of that obtained by direct extraction of a liquid bacterial culture. The latter is a minimum estimate of the relative recovery of microbial DNA, since liquid cultures include dissolved nucleic acids that are retained inefficiently by the filter. In conclusion, we demonstrate that nucleic acids can be extracted from microorganisms on AAO filters with an efficiency similar to that achievable by direct extraction of microbes in suspension or in pellets. These filters are therefore a convenient means by which to harvest total microbial communities from multiple aqueous samples in parallel for subsequent molecular analyses. PMID:24747903

Mueller, Jaclyn A; Culley, Alexander I; Steward, Grieg F

2014-07-01

407

Synthesis of reactive nucleic acid analogues and their application for the study of structure and functions of biopolymers  

NASA Astrophysics Data System (ADS)

Data on the synthesis of reactive derivatives of nucleic acid analogues and their application for the study of structure and functions of biopolymers are generalised. The main types of such analogues including photoactivated reagents containing azidoaryl, halogeno, and thiol groups, psoralen and its derivatives, platinum-based reagents, and nucleic acid analogues containing substituted pyrophosphate or acyl phosphate internucleotide groups are presented. The mechanisms of interaction of these compounds with proteins and nucleic acids are considered. The prospects for the in vivo application of reactive nucleic acids in various systems are discussed. The bibliography includes 76 references.

Kanevskii, Igor'E.; Kuznetsova, Svetlana A.

1998-07-01

408

Biomedical publications of Prof. David N. Nikogosyan, made in UCC UV-induced nucleic acid-protein cross-linking  

E-print Network

Biomedical publications of Prof. David N. Nikogosyan, made in UCC UV-induced nucleic acid-protein cross-linking 1. E.N. Dobrov, D.N. Nikogosyan: UV-induced nucleic acid-protein cross-linking: manual acids in collagen. J. Photochem. Photobiol. B: Biol., 47(1), 63-67 (1998) 2. D.N. Nikogosyan, H. Görner

Nikogosyan, David N.

409

Influence of Plasma Processing on Recovery and Analysis of Circulating Nucleic Acids  

PubMed Central

Circulating nucleic acids (CNAs) are under investigation as a liquid biopsy in cancer. However there is wide variation in blood processing and methods for isolation of circulating free DNA (cfDNA) and microRNAs (miRNAs). Here we compare the extraction efficiency and reproducibility of 4 commercially available kits for cfDNA and 3 for miRNA using spike-in of reference templates. We also compare the effects of increasing time between venepuncture and centrifugation and differential centrifugation force on recovery of CNAs. cfDNA was quantified by TaqMan qPCR and targeted deep sequencing. miRNA profiles were assessed with TaqMan low-density arrays and assays. The QIAamp® DNA Blood Mini and Circulating nucleic acid kits gave the highest recovery of cfDNA and efficient recovery (>90%) of a 564bp spike-in. Moreover, targeted sequencing revealed overlapping cfDNA profiles and variant depth, including detection of HER2 gene amplification, using the Ion AmpliSeq™Cancer Hotspot Panel v2. Highest yields of miRNA and the synthetic Arabidopsis thaliana miR-159a spike-in were obtained using the miRNeasy Serum/Plasma kit, with saturation above 200 µl of plasma. miRNA profiles showed significant variation with increasing time before centrifugation (p<0.001) and increasing centrifugation force, with depletion of platelet associated miRNAs, whereas cfDNA was unaffected. However, sample replicates showed excellent reproducibility on TaqMan low density arrays (? = 0.96, p<0.0001). We also successfully generated miRNA profiles for plasma samples stored > 12 years, highlighting the potential for analysis of stored sample biobanks. In the era of the liquid biopsy, standardisation of methods is required to minimise variation, particularly for miRNA. PMID:24205045

Zahra, Nathalie; Primrose, Lindsay; Elshaw, Shona R.; Pringle, J. Howard; Blighe, Kevin; Marchese, Stephanie D.; Hills, Allison; Woodley, Laura; Stebbing, Justin; Coombes, R. Charles; Shaw, Jacqueline A.

2013-01-01

410

[Circulating nucleic acids in blood of patients with stomach and colon neoplasms].  

PubMed

Concentrations of extracellular deoxy- and ribonucleic acids in blood plasma and cell-surface-bound of blood cells were investigated in healthy donors and patients with malignant gastrointestinal tumors. Our results indicate that high concentration of extracellular DNA in blood plasma along with decreased level of extracellular RNA on the surface of blood cells correlate with development of gastrointestinal cancer. Ratio of nucleic acids in plasma to total amount of nucleic acids circulated in blood is a characteristic parameter distinguishing cancer patients from healthy persons. PMID:16104395

Tamkovich, S N; Bryzgunova, O E; Rykova, E Iu; Kolesnikova, E V; Shelestiuk, P I; Laktionov, P P; Vlasov, V V

2005-01-01

411

Recent Advances in Delivery of Drug-Nucleic Acid Combinations for Cancer Treatment  

PubMed Central

Cancer treatment that uses a combination of approaches with the ability to affect multiple disease pathways has been proven highly effective in the treatment of many cancers. Combination therapy can include multiple chemotherapeutics or combinations of chemotherapeutics with other treatment modalities like surgery or radiation. However, despite the widespread clinical use of combination therapies, relatively little attention has been given to the potential of modern nanocarrier delivery methods, like liposomes, micelles, and nanoparticles, to enhance the efficacy of combination treatments. This lack of knowledge is particularly notable in the limited success of vectors for the delivery of combinations of nucleic acids with traditional small molecule drugs. The delivery of drug-nucleic acid combinations is particularly challenging due to differences in the physicochemical properties of the two types of agents. This review discusses recent advances in the development of delivery methods using combinations of small molecule drugs and nucleic acid therapeutics to treat cancer. This review primarily focuses on the rationale used for selecting appropriate drug-nucleic acid combinations as well as progress in the development of nanocarriers suitable for simultaneous delivery of drug-nucleic acid combinations. PMID:23624358

Li, Jing; Wang, Yan; Zhu, Yu; Oupický, David

2013-01-01

412

Phytoagents for Cancer Management: Regulation of Nucleic Acid Oxidation, ROS, and Related Mechanisms  

PubMed Central

Accumulation of oxidized nucleic acids causes genomic instability leading to senescence, apoptosis, and tumorigenesis. Phytoagents are known to reduce the risk of cancer development; whether such effects are through regulating the extent of nucleic acid oxidation remains unclear. Here, we outlined the role of reactive oxygen species in nucleic acid oxidation as a driving force in cancer progression. The consequential relationship between genome instability and cancer progression highlights the importance of modulation of cellular redox level in cancer management. Current epidemiological and experimental evidence demonstrate the effects and modes of action of phytoagents in nucleic acid oxidation and provide rationales for the use of phytoagents as chemopreventive or therapeutic agents. Vitamins and various phytoagents antagonize carcinogen-triggered oxidative stress by scavenging free radicals and/or activating endogenous defence systems such as Nrf2-regulated antioxidant genes or pathways. Moreover, metal ion chelation by phytoagents helps to attenuate oxidative DNA damage caused by transition metal ions. Besides, the prooxidant effects of some phytoagents pose selective cytotoxicity on cancer cells and shed light on a new strategy of cancer therapy. The “double-edged sword” role of phytoagents as redox regulators in nucleic acid oxidation and their possible roles in cancer prevention or therapy are discussed in this review. PMID:24454991

Shyur, Lie-Fen

2013-01-01

413

Cationic liposome-nucleic acid complexes: liquid crystal phases with applications in gene therapy  

PubMed Central

Cationic liposome (CL) carriers of nucleic acids are primarily studied because of their applications in gene delivery and gene silencing with CL-DNA and CL-siRNA (short-interfering RNA) complexes, respectively, and their implications to ongoing clinical gene therapy trials worldwide. A series of synchrotron-based small-angle-x-ray scattering studies, dating back to 1997, has revealed that CL-nucleic acid complexes spontaneously assemble into distinct novel liquid crystalline phases of matter. Significantly, transfection efficiency (TE; a measure of expression of an exogenous gene that is transferred into the cell by the lipid carrier) has been found to be dependent on the liquid crystalline structure of complexes, with lamellar complexes showing strong dependence on membrane charge density (?M) and non-lamellar complexes exhibiting TE behavior independent of?M. The review describes our current understanding of the structures of different liquid crystalline CL-nucleic acid complexes including the recently described gyroid cubic phase of CL-siRNA complexes used in gene silencing. It further makes apparent that the long-term goal of developing optimized liquid crystalline CL-nucleic acid complexes for successful medical applications requires a comprehensive understanding of the nature of the interactions of distinctly structured complexes with cell membranes and events leading to release of active nucleic acids within the cell cytoplasm. PMID:22778490

Safinya, C. R.; Ewert, K. K.; Leal, Cecília

2011-01-01

414

In search of the nature of specific nucleic acid-protein interactions.  

PubMed

The theory of "codon-amino acid coevolution" was first proposed by Woese in 1967. It suggests that there is a stereochemical matching - that is, affinity - between amino acids and certain of the base triplet sequences that code for those amino acids. We have constructed a Common Periodic Table of Codons and Amino Acids, where the Nucleic Acid Table showed perfect axial symmetry for codons and the corresponding Amino Acid Table also displayed periodicity regarding the biochemical properties (charge and hydrophobicity) of the 20 amino acids and the position of the stop signals. The Table indicates that the middle (2nd) amino acid in the codon has a prominent role in determining some of the structural features of the amino acids. The possibility that physical contact between codons and amino acids might exist was tested on restriction enzymes. Many recognition site-like sequences were found in the coding sequences of these enzymes and as many as 73 examples of codon-amino acid co-location were observed in the 7 known 3D structures (December 2003) of endonuclease-nucleic acid complexes. These results indicate that the smallest possible units of specific nucleic acid-protein interaction are indeed the stereochemically compatible codons and amino acids. PMID:16003939

Biro, J C; Benyó, Z; Sansom, C; Benyó, B

2005-01-01

415

Identification of Dekkera bruxellensis (Brettanomyces) from Wine by Fluorescence In Situ Hybridization Using Peptide Nucleic Acid Probes  

PubMed Central

A new fluorescence in situ hybridization method using peptide nucleic acid (PNA) probes for identification of Brettanomyces is described. The test is based on fluorescein-labeled PNA probes targeting a species-specific sequence of the rRNA of Dekkera bruxellensis. The PNA probes were applied to smears of colonies, and results were interpreted by fluorescence microscopy. The results obtained from testing 127 different yeast strains, including 78 Brettanomyces isolates from wine, show that the spoilage organism Brettanomyces belongs to the species D. bruxellensis and that the new method is able to identify Brettanomyces (D. bruxellensis) with 100% sensitivity and 100% specificity. PMID:11157265

Stender, Henrik; Kurtzman, Cletus; Hyldig-Nielsen, Jens J.; Sørensen, Ditte; Broomer, Adam; Oliveira, Kenneth; Perry-O'Keefe, Heather; Sage, Andrew; Young, Barbara; Coull, James

2001-01-01

416

Microwell array-mediated delivery of lipoplexes containing nucleic acids for enhanced therapeutic efficacy.  

PubMed

Many delivery methods have been developed to improve the therapeutic efficacy and facilitate the clinical translation of nucleic acids-based therapeutics. We present a facile microwell array to mediate the delivery of nucleic acids carried by lipoplexes, which combines the advantages of lipoplexes as an efficient carrier system, the surface mediated delivery, and the control of surface topography. This method shows much higher transfection efficiency than conventional transfection method for oligodeoxynucleotides and microRNAs, and thus significantly reduces the effective therapeutic dosages. Microwell array is also a very flexible platform. Multifunctional lipoplexes containing both nucleic acid therapeutics and imaging reagents can be easily prepared in the microwell array and efficiently delivered to cells, demonstrating its potential applications in theranostic medicine. PMID:25319649

Wu, Yun; Gallego-Perez, Daniel; Lee, L James

2015-01-01

417

Analyses of nuclear proteins and nucleic Acid structures using atomic force microscopy.  

PubMed

Since the inception of atomic force microscopy (AFM) in 1986, the value of this technology for exploring the structure and biophysical properties of a variety of biological samples has been increasingly recognized. AFM provides the opportunity to both image samples at nanometer resolution and also measure the forces on the surface of the sample. Here, we describe a variety of methods for studying nuclear samples including single nucleic acid molecules, higher-order chromatin structures, the nucleolus, and the nucleus. Protocols to prepare nucleic acids, nucleic acid-protein complexes, reconstituted chromatin, the cell nucleus, and the nucleolus are included, as well as protocols describing how to prepare the AFM substrate and the AFM tip. Finally, we describe how to perform conventional imaging, high-speed imaging, recognition imaging, force spectroscopy, and nanoindentation experiments. PMID:25555579

Gilmore, Jamie L; Yoshida, Aiko; Takahashi, Hirohide; Deguchi, Katashi; Kobori, Toshiro; Louvet, Emilie; Kumeta, Masahiro; Yoshimura, Shige H; Takeyasu, Kunio

2015-01-01

418

Development of Chemiluminescent Lateral Flow Assay for the Detection of Nucleic Acids  

PubMed Central

Rapid, sensitive detection methods are of utmost importance for the identification of pathogens related to health and safety. Herein we report the development of a nucleic acid sequence-based lateral flow assay which achieves a low limit of detection using chemiluminescence. On-membrane enzymatic signal amplification is used to reduce the limit of detection to the sub-femtomol level. To demonstrate this assay, we detected synthetic nucleic acid sequences representative of Trypanosoma mRNA, the causative agent for African sleeping sickness, with relevance in human and animal health in sub-Saharan Africa. The intensity of the chemiluminescent signal was evaluated by using a charge-coupled device as well as a microtiter plate reader. We demonstrated that our lateral flow chemiluminescent assay has a very low limit of detection and is easy to use. The limit of detection was determined to be 0.5 fmols of nucleic acid target.

Wang, Yuhong; Fill, Catherine; Nugen, Sam R.

2012-01-01

419

Fluorescence enhancement of yttrium(III)-rutin by nucleic acids in the presence of cetyltrimethylammonium bromide  

NASA Astrophysics Data System (ADS)

It is found that nucleic acids can enhance the fluorescence intensity of yttrium(III) (Y 3+)-rutin in presence of cetyltrimethylammonium bromide (CTMAB) system. In hexamethylenetetramine (HMTA)-HCl buffer, the maximum enhanced fluorescence is produced, with maximum excitation and emission wavelengths at 452 and 520 nm, respectively. Based on this, a new fluorimetric method of determination of nucleic acids is proposed. Under optimum conditions, the enhanced fluorescence intensity is proportion to the concentration of nucleic acids in the range of 1.0 × 10 -7 to 1.0 × 10 -5 g/ml for fish sperm DNA (fsDNA), 1.0 × 10 -7 to 4.6 × 10 -6 g/ml for yeast RNA (yRNA), their detection limits (S/N = 3) are 7.5 × 10 -8, 8.0 × 10 -8 g/ml, respectively. The interaction mechanism is also studied.

Wu, Xia; Guo, Changying; Wang, Fei; Yang, Jinghe; Ran, Dehuan; Zheng, Jinhua; Wu, Jinbo

2006-11-01

420

Advances in polymeric and inorganic vectors for nonviral nucleic acid delivery  

PubMed Central

Nonviral systems for nucleic acid delivery offer a host of potential advantages compared with viruses, including reduced toxicity and immunogenicity, increased ease of production and less stringent vector size limitations, but remain far less efficient than their viral counterparts. In this article we review recent advances in the delivery of nucleic acids using polymeric and inorganic vectors. We discuss the wide range of materials being designed and evaluated for these purposes while considering the physical requirements and barriers to entry that these agents face and reviewing recent novel approaches towards improving delivery with respect to each of these barriers. Furthermore, we provide a brief overview of past and ongoing nonviral gene therapy clinical trials. We conclude with a discussion of multifunctional nucleic acid carriers and future directions. PMID:22826857

Sunshine, Joel C; Bishop, Corey J; Green, Jordan J

2014-01-01

421

Spherical Nucleic Acid Nanoparticle Conjugates Enhance G-Quadruplex Formation and Increase Serum Protein Interactions**  

PubMed Central

To understand the effect of three-dimensional oligonucleotide structure on protein corona formation, we studied the identity and quantity of human serum proteins that bind to spherical nucleic acid (SNA) nanoparticle conjugates. SNAs exhibit cellular uptake properties that are remarkably different from those of linear nucleic acids, which have been related to their interaction with certain classes of proteins. Through a proteomic analysis, this work shows that the protein binding properties of SNAs are sequence-specific and supports the conclusion that the oligonucleotide tertiary structure can significantly alter the chemical composition of the SNA protein corona. This knowledge will impact our understanding of how nucleic acid-based nanostructures, and SNAs in particular, function in complex biological milieu. PMID:25393322

Chinen, Alyssa B.; Guan, Chenxia M.

2014-01-01

422

Spherical nucleic Acid nanoparticle conjugates enhance g-quadruplex formation and increase serum protein interactions.  

PubMed

To understand the effect of three-dimensional oligonucleotide structure on protein corona formation, we studied the identity and quantity of human serum proteins that bind to spherical nucleic acid (SNA) nanoparticle conjugates. SNAs exhibit cellular uptake properties that are remarkably different from those of linear nucleic acids, which have been related to their interaction with certain classes of proteins. Through a proteomic analysis, this work shows that the protein binding properties of SNAs are sequence-specific and supports the conclusion that the oligonucleotide tertiary structure can significantly alter the chemical composition of the SNA protein corona. This knowledge will impact our understanding of how nucleic acid-based nanostructures, and SNAs in particular, function in complex biological milieu. PMID:25393322

Chinen, Alyssa B; Guan, Chenxia M; Mirkin, Chad A

2015-01-01

423

Intracellular mRNA regulation with self-assembled locked nucleic acid polymer nanoparticles.  

PubMed

We present an untemplated, single-component antisense oligonucleotide delivery system capable of regulating mRNA abundance in live human cells. While most approaches to nucleic acid delivery rely on secondary carriers and complex multicomponent charge-neutralizing formulations, we demonstrate efficient delivery using a simple locked nucleic acid (LNA)-polymer conjugate that assembles into spherical micellar nanoparticles displaying a dense shell of nucleic acid at the surface. Cellular uptake of soft LNA nanoparticles occurs rapidly within minutes as evidenced by flow cytometry and fluorescence microscopy. Importantly, these LNA nanoparticles knockdown survivin mRNA, an established target for cancer therapy, in a sequence-specific fashion as analyzed by RT-PCR. PMID:24827740

Rush, Anthony M; Nelles, David A; Blum, Angela P; Barnhill, Sarah A; Tatro, Erick T; Yeo, Gene W; Gianneschi, Nathan C

2014-05-28

424

Beyond DNA origami: A look on the bright future of nucleic acid nanotechnology  

PubMed Central

Nucleic acid nanotechnology exploits the programmable molecular recognition properties of natural and synthetic nucleic acids to assemble structures with nanometer-scale precision. In 2006, DNA origami transformed the field by providing a versatile platform for self-assembly of arbitrary shapes from one long DNA strand held in place by hundreds of short, site-specific (spatially addressable) DNA ”staples”. This revolutionary approach has led to the creation of a multitude of 2D and 3D scaffolds that form the basis for functional nanodevices. Not limited to nucleic acids, these nanodevices can incorporate other structural and functional materials, such as proteins and nanoparticles, making them broadly useful for current and future applications in emerging fields such as nanomedicine, nanoelectronics, and alternative energy. PMID:22131292

Michelotti, Nicole; Johnson-Buck, Alexander; Manzo, Anthony J.

2012-01-01

425

Salt Contribution to the Flexibility of Single-stranded Nucleic Acid of Finite Length  

E-print Network

Nucleic acids are negatively charged macromolecules and their structure properties are strongly coupled to metal ions in solutions. In this paper, the salt effects on the flexibility of single stranded (ss) nucleic acid chain ranging from 12 to 120 nucleotides are investigated systematically by the coarse grained Monte Carlo simulations where the salt ions are considered explicitly and the ss chain is modeled with the virtual bond structural model. Our calculations show that, the increase of ion concentration causes the structural collapse of ss chain and multivalent ions are much more efficient in causing such collapse, and trivalent and small divalent ions can both induce more compact state than a random relaxation state. We found that monovalent, divalent and trivalent ions can all overcharge ss chain, and the dominating source for such overcharging changes from ion exclusion volume effect to ion Coulomb correlations. In addition, the predicted Na and Mg dependent persistence length lp of ss nucleic acid a...

Wang, Feng-Hua; Tan, Zhi-Jie

2012-01-01

426

Nucleic acid structure characterization by small angle X-ray scattering (SAXS)  

PubMed Central

Small angle X-ray scattering (SAXS) is a powerful method for investigating macromolecular structure in solution. SAXS data provide information about the size and shape of a molecule with a resolution of approximately 2–3 nm. SAXS is particularly useful for the investigation of nucleic acids, which scatter X-rays strongly due to the electron-rich phosphate backbone. Therefore, SAXS has become an increasingly popular method for modeling nucleic acid structures, an endeavor made tractable by the highly regular helical nature of nucleic acid secondary structures. Recently, we used SAXS in combination with NMR to filter and refine all-atom models of a U2/U6 small nuclear RNA complex. In this unit we present general protocols for sample preparation, data acquisition, and data analysis and processing. Additionally, examples of correctly and incorrectly processed SAXS data and expected results are provided. PMID:23255205

Burke, Jordan E.; Butcher, Samuel E.

2013-01-01

427

Visualising single molecules of HIV-1 and miRNA nucleic acids  

PubMed Central

Background The scarcity of certain nucleic acid species and the small size of target sequences such as miRNA, impose a significant barrier to subcellular visualization and present a major challenge to cell biologists. Here, we offer a generic and highly sensitive visualization approach (oligo fluorescent in situ hybridization, O-FISH) that can be used to detect such nucleic acids using a single-oligonucleotide probe of 19–26 nucleotides in length. Results We used O-FISH to visualize miR146a in human and avian cells. Furthermore, we reveal the sensitivity of O-FISH detection by using a HIV-1 model system to show that as little as 1–2 copies of nucleic acids can be detected in a single cell. We were able to discern newly synthesized viral cDNA and, moreover, observed that certain HIV RNA sequences are only transiently available for O-FISH detection. Conclusions Taken together, these results suggest that the O-FISH method can potentially be used for in situ probing of, as few as, 1–2 copies of nucleic acid and, additionally, to visualize small RNA such as miRNA. We further propose that the O-FISH method could be extended to understand viral function by probing newly transcribed viral intermediates; and discern the localisation of nucleic acids of interest. Additionally, interrogating the conformation and structure of a particular nucleic acid in situ might also be possible, based on the accessibility of a target sequence. PMID:23590669

2013-01-01

428

Characterisation of the nucleic-acid-binding activity of KH domains. Different properties of different domains.  

PubMed

The KH module is a sequence motif recently identified in a number of diversified RNA-binding proteins and suggested to be the functional element responsible for RNA binding. So far, however, this hypothesis has not received direct experimental support. We have expressed the three KH-domains from heterogeneous nuclear ribonucleoprotein K (hnRNP-K), the poly(C)-binding proteins PCBP-1 and PCBP-2, the first three to four domains from the high-density binding protein HBP, the one and a half domain from the archaeon Halobacterium halobium ORF139 and one and a half domain of the fragile-X protein FMR1 in Escherichia coli and analysed their nucleic-acid-binding properties in vitro. The results showed that the in vitro poly(rC)-binding activity of hnRNP-K can be assigned to KH-domain 3, whereas both domains 1 and 3 in the PCBPs bind poly(rC). In addition, all these domains exhibit binding activity towards other nucleic acids, albeit at a significantly lower level. The first KH domain from the FMR1 protein binds poly(rG) and single-stranded and double-stranded DNA. The N-terminal three or four domains from HBP bind poly(rG) and, at a much lower level, single-stranded and double-stranded DNA. Thus, single KH domains are discrete and independent nucleic-acid-binding units. Moreover, different KH domains bind different nucleic acids, suggesting that KH domains are composed of a conserved, weakly nucleic-acid-binding, structure that is fine tuned, by sequence variation, resulting in sequence-specific nucleic-acid-binding entities. PMID:8917439

Dejgaard, K; Leffers, H

1996-10-15

429

Photochemistry of nucleic Acid bases and their thio- and aza-analogues in solution.  

PubMed

The steady-state and time-resolved photochemistry of the natural nucleic acid bases and their sulfur- and nitrogen-substituted analogues in solution is reviewed. Emphasis is given to the experimental studies performed over the last 3-5 years that showcase topical areas of scientific inquiry and those that require further scrutiny. Significant progress has been made toward mapping the radiative and nonradiative decay pathways of nucleic acid bases. There is a consensus that ultrafast internal conversion to the ground state is the primary relaxation pathway in the nucleic acid bases, whereas the mechanism of this relaxation and the level of participation of the (1)??*, (1) n?*, and (3)??* states are still matters of debate. Although impressive research has been performed in recent years, the microscopic mechanism(s) by which the nucleic acid bases dissipate excess vibrational energy to their environment, and the role of the N-glycosidic group in this and in other nonradiative decay pathways, are still poorly understood. The simple replacement of a single atom in a nucleobase with a sulfur or nitrogen atom severely restricts access to the conical intersections responsible for the intrinsic internal conversion pathways to the ground state in the nucleic acid bases. It also enhances access to ultrafast and efficient intersystem crossing pathways that populate the triplet manifold in yields close to unity. Determining the coupled nuclear and electronic pathways responsible for the significantly different photochemistry in these nucleic acid base analogues serves as a convenient platform to examine the current state of knowledge regarding the photodynamic properties of the DNA and RNA bases from both experimental and computational perspectives. Further investigations should also aid in forecasting the prospective use of sulfur- and nitrogen-substituted base analogues in photochemotherapeutic applications. PMID:25238718

Pollum, Marvin; Martínez-Fernández, Lara; Crespo-Hernández, Carlos E

2015-01-01

430

Nucleic Acid-based Detection of Bacterial Pathogens Using Integrated Microfluidic Platform Systems  

PubMed Central

The advent of nucleic acid-based pathogen detection methods offers increased sensitivity and specificity over traditional microbiological techniques, driving the development of portable, integrated biosensors. The miniaturization and automation of integrated detection systems presents a significant advantage for rapid, portable field-based testing. In this review, we highlight current developments and directions in nucleic acid-based micro total analysis systems for the detection of bacterial pathogens. Recent progress in the miniaturization of microfluidic processing steps for cell capture, DNA extraction and purification, polymerase chain reaction, and product detection are detailed. Discussions include strategies and challenges for implementation of an integrated portable platform. PMID:22412335

Lui, Clarissa; Cady, Nathaniel C.; Batt, Carl A.

2009-01-01

431

Sfold: Software for Statistical Folding and Rational Design of Nucleic Acids  

NSDL National Science Digital Library

Available free of charge to any researcher for non-commercial applications, Sfold "predicts probable RNA secondary structures, assesses target accessibility, and provides tools for the rational design of RNA-targeting nucleic acids." Sfold is offered through the Wadsworth center of the New York State Department of Health. Sfold application modules allow users to target accessibility prediction and rational design of siRNA, antisense oligonucelotides and nucleic acid probes, _trans_-cleaving ribozymes, and to generate general features and output for statistical RNA folding.

432

Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures  

PubMed Central

The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids. PMID:22525788

šponer, Ji?í; Cang, Xiaohui; Cheatham, Thomas E.

2013-01-01

433

Methods and kits for nucleic acid analysis using fluorescence resonance energy transfer  

DOEpatents

A method for detecting the presence of a target nucleotide or sequence of nucleotides in a nucleic acid is disclosed. The method is comprised of forming an oligonucleotide labeled with two fluorophores on the nucleic acid target site. The doubly labeled oligonucleotide is formed by addition of a singly labeled dideoxynucleoside triphosphate to a singly labeled polynucleotide or by ligation of two singly labeled polynucleotides. Detection of fluorescence resonance energy transfer upon denaturation indicates the presence of the target. Kits are also provided. The method is particularly applicable to genotyping.

Kwok, Pui-Yan (Clayton, MO); Chen, Xiangning (St. Louis, MO)

1999-01-01

434

Highly selective and sensitive nucleic acid detection based on polysaccharide-functionalized silver nanoparticles  

NASA Astrophysics Data System (ADS)

Polysaccharide-functionalized silver nanoparticles (Oc-AgNPs) with a mean diameter of 15 nm were utilized as a novel and effective fluorescence-sensing platform for nucleic acid detection. Tests on the oligonucleotide sequences associated with the human immunodeficiency virus as a model system showed that the Oc-AgNPs effectively absorbed and quenched dye-labeled single-stranded DNA through strong hydrogen bonding interactions and slight electrostatic attractive interactions. The proposed system efficiently differentiated between complementary and mismatched nucleic acid sequences with high selectivity and good reproducibility at room temperature.

Yan, Jing-Kun; Ma, Hai-Le; Cai, Pan-Fu; Wu, Jian-Yong

2015-01-01

435

Nucleic acid and protein structures and interactions in viruses investigated by laser Raman spectroscopy  

NASA Astrophysics Data System (ADS)

Raman spectroscopy may be profitably exploited to determine details of protein and nucleic acid structures and their mutual interactions in viruses and gene regulatory complexes. Present applications use data obtained from model nucleic acid crystals, fibers and solutions to reveal preferred backbone and nucleoside conformations for different morphological states of DNA and RNA in plant (TMV, BDMV) and bacterial viruses (P22, Pfl, Xf, Pf3, fd, Ifl, IKe). Interpretation of the results is enhanced by deconvolution methods which, in favorable cases, permit quantitative conclusions regarding macromolecular structures. Both equilibrium and dynamic Raman applications are described.

Thomas, George J.

1986-03-01

436

Nucleic acids from long-term preserved FFPE tissues are suitable for downstream analyses.  

PubMed

Tissues used for clinical diagnostics are mostly formalin-fixed and paraffin-embedded (FFPE) which provides many advantages. However, the quality of the obtained nucleic acids (NA) is reduced and this turns out to be a challenge for further molecular analyses. Although the spectrum of analyses of NA extracted from FFPE tissue has increased, the standard operating procedures for NA isolation from old tissue blocks still need to be improved. Here, we compared the efficiency of different NA extraction methods, using FFPE tissues of variable age and origin, with respect to downstream analyses. Our study showed that the phenol-chloroform isoamyl alcohol (PCI) and the commercial Qiagen protocol yielded samples with highest purity. The PCI protocol delivered the longest amplicons even from samples from the 1970s. We developed a short (1 h) tissue lysis procedure that turned out to be highly time- and cost-effective when DNA quality was tested using single and multiplex PCR. Compared to a 1-day lysis-protocol, the amplicons were only 100 bp shorter. In addition, single-copy genes used in daily routine were successfully amplified from long-term stored FFPE samples following 1-h tissue-lysis. The RNA integrity numbers (RIN) determined on RNA isolated from FFPE tissues indicated degraded RNA; however, all RINs were above the generally agreed threshold of 1.4. We showed that, depending on the purpose of the analysis, NA retrieved from FFPE tissues older than 40 years may be successfully used for molecular analysis. PMID:22270699

Ludyga, Natalie; Grünwald, Barbara; Azimzadeh, Omid; Englert, Sonja; Höfler, Heinz; Tapio, Soile; Aubele, Michaela

2012-02-01

437

Detecting and genotyping Escherichia coli O157:H7 using multiplexed PCR and nucleic acid microarrays  

SciTech Connect

Rapid detection and characterization of food borne pathogens such as Escherichia coli O157:H7 is crucial for epidemiological investigations and food safety surveillance. As an alternative to conventional technologies, we examined the sensitivity and specificity of nucleic acid microarrays for detecting and genotyping E. coli O157:H7. The array was composed of oligonucleotide probes (25-30 mer) complementary to four virulence loci (intimin, Shiga-like toxins I and II, and hemolysin A). Target DNA was amplified from whole cells or from purified DNA via single or multiplexed polymerase chain reaction (PCR), and PCR products were hybridized to the array without further modification or purification. The array was 32-fold more sensitive than gel electrophoresis and capable of detecting amplification products from < 1 cell equivalent of genomic DNA (1 fg). Immunomagnetic capture, PCR and a microarray were subsequently used to detect 55 CFUs ml-1 (E. coli O157:H7) from chicken rinsate without the aid of pre-enrichment. Four isolates of E. coli O157:H7 and one isolate of O91:H2, for which genotypic data were available, were unambiguously genotyped with this array. Glass based microarrays are relatively simple to construct and provide a rapid and sensitive means to detect multiplexed PCR products and the system is amenable to automation.

Call, Douglas R.; Brockman, Fred J.; Chandler, Darrell P.

2001-07-05

438

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

E-print Network

CINT Science Highlight ­ September 22, 2010 NanoCluster Beacon detects specific nucleic acid target nanoclusters (DNA/Ag NCs) can be used to detect specific nucleic acid targets. The nanoclusters circumvent many nanoclusters (DNA/Ag NCs) between highly fluorescent and weakly fluorescent states. This reversible

439

Evidence for novel viruses by analysis of nucleic acids in virus-like particle fractions from Ambrosia psilostachya  

Microsoft Academic Search

To test the hypothesis that many viruses remain to be discovered in plants, a procedure was developed to sequence nucleic acids cloned randomly from virus-like particle fractions of plant homogenates. As a test of the efficiency of the procedure we targeted Ambrosia psilostachya, western ragweed, plants growing at the Tallgrass Prairie Preserve of northeastern Oklahoma. Amplifiable nucleic acid was found

Ulrich Melcher; Vijay Muthukumar; Graham B. Wiley; Byoung Eun Min; Michael W. Palmer; Jeanmarie Verchot-Lubicz; Akhtar Ali; Richard S. Nelson; Bruce A. Roe; Vaskar Thapa; Margaret L. Pierce

2008-01-01

440

"cgDNAmanuscriptfinal" --2014/9/5 --8:05 --page 1 --#1 Published online Nucleic Acids Research, , Vol. , No. 18  

E-print Network

"cgDNAmanuscriptfinal" -- 2014/9/5 -- 8:05 -- page 1 -- #1 Published online Nucleic Acids Research), and (11, a webserver to access various databases and models of nucleic acid flexibility). c The Author

Gonzalez, Oscar

441

Triazole linkages and backbone branches in nucleic acids for biological and extra-biological applications  

NASA Astrophysics Data System (ADS)

The recently increasing evidence of nucleic acids' alternative roles in biology and potential as useful nanomaterials and therapeutic agents has enabled the development of useful probes, elaborate nanostructures and therapeutic effectors based on nucleic acids. The study of alternative nucleic acid structure and function, particularly RNA, hinges on the ability to introduce site-specific modifications that either provide clues to the nucleic acid structure function relationship or alter the nucleic acid's function. Although the available chemistries allow for the conjugation of useful labels and molecules, their limitations lie in their tedious conjugation conditions or the lability of the installed probes. The development and optimization of click chemistry with RNA now provides the access to a robust and orthogonal conjugation methodology while providing stable conjugates. Our ability to introduce click reactive groups enzymatically, rather than only in the solid-phase, allows for the modification of larger, more cell relevant RNAs. Additionally, ligation of modified RNAs with larger RNA constructs through click chemistry represents an improvement over traditional ligation techniques. We determined that the triazole linkage generated through click chemistry is compatible in diverse nucleic acid based biological systems. Click chemistry has also been developed for extra-biological applications, particularly with DNA. We have expanded its use to generate useful polymer-DNA conjugates which can form controllable soft nanoparticles which take advantage of DNA's properties, i.e. DNA hybridization and computing. Additionally, we have generated protein-DNA conjugates and assembled protein-polymer hybrids mediated by DNA hybridization. The use of click chemistry in these reactions allows for the facile synthesis of these unnatural conjugates. We have also developed backbone branched DNA through click chemistry and showed that these branched DNAs are useful in generating well-defined architectures based solely on DNA. While backbone branched DNAs are useful for nanotechnological applications, backbone branches in RNA occur in nature and are involved in the distinct but related processes of splicing, debranching and RNAi. Therefore we have developed protocols for the synthesis of backbone branched nucleic acids in the solid-phase using photoprotecting groups. Using the synthesized backbone branched RNAs we have uncovered a specific substrate requirement of debranching enzyme which distinguishes it from other homologous proteins with alternative functions. Finally, through the marriage of click chemistry and backbone branches, we have produced useful progeny in the synthesis of lariat RNAs. We investigated the potential of these lariats as therapeutic agents by synthesizing siRNA sequences as lariats. We showed that these lariats are efficiently debranched by debranching enzyme and are able to induce an RNAi response in vivo. Altogether, the development of click chemistry and backbone branched nucleic acids represents a significant advantage in the ability to modify nucleic acid structure and affect its function. I envision that these methods can become generally useful to probe nucleic acid systems, useful nanomaterials and functional effectors in nucleic acid based therapies.

Paredes, Eduardo

442

Investigation of the tautomeric equilibrium of nucleic acid bases in aqueous solution  

Microsoft Academic Search

Relative constants of acidity and basicity of nucleic acid bases (NABs) and their tautomeric forms are calculated. The general\\u000a characteristic of the effect of an aqueous solvent on the tautomeric equilibrium of NABs is formulated. It is shown that during\\u000a the tautomeric transformation of NABs their acid-base properties change to the opposite ones. One of possible causes of the\\u000a formation

G. N. Ten; V. I. Baranov

2007-01-01

443

'Caged' peptide nucleic acids activated by red light in a singlet oxygen mediated process.  

PubMed

Common 'caged' nucleic acid binders, which can be applied for temporal and spatial control of gene expression, are activated by high energy light (<450 nm). The light of this type is damaging to cells and is strongly absorbed by cellular components. Therefore, shifting the triggering light to the visible region (>550 nm) is highly desirable. Herein we report on a cyclic peptide nucleic acid (PNA), whose backbone contains a 9,10-dialkoxy-substituted anthracene linker. The sequence of this compound was selected to be complementary to a representative microRNA (miR-92). We demonstrated that the cyclic PNA does not bind complementary nucleic acids and is, correspondingly, 'caged'. Its uncaging can be conducted by its exposure to red light (635 nm) in the presence of pyropheophorbide-a. The latter process is mediated by singlet oxygen ((1)O2), which cleaves the 9,10-dialcoxyanthracene linker within the PNA with formation of a linear PNA, an efficient binder of the complementary ribonucleic acid. This is the first example of a red light-activated, 'caged' peptide nucleic acid. PMID:24268552

König, Sandra G; Mokhir, Andriy

2013-12-15

444

Structural aspects of catalytic mechanisms of endonucleases and their binding to nucleic acids  

SciTech Connect

Endonucleases (EC 3.1) are enzymes of the hydrolase class that catalyze the hydrolytic cleavage of deoxyribonucleic and ribonucleic acids at any region of the polynucleotide chain. Endonucleases are widely used both in biotechnological processes and in veterinary medicine as antiviral agents. Medical applications of endonucleases in human cancer therapy hold promise. The results of X-ray diffraction studies of the spatial organization of endonucleases and their complexes and the mechanism of their action are analyzed and generalized. An analysis of the structural studies of this class of enzymes showed that the specific binding of enzymes to nucleic acids is characterized by interactions with nitrogen bases and the nucleotide backbone, whereas the nonspecific binding of enzymes is generally characterized by interactions only with the nucleic-acid backbone. It should be taken into account that the specificity can be modulated by metal ions and certain low-molecular-weight organic compounds. To test the hypotheses about specific and nonspecific nucleic-acid-binding proteins, it is necessary to perform additional studies of atomic-resolution three-dimensional structures of enzyme-nucleic-acid complexes by methods of structural biology.

Zhukhlistova, N. E.; Balaev, V. V.; Lyashenko, A. V.; Lashkov, A. A., E-mail: alashkov83@gmail.com [Russian Academy of Sciences, Shubnikov Institute of Crystallography (Russian Federation)

2012-05-15

445

W526W530 Nucleic Acids Research, 2007, Vol. 35, Web Server issue doi:10.1093/nar/gkm401  

E-print Network

W526­W530 Nucleic Acids Research, 2007, Vol. 35, Web Server issue doi:10.1093/nar/gkm401 Patch surfaces are usually indicative of nucleic acid binding interfaces. Interestingly, many proteins which are not involved in nucleic acid binding possess large positive patches on their surface as well. In some cases

Mandel-Gutfreund, Yael

446

39743987 Nucleic Acids Research, 2007, Vol. 35, No. 12 Published online 6 June 2007 doi:10.1093/nar/gkm375  

E-print Network

3974­3987 Nucleic Acids Research, 2007, Vol. 35, No. 12 Published online 6 June 2007 doi:10.1093/nar/gkm375 Effects of nucleic acid local structure and magnesium ions on minus-strand transfer mediated by the nucleic acid chaperone activity of HIV-1 nucleocapsid protein Tiyun Wu, Susan L. Heilman

Levin, Judith G.

447

40 CFR 174.507 - Nucleic acids that are part of a plant-incorporated protectant; exemption from the requirement of...  

Code of Federal Regulations, 2013 CFR

...2013-07-01 2013-07-01 false Nucleic acids that are part of a plant-incorporated...Tolerance Exemptions § 174.507 Nucleic acids that are part of a plant-incorporated...of a tolerance. Residues of nucleic acids that are part of a...

2013-07-01

448

40 CFR 174.507 - Nucleic acids that are part of a plant-incorporated protectant; exemption from the requirement of...  

Code of Federal Regulations, 2011 CFR

...2011-07-01 2011-07-01 false Nucleic acids that are part of a plant-incorporated...Tolerance Exemptions § 174.507 Nucleic acids that are part of a plant-incorporated...of a tolerance. Residues of nucleic acids that are part of a...

2011-07-01

449

40 CFR 174.507 - Nucleic acids that are part of a plant-incorporated protectant; exemption from the requirement of...  

...2014-07-01 2014-07-01 false Nucleic acids that are part of a plant-incorporated...Tolerance Exemptions § 174.507 Nucleic acids that are part of a plant-incorporated...of a tolerance. Residues of nucleic acids that are part of a...

2014-07-01

450

40 CFR 174.507 - Nucleic acids that are part of a plant-incorporated protectant; exemption from the requirement of...  

Code of Federal Regulations, 2012 CFR

...2012-07-01 2012-07-01 false Nucleic acids that are part of a plant-incorporated...Tolerance Exemptions § 174.507 Nucleic acids that are part of a plant-incorporated...of a tolerance. Residues of nucleic acids that are part of a...

2012-07-01

451

Volume 16 Number 4 1988 Nucleic Acids Research Synthesis of a thymidine phosphoramidite labelled with 13C at C6 relaxation studies of the loop  

E-print Network

Volume 16 Number 4 1988 Nucleic Acids Research Synthesis of a thymidine phosphoramidite labelled are difficult to obtain. © I R L Press Limited, Oxford, England. 1529 Nucleic Acids ResearchVolume 16 Number 4 1988 #12;Nucleic Acids Research In particular, the measurement of several carbon relaxation parameters

Boxer, Steven G.

452

9034 Chem. Commun., 2010, 46, 90349036 This journal is c The Royal Society of Chemistry 2010 Sustained release of nucleic acids from polymeric nanoparticles using  

E-print Network

Sustained release of nucleic acids from polymeric nanoparticles using microemulsion precipitation for producing biodegradable nanoparticles for sustained nucleic acid release is presented. The nanoparticles-butanol. The possibility of using nucleic acids for pharmacological purposes has gained a new impetus with the discovery

Zare, Richard N.

453

* arjang@stanford.edu; phone 1 650 725-3658; fax 1 650 725-3383 Bioluminescence Regenerative Cycle (BRC) System for Nucleic Acid  

E-print Network

(BRC) System for Nucleic Acid Quantification Assays Arjang Hassibi*ac , Thomas H. Leea , Ronald W for nucleic acid quantification has been developed where the number of pyrophosphate molecules (PPi) released during polymerization of the target nucleic acid is counted and correlated to DNA copy number

Lee, Thomas H.

454

40 CFR 174.507 - Nucleic acids that are part of a plant-incorporated protectant; exemption from the requirement of...  

Code of Federal Regulations, 2010 CFR

...2010-07-01 2010-07-01 false Nucleic acids that are part of a plant-incorporated...Tolerance Exemptions § 174.507 Nucleic acids that are part of a plant-incorporated...of a tolerance. Residues of nucleic acids that are part of a...

2010-07-01

455

Preprint copy of chapter from Functional Nucleic Acids for Sensing and Other Ana-lytical Applications, Y. Lu and Y. Li, eds.; Springer: New York, 2007.  

E-print Network

Preprint copy of chapter from Functional Nucleic Acids for Sensing and Other Ana- lytical Applications, Y. Lu and Y. Li, eds.; Springer: New York, 2007. Artificial functional nucleic acids: Aptamers nucleic acids. In vitro selection is the experimental process by which large random-sequence pools of RNA

Silverman, Scott K.

456

Understanding nonviral nucleic acid delivery with quantum dot-FRET nanosensors  

PubMed Central

Nonviral delivery of nucleic acids is a potentially safe and viable therapeutic modality for inherited and acquired diseases. However, current systems have proven too inefficient for widespread clinical translation. The rational design of improved carriers depends on a quantitative, mechanistic understanding of the rate-limiting barriers to efficient intracellular delivery. Separation of the nucleic acid from the carrier is one of the barriers, which may be analyzed by Förster resonance energy transfer (FRET), a mechanism used to detect interactions between fluorescently labeled molecules. When applied to the molecular components of polymer or lipid-based nanocomplexes, FRET provides information on their complexation status, uptake, release and degradation. Recently, the design of FRET systems incorporating quantum dots as energy donors has led to improved signal stability, allowing prolonged measurements, as well as increased sensitivity, enabling direct detection and the potential for multiplexing. The union of quantum dots and FRET is providing new insights into the mechanisms of nonviral nucleic acid delivery through convergent characterization of delivery barriers, and has the potential to accelerate the design of improved carriers to realize the potential of nucleic acid therapeutics and gene medicine. PMID:22471720

Grigsby, Christopher L; Ho, Yi-Ping; Leong, Kam W

2012-01-01

457

Liquid chromatography of nucleic acid components and their analogues on hydroxyethyl methacrylate gels.  

PubMed

Spheron hydroxyethyl methacrylate gels are advantageous sorbents for the high-performance liquid chromatography of various nucleic acid components and their analogues. In aqueous media these compounds are reversible sorbed on the surface of the gel. Differences in the sorption characteristics of particular derivatives enable good separations of even relatively complicated mixtures to be achieved. PMID:838791

Borák, J; Smrz, M

1977-03-11

458

ll cells contain lots of big molecules, especially proteins, nucleic acids and  

E-print Network

A ll cells contain lots of big molecules, especially proteins, nucleic acids and complex sugars- escent proteins in animal cells -- both within the cytoplasm and inside two cellu- lar compartments consequences that could affect many aspects of cellular function. Yet most bio- chemical studies

Weston, Ken

459

Biopolymers Celebrates 50 Years of Nucleic Acids Research DNA AND RNA OVER HALF A CENTURY  

E-print Network

, which was quickly amended to include such non-canonical events as reverse transcription of RNA into DNAEditorial Biopolymers Celebrates 50 Years of Nucleic Acids Research DNA AND RNA OVER HALF A CENTURY of the DNA double helix by James Watson and Francis Crick 60 years ago, our grasp of the cen- tral role

Walter, Nils G.

460

Isothermal Amplification Methods for the Detection of Nucleic Acids in Microfluidic Devices  

PubMed Central

Diagnostic tools for biomolecular detection need to fulfill specific requirements in terms of sensitivity, selectivity and high-throughput in order to widen their applicability and to minimize the cost of the assay. The nucleic acid amplification is a key step in DNA detection assays. It contributes to improving the assay sensitivity by enabling the detection of a limited number of target molecules. The use of microfluidic devices to miniaturize amplification protocols reduces the required sample volume and the analysis times and offers new possibilities for the process automation and integration in one single device. The vast majority of miniaturized systems for nucleic acid analysis exploit the polymerase chain reaction (PCR) amplification method, which requires repeated cycles of three or two temperature-dependent steps during the amplification of the nucleic acid target sequence. In contrast, low temperature isothermal amplification methods have no need for thermal cycling thus requiring simplified microfluidic device features. Here, the use of miniaturized analysis systems using isothermal amplification reactions for the nucleic acid amplification will be discussed.

Zanoli, Laura Maria; Spoto, Giuseppe

2012-01-01

461

Rapid Detection of Noroviruses in Fecal Samples and Shellfish by Nucleic Acid Sequence-based Amplification  

Microsoft Academic Search

The purpose of this study was to determine the efficacy of a nucleic acid sequence-based amplification (NASBA) method of detecting noroviruses in artificially and naturally contaminated shellfish. We used 58 fecal samples that tested positive for noroviruses with electron microscopy (EM) to develop an NASBA assay for these viruses. Oligonucleotide primers targeting the polymerase coding region were used to amplify

Xiaoxia Kou; Qingping Wu; Jumei Zhang; Hongying Fan

2006-01-01

462

Inhibition of Translation and Bacterial Growth by Peptide Nucleic Acid Targeted to Ribosomal RNA  

Microsoft Academic Search

Peptide nucleic acid (PNA) is a DNA mimic that has shown considerable promise as a lead compound for developing gene therapeutic drugs. We report that PNAs targeted to functional and accessible sites in ribosomal RNA can inhibit translation in an Escherichia coli cell-free transcription\\/translation system, with 50% reductions caused by nanomolar PNA concentrations. The effect in vitro is quantitatively similar

Liam Good; Peter E. Nielsen

1998-01-01

463

A Rate-independent Technique for Analysis of Nucleic Acid Sequences: Evolutionary Parsimony  

Microsoft Academic Search

The method of evolutionary parsimony-or operator invariants-is a technique of nucleic acid sequence analysis related to parsimony analysis and explicitly de- signed for determining evolutionary relationships among four distantly related taxa. The method is independent of substitution rates because it is derived from consid- eration of the group properties of substitution operators rather than from an analysis of the probabilities

James A. Lake

1987-01-01

464

Introductory Course Based on a Single Problem: Learning Nucleic Acid Biochemistry from AIDS Research  

ERIC Educational Resources Information Center

In departure from the standard approach of using several problems to cover specific topics in a class, I use a single problem to cover the contents of the entire semester-equivalent biochemistry classes. I have developed a problem-based service-learning (PBSL) problem on HIV/AIDS to cover nucleic acid concepts that are typically taught in the…

Grover, Neena

2004-01-01

465

A Second Generation Force Field for the Simulation of Proteins, Nucleic Acids, and Organic Molecules  

Microsoft Academic Search

We present the derivation of a new molecular mechanical force field for simulating the structures, conformational energies, and interaction energies of proteins, nucleic acids, and many related organic molecules in condensed phases. This effective two-body force field is the successor to the Weiner et al. force field and was developed with some of the same philosophies, such as the use

Wendy D. Cornell; Piotr Cieplak; Christopher I. Bayly; Ian R. Gould; Kenneth M. Merz; David M. Ferguson; David C. Spellmeyer; Thomas Fox; James W. Caldwell

1995-01-01

466

High efficiency transformation of intact yeast cells using single stranded nucleic acids as a carrier  

Microsoft Academic Search

A method, using LiAc to yield competent cells, is described that increased the efficiency of genetic transformation of intact cells of Saccharomyces cerevisiae to more than 1 × 105 transformants per microgram of vector DNA and to 1.5% transformants per viable cell. The use of single stranded, or heat denaturated double stranded, nucleic acids as carrier resulted in about a

Robert H. Schiestl; R. Daniel Gietz

1989-01-01

467

The Chemistry of Polymers, Proteins, and Nucleic Acids: A Short Course on Macromolecules for Secondary Schools.  

ERIC Educational Resources Information Center

Describes a unit on macromolecules that has been used in the 12th grade of many Israeli secondary schools. Topic areas in the unit include synthetic polymers, biological macromolecules, and nucleic acids. A unit outline is provided in an appendix. (JN)

Lulav, Ilan; Samuel, David

1985-01-01

468

Integrated printed circuit board device for cell lysis and nucleic acid extraction.  

PubMed

Preparation of raw, untreated biological samples remains a major challenge in microfluidics. We present a novel microfluidic device based on the integration of printed circuit boards and an isotachophoresis assay for sample preparation of nucleic acids from biological samples. The device has integrated resistive heaters and temperature sensors as well as a 70 ?m × 300 ?m × 3.7 cm microfluidic channel connecting two 15 ?L reservoirs. We demonstrated this device by extracting pathogenic nucleic acids from 1 ?L dispensed volume of whole blood spiked with Plasmodium falciparum. We dispensed whole blood directly onto an on-chip reservoir, and the system's integrated heaters simultaneously lysed and mixed the sample. We used isotachophoresis to extract the nucleic acids into a secondary buffer via isotachophoresis. We analyzed the convective mixing action with micro particle image velocimetry (micro-PIV) and verified the purity and amount of extracted nucleic acids using off-chip quantitative polymerase chain reaction (PCR). We achieved a clinically relevant limit of detection of 500 parasites per microliter. The system has no moving parts, and the process is potentially compatible with a wide range of on-chip hybridization or amplification assays. PMID:23046297

Marshall, Lewis A; Wu, Liang Li; Babikian, Sarkis; Bachman, Mark; Santiago, Juan G

2012-11-01

469

Nucleic Acids Research, Vol. 18, NO. 3 589 The distribution of restriction enzyme sites in Escherichia  

E-print Network

Nucleic Acids Research, Vol. 18, NO. 3 589 The distribution of restriction enzyme sites restriction enzymes and coveringnearly the entire genome (l), affords us with a unique opportunity to examine set of restriction enzymes would help to minimize the amount of work required. Results presented here

Waterman, Michael S.

470

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

E-print Network

(Figure 2). Indeed, the majority of the TAR RNA was found in the flow-through fraction with the PAC for high-affinity RNA ligands using spatial arraying strategies.4 However, it is not currently known if immobilization of a PAC affects binding to RNA targets. Similar compounds have been shown to bind nucleic acids

Beal, Peter A.

471

Affi-Gel Blue for nucleic acid removal and early enrichment of nucleotide binding proteins.  

PubMed

Passage of an extract or supernatant fraction through a column of Affi-Gel Blue and batchwise elution can be a rapid and effective early procedure for removal of nucleic acid, concentration of the sample and purification of nucleotide binding proteins. PMID:19892181

Deutscher, Murray P

2009-01-01

472

Specific zinc-finger architecture required for HIV-1 nucleocapsid protein's nucleic acid chaperone function  

NASA Astrophysics Data System (ADS)

The nucleocapsid protein (NC) of HIV type 1 (HIV-1) is a nucleic acid chaperone that facilitates the rearrangement of nucleic acid secondary structure during reverse transcription. HIV-1 NC contains two CCHC-type zinc binding domains. Here, we use optical tweezers to stretch single -DNA molecules through the helix-to-coil transition in the presence of wild-type and several mutant forms of HIV-1 NC with altered zinc-finger domains. Although all forms of NC lowered the cooperativity of the DNA helix-coil transition, subtle changes in the zinc-finger structures reduced NC's effect on the transition. The change in cooperativity of the DNA helix-coil transition correlates strongly with in vitro nucleic acid chaperone activity measurements and in vivo HIV-1 replication studies using the same NC mutants. Moreover, Moloney murine leukemia virus NC, which contains a single zinc finger, had little effect on transition cooperativity. These results suggest that a specific two-zinc-finger architecture is required to destabilize nucleic acids for optimal chaperone activity during reverse transcription in complex retroviruses such as HIV-1.

Williams, Mark C.; Gorelick, Robert J.; Musier-Forsyth, Karin

2002-06-01

473

Aurintricarboxylic acid modulates the affinity of hepatitis C virus NS3 helicase for both nucleic acid and ATP‡  

PubMed Central

Aurintricarboxylic acid (ATA) is a potent inhibitor of many enzymes needed for cell and virus replication, such as polymerases, helicases, nucleases, and topoisomerases. This study examines how ATA interacts with the helicase encoded by the hepatitis C virus (HCV) to reveal that ATA interferes with both nucleic acid and ATP binding to the enzyme. We show that ATA directly binds HCV helicase to prevent the enzyme from interacting with nucleic acids and to modulate the affinity of HCV helicase for ATP, the fuel for helicase action. Amino acid substitutions in the helicase DNA binding cleft or its ATP binding site alter the ability of ATA to disrupt helicase-DNA interactions. These data, along with molecular modeling results, support the notion that an ATA polymer binds between Arg467 and Glu493 to prevent the helicase from binding either ATP or nucleic acids. We also characterize how ATA affects the kinetics of helicase-catalyzed ATP hydrolysis, and thermodynamic parameters describing the direct interaction between HCV helicase and ATA using microcalorimetry. The thermodynamics of ATA binding to HCV helicase reveal that ATA binding does not mimic nucleic acid binding in that ATA binding is driven by a smaller enthalpy change and an increase in entropy. PMID:23947785

Shadrick, William R.; Mukherjee, Sourav; Hanson, Alicia M.; Sweeney, Noreena L.; Frick, David N.

2013-01-01

474

RNA:DNA Ratio and Other Nucleic Acid Derived Indices in Marine Ecology  

PubMed Central

Some of most used indicators in marine ecology are nucleic ac