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1

Nucleic acid isolation  

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 reduces 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 effect on the protocol.

Longmire, J.L.; Lewis, A.K.; Hildebrand, C.E.

1988-01-21

2

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

3

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

4

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

5

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

6

Isolated nucleic acids encoding antipathogenic polypeptides and uses thereof  

DOEpatents

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

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

2010-04-20

7

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

Microsoft Academic Search

A self-contained, integrated, disposable, sample-to-answer, polycarbonate microfluidic cassette for nucleic acid—based detection\\u000a of pathogens at the point of care was designed, constructed, and tested. The cassette comprises on-chip sample lysis, nucleic\\u000a acid isolation, enzymatic amplification (polymerase chain reaction and, when needed, reverse transcription), amplicon labeling,\\u000a and detection. On-chip pouches and valves facilitate fluid flow control. All the liquids and dry

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

2010-01-01

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

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

10

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

11

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

12

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

13

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

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. (Madison, WI); Lyamichev, Victor L. (Madison, WI); Brow, Mary Ann D. (Madison, WI); Dahlberg, James E. (Madison, WI)

2007-12-11

15

Nucleic acid detection assays  

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

2005-04-05

16

Nucleic acid detection compositions  

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 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

17

Nucleic acid detection kits  

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 nucleic acid from various viruses in a sample.

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

2005-03-29

18

Isolation of nucleic acids and cultures from fossil ice and permafrost  

Microsoft Academic Search

Owing to their constant low temperatures, glacial ice and permafrost might contain the oldest nucleic acids and microbial cells on Earth, which could prove key to reconstructing past ecosystems and for the planning of missions to other planets. However, recent claims concerning viable cells and microbial nucleic acids obtained from ice- and permafrost cores from hundreds of thousands to millions

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

2004-01-01

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. 7 figs.

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

1997-04-01

20

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

21

Method and Apparatus for Automated Isolation of Nucleic Acids from Small Cell Samples  

NASA Technical Reports Server (NTRS)

RNA isolation is a ubiquitous need, driven by current emphasis on microarrays and miniaturization. With commercial systems requiring 100,000 to 1,000,000 cells for successful isolation, there is a growing need for a small-footprint, easy-to-use device that can harvest nucleic acids from much smaller cell samples (1,000 to 10,000 cells). The process of extraction of RNA from cell cultures is a complex, multi-step one, and requires timed, asynchronous operations with multiple reagents/buffers. An added complexity is the fragility of RNA (subject to degradation) and its reactivity to surface. A novel, microfluidics-based, integrated cartridge has been developed that can fully automate the complex process of RNA isolation (lyse, capture, and elute RNA) from small cell culture samples. On-cartridge cell lysis is achieved using either reagents or high-strength electric fields made possible by the miniaturized format. Traditionally, silica-based, porous-membrane formats have been used for RNA capture, requiring slow perfusion for effective capture. In this design, high efficiency capture/elution are achieved using a microsphere-based "microfluidized" format. Electrokinetic phenomena are harnessed to actively mix microspheres with the cell lysate and capture/elution buffer, providing important advantages in extraction efficiency, processing time, and operational flexibility. Successful RNA isolation was demonstrated using both suspension (HL-60) and adherent (BHK-21) cells. Novel features associated with this development are twofold. First, novel designs that execute needed processes with improved speed and efficiency were developed. These primarily encompass electric-field-driven lysis of cells. The configurations include electrode-containing constructs, or an "electrode-less" chip design, which is easy to fabricate and mitigates fouling at the electrode surface; and the "fluidized" extraction format based on electrokinetically assisted mixing and contacting of microbeads in a shape-optimized chamber. A secondary proprietary feature is in the particular layout integrating these components to perform the desired operation of RNA isolation. Apart from a novel functional capability, advantages of the innovation include reduced or eliminated use of toxic reagents, and operator-independent extraction of RNA.

Sundaram, Shivshankar; Prabhakarpandian, Balabhaskar; Pant, Kapil; Wang, Yi

2014-01-01

22

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

23

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

24

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

25

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

26

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

27

Geranyl diphosphate synthase molecules, and nucleic acid molecules encoding same  

DOEpatents

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

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

2008-06-24

28

Nucleic Acid 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.

29

Nucleic Acid Detection Methods  

DOEpatents

The invention relates to methods for rapidly determining the sequence and/or length a target sequence. The target sequence may be a series of known or unknown repeat sequences which are hybridized to an array of probes. The hybridized array is digested with a single-strand nuclease and free 3'-hydroxyl groups extended with a nucleic acid polymerase. Nuclease cleaved heteroduplexes can be easily distinguish from nuclease uncleaved heteroduplexes by differential labeling. Probes and target can be differentially labeled with detectable labels. Matched target can be detected by cleaving resulting loops from the hybridized target and creating free 3-hydroxyl groups. These groups are recognized and extended by polymerases added into the reaction system which also adds or releases one label into solution. Analysis of the resulting products using either solid phase or solution. These methods can be used to detect characteristic nucleic acid sequences, to determine target sequence and to screen for genetic defects and disorders. Assays can be conducted on solid surfaces allowing for multiple reactions to be conducted in parallel and, if desired, automated.

Smith, Cassandra L. (Boston, MA); Yaar, Ron (Brookline, MA); Szafranski, Przemyslaw (Boston, MA); Cantor, Charles R. (Boston, MA)

1998-05-19

30

Nucleic acid detection methods  

DOEpatents

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

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

1998-05-19

31

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

32

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

33

Evaluation of nucleic acid probe for rapid identification of Mycobacterium tuberculosis complex in extra-pulmonary culture isolates.  

PubMed

Patients infected with Non-tuberculous mycobacteria (NTM) usually do not respond to conventional anti-tubercular treatment and are misdiagnosed as infection with multi-drug resistant strains of mycobacterium tuberculosis (M.tb) due to lack of correct species identification, particularly in the developing countries like India. One of the challenges faced by clinicians in the treatment of tuberculosis is the absence of an easy, reliable and rapid identification tool that can accurately differentiate disease caused by M.tb complex from NTM. Keeping this in consideration, the performance of species specific nucleic acid probe i.e. Accuprobe was assessed and compared with conventional niacin production, nitrate reductase assay techniques for identification of M.tb complex in 80 mycobacterial isolates obtained from different extra-pulmonary sites. Accuprobe identified 62 isolates (77.5%) as M. tuberculosis complex and remaining 18 isolates (22.5%) as NTM whereas 64 isolates (80%) were identified as M.tb and rest 16 (20%) were interpreted as NTM by conventional biochemical techniques. The overall agreement between both techniques was 96.9% The sensitivity, specificity, positive predictive value(PPV) and negative predictive value (NPV) shown by accuprobe were 96.9%, 100%, 96.9%, and 88.9% respectively. Thus, accuprobe has showed impressive sensitivity and specificity giving results in < 3 hrs from culture-positive isolates and have sure edge over conventional biochemical methods which are, nonetheless, labour intensive and cumbersome to perform thus delaying prompt mycobacterial identification. PMID:23785877

Verma, J S; Rawat, D; Manzoor, N; Deb, M; Nair, D

2011-03-01

34

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

35

The Nucleic Acid Database (NDB)  

NSDL National Science Digital Library

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

36

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

37

Reduced PCR Sensitivity Due to Impaired DNA Recovery with the MagNA Pure LC Total Nucleic Acid Isolation Kit  

PubMed Central

The increasing demand for molecular diagnostics in clinical microbiology laboratories necessitates automated sample processing. In the present study, we evaluated the performance of the MagNA Pure LC total nucleic acid isolation kit (M extraction) in comparison with the manual method (Si extraction) according to Boom et al. (R. Boom, C. J. A. Sol, M. M. M. Salimans, C. L. Jansen, P. M. Wertheim-van Dillen, and J. van der Noordaa, J. Clin. Microbiol. 28:495-503, 1990) for the detection of viral DNA by competitive quantitative PCR. Reconstruction experiments with HindIII-digested phage lambda DNA and HaeIII-digested ?X174 DNA showed that the recovery of DNA from phosphate-buffered saline, cerebrospinal fluid, EDTA-anticoagulated plasma, and EDTA-anticoagulated whole blood by M extraction is, on average, 6.6-fold lower compared to Si extraction. PCR signals of spiked PCR control DNAs for Epstein-Barr virus and varicella-zoster virus were also between 1.9- and 14.2-fold lower after M extraction compared to Si extraction, also suggesting impaired DNA recovery. M extraction of spiked cytomegalovirus strain AD 169 in whole blood showed a 5- to 10-fold reduction in PCR sensitivity compared to Si extraction. This reduction of PCR sensitivity was also observed when clinical whole blood samples were processed by M extraction. Before implementing M extraction, the clinical consequences of the reduced recovery should first be considered, especially when maximal sensitivity is required. PMID:16145116

Schuurman, Tim; van Breda, Alex; de Boer, Richard; Kooistra-Smid, Mirjam; Beld, Marcel; Savelkoul, Paul; Boom, René

2005-01-01

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

Applications of peptide nucleic acids  

Microsoft Academic Search

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

Peter E Nielsen

1999-01-01

44

Method for sequencing nucleic acid molecules  

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

2006-05-30

45

Method for sequencing nucleic acid molecules  

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

2006-06-06

46

Matrix isolation infrared studies of nucleic acid constituents. Part 4. Guanine and 9-methylguanine monomers and their keto—enol tautomerism  

NASA Astrophysics Data System (ADS)

Infrared absorption spectra have been studied for matrix isolated guanine and 9-methylguanine, which is a formal analogue of the natural nucleoside found in DNA and RNA. Three related compounds (isocytosine, 2-amino-5-chloropyrimidine and 2-dimethyl-amino-6-hydroxypurine) have also been examined. The spectra provide evidence for the existence of guanine and of 9-methylguanine as mixtures of the enol-amino and keto-amino tautomers, although the keto-amino tautomer is the only tautomeric form found in solution and in solid. The estimated enol—keto equilibrium constant fund in nitrogen matrices K = [E]/[K] is about 3.6 for guanine and 5.9 for 9-methylguanine. The significance of these results is evaluated in relation to the types of tautomers found in natural nucleic acids and to the concept of spontaneous and induced mutations caused by mis-pairing of the bases in the nucleic acids.

Szczepaniak, Krystyna; Szczesniak, Marian

1987-01-01

47

Identification of Bacillus strains isolated from milk and cream with classical and nucleic acid hybridization methods.  

PubMed

A total of 529 bacterial strains have been isolated from milk and cream sampled at different sites in a dairy production plant under conditions selective for aerobic sporeforming bacteria. Identification with classical methods based on morphological, physiological and biochemical criteria showed Bacillus licheniformis to be the most frequently occurring Bacillus sp. The investigation also revealed 62 unidentified strains. Classical identification methods were time consuming (3-7 d), lacked specificity and--because of their dependence on phenotypic gene expression--sometimes produced ambiguous results. Consequently, a colony hybridization method developed for the identification of B. licheniformis strains and using nonradioactive labelled 23S rRNA targeted oligonucleotide probes was also used. Identification of B. licheniformis with both classical and hybridization methods revealed diverging identification results for 70 strains. PMID:7829756

Tatzel, R; Ludwig, W; Schleifer, K H; Wallnöfer, P R

1994-11-01

48

Nucleic acids, compositions and uses thereof  

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

2012-02-21

49

Nucleic acid compositions and the encoding proteins  

DOEpatents

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

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

2014-09-02

50

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

51

Self-assembling multimeric nucleic acid constructs  

DOEpatents

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

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

1996-10-01

52

Self-assembling multimeric nucleic acid constructs  

DOEpatents

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

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

1999-10-12

53

Self-assembling multimeric nucleic acid constructs  

DOEpatents

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

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

1996-01-01

54

Double stranded nucleic acid biochips  

DOEpatents

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

Chernov, Boris; Golova, Julia

2006-05-23

55

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

56

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.

57

Optimizing the specificity of nucleic acid hybridization  

Microsoft Academic Search

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

Sherry Xi Chen; David Yu Zhang; Peng Yin

2012-01-01

58

Antisense properties of peptide nucleic acid  

Microsoft Academic Search

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

H. Jakob Larsen; Thomas Bentin; Peter E Nielsen

1999-01-01

59

An Introduction to Peptide Nucleic Acid  

Microsoft Academic Search

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

Peter E. Nielsen; Michael Egholm

1999-01-01

60

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

61

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

62

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

DOEpatents

A method is provided for detecting nucleic acid sequence aberrations using two immobilization steps. According to the method, a nucleic acid sequence aberration is detected by detecting nucleic acid sequences having both a first nucleic acid sequence type (e.g., from a first chromosome) and a second nucleic acid sequence type (e.g., from a second chromosome), the presence of the first and the second nucleic acid sequence type on the same nucleic acid sequence indicating the presence of a nucleic acid sequence aberration. In the method, immobilization of a first hybridization probe is used to isolate a first set of nucleic acids in the sample which contain the first nucleic acid sequence type. Immobilization of a second hybridization probe is then used to isolate a second set of nucleic acids from within the first set of nucleic acids which contain the second nucleic acid sequence type. The second set of nucleic acids are then detected, their presence indicating the presence of a nucleic acid sequence aberration. 14 figs.

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

1998-03-24

63

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

DOEpatents

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

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

1998-01-01

64

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

65

Polypeptides having cellulolytic enhancing activity and nucleic acids encoding same  

SciTech Connect

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

66

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

67

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

SciTech Connect

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

Bavykin, Sergei (Darien, IL)

2011-01-18

68

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

69

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.

70

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

71

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

72

Replica amplification of nucleic acid arrays  

SciTech Connect

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

73

Amplification of trace amounts of nucleic acids  

DOEpatents

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

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

2008-06-17

74

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

75

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

76

Method of Identifying a Base in a Nucleic Acid  

DOEpatents

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

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

1999-01-01

77

Probe kit for 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)

2001-01-01

78

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

79

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

80

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

81

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

82

Nucleic Acid Aptamers: an Emerging Frontier in Cancer Therapy  

PubMed Central

The last two decades have witnessed the development and application of nucleic acid aptamers in a variety of fields, including target analysis, disease therapy, and molecular and cellular engineering. The efficient and widely applicable aptamer selection, reproducible chemical synthesis and modification, generally impressive target binding selectivity and affinity, relatively rapid tissue penetration, low immunogenicity, and rapid systemic clearance make aptamers ideal recognition elements for use as therapeutics or for in vivo delivery of therapeutics. In this feature article, we discuss the development and biomedical application of nucleic acid aptamers, with emphasis on cancer cell aptamer isolation, targeted cancer therapy, oncology biomarker identification and drug discovery. PMID:22951893

Zhu, Guizhi; Ye, Mao; Donovan, Michael J.; Song, Erqun; Zhao, Zilong

2013-01-01

83

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

84

A chromatographic comparison of the nucleic acids from isologous newborn, adult and neoplastic thymus  

Microsoft Academic Search

SUMMARY The total tissue nucleic acids (DNA and RNA) have been isolated from normal and neoplastic mouse thymus glands and chromatographically fractionated. Significant differences in the chromatographic distribution of the nucleic acids from normal adult thymus and x-radiation-induced thymic lymphosarcoma were found. Chromatographic patterns intermediate between normal and tumor were found in the thymuses of irradi- ated animals prior to

KENDRIC C. SMITH; H S Kaplan

1961-01-01

85

Fmoc mediated synthesis of Peptide Nucleic Acids  

Microsoft Academic Search

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

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

1995-01-01

86

Novel Biochip Platform for Nucleic Acid Analysis  

PubMed Central

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

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

2012-01-01

87

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)

2000-02-04

88

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.

89

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.

90

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.

91

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

92

Method for identifying and quantifying nucleic acid sequence aberrations  

DOEpatents

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

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

1998-01-01

93

Advances in magnetofection—magnetically guided nucleic acid delivery  

NASA Astrophysics Data System (ADS)

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

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

2005-05-01

94

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

95

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

96

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.

97

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

98

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.

99

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

100

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.

101

Thermodynamic analysis of nylon nucleic acids.  

PubMed

The stability and structure of nylon nucleic acid duplexes with complementary DNA and RNA strands was examined. Thermal denaturing studies of a series of oligonucleotides that contained nylon nucleic acids (1-5 amide linkages) revealed that the amide linkage significantly enhanced the binding affinity of nylon nucleic acids towards both complementary DNA (up to 26 degrees C increase in the thermal transition temperature (T(m)) for five linkages) and RNA (around 15 degrees C increase in T(m) for five linkages) compared with nonamide linked precursor strands. For both DNA and RNA complements, increasing derivatization decreased the melting temperatures of uncoupled molecules relative to unmodified strands; by contrast, increasing lengths of coupled copolymer raised T(m) from less to slightly greater than T(m) of unmodified strands. Thermodynamic data extracted from melting curves and CD spectra of nylon nucleic acid duplexes were consistent with loss of stability due to incorporation of pendent groups on the 2'-position of ribose and recovery of stability upon linkage of the side chains. PMID:18543259

Liu, Yu; Wang, Risheng; Ding, Liang; Sha, Ruojie; Lukeman, Philip S; Canary, James W; Seeman, Nadrian C

2008-07-01

102

Common structural features of nucleic acid polymerases  

Microsoft Academic Search

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

P. Cramer

2002-01-01

103

Phospholipid membrane permeability of peptide nucleic acid  

Microsoft Academic Search

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

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

1995-01-01

104

Cellular delivery of peptide nucleic acid (PNA)  

Microsoft Academic Search

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

Uffe Koppelhus; Peter E. Nielsen

2003-01-01

105

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

106

Non-instrumented nucleic acid amplification assay  

NASA Astrophysics Data System (ADS)

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

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

2008-02-01

107

Topological constraints in nucleic acid hybridization kinetics  

E-print Network

, Harry M. T. Choi1 , Andrew J. Spakowitz, Zhen-Gang Wang and Niles A. Pierce1,2, * Department of Chemical illustrates the potential for topological effects to influence the kinetics and function of nucleic acid of double-stranded knots and catenanes (8). Topological effects also influence the regulatory mechanisms

Straight, Aaron

108

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

109

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

110

Leukocyte protease binding to nucleic acids promotes nuclear localization and cleavage of nucleic acid binding proteins.  

PubMed

Killer lymphocyte granzyme (Gzm) serine proteases induce apoptosis of pathogen-infected cells and tumor cells. Many known Gzm substrates are nucleic acid binding proteins, and the Gzms accumulate in the target cell nucleus by an unknown mechanism. In this study, we show that human Gzms bind to DNA and RNA with nanomolar affinity. Gzms cleave their substrates most efficiently when both are bound to nucleic acids. RNase treatment of cell lysates reduces Gzm cleavage of RNA binding protein targets, whereas adding RNA to recombinant RNA binding protein substrates increases in vitro cleavage. Binding to nucleic acids also influences Gzm trafficking within target cells. Preincubation with competitor DNA and DNase treatment both reduce Gzm nuclear localization. The Gzms are closely related to neutrophil proteases, including neutrophil elastase (NE) and cathepsin G. During neutrophil activation, NE translocates to the nucleus to initiate DNA extrusion into neutrophil extracellular traps, which bind NE and cathepsin G. These myeloid cell proteases, but not digestive serine proteases, also bind DNA strongly and localize to nuclei and neutrophil extracellular traps in a DNA-dependent manner. Thus, high-affinity nucleic acid binding is a conserved and functionally important property specific to leukocyte serine proteases. Furthermore, nucleic acid binding provides an elegant and simple mechanism to confer specificity of these proteases for cleavage of nucleic acid binding protein substrates that play essential roles in cellular gene expression and cell proliferation. PMID:24771851

Thomas, Marshall P; Whangbo, Jennifer; McCrossan, Geoffrey; Deutsch, Aaron J; Martinod, Kimberly; Walch, Michael; Lieberman, Judy

2014-06-01

111

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

112

Human jagged polypeptide, encoding nucleic acids and methods of use  

DOEpatents

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

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

2000-01-01

113

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

114

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

115

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.

116

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

117

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

118

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

119

Diagnostic applications of nucleic acid circuits.  

PubMed

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

Jung, Cheulhee; Ellington, Andrew D

2014-06-17

120

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; Foote, Robert S.

2003-12-09

121

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

SciTech Connect

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

122

Nucleic acid-specific suppressor T cells.  

PubMed Central

The concept of using cell-bound antigens as tolerogen was applied to nucleic acid. Nucleoside was linked directly to spleen cell suspensions. Intravenous administration of nucleoside coupled to isogeneic spleen cells into mice generated suppressor cells that diminished the formation of antibody-forming cells either to a T-dependent antigen in vivo or to a T-independent antigen in vitro. Suppressor cells were nucleoside specific, but the specificity of immune suppression seems to be somewhat broader than that of tolerance to a single nucleoside. The ability to raise nucleic acid-specific suppressor T cells may have implications for both the pathogenesis and treatment of systemic lupus erythematosus. PMID:6445559

Borel, Y; Young, M C

1980-01-01

123

Nucleic acid detection systems for enteroviruses.  

PubMed Central

The enteroviruses comprise nearly 70 human pathogens responsible for a wide array of diseases including poliomyelitis, meningitis, myocarditis, and neonatal sepsis. Current diagnostic tests for the enteroviruses are limited in their use by the slow growth, or failure to grow, of certain serotypes in culture, the antigenic diversity among the serotypes, and the low titer of virus in certain clinical specimens. Within the past 6 years, applications of molecular cloning techniques, in vitro transcription vectors, automated nucleic acid synthesis, and the polymerase chain reaction have resulted in significant progress toward nucleic acid-based detection systems for the enteroviruses that take advantage of conserved genomic sequences across many, if not all, serotypes. Similar approaches to the study of enteroviral pathogenesis have already produced dramatic advances in our understanding of how these important viruses cause their diverse clinical spectra. PMID:1649002

Rotbart, H A

1991-01-01

124

Peptide nucleic acid delivery to human mitochondria  

Microsoft Academic Search

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

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

1999-01-01

125

Therapeutic Potential of Antisense Nucleic Acid Molecules  

NSDL National Science Digital Library

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

Joanna B. Opalinska (Pommeranian Medical Academy; Department of Hematology REV)

2003-10-28

126

Diversity of the 47-kD HtrA Nucleic Acid and Translated Amino Acid Sequences from 17 Recent Human Isolates of Orientia  

PubMed Central

Abstract Orientia tsutsugamushi, the etiologic agent of potentially fatal scrub typhus, is characterized by a high antigenic diversity, which complicates the development of a broadly protective vaccine. Efficacy studies in murine and nonhuman primate models demonstrated the DNA vaccine candidate pKarp47, based upon the O. tsutsugamushi Karp 47-kD HtrA protein gene, to be a successful immunoprophylactic against scrub typhus. To characterize 47-kD HtrA protein diversity among human isolates of Orientia, we sequenced the full open reading frame (ORF) of the 47-kD HtrA gene and analyzed the translated amino acid sequences of 17 patient isolates from Thailand (n=13), Laos (n=2), Australia (n=1), and the United Arab Emirates (UAE) (n=1) and 9 reference strains: Karp (New Guinea), Kato (Japan), Ikeda (Japan), Gilliam (Burma), Boryong (Korea), TA763, TH1811 and TH1817 (Thailand), and MAK243 (China). The percentage identity (similarity) of translated amino acid sequences between 16 new isolates and 9 reference strains of O. tsutsugamushi ranged from 96.4% to 100% (97.4% to 100%). However, inclusion of the recently identified Orientia chuto sp. nov. reduced identity (similarity) values to 82.2% to 83.3% (90.4% to 91.4%). These results demonstrate the diversity of Orientia 47-kD HtrA among isolates encountered by humans and therefore provide support for the necessity of developing a broadly protective scrub typhus vaccine that takes this diversity into account. PMID:23590326

Jiang, Ju; Paris, Daniel H.; Blacksell, Stuart D.; Aukkanit, Nuntipa; Newton, Paul N.; Phetsouvanh, Rattanaphone; Izzard, Leonard; Stenos, John; Graves, Stephen R.; Day, Nicholas P.J.

2013-01-01

127

Carbohydrate Polymers for Nonviral Nucleic Acid Delivery  

PubMed Central

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

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

2014-01-01

128

[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

129

Optimizing the specificity of nucleic acid hybridization  

NASA Astrophysics Data System (ADS)

The specific hybridization of complementary sequences is an essential property of nucleic acids, enabling diverse biological and biotechnological reactions and functions. However, the specificity of nucleic acid hybridization is compromised for long strands, except near the melting temperature. Here, we analytically derived the thermodynamic properties of a hybridization probe that would enable near-optimal single-base discrimination and perform robustly across diverse temperature, salt and concentration conditions. We rationally designed ‘toehold exchange’ probes that approximate these properties, and comprehensively tested them against five different DNA targets and 55 spurious analogues with energetically representative single-base changes (replacements, deletions and insertions). These probes produced discrimination factors between 3 and 100+ (median, 26). Without retuning, our probes function robustly from 10 °C to 37 °C, from 1 mM Mg2+ to 47 mM Mg2+, and with nucleic acid concentrations from 1 nM to 5 µM. Experiments with RNA also showed effective single-base change discrimination.

Zhang, David Yu; Chen, Sherry Xi; Yin, Peng

2012-03-01

130

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.

131

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

132

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

133

Helicase-dependent amplification of nucleic acids.  

PubMed

Helicase-dependent amplification (HDA) is a novel method for the isothermal in vitro amplification of nucleic acids. The HDA reaction selectively amplifies a target sequence by extension of two oligonucleotide primers. Unlike the polymerase chain reaction (PCR), HDA uses a helicase enzyme to separate the deoxyribonucleic acid (DNA) strands, rather than heat denaturation. This allows DNA amplification without the need for thermal cycling. The helicase used in HDA is a helicase super family II protein obtained from a thermophilic organism, Thermoanaerobacter tengcongensis (TteUvrD). This thermostable helicase is capable of unwinding blunt-end nucleic acid substrates at elevated temperatures (60° to 65°C). The HDA reaction can also be coupled with reverse transcription for ribonucleic acid (RNA) amplification. The products of this reaction can be detected during the reaction using fluorescent probes when incubations are conducted in a fluorimeter. Alternatively, products can be detected after amplification using a disposable amplicon containment device that contains an embedded lateral flow strip. PMID:24510297

Cao, Yun; Kim, Hyun-Jin; Li, Ying; Kong, Huimin; Lemieux, Bertrand

2013-01-01

134

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

135

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

136

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

137

EGVII endoglucanase and nucleic acids encoding the same  

SciTech Connect

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

138

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

139

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

140

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

141

ORIGIN OF LIFE: A Simpler Nucleic Acid  

NSDL National Science Digital Library

Access to the article is free, however registration and sign-in are required. What was the genetic material of the earliest life forms on Earth if it was not RNA? As Orgel explains in his Perspective, the answer may be simpler nucleic acid polymers perhaps like the RNA analogs called (L)-a-threofuranosyl oligonucleotides or TNAs (Schöning et al.). These molecules have threose rather than ribose in their sugar-phosphate backbones and yet retain many of the properties of RNA including the ability to pair up in double helices.

Leslie Orgel (Salk Institute for Biomedical Study; )

2000-11-17

142

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); Raja, Mugasimangalam C. (Downers Grove, IL)

2001-01-01

143

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

144

Electrocatalysis in proteins, nucleic acids and carbohydrates.  

PubMed

The ability of proteins to catalyze hydrogen evolution has been known for more than 80 years, but the poorly developed d.c. polarographic "pre-sodium wave" was of little analytical use. Recently, we have shown that by using constant current chronopotentiometric stripping analysis, proteins produce a well-developed peak H at hanging mercury drop and solid amalgam electrodes. Peak H sensitively reflects changes in protein structures due to protein denaturation, single amino acid exchange, etc. at the picomole level. Unmodified DNA and RNA do not yield such a peak, but they produce electrocatalytic voltammetric signals after modification with osmium tetroxide complexes with nitrogen ligands [Os(VIII)L], binding covalently to pyrimidine bases in nucleic acids. Recently, it has been shown that six-valent [Os(VI)L] complexes bind to 1,2-diols in polysaccharides and oligosaccharides, producing voltammetric responses similar to those of DNA-Os(VIII)L adducts. Electrocatalytic peaks produced by Os-modified nucleic acids, proteins (reaction with tryptophan residues) and carbohydrates are due to the catalytic hydrogen evolution, allowing determination of oligomers at the picomolar level. PMID:22287069

Pale?ek, Emil; Bartošík, Martin; Ostatná, Veronika; Trefulka, Mojmír

2012-02-01

145

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

2010-04-01

146

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

Federal Register 2010, 2011, 2012, 2013, 2014

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

2013-06-19

147

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

E-print Network

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

Borguet, Eric

148

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

Code of Federal Regulations, 2011 CFR

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

2011-04-01

149

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

Code of Federal Regulations, 2012 CFR

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

2012-04-01

150

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

Code of Federal Regulations, 2014 CFR

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

2014-04-01

151

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

152

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

153

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

154

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.

155

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

156

A Robust Technique for Assembly of Nucleic Acid Hybridization Chips Based on Electrochemically  

E-print Network

A Robust Technique for Assembly of Nucleic Acid Hybridization Chips Based on Electrochemically and Biochemical Engineering, University of Maryland, Baltimore County, Maryland 21250 A nucleic acid hybridization evaluated. Hybridization of target nucleic acid was quantifiable, reproducible, and robust; the surface

Rubloff, Gary W.

157

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

158

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

159

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

160

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

Code of Federal Regulations, 2014 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...

2014-04-01

161

Nucleic acid interactions with pyrite surfaces  

NASA Astrophysics Data System (ADS)

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

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

2008-09-01

162

The nucleic acid-sensing inflammasomes.  

PubMed

Inflammasomes are oligomeric signaling complexes that promote caspase activation and maturation of proinflammatory cytokines. Structural and biophysical studies have shed light on the mechanisms of nucleic acid recognition and signaling complex assembly involving the AIM2 (absent in myeloma 2) and IFI16 (?-interferon-inducible protein 16) inflammasomes. However, our understanding of the mechanisms of the NLRP3 (nucleotide-binding oligomerization-like receptor family, pyrin domain-containing protein 3) activation, either by nucleic acids or by other reported stimuli, has remained elusive. Exciting recent progress on the filament formation by the ASC (apoptosis-associated speck-like protein containing a caspase recruitment domain) pyrin domain and the IFI16-double stranded DNA complex has established that the formation of higher order polymers is one of the general mechanisms for signaling platform assembly in innate immune system. The paradigm-changing discovery of the extracellular function of the NLRP3-ASC inflammasome has opened the door for therapeutic targeting the inflammasome filament formation for various clinical conditions. Future characterization of the canonical and non-canonical inflammasome complexes will undoubtedly reveal more surprises on their structure and function and enrich our understanding of the molecular mechanisms of ligand recognition, activation, and regulation. PMID:25879287

Xiao, Tsan Sam

2015-05-01

163

Assembly of barcode-like nucleic acid nanostructures.  

PubMed

Barcode-like (BC) nanopatterns from programmed self-assembly of nucleic acids (DNA and RNA) are reported. BC nanostructures are generated by the introduction of open spaces at selected sites to an otherwise closely packed, plain, rectangle nucleic acid nanostructure. This strategy is applied to nanostructures assembled from both origami approach and single stranded tile approach. PMID:24978689

Wang, Pengfei; Tian, Cheng; Li, Xiang; Mao, Chengde

2014-10-15

164

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

165

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

166

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

167

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

168

Peptide Nucleic Acid-Assisted Topological Labeling of Duplex DNA  

Microsoft Academic Search

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

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

2001-01-01

169

Structural and biological properties of peptide nucleic acid (PNA)  

Microsoft Academic Search

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

Peter E. Nielsen

1998-01-01

170

XVIth symposium on chemistry of nucleic acid components.  

PubMed

SCNAC, the XVIth Symposium on Chemistry of Nucleic Acid Components, was held in ?eský Krumlov (Czech Republic) in June. This year's symposium, which covered the chemistry, biochemistry, biophysics and chemical biology of nucleobases, nucleosides, nucleotides and nucleic acids attracted more than 150 participants from 21 countries to its lectures, oral communications and poster presentations. PMID:25250893

Gheerardijn, Vicky; Madder, Annemieke

2014-11-24

171

Annotating Nucleic Acid-Binding Function Based on Protein Structure  

E-print Network

Annotating Nucleic Acid-Binding Function Based on Protein Structure Eric W. Stawiski1 , Lydia M. Gregoret2 * and Yael Mandel-Gutfreund2 1 Department of Molecular, Cell and Developmental Biology University an automated approach to predict nucleic-acid-binding (NA-binding) proteins, specifi- cally DNA

Mandel-Gutfreund, Yael

172

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.

173

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

Microsoft Academic Search

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

Nicke Svanvik; Gunnar Westman; Dongyuan Wang; Mikael Kubista

2000-01-01

174

Quantitative thermodynamic predication of interactions between nucleic acid and non-nucleic acid species using Microsoft excel.  

PubMed

Proper design of nucleic acid sequences is crucial for many applications. We have previously established a thermodynamics-based quantitative model to help design aptamer-based nucleic acid probes by predicting equilibrium concentrations of all interacting species. To facilitate customization of this thermodynamic model for different applications, here we present a generic and easy-to-use platform to implement the algorithm of the model with Microsoft(®) Excel formulas and VBA (Visual Basic for Applications) macros. Two Excel spreadsheets have been developed: one for the applications involving only nucleic acid species, the other for the applications involving both nucleic acid and non-nucleic acid species. The spreadsheets take the nucleic acid sequences and the initial concentrations of all species as input, guide the user to retrieve the necessary thermodynamic constants, and finally calculate equilibrium concentrations for all species in various bound and unbound conformations. The validity of both spreadsheets has been verified by comparing the modeling results with the experimental results on nucleic acid sequences reported in the literature. This Excel-based platform described here will allow biomedical researchers to rationalize the sequence design of nucleic acid probes using the thermodynamics-based modeling even without relevant theoretical and computational skills. PMID:23849929

Zou, Jiaqi; Li, Na

2013-09-01

175

Highly stable duplex formation by artificial nucleic acids acyclic threoninol nucleic acid (aTNA) and serinol nucleic acid (SNA) with acyclic scaffolds.  

PubMed

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

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

2013-10-11

176

Scanning Tunneling Microscopy of Nucleic Acids  

NASA Astrophysics Data System (ADS)

The scanning tunneling microscope (STM) has been used to measure properties of poly(rA)\\cdot poly(rU) and DNA, such as helical pitch, half-period oscillations that were interpreted as the alternation between the major and minor grooves, and interhelical spacing. Average pitches were measured by two-dimensional Fourier transforms and by topographic profiles along the fiber axes. Values were typically 7 percent less than standard dimensions of A-form RNA and B-form DNA fibers. This result is compatible with the mild dehydration that occurred under air-drying conditions. More extensive dehydration typically led to 19 percent shrinkage. Analysis of specific regions allowed local variations in helical pitch as small as 1 angstrom to be detected, thus demonstrating that the STM can visualize functionally significant modulations of nucleic acid structure.

Lee, Gil; Arscott, Patricia G.; Bloomfield, Victor A.; Fennell Evans, D.

1989-04-01

177

ENDOCYTOSIS PATHWAYS FOR NUCLEIC ACID THERAPEUTICS  

PubMed Central

The development of nanoscale delivery vehicles for siRNAs is a current topic of considerable importance. However, little is understood about the exact trafficking mechanisms for siRNA-vehicle complexes across the plasma membrane and into the cytoplasm. While some information can be gleaned from studies on delivery of plasmid DNA, the different delivery requirements for these two vehicles makes drawing specific conclusions a challenge. However, using chemical inhibitors of different endocytosis pathways, studies on which endocytotic pathways are advantageous and deleterious for the delivery of nucleic acid drugs are emerging. Using this information as a guide, it is expected that the future development of effective siRNA delivery vehicles and therapeutics will be greatly improved. PMID:23956796

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

2013-01-01

178

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

179

Nucleic Acids Research, 1992, Vol. 20, No. 23 6297-6301 The isolation of transcription factors from Xgtl 1 cDNA  

E-print Network

. Similarly a fusion protein in which the acidic activation domain of HSV VP16 was linked to the cloned factor of proteins to bind to DNA in a sequence-specific manner has been used to clone a number of mammalianDNA expression library with a concatenated Su2 factor binding site, we isolated a cDNA which encodes a protein

Gaston, Kevin

180

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

181

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

182

ATR-IR spectroscopy as applied to nucleic acid films.  

PubMed

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. PMID:15911421

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

2005-07-01

183

THE EFFECT OF NUCLEIC ACIDS AND OF CARBOHYDRATES ON THE FORMATION OF STREPTOLYSIN  

PubMed Central

1. Ribonucleic acid of yeast causes the formation of a potent hemolysin in broth cultures of Streptococcus pyogenes. 2. The hemolysin whose formation is induced by yeast ribonucleic acid appears to be identical with streptolysin S. 3. Desoxyribonucleic acid, products of acid or alkaline hydrolysis of ribonucleic acid, or many other substances tested, fail to produce a similar effect. 4. Digestion by ribonuclease increases markedly the streptolysin-inducing activity of certain preparations of ribonucleic acid. 5. A fraction (AF) of yeast nucleic acid has been isolated which possesses approximately 100 times the streptolysin-inducing capacity of the starting material. Some of the properties which distinguish AF, a polynucleotide, from ordinary yeast nucleic acid are described. AF is associated with the ribonuclease-resistant fraction of yeast nucleic acid. 6. Ribonucleic acid prepared from streptococci, wheat germ, and mammalian liver, and subsequently treated with ribonuclease, is about as active in causing streptolysin formation as ribonuclease-treated yeast nucleic acid. 7. Ribonucleic acid of tobacco mosaic virus, tested under comparable conditions, was found to be inactive. 8. Ribonucleic acid prepared from streptococci, wheat germ, and tobacco mosaic virus resembles yeast nucleic acid in possessing a ribonuclease-resistant fraction. 9. In addition to AF, a factor (or factors), present in meat infusion and in peptone, was found to be required for the formation of streptolysin. 10. The factor can be partially replaced by any one of several carbohydrates, the most active being maltose, glucosamine, and trehalose, in that order. 11. When appropriate concentrations of AF, maltose, and glucose are used, the nucleic acid-induced streptolysin can be produced in a medium whose chemical composition is essentially defined. PMID:18873865

Bernheimer, Alan W.; Rodbart, Marcelle

1948-01-01

184

Methods and compositions for efficient nucleic acid sequencing  

DOEpatents

Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

Drmanac, Radoje

2006-07-04

185

Electrical and Electrochemical Monitoring of Nucleic Acid Amplification  

PubMed Central

Nucleic acid amplification is a gold standard technique for analyzing a tiny amount of nucleotides in molecular biology, clinical diagnostics, food safety, and environmental testing. Electrical and electrochemical monitoring of the amplification process draws attention over conventional optical methods because of the amenability toward point-of-care applications as there is a growing demand for nucleic acid sensing in situations outside the laboratory. A number of electrical and electrochemical techniques coupled with various amplification methods including isothermal amplification have been reported in the last 10?years. In this review, we highlight recent developments in the electrical and electrochemical monitoring of nucleic acid amplification. PMID:25798440

Goda, Tatsuro; Tabata, Miyuki; Miyahara, Yuji

2015-01-01

186

Lateral flow biosensors for the detection of nucleic acid.  

PubMed

The detection of nucleic acid is of central importance for the diagnosis of genetic diseases, infectious agents, and biowarfare agents. Traditional strategies and technologies for nucleic acid detection are time-consuming and labor-intensive. Recently, isothermal strand-displacement reaction-based lateral flow biosensors have attracted a great deal of research interest because they are sensitive, simple, fast, and easy to use. Here, we describe a lateral flow biosensor based on isothermal strand-displacement polymerase reaction and gold nanoparticles for the visual detection of nucleic acid. PMID:24026695

Zeng, Lingwen; Lie, Puchang; Fang, Zhiyuan; Xiao, Zhuo

2013-01-01

187

Methods and compositions for efficient nucleic acid sequencing  

DOEpatents

Disclosed are novel methods and compositions for rapid and highly efficient nucleic acid sequencing based upon hybridization with two sets of small oligonucleotide probes of known sequences. Extremely large nucleic acid molecules, including chromosomes and non-amplified RNA, may be sequenced without prior cloning or subcloning steps. The methods of the invention also solve various current problems associated with sequencing technology such as, for example, high noise to signal ratios and difficult discrimination, attaching many nucleic acid fragments to a surface, preparing many, longer or more complex probes and labelling more species.

Drmanac, Radoje (850 E. Greenwich Pl., Palo Alto, CA 94303)

2002-01-01

188

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

E-print Network

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

Liu, David R.

189

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

190

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.

191

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.

192

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

193

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

194

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.

195

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

196

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

197

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

198

21 CFR 866.3225 - Enterovirus nucleic acid assay.  

Code of Federal Regulations, 2012 CFR

... 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) Identification . An...

2012-04-01

199

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

200

Optimization of Encoded Hydrogel Particles for Nucleic Acid Quantification  

E-print Network

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

Pregibon, Daniel C.

201

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

202

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

203

Nucleic acid in-situ hybridization detection of infectious agents  

NASA Astrophysics Data System (ADS)

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

Thompson, Curtis T.

2000-04-01

204

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

205

Nucleic Acid Amplification Testing for Neisseria gonorrhoeae  

PubMed Central

Nucleic acid amplification tests (NAATs) for the detection of Neisseria gonorrhoeae became available in the early 1990s. Although offering several advantages over traditional detection methods, N. gonorrhoeae NAATs do have some limitations. These include cost, risk of carryover contamination, inhibition, and inability to provide antibiotic resistance data. In addition, there are sequence-related limitations that are unique to N. gonorrhoeae NAATs. In particular, false-positive results are a major consideration. These primarily stem from the frequent horizontal genetic exchange occurring within the Neisseria genus, leading to commensal Neisseria species acquiring N. gonorrhoeae genes. Furthermore, some N. gonorrhoeae subtypes may lack specific sequences targeted by a particular NAAT. Therefore, NAAT false-negative results because of sequence variation may occur in some gonococcal populations. Overall, the N. gonorrhoeae species continues to present a considerable challenge for molecular diagnostics. The need to evaluate N. gonorrhoeae NAATs before their use in any new patient population and to educate physicians on the limitations of these tests is emphasized in this review. PMID:16436629

Whiley, David M.; Tapsall, John W.; Sloots, Theo P.

2006-01-01

206

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

207

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

208

Electrochemical Molecular Analysis Without Nucleic Acid Amplification  

PubMed Central

Electrochemical biosensors have revolutionized glucose monitoring but have not yet fulfilled their promise of a low cost, direct detection replacement for genetic amplification tests such as PCR [K. Kerman, M. Kobayashi, E. Tamiya, Recent trends in electro-chemical DNA biosensor technology, Meas. Sci. Technol. 15 (2004) R1-R11; A. Chaubey, B.D. Malhotra, Mediated biosensors. Biosens. Bioelectron. 17 (6-7) (2002) 441-456]. It has been anticipated that the integration of nanoscale chemical structures such as self-assembled monolayers with electrochemical biosensors would increase sensitivity by decreasing inherent system noise. We have designed a novel biosensing approach incorporating such integration and achieved rapid, ultra-low concentration sensitivities without target amplification. Raw samples are mixed with lysis buffer to allow hybridization of nucleic acid targets with anchor and signal probes before immobilizing a signaling enzyme proximate to the biosensor surface. A bias potential is subsequently applied and the secondary byproduct of a cyclic peroxidase reaction measured. Further studies have demonstrated the application of our approach in protein, clinical chemistry, and ionic assays. PMID:16213156

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

2006-01-01

209

Coordination polymer nanobelts for nucleic acid detection  

NASA Astrophysics Data System (ADS)

Herein, coordination polymer nanobelts (CPNBs) were prepared rapidly and on a large scale, by directly mixing aqueous AgNO3 solution and an ethanol solution of 4, 4'-bipyridine at room temperature. The application of such CPNBs as a fluorescent sensing platform for nucleic acid detection was further explored. CPNB is a ?-rich structure, the strong ?-? stacking interactions between unpaired DNA bases and CPNB leads to adsorption of fluorescently labeled single-stranded DNA (ssDNA) accompanied by 66% fluorescence quenching. However, the presence of target ssDNA will hybridize with the probe. The resultant helix cannot be adsorbed by CPNB due to its rigid conformation and the absence of unpaired DNA bases. Thus, a significant fluorescence enhancement, 73% fluorescence recovery, was observed in DNA detection as long as the target exists. The present system has excellent sensitivity; a substantial fluorescence enhancement was observed when the concentration of the target was as low as 5 nM. It also exhibits outstanding discrimination ability down to a single-base mismatch.

Luo, Yonglan; Liao, Fang; Lu, Wenbo; Chang, Guohui; Sun, Xuping

2011-05-01

210

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

Microsoft Academic Search

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

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

2003-01-01

211

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

212

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

E-print Network

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

Sagot, Marie-France

213

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

Microsoft Academic Search

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

Darrell P. Chandler; Ann E. Jarrell

2003-01-01

214

Isolation and Detection of Enterovirus RNA from Large-Volume Water Samples by Using the NucliSens miniMAG System and Real-Time Nucleic Acid Sequence-Based Amplification  

PubMed Central

Concentration of water samples is a prerequisite for the detection of the low virus levels that are present in water and may present a public health hazard. The aim of this study was to develop a rapid, standardized molecular method for the detection of enteroviruses in large-volume surface water samples, using a concentration method suitable for the detection of infectious viruses as well as virus RNA. Concentration of water was achieved by a conventional filter adsorption-elution method and ultrafiltration, resulting in a 10,000-fold concentration of the sample. Isolation of virus RNA by a silica-based RNA extraction method was compared with the nonmagnetic and magnetic NucliSens RNA isolation methods. By using the silica-based RNA extraction method in two out of five samples, enterovirus RNA was detected, whereas four out of five samples were positive following RNA isolation with magnetic silica beads. Moreover, estimated RNA levels increased at least 100 to 500 times. Furthermore, we compared enterovirus detection by an in-house reverse transcription (RT)-PCR with a novel commercially available real-time nucleic acid sequence-based amplification (NASBA) assay. We found that the rapid real-time NASBA assay was slightly less sensitive than our in-house RT-PCR. The advantages, however, of a commercial real-time NASBA assay, like the presence of an internal control RNA, standardization, and enormous decrease in turnaround time, makes it an attractive alternative to RT-PCR. PMID:16000783

Rutjes, Saskia A.; Italiaander, Ronald; van den Berg, Harold H. J. L.; Lodder, Willemijn J.; de Roda Husman, Ana Maria

2005-01-01

215

Recent Progress in Nucleic Acid Aptamer-Based Biosensors and Bioassays  

PubMed Central

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

Mok, Wendy; Li, Yingfu

2008-01-01

216

Nucleic acid-based nanoengineering: novel structures for biomedical applications  

PubMed Central

Nanoengineering exploits the interactions of materials at the nanometre scale to create functional nanostructures. It relies on the precise organization of nanomaterials to achieve unique functionality. There are no interactions more elegant than those governing nucleic acids via Watson–Crick base-pairing rules. The infinite combinations of DNA/RNA base pairs and their remarkable molecular recognition capability can give rise to interesting nanostructures that are only limited by our imagination. Over the past years, creative assembly of nucleic acids has fashioned a plethora of two-dimensional and three-dimensional nanostructures with precisely controlled size, shape and spatial functionalization. These nanostructures have been precisely patterned with molecules, proteins and gold nanoparticles for the observation of chemical reactions at the single molecule level, activation of enzymatic cascade and novel modality of photonic detection, respectively. Recently, they have also been engineered to encapsulate and release bioactive agents in a stimulus-responsive manner for therapeutic applications. The future of nucleic acid-based nanoengineering is bright and exciting. In this review, we will discuss the strategies to control the assembly of nucleic acids and highlight the recent efforts to build functional nucleic acid nanodevices for nanomedicine. PMID:23050076

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

2011-01-01

217

Methods And Devices For Characterizing Duplex Nucleic Acid Molecules  

DOEpatents

Methods and devices are provided for characterizing a duplex nucleic acid, e.g., a duplex DNA molecule. In the subject methods, a fluid conducting medium that includes a duplex nucleic acid molecule is contacted with a nanopore under the influence of an applied electric field and the resulting changes in current through the nanopore caused by the duplex nucleic acid molecule are monitored. The observed changes in current through the nanopore are then employed as a set of data values to characterize the duplex nucleic acid, where the set of data values may be employed in raw form or manipulated, e.g., into a current blockade profile. Also provided are nanopore devices for practicing the subject methods, where the subject nanopore devices are characterized by the presence of an algorithm which directs a processing means to employ monitored changes in current through a nanopore to characterize a duplex nucleic acid molecule responsible for the current changes. The subject methods and devices find use in a variety of applications, including, among other applications, the identification of an analyte duplex DNA molecule in a sample, the specific base sequence at a single nulceotide polymorphism (SNP), and the sequencing of duplex DNA molecules.

Akeson, Mark (Santa Cruz, CA); Vercoutere, Wenonah (Santa Cruz, CA); Haussler, David (Santa Cruz, CA); Winters-Hilt, Stephen (Santa Cruz, CA)

2005-08-30

218

Interaction of resveratrol and genistein with nucleic acids.  

PubMed

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

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

2005-03-31

219

Presence of human immunodeficiency virus nucleic acids in wastewater and their detection by polymerase chain reaction.  

PubMed Central

The human immunodeficiency virus type 1 (HIV-1) released by infected individuals or present in human and hospital wastes can potentially cause contamination problems. The presence of HIV-1 was investigated in 16 environmental samples, including raw wastewater, sludge, final effluent, soil, and pond water, collected from different locations. A method was developed to extract total nucleic acids in intact form directly from the raw samples or from the viral concentrates of the raw samples. The isolated nucleic acids were analyzed for the presence of HIV-1 by using in vitro amplification of the target sequences by the polymerase chain reaction (PCR) method. HIV-1-specific proviral DNA and viral RNA were detected in the extracted nucleic acids obtained from three wastewater samples by this method. The specificity of the PCR-amplified products was determined by Southern blot hybridization with an HIV-1-specific oligonucleotide probe, SK19. The isolated nucleic acids from wastewater samples were also screened for the presence of poliovirus type 1, representing a commonly found enteric virus, and simian immunodeficiency virus, representing, presumably, rare viruses. While poliovirus type 1 viral RNA was found in all of the wastewater samples, none of the samples yielded a simian immunodeficiency virus-specific product. No PCR-amplified product was yielded when wastewater samples were directly used for the detection of HIV-1 and poliovirus type 1. The wastewater constituents appeared to be inhibitory to the enzymes reverse transcriptase and DNA polymerase.(ABSTRACT TRUNCATED AT 250 WORDS) Images PMID:1476440

Ansari, S A; Farrah, S R; Chaudhry, G R

1992-01-01

220

Point-of-care nucleic acid testing for infectious diseases  

PubMed Central

Nucleic acid testing for infectious diseases at the point of care is beginning to enter clinical practice in developed and developing countries; especially for applications requiring fast turnaround times, and in settings where a centralized laboratory approach faces limitations. Current systems for clinical diagnostic applications are mainly PCR-based, can only be used in hospitals, and are still relatively complex and expensive. Integrating sample preparation with nucleic acid amplification and detection in a cost-effective, robust, and user-friendly format remains challenging. This review describes recent technical advances that might be able to address these limitations, with a focus on isothermal nucleic acid amplification methods. It briefly discusses selected applications related to the diagnosis and management of tuberculosis, HIV, and perinatal and nosocomial infections. PMID:21377748

Niemz, Angelika; Ferguson, Tanya M.; Boyle, David S.

2013-01-01

221

Nucleic acid-protein interactions: Wedding for love or circumstances?  

PubMed

The sixth Figeac meeting on nucleic acid-protein interactions was held in Figeac, France, from September 26th to October 1st, 2008. It was organized by the working group "nucleic acid-protein interactions and gene expression" from the French Society for Biochemistry and Molecular Biology. This report briefly summarizes the presentations by 40 speakers during the four plenary sessions, which were organised as follows: (1) nucleic acids: targets and tools, (2) RNA superstar, (3) nuclear structure and dynamics, and (4) new concepts - new approaches. A total of 22 plenary lectures, 18 oral communications and 40 posters were presented over the 5 days, providing a highly stimulating environment for scientific exchange between the approximately 80 participants (biochemists, physicists, bio-informaticians and molecular and cellular biologists). PMID:19422875

Lavelle, Christophe; Buckle, Malcolm

2009-08-01

222

Nature and Magnitude of Aromatic Stacking of Nucleic Acid Bases  

SciTech Connect

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

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

2008-04-07

223

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

224

Intracellular protein and nucleic acid measured in eight cell types using deep-ultraviolet mass mapping.  

PubMed

We present measurements by deep-ultraviolet mass mapping of nucleic acid (NA) and protein for five commonly cultured and three primary cell types. The dry mass distribution at submicron resolution was determined on a single-cell basis for 250-500 cells from each of these types. Since the method carries a direct reference to a spectrophotometric standard (molar extinction coefficient), we are able to calibrate the absolute weight distributions both on a cell-to-cell basis within each type and across types. We also provide a calibration in absolute mass units for fluorescence-based measurements (flow cytometry and fluorescence microscopy). As might be expected the cultured cell lines show a high concentration of nucleic acids in the nuclear compartment, much larger than the genomic 2C number even in the G1 stage. The whole-cell nucleic-acid/protein ratio was found to be a characteristic of cell lines that persists independent of cell cycle and, as a result, this ratio has some value for phenotyping. Primary chicken red blood cells (cRBC), often used as a cytometry standard, were determined to have a nuclear-isolated nucleic acid content much closer to the genomic number than the cultured cell lines (cRBC: 3.00 pg total NA, 2.30 pg DNA, and 0.70 pg RNA). The individual blastomeres (n = 54) from mouse embryos at eight-cell stage were measured and found to vary by more than a factor or two in total protein and nucleic acid content (0.8-2.3 ng total protein, 70-150 pg total NA). The ratio of nucleic acid to protein was more nearly constant for each blastomere from a particular embryo and this ratio was found to be an identifying characteristic that varies from embryo to embryo obtained from a single flushing of a mouse. PMID:23504822

Cheung, Man C; LaCroix, Rebecca; McKenna, Brian K; Liu, Ling; Winkelman, James; Ehrlich, Daniel J

2013-06-01

225

Nucleic acid structure analysis: Local, mathematically rigorous, comparable  

SciTech Connect

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

Babcock, M.S.

1993-01-01

226

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

227

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

228

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

NASA Astrophysics Data System (ADS)

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

Forties, Robert; Bundschuh, Ralf

2009-03-01

229

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

230

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

231

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

232

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

233

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

Federal Register 2010, 2011, 2012, 2013, 2014

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

2012-03-19

234

DNA-Templated Polymerization of Side-Chain-Functionalized Peptide Nucleic Acid Aldehydes  

E-print Network

DNA-Templated Polymerization of Side-Chain-Functionalized Peptide Nucleic Acid Aldehydes Ralph E previously reported the efficient and sequence-specific DNA-templated polymerization of peptide nucleic acid-specific DNA-templated polymerization of unfunc- tionalized peptide nucleic acid (PNA) aldehydes using

Liu, David R.

235

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

E-print Network

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

Liu, David R.

236

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

Microsoft Academic Search

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

Peter E Nielsen

2001-01-01

237

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

Microsoft Academic Search

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

ARGHYA RAY; BENGT NORDEN

238

Nucleic Acids Research doi:10.1093/nar/gkn433  

E-print Network

Nucleic Acids Research doi:10.1093/nar/gkn433 First published online 14 Jul 2008;Nucleic Acids Res. Hilda David-Eden and Yael Mandel-Gutfreund Revealing unique properties of the ribosome using a network://nar.oxfordjournals.org Additional information about Nucleic Acids Research, including how to subscribe can be found at Published

Mandel-Gutfreund, Yael

239

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.

240

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

241

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

242

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

243

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

E-print Network

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

244

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

245

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

246

SINGLE MOLECULE DETECTION OF TUBERCULOSIS NUCLEIC ACID USING DARK FIELD TETHERED PARTICLE MOTION  

E-print Network

SINGLE MOLECULE DETECTION OF TUBERCULOSIS NUCLEIC ACID USING DARK FIELD TETHERED PARTICLE MOTION for tuberculosis nucleic acid detection re- quire amplification and labeling before detection is possible. We of an exquisitely sensitive method of detecting the presence of nucleic acids derived from human pathogens directly

Stallinga, Sjoerd

247

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

248

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

249

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.

250

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

251

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.

252

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

253

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.

254

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

255

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

256

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 of alternative nucleotides would support the assembly of nucleic acid polymers containing nonheritable backbone of heterogeneous nucleic acid molecules could evolve reproducible function. For such evolution to be possible

Heller, Eric

257

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.

258

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.

259

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

260

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

261

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.

262

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.

263

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.

264

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

265

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

266

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

267

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.

268

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

269

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

E-print Network

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

Benedek, George B.

270

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.

271

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

272

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

273

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

E-print Network

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

274

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

275

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

E-print Network

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

Fernando, Chrisantha

276

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

277

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

278

Modern mass spec based (Because nucleic acids are overrated)  

E-print Network

Modern mass spec based proteomics (Because nucleic acids are overrated) #12;Presentation outlinePIT) Protein mass spectrometry Protein separation Data analysis -> #12;Protein mass spectrometry Mass spec Wilhelm Wien (Foundation), 1898 Sir Joseph Thomson (Neon isotopes) , 1913 Beginning of protein mass spec

Goldschmidt, Christina

279

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

280

Mosaic protein and nucleic acid vaccines against hepatitis C virus  

DOEpatents

The invention relates to immunogenic compositions useful as HCV vaccines. Provided are HCV mosaic polypeptide and nucleic acid compositions which provide higher levels of T-cell epitope coverage while minimizing the occurrence of unnatural and rare epitopes compared to natural HCV polypeptides and consensus HCV sequences.

Yusim, Karina; Korber, Bette T. M.; Kuiken, Carla L.; Fischer, William M.

2013-06-11

281

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

Microsoft Academic Search

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

Dwaine A. Braasch; David R. Corey

2001-01-01

282

Liver cell specific targeting of peptide nucleic acid oligomers  

Microsoft Academic Search

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

Xiao Zhang; Carla G Simmons; David R Corey

2001-01-01

283

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

284

Inhibition of miRNA maturation by peptide nucleic acids.  

PubMed

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

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

2014-01-01

285

Structure, stability and behaviour of nucleic acids in ionic liquids  

PubMed Central

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

2014-01-01

286

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

287

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

PubMed Central

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

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

2013-01-01

288

Nucleic acids encoding human trithorax protein  

DOEpatents

In accordance with the present invention, there is provided an isolated peptide having the characteristics of human trithorax protein (as well as DNA encoding same, antisense DNA derived therefrom and antagonists therefor). The invention peptide is characterized by having a DNA binding domain comprising multiple zinc fingers and at least 40% amino acid identity with respect to the DNA binding domain of Drosophila trithorax protein and at least 70% conserved sequence with respect to the DNA binding domain of Drosophila trithorax protein, and wherein said peptide is encoded by a gene located at chromosome 11 of the human genome at q23. Also provided are methods for the treatment of subject(s) suffering from immunodeficiency, developmental abnormality, inherited disease, or cancer by administering to said subject a therapeutically effective amount of one of the above-described agents (i.e., peptide, antagonist therefor, DNA encoding said peptide or antisense DNA derived therefrom). Also provided is a method for the diagnosis, in a subject, of immunodeficiency, developmental abnormality, inherited disease, or cancer associated with disruption of chromosome 11 at q23.

Evans, Glen A. (Encinitas, CA); Djabali, Malek (Marseilles, FR); Selleri, Licia (Del Mar, CA); Parry, Pauline (San Diego, CA)

2001-01-01

289

Polymers for nucleic acid transfer-an overview.  

PubMed

For the last five decades cationic polymers have been used for nucleic acids transfection. Our understanding of polymer-nucleic acid interactions and their rational use in delivery has continuously increased. The great improvements in macromolecular chemistry and the recognition of distinct biological extra- and intracellular delivery hurdles triggered several breakthrough developments, including the discovery of natural and synthetic polycations for compaction of nucleic acids into stable nanoparticles termed polyplexes; the incorporation of targeting ligands and surface-shielding of polyplexes to enable receptor-mediated gene delivery into defined target tissues; and strongly improved intracellular transfer efficacy by better endosomal escape of vesicle-trapped polyplexes into the cytosol. These experiences triggered the development of second-generation polymers with more dynamic properties, such as endosomal pH-responsive release mechanisms, or biodegradable units for improved biocompatibility and intracellular release of the nucleic acid pay load. Despite a better biological understanding, significant challenges such as efficient nuclear delivery and persistence of gene expression persist. The therapeutic perspectives widened from pDNA-based gene therapy to application of novel therapeutic nucleic acids including mRNA, siRNA, and microRNA. The finding that different therapeutic pay loads require different tailor-made carriers complicates preclinical developments. Convincing evidence of medical efficacy still remains to be demonstrated. Bioinspired multifunctional polyplexes resembling "synthetic viruses" appear as attractive opportunity, but provide additional challenges: how to identify optimum combinations of functional delivery units, and how to prepare such polyplexes reproducibly in precise form? Design of sequence-defined polymers, screening of combinatorial polymer and polyplex libraries are tools for further chemical evolution of polyplexes. PMID:25409608

Wagner, Ernst

2014-01-01

290

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

PubMed Central

The extraction and purification of nucleic acids from complex samples (e.g. blood, biopsied tissue, cultured cells, food) is an essential prerequisite for many applications in biology including genotyping, transcriptional analysis, systems biology, epigenetic analysis, and virus/bacterial detection. In this report, we describe a new process of nucleic acid extraction that utilizes “pinned” aqueous/organic liquid interfaces in microchannels to streamline the extraction mechanism, replacing all washing steps with a single traverse of an immiscible fluid barrier, termed Immiscible Filtration Assisted by Surface Tension (IFAST). Nucleic acids in biological samples are bound to paramagnetic particles and then drawn across the IFAST device (or array of IFAST devices) using a magnet. While the strength of the IFAST barrier is suitable for separation of nucleic acids from lysate in its current embodiment, its permeability can be selectively adapted by adjusting the surface tensions/energies associated with the cell lysate, the immiscible phase, and the device surface, enabling future expansion to other non-nucleic acid applications. Importantly, processing time is reduced from 15–45 minutes to less than 5 minutes while maintaining purity, yield, and scalability equal to or better than prevailing methods. Operation is extremely simple and no additional lab infrastructure is required. The IFAST technology thus significantly enhances researchers’ abilities to isolate and analyze nucleic acids, a process which is critical and ubiquitous in an extensive array of scientific fields. PMID:21423999

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

2011-01-01

291

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

292

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

Microsoft Academic Search

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

Robert H. E Hudson; Ge Li; Joseph Tse

2002-01-01

293

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

DOEpatents

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

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

2011-12-06

294

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

295

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

296

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.

297

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

298

A partition function algorithm for interacting nucleic acid strands  

PubMed Central

Recent interests, such as RNA interference and antisense RNA regulation, strongly motivate the problem of predicting whether two nucleic acid strands interact. Motivation: Regulatory non-coding RNAs (ncRNAs) such as microRNAs play an important role in gene regulation. Studies on both prokaryotic and eukaryotic cells show that such ncRNAs usually bind to their target mRNA to regulate the translation of corresponding genes. The specificity of these interactions depends on the stability of intermolecular and intramolecular base pairing. While methods like deep sequencing allow to discover an ever increasing set of ncRNAs, there are no high-throughput methods available to detect their associated targets. Hence, there is an increasing need for precise computational target prediction. In order to predict base-pairing probability of any two bases in interacting nucleic acids, it is necessary to compute the interaction partition function over the whole ensemble. The partition function is a scalar value from which various thermodynamic quantities can be derived. For example, the equilibrium concentration of each complex nucleic acid species and also the melting temperature of interacting nucleic acids can be calculated based on the partition function of the complex. Results: We present a model for analyzing the thermodynamics of two interacting nucleic acid strands considering the most general type of interactions studied in the literature. We also present a corresponding dynamic programming algorithm that computes the partition function over (almost) all physically possible joint secondary structures formed by two interacting nucleic acids in O(n6) time. We verify the predictive power of our algorithm by computing (i) the melting temperature for interacting RNA pairs studied in the literature and (ii) the equilibrium concentration for several variants of the OxyS–fhlA complex. In both experiments, our algorithm shows high accuracy and outperforms competitors. Availability: Software and web server is available at http://compbio.cs.sfu.ca/taverna/pirna/ Contact: cenk@cs.sfu.ca; backofen@informatik.uni-freiburg.de Supplementary information: Supplementary data are avaliable at Bioinformatics online. PMID:19478011

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

2009-01-01

299

Acyclicl-threoninol nucleic acid (l-aTNA) with suitable structural rigidity cross-pairs with DNA and RNA.  

PubMed

We report the hybridization properties of a novel artificial nucleic acid: acyclicl-threoninol nucleic acid (l-aTNA). l-aTNA formed a more stable duplex with DNA and RNA than either d-aTNA or serinol nucleic acid (SNA) as the rigidity of the l-form was more optimal for interaction with natural nucleic acids. PMID:25633432

Murayama, Keiji; Kashida, Hiromu; Asanuma, Hiroyuki

2015-03-31

300

Performance Characteristics of a Quantitative Hepatitis C Virus RNA Assay Using COBAS AmpliPrep Total Nucleic Acid Isolation and COBAS TaqMan Hepatitis C Virus Analyte-Specific Reagent  

PubMed Central

Performance characteristics of a hepatitis C virus (HCV) RNA quantification assay comprised automated specimen extraction [COBAS AmpliPrep (CAP) using total nucleic acid isolation reagents (TNAI)], and real-time polymerase chain reaction [COBAS TaqMan 48 HCV with analyte-specific reagents (CTM48)] were determined. CAP TNAI/CTM48 performed linearly from approximately 2.0 to at least 6.7 log10 IU/ml for HCV genotypes (Gts) 1, 2, and 3. The limit of detection for the World Health Organization International Standard was 23 IU/ml. Variabilities ranged from 1.3 to 2.1%. Excellent quantitative agreement was observed in clinical samples using CTM48 and two different methods for HCV RNA extraction (CAP TNAI and BioRobot M48; regression line slope, 0.98; y-intercept, 0.11; R2, 0.98; mean difference, 0.003). Good agreement was also observed between CAP TNAI/CTM48 and COBAS Amplicor Monitor (regression line slope, 0.94; y-intercept, 0.08; R2, 0.96), although HCV RNA concentrations were on average greater by COBAS Amplicor Monitor (mean difference ?0.27 log10 IU/ml). Better overall agreement was observed for Gt 1 than non-Gt 1 specimens when comparing extraction and quantification methods; however, no consistent genotype-dependent quantification bias was observed. These data suggest that CAP TNAI/CTM48 offers an alternative method for the quantification of HCV in plasma samples. PMID:18276771

Forman, Michael S.; Valsamakis, Alexandra

2008-01-01

301

Recent Developments in Peptide-Based Nucleic Acid Delivery  

PubMed Central

Despite the fact that non-viral nucleic acid delivery systems are generally considered to be less efficient than viral vectors, they have gained much interest in recent years due to their superior safety profile compared to their viral counterpart. Among these synthetic vectors are cationic polymers, branched dendrimers, cationic liposomes and cell-penetrating peptides (CPPs). The latter represent an assortment of fairly unrelated sequences essentially characterised by a high content of basic amino acids and a length of 10–30 residues. CPPs are capable of mediating the cellular uptake of hydrophilic macromolecules like peptides and nucleic acids (e.g. siRNAs, aptamers and antisense-oligonucleotides), which are internalised by cells at a very low rate when applied alone. Up to now, numerous sequences have been reported to show cell-penetrating properties and many of them have been used to successfully transport a variety of different cargos into mammalian cells. In recent years, it has become apparent that endocytosis is a major route of internalisation even though the mechanisms underlying the cellular translocation of CPPs are poorly understood and still subject to controversial discussions. In this review, we will summarise the latest developments in peptide-based cellular delivery of nucleic acid cargos. We will discuss different mechanisms of entry, the intracellular fate of the cargo, correlation studies of uptake versus biological activity of the cargo as well as technical problems and pitfalls. PMID:19325804

Veldhoen, Sandra; Laufer, Sandra D.; Restle, Tobias

2008-01-01

302

Hands-free sample preparation platform for nucleic acid analysis.  

PubMed

A Lab-On-Chip system with an instrument is presented which is capable of performing total sample preparation and automated extraction of nucleic acid from human cell samples fixed in a methanol based solution. The target application is extraction of mRNA from cervical liquid based cytology specimens for detection of transformed HPV-infections. The device accepts 3 ml of sample and performs the extraction in a disposable polymer chip of credit card size. All necessary reagents for cell lysis, washing, and elution are stored on-chip and the extraction is performed in two filter stages; one for cell pre-concentration and the other for nucleic acid capture. Tests performed using cancer cell lines and cervical liquid based cytology specimens confirm the extraction of HPV-mRNA by the system. PMID:19904407

Baier, T; Hansen-Hagge, T E; Gransee, R; Crombé, A; Schmahl, S; Paulus, C; Drese, K S; Keegan, H; Martin, C; O'Leary, J J; Furuberg, L; Solli, L; Grønn, P; Falang, I M; Karlgård, A; Gulliksen, A; Karlsen, F

2009-12-01

303

Nucleic acid aptamers: research tools in disease diagnostics and therapeutics.  

PubMed

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

Santosh, Baby; Yadava, Pramod K

2014-01-01

304

Selected Nucleic Acid Precursors in Studies of Aquatic Microbial Ecology  

PubMed Central

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

Karl, David M.

1982-01-01

305

Detection of nucleic acid hybrids by prolonged chemiluminescence  

SciTech Connect

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

Dattagupta, N.; Clemens, A.H.

1988-12-27

306

Nucleic acid-free mutation of prion strains  

PubMed Central

While prions share the ability to propagate strain information with nucleic acid-based pathogens, it is unclear how they mutate and acquire fitness in the absence of this informational component. Because prion diseases occur as epidemics, understanding this mechanism is of paramount importance for implementing control strategies to limit their spread and for evaluating their zoonotic potential. Here we review emerging evidence indicating how prion protein primary structures, in concert with PrPSc conformational compatibility, determine prion strain mutation. PMID:20948302

2010-01-01

307

Developing nucleic acid-based electrical detection systems  

PubMed Central

Development of nucleic acid-based detection systems is the main focus of many research groups and high technology companies. The enormous work done in this field is particularly due to the broad versatility and variety of these sensing devices. From optical to electrical systems, from label-dependent to label-free approaches, from single to multi-analyte and array formats, this wide range of possibilities makes the research field very diversified and competitive. New challenges and requirements for an ideal detector suitable for nucleic acid analysis include high sensitivity and high specificity protocol that can be completed in a relatively short time offering at the same time low detection limit. Moreover, systems that can be miniaturized and automated present a significant advantage over conventional technology, especially if detection is needed in the field. Electrical system technology for nucleic acid-based detection is an enabling mode for making miniaturized to micro- and nanometer scale bio-monitoring devices via the fusion of modern micro- and nanofabrication technology and molecular biotechnology. The electrical biosensors that rely on the conversion of the Watson-Crick base-pair recognition event into a useful electrical signal are advancing rapidly, and recently are receiving much attention as a valuable tool for microbial pathogen detection. Pathogens may pose a serious threat to humans, animal and plants, thus their detection and analysis is a significant element of public health. Although different conventional methods for detection of pathogenic microorganisms and their toxins exist and are currently being applied, improvements of molecular-based detection methodologies have changed these traditional detection techniques and introduced a new era of rapid, miniaturized and automated electrical chip detection technologies into pathogen identification sector. In this review some developments and current directions in nucleic acid-based electrical detection are discussed. PMID:16512917

Gabig-Ciminska, Magdalena

2006-01-01

308

Molecular modeling of nucleic Acid structure: electrostatics and solvation.  

PubMed

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 its 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 a way of sampling conformational space for a better understanding of the relevance of a given model. This discussion highlighted the major limitations with modeling in general. When sampling conformational space effectively, difficult issues are encountered, such as 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 subjects are discussed in detail in this unit. Curr. Protoc. Nucleic Acid Chem. 55:7.9.1-7.9.27. © 2014 by John Wiley & Sons, Inc. PMID:25631536

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

2014-01-01

309

DNA-like double helix formed by peptide nucleic acid  

Microsoft Academic Search

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

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

1994-01-01

310

Inhibition of a DNA-helicase by peptide nucleic acids  

Microsoft Academic Search

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

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

1999-01-01

311

Inhibiting transcription of chromosomal DNA with antigene peptide nucleic acids  

Microsoft Academic Search

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

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

2005-01-01

312

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

PubMed Central

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

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

2009-01-01

313

Method and apparatus for staining immobilized nucleic acids  

SciTech Connect

A method for staining immobilized nucleic acids includes the following steps: 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.M.; Foote, R.S.; Jacobson, S.C.

2000-05-02

314

Antisense and Antigene Properties of Peptide Nucleic Acids  

Microsoft Academic Search

Peptide nucleic acids (PNAs) are polyamide oligomers that can strand invade duplex DNA, causing displacement of one DNA strand and formation of a D-loop. Binding of either a T10 PNA or a mixed sequence 15-mer PNA to the transcribed strand of a G-free transcription cassette caused 90 to 100 percent site-specific termination of pol II transcription elongation. When a T10

Jeffery C. Hanvey; Nancy J. Peffer; John E. Bisi; Stephen A. Thomson; Rodolfo Cadilla; John A. Josey; Daniel J. Ricca; C. Fred Hassman; Michele A. Bonham; Karin G. Au; Stephen G. Carter; David A. Bruckenstein; Ann L. Boyd; Stewart A. Noble; Lee E. Babiss

1992-01-01

315

System for portable nucleic acid testing in low resource settings  

NASA Astrophysics Data System (ADS)

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

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

2013-03-01

316

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

317

Cell-free Nucleic Acids as Potential Markers for Preeclampsia  

Microsoft Academic Search

Preeclampsia is one of the leading causes of maternal and fetal\\/neonatal mortality and morbidity worldwide. Therefore, widely applicable and affordable tests are needed to make an early diagnosis before the occurrence of the clinical symptoms. Circulating cell-free nucleic acids in plasma and serum are novel biomarkers with promising clinical applications in different medical fields, including prenatal diagnosis.Quantitative changes of cell-free

S. Hahn; C. Rusterholz; I. Hösli; O. Lapaire

2011-01-01

318

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

319

IR-UV photochemistry of protein-nucleic acid systems  

SciTech Connect

UV light has often been used to induce the formation of covalent bonds between DNA (or RNA) and tightly-bound protein molecules. However, the internal photoreactions of nucleic acids and proteins limit the yield and complicate the analysis of intermolecular crosslinks. In an ongoing search for improved reaction specificity or new photoreactions in these systems, we have employed UV photons from a Nd:YAG-pumped dye laser and mid-IR photons from the Vanderbilt FEL. Having crosslinked several protein-nucleic acid systems with nanosecond UV laser pulses, we are currently studying the effect of various IR wavelengths on a model system (gene 32 protein and poly[dT]). We have found that irradiation with sufficiently intense FEL macropulses creates an altered form of gene 32 protein which was not observed with UV-only irradiation. The electrophoretic nobility of the product is consistent with the formation of a specific protein-protein crosslink. No evidence of the non-specific protein damage typically induced by UV light is found. The yield of the new photoproduct is apparently enhanced by exposure to FEL macropulses which are synchronized with UV laser pulses. With ideal exposure parameters, the two-color reaction effectively competes with UV-only reactions. Experiments designed to determine the reaction mechanism and to demonstrate FEL-induced reactions in other protein-nucleic acid systems are currently underway.

Kozub, J.; Edwards, G. [Vanderbilt Univ., Nashville, TN (United States)

1995-12-31

320

Identification and characterization of a cell membrane nucleic acid channel.  

PubMed

We have identified a 45-kDa protein purified from rat renal brush border membrane that binds short single-stranded nucleic acid sequences. This activity was purified, reconstituted in proteoliposomes, and then fused with model planar lipid bilayers. In voltage-clamp experiments, the reconstituted 45-kDa protein functioned as a gated channel that allows the passage of nucleic acids. Channel activity was observed immediately after addition of oligonucleotide. Channel activity was not observed in the absence of purified protein or of oligonucleotide or when protein was heat-inactivated prior to forming proteoliposomes. In the presence of symmetrical buffered solution and oligonucleotide, current passed linearly over the range of holding potentials tested. Conductance was 10.4 +/- 0.4 picosiemens (pS) and reversal potential was 0.2 +/- 1.7 mV. There was no difference in channel conductance or reversal potential between phosphodiester and phosphorothioate oligonucleotides. Ion-substitution experiments documented a shift in reversal potential only when a concentration gradient for oligonucleotide was established, indicating that movement of oligonucleotide alone was responsible for current. Movement of oligonucleotide across the bilayer was confirmed by using 32P-labeled oligonucleotides. Channel open probability decreased significantly in the presence of heparan sulfate. These studies provide evidence for a cell surface channel that conducts nucleic acids. PMID:9465118

Hanss, B; Leal-Pinto, E; Bruggeman, L A; Copeland, T D; Klotman, P E

1998-02-17

321

Comparison of Automated Nucleic Acid Extraction Methods with Manual Extraction  

PubMed Central

Automated nucleic acid extractors can improve workflow and decrease variability in the clinical laboratory. We evaluated Qiagen EZ1 (Valencia, CA) and bioMérieux (Durham, NC) easyMAG extractors compared with Qiagen manual extraction using targets and matrices commonly available in the clinical laboratory. Pooled samples were spiked with various organisms, serially diluted, and extracted in duplicate. The organisms/matrices were Bordetella pertussis/bronchoalveolar lavage, herpes simplex virus II/cerebrospinal fluid, coxsackievirus A9/cerebrospinal fluid, BK virus/plasma, and Mycoplasma pneumoniae/endotracheal tube samples. Extracts were amplified in duplicate using real-time PCR assays, and amplification of the target at a cycle threshold of 35 using the manual method was used for comparison. Amplification efficiency of nucleic acids extracted by automated methods was similar to that by the manual method except for a loss of efficiency for M. pneumoniae in endotracheal tube samples. The EZ1 viral kit 2.0 gave better results for coxsackievirus A9 than the EZ1 viral kit version 1.0. At the lowest limit of detection (past a cycle threshold of 35), the easyMAG was more likely to produce amplifiable nucleic acid than were either the EZ1 or manual extraction. Operational complexity, defined as the number of manipulations required to obtain an extracted sample, was the lowest for the easyMAG. The easyMAG was the most expensive of the methods, followed by the EZ1 kit and manual extraction. PMID:18556770

Dundas, Nicola; Leos, N. Kristine; Mitui, Midori; Revell, Paula; Rogers, Beverly Barton

2008-01-01

322

Efficient, validated method for detection of mycobacterial growth in liquid culture media by use of bead beating, magnetic-particle-based nucleic Acid isolation, and quantitative PCR.  

PubMed

Pathogenic mycobacteria are difficult to culture, requiring specialized media and a long incubation time, and have complex and exceedingly robust cell walls. Mycobacterium avium subsp. paratuberculosis (MAP), the causative agent of Johne's disease, a chronic wasting disease of ruminants, is a typical example. Culture of MAP from the feces and intestinal tissues is a commonly used test for confirmation of infection. Liquid medium offers greater sensitivity than solid medium for detection of MAP; however, support for the BD Bactec 460 system commonly used for this purpose has been discontinued. We previously developed a new liquid culture medium, M7H9C, to replace it, with confirmation of growth reliant on PCR. Here, we report an efficient DNA isolation and quantitative PCR methodology for the specific detection and confirmation of MAP growth in liquid culture media containing egg yolk. The analytical sensitivity was at least 10(4)-fold higher than a commonly used method involving ethanol precipitation of DNA and conventional PCR; this may be partly due to the addition of a bead-beating step to manually disrupt the cell wall of the mycobacteria. The limit of detection, determined using pure cultures of two different MAP strains, was 100 to 1,000 MAP organisms/ml. The diagnostic accuracy was confirmed using a panel of cattle fecal (n = 54) and sheep fecal and tissue (n = 90) culture samples. This technique is directly relevant for diagnostic laboratories that perform MAP cultures but may also be applicable to the detection of other species, including M. avium and M. tuberculosis. PMID:25609725

Plain, Karren M; Waldron, Anna M; Begg, Douglas J; de Silva, Kumudika; Purdie, Auriol C; Whittington, Richard J

2015-04-01

323

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

324

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

325

Nucleic Acids Research, Vol. 20, No. 3 613 An alfalfa cDNA encodes a protein with similarity to  

E-print Network

Nucleic Acids Research, Vol. 20, No. 3 613 An alfalfa cDNA encodes a protein with similarity to an understanding of the function of these proteins in RNA processing. We have isolated an alfalfa cDNA whose, the putative alfalfa protein is clearly related to the human snRNP-E protein. However, since the protein

Hirt, Heribert

326

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

327

Microchip Module for Blood Sample Preparation and Nucleic Acid Amplification Reactions  

PubMed Central

A computer numerical control-machined plexiglas-based microchip module was designed and constructed for the integration of blood sample preparation and nucleic acid amplification reactions. The microchip module is comprised of a custom-made heater-cooler for thermal cycling, a series of 254 ?m?×?254 ?m microchannels for transporting human whole blood and reagents in and out of an 8–9 ?L dual-purpose (cell isolation and PCR) glass-silicon microchip. White blood cells were first isolated from a small volume of human whole blood (<3 ?L) in an integrated cell isolation–PCR microchip containing a series of 3.5-?m feature-sized “weir-type” filters, formed by an etched silicon dam spanning the flow chamber. A genomic target, a region in the human coagulation Factor V gene (226-bp), was subsequently directly amplified by microchip-based PCR on DNA released from white blood cells isolated on the filter section of the microchip mounted onto the microchip module. The microchip module provides a convenient means to simplify nucleic acid analyses by integrating two key steps in genetic testing procedures, cell isolation and PCR and promises to be adaptable for additional types of integrated assays. PMID:11230164

Yuen, Po Ki; Kricka, Larry J.; Fortina, Paolo; Panaro, Nicholas J.; Sakazume, Taku; Wilding, Peter

2001-01-01

328

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

329

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

Microsoft Academic Search

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

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

2001-01-01

330

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.

331

Origin of overstretching transitions in single-stranded nucleic acids.  

PubMed

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. PMID:24237568

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

2013-11-01

332

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

333

Nucleic acid modifications in bacterial pathogens - impact on pathogenesis, diagnosis, and therapy  

E-print Network

Nucleic acids are subject to extensive chemical modification by all organisms. These modifications display incredible structural diversity, and some are essential for survival. Intriguingly, several of these modifications ...

Russell, Brandon S. (Brandon Skylur)

2014-01-01

334

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

335

BGL3 beta-glucosidase and nucleic acids encoding the same  

DOEpatents

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

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

2011-06-14

336

BGL3 beta-glucosidase and nucleic acids encoding the same  

DOEpatents

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

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

2008-04-01

337

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

338

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

339

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

340

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

341

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

342

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

343

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

344

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

E-print Network

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

Beal, Peter A.

345

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

346

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

347

Structure and kinetics of lipid-nucleic acid complexes.  

PubMed

The structure and function of lipid-based complexes (lipoplexes) have been widely investigated as cellular delivery vehicles for nucleic acids-DNA and siRNA. Transfection efficiency in applications such as gene therapy and gene silencing has been clearly linked to the local, nano-scale organization of the nucleic acid in the vehicle, as well as to the global properties (e.g. size) of the carriers. This review focuses on both the structure of DNA and siRNA complexes with cationic lipids, and the kinetics of structure evolution during complex formation. The local organization of the lipoplexes is largely set by thermodynamic, equilibrium forces, dominated by the lipid preferred phase. As a result, complexation of linear lambda-phage DNA, circular plasmid DNA, or siRNA with lamellae-favoring lipids (or lipid mixtures) forms multi-lamellar L(?)(C) liquid crystalline arrays. Complexes created with lipids that have bulky tail groups may form inverted hexagonal HII(C) phases, or bicontinuous cubic Q(II)(C) phases. The kinetics of complex formation dominates the large-scale, global structure and the properties of lipoplexes. Furthermore, the time-scales required for the evolution of the equilibrium structure may be much longer than expected. In general, the process may be divided into three distinct stages: An initial binding, or adsorption step, where the nucleic acid binds onto the surface of the cationic vesicles. This step is relatively rapid, occurring on time scales of order of milliseconds, and largely insensitive to system parameters. In the second step, vesicles carrying adsorbed nucleic acid aggregate to form larger complexes. This step is sensitive to the lipid characteristics, in particular the bilayer rigidity and propensity to rupture, and to the lipid to nucleic acid (L/D) charge ratio, and is characterized by time scales of order seconds. The last and final step is that of internal rearrangement, where the overall global structure remains constant while local adjustment of the nucleic acid/lipid organization takes place. This step may occur on unusually long time scales of order hours or longer. This rate, as well, is highly sensitive to lipid characteristics, including membrane fluidity and rigidity. While the three step process is consistent with many experimental observations to date, improving the performance of these non-viral vectors requires better understanding of the correlations between the parameters that influence lipoplexes' formation and stability and the specific rate constants i.e., the timescales required to obtain the equilibrium structures. Moreover, new types of cellular delivery agents are now emerging, such as antimicrobial peptide complexes with anionic lipids, and other proteins and small-molecule lipid carriers, suggesting that better understanding of lipoplex kinetics would apply to a variety of new systems in biotechnology and nanomedicine. PMID:24529969

Dan, Nily; Danino, Dganit

2014-03-01

348

Poly(alkylene oxide) Copolymers for Nucleic Acid Delivery  

PubMed Central

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

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

2012-01-01

349

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

350

New crystal structures of nucleic acids and their complexes.  

PubMed

In the past year, X-ray crystallographic studies of representatives of all nucleic acid structural types have been reported. Among the most interesting structures are the parallel DNA tetraplex formed by d(TGGGGT), the four-stranded structure formed by d(CCCT) and a double drug bound side by side in an antiparallel orientation to the minor groove of a B-DNA. Certainly, the structure that has received most attention is that of the first complex of a ribozyme with an inhibitor DNA. PMID:7583626

Wahl, M C; Sundaralingam, M

1995-06-01

351

Fluorecently labeled bionanotransporters of nucleic acid based on carbon nanotubes  

E-print Network

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

Novopashina, D S; Venyaminova, A G

2012-01-01

352

Recognition of Chromosomal DNA Inside Cells by Locked Nucleic Acids  

PubMed Central

Sequence-selective recognition of DNA inside cells by oligonucleotides would provide valuable insights into cellular processes and new leads for therapeutics. Recent work, however, has shown that noncoding RNA transcripts overlap chromosomal DNA. These RNAs provide alternate targets for oligonucleotides designed to bind promoter DNA, potentially overturning previous assumptions about mechanism. Here, we show that antigene locked nucleic acids (agLNAs) reduce RNA levels of targeted genes, block RNA polymerase and transcription factor association at gene promoters, and bind to chromosomal DNA. These data suggest that the mechanism of LNAs involves recognition of chromosomal DNA and that LNAs are bona fide antigene molecules. PMID:19053275

Beane, Randall; Gabillet, Sylvie; Montaillier, Christophe; Arar, Khalil; Corey, David R.

2009-01-01

353

Cationic lipid saturation influences intracellular delivery of encapsulated nucleic acids  

Microsoft Academic Search

An analogous series of cationic lipids (1,2-distearyloxy-N,N-dimethyl-3-aminopropane (DSDMA), 1,2-dioleyloxy-N,N-dimethyl-3-aminopropane (DODMA), 1,2-dilinoleyloxy-N,N-dimethyl-3-aminopropane (DLinDMA) and 1,2-dilinolenyloxy-N,N-dimethyl-3-aminopropane (DLenDMA)) possessing 0, 1, 2 or 3 double bonds per alkyl chain respectively, was synthesized to determine the correlation between lipid saturation, fusogenicity and efficiency of intracellular nucleic acid delivery. 31P-NMR analysis suggests that as saturation increases, from 2 to 0 double bonds, lamellar (L?) to

James Heyes; Lorne Palmer; Kaz Bremner; Ian MacLachlan

2005-01-01

354

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

355

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

DOEpatents

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

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

2013-07-23

356

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

357

Electrostatic free energy landscapes for nucleic acid helix assembly  

PubMed Central

Metal ions are crucial for nucleic acid folding. From the free energy landscapes, we investigate the detailed mechanism for ion-induced collapse for a paradigm system: loop-tethered short DNA helices. We find that Na+ and Mg2+ play distinctive roles in helix–helix assembly. High [Na+] (>0.3 M) causes a reduced helix–helix electrostatic repulsion and a subsequent disordered packing of helices. In contrast, Mg2+ of concentration >1 mM is predicted to induce helix–helix attraction and results in a more compact and ordered helix–helix packing. Mg2+ is much more efficient in causing nucleic acid compaction. In addition, the free energy landscape shows that the tethering loops between the helices also play a significant role. A flexible loop, such as a neutral loop or a polynucleotide loop in high salt concentration, enhances the close approach of the helices in order to gain the loop entropy. On the other hand, a rigid loop, such as a polynucleotide loop in low salt concentration, tends to de-compact the helices. Therefore, a polynucleotide loop significantly enhances the sharpness of the ion-induced compaction transition. Moreover, we find that a larger number of helices in the system or a smaller radius of the divalent ions can cause a more abrupt compaction transition and a more compact state at high ion concentration, and the ion size effect becomes more pronounced as the number of helices is increased. PMID:17145719

Tan, Zhi-Jie; Chen, Shi-Jie

2006-01-01

358

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

359

Rapid and simple method for purification of nucleic acids.  

PubMed

We have developed a simple, rapid, and reliable protocol for the small-scale purification of DNA and RNA from, e.g., human serum and urine. The method is based on the lysing and nuclease-inactivating properties of the chaotropic agent guanidinium thiocyanate together with the nucleic acid-binding properties of silica particles or diatoms in the presence of this agent. By using size-fractionated silica particles, nucleic acids (covalently closed circular, relaxed circular, and linear double-stranded DNA; single-stranded DNA; and rRNA) could be purified from 12 different specimens in less than 1 h and were recovered in the initial reaction vessel. Purified DNA (although significantly sheared) was a good substrate for restriction endonucleases and DNA ligase and was recovered with high yields (usually over 50%) from the picogram to the microgram level. Copurified rRNA was recovered almost undegraded. Substituting size-fractionated silica particles for diatoms (the fossilized cell walls of unicellular algae) allowed for the purification of microgram amounts of genomic DNA, plasmid DNA, and rRNA from cell-rich sources, as exemplified for pathogenic gram-negative bacteria. In this paper, we show representative experiments illustrating some characteristics of the procedure which may have wide application in clinical microbiology. PMID:1691208

Boom, R; Sol, C J; Salimans, M M; Jansen, C L; Wertheim-van Dillen, P M; van der Noordaa, J

1990-03-01

360

Thermodynamics of RNA duplexes modified with unlocked nucleic acid nucleotides  

PubMed Central

Thermodynamics provides insights into the influence of modified nucleotide residues on stability of nucleic acids and is crucial for designing duplexes with given properties. In this article, we introduce detailed thermodynamic analysis of RNA duplexes modified with unlocked nucleic acid (UNA) nucleotide residues. We investigate UNA single substitutions as well as model mismatch and dangling end effects. UNA residues placed in a central position makes RNA duplex structure less favourable by 4.0–6.6?kcal/mol. Slight destabilization, by ?0.5–1.5?kcal/mol, is observed for 5?- or 3?-terminal UNA residues. Furthermore, thermodynamic effects caused by UNA residues are extremely additive with ?G°37 conformity up to 98%. Direct mismatches involving UNA residues decrease the thermodynamic stability less than unmodified mismatches in RNA duplexes. Additionally, the presence of UNA residues adjacent to unpaired RNA residues reduces mismatch discrimination. Thermodynamic analysis of UNA 5?- and 3?-dangling ends revealed that stacking interactions of UNA residues are always less favourable than that of RNA residues. Finally, circular dichroism spectra imply no changes in overall A-form structure of UNA–RNA/RNA duplexes relative to the unmodified RNA duplexes. PMID:20562222

Pasternak, Anna; Wengel, Jesper

2010-01-01

361

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

362

Nucleic Acid Drugs for Prevention of Cardiac Rejection  

PubMed Central

Heart transplantation has been broadly performed in humans. However, occurrence of acute and chronic rejection has not yet been resolved. Several inflammatory factors, such as cytokines and adhesion molecules, enhance the rejection. The graft arterial disease (GAD), which is a type of chronic rejection, is characterized by intimal thickening comprised of proliferative smooth muscle cells. Specific treatments that target the attenuation of acute rejection and GAD formation have not been well studied in cardiac transplantation. Recent progress in the nucleic acid drugs, such as antisense oligodeoxynucleotides (ODNs) to regulate the transcription of disease-related genes, has important roles in therapeutic applications. Transfection of cis-element double-stranded DNA, named as “decoy,” has been also reported to be a useful nucleic acid drug. This decoy strategy has been not only a useful method for the experimental studies of gene regulation but also a novel clinical strategy. In this paper, we reviewed the experimental results of NF-?B, E2F, AP-1, and STAT-1 decoy and other ODNs using the experimental heart transplant models. PMID:20069118

Suzuki, Jun-ichi; Isobe, Mitsuaki; Morishita, Ryuichi; Nagai, Ryozo

2009-01-01

363

Peptide vectors for the nonviral delivery of nucleic acids.  

PubMed

Over the past two decades, gene therapy has garnered tremendous attention and is heralded by many as the ultimate cure to treat diseases such as cancer, viral infections, and inherited genetic disorders. However, the therapeutic applications of nucleic acids extend beyond the delivery of double-stranded DNA and subsequent expression of deficient gene products in diseased tissue. Other strategies include antisense oligonucleotides and most notably RNA interference (RNAi). Antisense strategies bear great potential for the treatment of diseases that are caused by misspliced mRNA, and RNAi is a universal and extraordinarily efficient tool to knock down the expression of virtually any gene by specific degradation of the desired target mRNA. However, because of the hurdles associated with effective delivery of nucleic acids across a cell membrane, the initial euphoria surrounding siRNA therapy soon subsided. The ability of oligonucleotides to cross the plasma membrane is hampered by their size and highly negative charge. Viral vectors have long been the gold standard to overcome this barrier, but they are associated with severe immunogenic effects and possible tumorigenesis. Cell-penetrating peptides (CPPs), cationic peptides that can translocate through the cell membrane independent of receptors and can transport cargo including proteins, small organic molecules, nanoparticles, and oligonucleotides, represent a promising class of nonviral delivery vectors. This Account focuses on peptide carrier systems for the cellular delivery of various types of therapeutic nucleic acids with a special emphasis on cell-penetrating peptides. We also emphasize the clinical relevance of this research through examples of promising in vivo studies. Although CPPs are often derived from naturally occurring protein transduction domains, they can also be artificially designed. Because CPPs typically include many positively charged amino acids, those electrostatic interactions facilitate the formation of complexes between the carriers and the oligonucleotides. One drawback of CPP-mediated delivery includes entrapment of the cargo in endosomes because uptake tends to be endocytic: coupling of fatty acids or endosome-disruptive peptides to the CPPs can overcome this problem. CPPs can also lack specificity for a single cell type, which can be addressed through the use of targeting moieties, such as peptide ligands that bind to specific receptors. Researchers have also applied these strategies to cationic carrier systems for nonviral oligonucleotide delivery, such as liposomes or polymers, but CPPs tend to be less cytotoxic than other delivery vehicles. PMID:22455499

Hoyer, Jan; Neundorf, Ines

2012-07-17

364

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

E-print Network

. The discovered glycol nucleic acid (GNA) uses the canonical Watson-Crick base pairing scheme combined of the Eschenmoser group on the chemical etiology of nucleic acid structure have demonstrated that Watson-Crick base. To reassure that the duplex relies on proper Watson-Crick base pairing, we also investigated the UV melting

Meggers, Eric

365

Nucleic acid binding and chaperone properties of HIV1 Gag and nucleocapsid proteins  

Microsoft Academic Search

The Gag polyprotein of HIV-1 is essential for retro- viral replication and packaging. The nucleocapsid (NC) protein is the primary region for the interac- tion 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 experi- ments. The NC

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

2006-01-01

366

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

Microsoft Academic Search

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

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

1997-01-01

367

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

Microsoft Academic Search

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

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

1999-01-01

368

Nucleic acid probes are molecules that complement or hybridize to a  

E-print Network

Nucleic acid probes are molecules that complement or hybridize to a specific mRNA or DNA sequence of rapid methods of nucleic acid sequencing and measurement made DNA and RNA the center of atten- tion computational methods of protein identification since analysis can involve thousands of peptide mass spectra

Levin, Judith G.

369

A rapid, sensitive, and selective bioluminescence resonance energy transfer (BRET)-based nucleic acid sensing system  

Microsoft Academic Search

Here we report the design of a bioluminescence resonance energy transfer (BRET)-based sensing system that could detect nucleic acid target in 5min with high sensitivity and selectivity. The sensing system is based on adjacent binding of oligonucleotide probes labeled with Renilla luciferase (Rluc) and quantum dot (Qd) on the nucleic acid target. Here Rluc, a bioluminescent protein that generates light

Manoj Kumar; Daohong Zhang; David Broyles; Sapna K. Deo

2011-01-01

370

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

Microsoft Academic Search

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

Besik I. Kankia

2004-01-01

371

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

Microsoft Academic Search

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

M. Y. Galperin; Guy Cochrane

2009-01-01

372

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

373

NAPS: a residue-level nucleic acid-binding prediction server  

E-print Network

NAPS: a residue-level nucleic acid-binding prediction server Matthew B. Carson, Robert Langlois achieved 79.1% accuracy, while the RNA-binding model reached an accuracy of 73.2%. The NAPS web server is freely available at http://proteomics.bioengr.uic.edu/NAPS. INTRODUCTION Nucleic acid-binding (NA

Lu, Hui

374

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

375

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

376

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

377

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

Microsoft Academic Search

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

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

2006-01-01

378

DyNAs: constitutional dynamic nucleic acid analogues.  

PubMed

Dynamic cationic polymers were generated in aqueous media from functionally complementary monomers bearing nucleobase groups. (1)H NMR spectroscopy was used to follow the polycondensation reaction of the nucleobase-appended dihydrazides 1 and 2 with the dialdehydes B and C. The reversibility of these polymers was established by proton NMR spectroscopy through exchange of the dihydrazide 2 with polymer 1 B. The polymers 1 B, 2 B, 1 C, and 2 C represent dynamic biopolymers of nucleic acid type, DyNAs. Electrostatic interaction of these polymers with polyanionic entities, such as polyphosphates, polynucleotides, and polyaspartic acid, was shown to take place. It induces a change in size of the dynamic polymer, as it responds by an increase in degree of polymerization to an increase of the overall anionic charge introduced, that is, to the total electrostatic interaction. PMID:16969774

Sreenivasachary, Nampally; Hickman, David T; Sarazin, Dominique; Lehn, Jean-Marie

2006-11-15

379

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

380

Trifluoromethylated Nucleic Acid Analogues Capable of Self-Assembly through Hydrophobic Interactions.  

PubMed

An artificial nucleic acid analogue capable of self-assembly into duplex merely through hydrophobic interactions is presented. The replacement of Watson-Crick hydrogen bonding with strictly hydrophobic interactions has the potential to confer new properties and facilitate the construction of complex DNA nanodevices. To study how the hydrophobic effect works during the self-assembly of nucleic acid bases, we have designed and synthesized a series of fluorinated nucleic acids (FNA) containing 3,5-bis(trifluoromethyl) benzene (F) and nucleic acids incorporating 3,5-dimethylbenzene (M) as hydrophobic base surrogates. Our experiments illustrate that two single-stranded nucleic acid oligomers could spontaneously organize into a duplex entirely by hydrophobic base pairing if the bases were size-complementary and the intermolecular forces were sufficiently strong. PMID:25285193

Wang, RuoWen; Wang, Chunming; Cao, Yang; Zhu, Zhi; Yang, Chaoyong; Chen, Jianzhong; Qing, Feng-Ling; Tan, Weihong

2014-10-01

381

Fluorescence energy transfer monitored competitive equilibria of nucleic acids: applications in thermodynamics and screening.  

PubMed

Precise thermodynamic characterization of nucleic acid complex stability is required to understand a variety of biologically significant events as well as to exploit the specific recognition capabilities of nucleic acids in biotechnology, diagnostics, and therapeutics. The development of a database of nucleic acid thermodynamics with sufficient precision to foster further developments in these areas requires new and improved measurement techniques. The combination of a competitive equilibrium titration with fluorescence energy transfer based detection provides a method for precise measurement of differences in free energy values for nucleic acid duplexes that far exceeds in precision those accessible via conventional methods. The method can be applied to detect and to characterize any deviation in a nucleic acid that alters duplex stability. Such deviations include, but are not limited to, mismatches; single nucleotide polymorphisms (SNP); chemically modified nucleotide bases, sugars or phosphates; and conformational anomalies or folding motifs, such as, loops or hairpins. PMID:11987182

Plum, G E; Breslauer, K J

382

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

383

Potential in vivo roles of nucleic acid triple-helices  

PubMed Central

The ability of double-stranded DNA to form a triple-helical structure by hydrogen bonding with a third strand is well established, but the biological functions of these structures remain largely unknown. There is considerable albeit circumstantial evidence for the existence of nucleic triplexes in vivo and their potential participation in a variety of biological processes including chromatin organization, DNA repair, transcriptional regulation and RNA processing has been investigated in a number of studies to date. There is also a range of possible mechanisms to regulate triplex formation through differential expression of triplex-forming RNAs, alteration of chromatin accessibility, sequence unwinding and nucleotide modifications. With the advent of next generation sequencing technology combined with targeted approaches to isolate triplexes, it is now possible to survey triplex formation with respect to their genomic context, abundance and dynamical changes during differentiation and development, which may open up new vistas in understanding genome biology and gene regulation. PMID:21525785

Buske, Fabian A

2011-01-01

384

Differentiation of respiratory syncytial virus subgroups with cDNA probes in a nucleic acid hybridization assay.  

PubMed Central

A new approach to respiratory syncytial (RS) virus subgroup determination was developed by using a simple nucleic acid filter hybridization technique. By this method, virus-infected cells are bound and fixed in a single step, and the viral RNA in the fixed-cell preparation is characterized directly by its ability to hybridize to cDNA probes specific for either the A or B subgroups of RS virus. The subgroup-specific probes were constructed from cDNA clones that corresponded to a portion of the extracellular domain of the RS virus G protein of either a subgroup B RS virus (8/60) or a subgroup A RS virus (A2). The cDNA probes were labeled with 32P and used to analyze RS virus isolates collected over a period of three decades. Replicate templates of infected cell preparations were hybridized with either the subgroup A or B probe. The subgroup assignments of 40 viruses tested by nucleic acid hybridization were in agreement with the results of subgroup determinations based on their reactivities with monoclonal antibodies, which previously has been the only method available for determining the subgroup classification of RS virus isolates. The nucleic acid hybridization assay has the advantage of providing broad-based discrimination of the two subgroups on the basis of nucleic acid homology, irrespective of minor antigenic differences that are detected in assays in which monoclonal antibodies are used. The nucleic acid hybridization technique provides a reliable method for RS virus subgroup characterization. Images PMID:2118548

Sullender, W M; Anderson, L J; Anderson, K; Wertz, G W

1990-01-01

385

[The substance of genetic information--nucleic acids].  

PubMed

If we look at the history of our knowledge of nucleic acids, we would see in the distant past of 140 years Friedrich Miescher who had identified the acidic substance within the cell nucleus, which he called nuclein. About 70 years after his initial observation, this substance was connected with genetic information. This very substantial finding happened during the World War II. This was the impulse that research of nucleic acids received to speed up continuously growing mountain of information, which is more and more difficult to understand. Another eruption of new information about our genome was the result of ten years of intensive cooperation of many manufacturers divided into two competitive blocks which offered us knowledge of nucleotide sequence of all 46 DNA molecules. The year 2000 became the landmark marking the start of the postgenomic era. It did not mean that human genome was totally explored, but the cornerstone has been settled. Since then, we could concentrate our efforts on variability; use of the project of 1,000 genomes brought many important findings, eg. copy number variability (CNV) exceeds the single nucleotide polymophisms (SNP). Also intergenomic relationships, studies on function and pathways began to be much more understandable by elucidation of the genome primary structure. NGS as a tool also accelerated the epigenetic research. All this improved molecular diagnostics by discovering many new markers playing their role in disease and treatment and allowed us to enter the field of multifactorial illnesses including cancer. The progress in diagnostic technologies which has happened during the last decade forced our research teams to include other professions - eg. bioinformatics. PMID:23102193

Brdi?ka, R

2012-01-01

386

78 FR 63476 - Draft Guidance for Industry: Use of Nucleic Acid Tests To Reduce the Risk of Transmission of West...  

Federal Register 2010, 2011, 2012, 2013, 2014

...Guidance for Industry: Use of Nucleic Acid Tests To Reduce the Risk of Transmission...Guidance for Industry: Use of Nucleic Acid Tests to Reduce the Risk of Transmission...recommends the use of an FDA-licensed nucleic acid test [[Page 63477

2013-10-24

387

76 FR 72950 - Draft Guidance for Industry: Use of Nucleic Acid Tests on Pooled and Individual Samples From...  

Federal Register 2010, 2011, 2012, 2013, 2014

...Guidance for Industry: Use of Nucleic Acid Tests on Pooled and Individual Samples...Guidance for Industry: Use of Nucleic Acid Tests (NAT) on Pooled and Individual...recommendations on the use of FDA-licensed nucleic acid tests (NAT) to screen blood donors...

2011-11-28

388

75 FR 22814 - Guidance for Industry: Nucleic Acid Testing (NAT) for Human Immunodeficiency Virus Type 1 (HIV-1...  

Federal Register 2010, 2011, 2012, 2013, 2014

...FDA-2005D-0261) Guidance for Industry: Nucleic Acid Testing (NAT) for Human Immunodeficiency...entitled ``Guidance for Industry: Nucleic Acid Testing (NAT) for Human Immunodeficiency...Immunodeficiency Virus Type 1 (HIV-1) Nucleic Acid Test (NAT) and Hepatitis C Virus...

2010-04-30

389

77 FR 68133 - Guidance for Industry: Use of Nucleic Acid Tests on Pooled and Individual Samples From Donors of...  

Federal Register 2010, 2011, 2012, 2013, 2014

...Guidance for Industry: Use of Nucleic Acid Tests on Pooled and Individual Samples...Guidance for Industry: Use of Nucleic Acid Tests on Pooled and Individual Samples...recommendations on the use of FDA- licensed nucleic acid tests (NAT) to screen blood donors...

2012-11-15

390

Locked Nucleic Acid Molecular Beacons Lin Wang, Chaoyong James Yang, Colin D. Medley, Steven A. Benner,*,, and Weihong Tan*,  

E-print Network

peptide nucleic acids (PNAs).8 However, these DNA analogues meet with problems, such as toxicity,6 selfLocked Nucleic Acid Molecular Beacons Lin Wang, Chaoyong James Yang, Colin D. Medley, Steven A locked nucleic acid (LNA) bases. Quantitative studies of genomic information have driven a strong demand

Tan, Weihong

391

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

392

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

E-print Network

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

393

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

394

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.

395

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.

396

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.

397

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.

398

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

E-print Network

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

Maizels, Nancy

399

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

400

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

401

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

402

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.

403

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.

404

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

405

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

406

Luminescent Probes for Ultrasensitive Detection of Nucleic Acids  

PubMed Central

Novel amino-reactive derivatives of lanthanide-based luminescent labels of enhanced brightness and metal retention were synthesized and used for the detection of complementary DNA oligonucleotides by molecular beacons. Time-resolved acquisition of the luminescent signal that occurs upon hybridization of the probe to the target enabled the avoidance of short-lived background fluorescence, markedly enhancing the sensitivity of detection, which was less than 1 pM. This value is about 50 to 100 times more sensitive than the level achieved with conventional fluorescence-based molecular beacons, and is 10 to 60 times more sensitive than previously reported for other lanthanide-based hybridization probes. These novel luminescent labels should significantly enhance the sensitivity of all type of nucleic acid hybridization probes, and could dramatically improve the detection limit of other biopolymers and small compounds that are used in a variety of biological applications. PMID:20085336

Krasnoperov, Lev N.; Marras, Salvatore A.E.; Kozlov, Maxim; Wirpsza, Laura; Mustaev, Arkady

2010-01-01

407

Nucleic Acid-Based Approaches for Detection of Viral Hepatitis  

PubMed Central

Context: To determining suitable nucleic acid diagnostics for individual viral hepatitis agent, an extensive search using related keywords was done in major medical library and data were collected, categorized, and summarized in different sections. Results: Various types of molecular biology tools can be used to detect and quantify viral genomic elements and analyze the sequences. These molecular assays are proper technologies for rapidly detecting viral agents with high accuracy, high sensitivity, and high specificity. Nonetheless, the application of each diagnostic method is completely dependent on viral agent. Conclusions: Despite rapidity, automation, accuracy, cost-effectiveness, high sensitivity, and high specificity of molecular techniques, each type of molecular technology has its own advantages and disadvantages. PMID:25789132

Behzadi, Payam; Ranjbar, Reza; Alavian, Seyed Moayed

2014-01-01

408

Diastereomer characterizations of nitroxide-labeled nucleic acids  

SciTech Connect

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

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

2008-07-04

409

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

410

Nucleic acid delivery with chitosan and its derivatives.  

PubMed

Chitosan is a naturally occurring cationic mucopolysaccharide. It is generally biocompatible, biodegradable, mucoadhesive, non-immunogenic and non-toxic. Although chitosan is able to condense nucleic acids (NA) (both DNA and RNA) and protect them from nuclease degradation, its poor water solubility and low transfection efficacy have impeded its use as an NA carrier. In order to overcome such limitations, a multitude of strategies for chitosan modification and formulation have been proposed. In this article, we will first give a brief overview of the physical and biological properties of chitosan. Then, with a special focus on plasmid DNA delivery, we will have a detailed discussion of the latest advances in chitosan-mediated NA transfer. For future research, the following three important areas will be discussed: chitosan-mediated therapeutic small RNA transfer, structure-activity relationships (SAR) in chitosan vector design, and chitosan-mediated oral/nasal NA therapy. PMID:19100795

Lai, Wing-Fu; Lin, Marie Chia-Mi

2009-03-19

411

Mfold web server for nucleic acid folding and hybridization prediction  

E-print Network

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 universally available web GUIs (Graphical User Interfaces),the server circumvents the problem of portability of this software. Detailed output,in the form of structure plots with or without reliability information,single strand frequency plots and ‘energy dot plots’, are available for the folding of single sequences. A variety of ‘bulk ’ servers give less information,but in a shorter time and for up to hundreds of sequences at once. The portal for the mfold web server is

Michael Zuker

2003-01-01

412

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

413

Nucleic Acid-Based Therapy Approaches for Huntington's Disease  

PubMed Central

Huntington's disease (HD) is caused by a dominant mutation that results in an unstable expansion of a CAG repeat in the huntingtin gene leading to a toxic gain of function in huntingtin protein which causes massive neurodegeneration mainly in the striatum and clinical symptoms associated with the disease. Since the mutation has multiple effects in the cell and the precise mechanism of the disease remains to be elucidated, gene therapy approaches have been developed that intervene in different aspects of the condition. These approaches include increasing expression of growth factors, decreasing levels of mutant huntingtin, and restoring cell metabolism and transcriptional balance. The aim of this paper is to outline the nucleic acid-based therapeutic strategies that have been tested to date. PMID:22288011

Vagner, Tatyana; Young, Deborah; Mouravlev, Alexandre

2012-01-01

414

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

415

Development of nucleic acid drugs for neurological disorders.  

PubMed

Novel therapeutic strategies using nucleic acid drugs, such as plasmid DNA (pDNA) and nuclear factor-?B (NF?B) decoy, have been sought for non-treatable neurological disorders. Among them, the application of pDNA has been extensively studied in diabetic neuropathy. Since growth factors, such as vascular endothelial growth factor (VEGF) and hepatocyte growth factor (HGF), have both neurotrophic and angiogenic properties, intramuscular injection of pDNA encoding these genes has been examined and shown to be effective for treatment in experimental animals and also in clinical trials. These growth factors have also been shown to accelerate neuroprotection, angiogenesis, and regeneration in the brain, and overexpression of these factors showed therapeutic effects in cerebral ischemia in rodents. Inhibition of inflammation is another strategy to treat cerebrovascular diseases. Recent studies suggest that NF?B plays critical roles in the formation of cerebral aneurysms, and inhibition of its function by NF?B decoy was shown to prevent cerebral aneurysm enlargement through inhibition of NF?B-mediated inflammation. In the field of neurodegenerative disease, the potential of pDNA as a tool for vaccination has attracted researchers since pDNA itself has shown adjuvant properties and the potential to induce immunity or immune tolerance. pDNA encoding disease antigens, such as amyloid-A? in Alzheimer disease or myelin basic protein in multiple sclerosis (MS), was shown to have therapeutic effects in rodents, and its efficacy and safety were reported in a phase I/II clinical study in MS. In this review, we discuss the potential and problems of nucleic acid drugs in neurological disorders. PMID:22762559

Shimamura, Munehisa; Sato, Naoyuki; Nakagami, Hironori; Taniyama, Yoshiaki; Morishita, Ryuichi

2012-01-01

416

Electrostatics of nucleic acid folding under conformational constraint.  

PubMed

RNA folding is enabled by interactions between the nucleic acid and its ion atmosphere, the mobile sheath of aqueous ions that surrounds and stabilizes it. Understanding the ion atmosphere requires the interplay of experiment and theory. However, even an apparently simple experiment to probe the ion atmosphere, measuring the dependence of DNA duplex stability upon ion concentration and identity, suffers from substantial complexity, because the unfolded ensemble contains many conformational states that are difficult to treat accurately with theory. To minimize this limitation, we measured the unfolding equilibrium of a DNA hairpin using a single-molecule optical trapping assay, in which the unfolded state is constrained to a limited set of elongated conformations. The unfolding free energy increased linearly with the logarithm of monovalent cation concentration for several cations, such that smaller cations tended to favor the folded state. Mg(2+) stabilized the hairpin much more effectively at low concentrations than did any of the monovalent cations. Poisson-Boltzmann theory captured trends in hairpin stability measured for the monovalent cation titrations with reasonable accuracy, but failed to do so for the Mg(2+) titrations. This finding is consistent with previous work, suggesting that Poisson-Boltzmann and other mean-field theories fail for higher valency cations where ion-ion correlation effects may become significant. The high-resolution data herein, because of the straightforward nature of both the folded and the unfolded states, should serve as benchmarks for the development of more accurate electrostatic theories that will be needed for a more quantitative and predictive understanding of nucleic acid folding. PMID:22369617

Anthony, Peter C; Sim, Adelene Y L; Chu, Vincent B; Doniach, Sebastian; Block, Steven M; Herschlag, Daniel

2012-03-14

417

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

418

Nucleic acid binding property of the gene products of rice stripe virus.  

PubMed

GST fusion proteins of the six gene products from RNAs 2,3 and 4 of the tenuivirus, Rice stripe virus (RSV), were used to study the nucleic acid binding activities in vitro. Three of the proteins, p3, pc3 and pc4, bound both single- and double-stranded cDNA of RSV RNA4 and also RNA3 transcribed from its cDNA clone, while p2, pc2-N (the N-terminal part of pc2) nor p4 bound the cDNA or RNA transcript. The binding activity of p3 is located in the carboxyl-terminus amino acid 154-194, which contains basic amino acid rich beta-sheets. The acidic amino acid-rich amino-terminus (amino acids 1-100) of p3 did not have nucleic acid binding activity. The related analogous gene product of the tenuivirus, Rice hoja blanca virus, is a suppressor of gene silencing and the possibility of the nucleic acid binding ability of RSV p3 being associated with this property is discussed. The C-terminal part of the RSV nucleocapsid protein, which also contains a basic region, binds nucleic acids, which is consistent with its function. The central and C-terminal regions of pc4 bind nucleic acid. It has been suggested that this protein is a cell-to-cell movement protein and nucleic acid binding would be in accord with this function. PMID:16025246

Liang, Delin; Ma, Xiangqiang; Qu, Zhicai; Hull, Roger

2005-10-01

419

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

420

BIOPHYSICAL PROPERTIES OF NUCLEIC ACIDS AT SURFACES RELEVANT TO MICROARRAY PERFORMANCE  

PubMed Central

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.

2014-01-01

421

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

422

Interaction of nucleic acid bases and Watson-Crick base pairs with fullerene: Computational study  

NASA Astrophysics Data System (ADS)

A first-principle investigation using the recently developed M05-2X density functional and the 6-311++G(d, p) basis set was performed to understand the nature of interaction between C 60 and nucleic acid bases and the Watson-Crick base pairs. It was found that C 60 forms stacking complexes with nucleic acid bases and base pairs. It was revealed that the strength of interaction of nucleic acid bases with C 60 follows the order: G > C > A > T > U, while the GC base pair forms stronger complex than the AT base pair with C 60.

Shukla, Manoj K.; Dubey, Madan; Zakar, Eugene; Namburu, Raju; Leszczynski, Jerzy

2010-06-01

423

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

NASA Astrophysics Data System (ADS)

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

Abramova, Tatyana V.; Silnikov, Vladimir N.

2011-05-01

424

Synthesis of Peptide nucleic acids containing a crosslinking agent and evaluation of their reactivities.  

PubMed

Peptide nucleic acids (PNAs) are structural mimics of nucleic acids that form stable hybrids with DNA and RNA. In addition, PNAs can invade double-stranded DNA. Due to these characteristics, PNAs are widely used as biochemical tools, for example, in antisense/antigene therapy. Interstrand crosslink formation in nucleic acids is one of the strategies for preparing a stable duplex by covalent bond formation. In this study, we have synthesized PNAs incorporating 4-amino-6-oxo-2-vinylpyrimidine (AOVP) as a crosslinking agent and evaluated their reactivities for targeting DNA and RNA. PMID:25781072

Akisawa, Takuya; Ishizawa, Yuki; Nagatsugi, Fumi

2015-01-01

425

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

426

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

427

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

NASA Astrophysics Data System (ADS)

Amino acids and nucleic acid bases are very important for the living organisms. Thus, their protection from decomposition, selection, pre-concentration and formation of biopolymers are important issues for understanding the origin of life on the Earth. Minerals could have played all of these roles. This paper discusses several aspects involving the adsorption of amino acids and nucleic acid bases onto minerals under conditions that could have been found on the prebiotic Earth; in particular, we recommend the use of minerals, amino acids, nucleic acid bases and seawater ions in prebiotic chemistry experiments. Several experiments involving amino acids, nucleic acid bases, minerals and seawater ions are also suggested, including: (a) using well-characterized minerals and the standardization of the mineral synthesis methods; (b) using primary chondrite minerals (olivine, pyroxene, etc.) and clays modified with metals (Cu, Fe, Ni, Mo, Zn, etc.); (c) determination of the possible products of decomposition due to interactions of amino acids and nucleic acid bases with minerals; (d) using minerals with more organophilic characteristics; (e) using seawaters with different concentrations of ions (i.e. Na+, Ca2+, Mg2+, SO4 2- and Cl-) (f) using non-protein amino acids (AIB, ?-ABA, ?-ABA, ?-ABA and ?-Ala and g) using nucleic acid bases other than adenine, thymine, uracil and cytosine. These experiments could be useful to clarify the role played by minerals in the origin of life on the Earth.

Zaia, Dimas A. M.

2012-10-01

428

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

PubMed Central

Context Recently, robotic-assisted laparoscopic prostatectomy has replaced open retropubic radical prostatectomy as the surgical procedure of choice. This less-invasive approach offers many advantages but exposes prostate tissue to longer periods of warm ischemia that may affect subsequent analysis of biomarkers. Objective To analyze the nucleic acid quality and quantity isolated from open versus laparoscopic prostatectomies. Design Nucleic acids were isolated from 10 open-obtained and 10 laparoscopic-obtained tissues stored in our prostate sample repository. Nucleic acid integrity was assessed via electrophoresis and polymerase chain reaction amplification of RNA and DNA targets ranging in size from 125 to 939 base pairs. Results The DNA yield, integrity, and polymerase chain reaction amplification were identical between samples obtained from both surgical approaches. The RNA integrity number and yield were similar, as was ?-2 microglobulin mRNA amplification up to 652 base pairs. However, 2 of 10 samples (20%) collected robotically showed decreased real-time reverse transcriptase-polymerase chain reaction amplification of prostate-specific antigen messenger RNA, especially with targets larger than 300 base pairs. Conclusions Generally, the quality and quantity of nucleic acids isolated from prostate tissue obtained via open or laparoscopic approaches are equivalent, suggesting that procurement of tissues is appropriate from either procedure. However, some loss of reverse transcriptase-polymerase chain reaction amplification of larger RNA targets was noted in the laparoscopic samples; appropriate design of assays to keep amplicon sizes small and the use of internal controls to assess RNA integrity is recommended. PMID:23544941

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

2013-01-01

429

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

430

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

Microsoft Academic Search

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

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

2001-01-01

431

Synthesis and characterization of peptide nucleic acid platinum nanoclusters  

NASA Astrophysics Data System (ADS)

Peptide nucleic acid (PNA) is an analogue of deoxyribonucleic acid (DNA) and possesses a neutral backbone that affords stronger hybridization, greater stability and higher specificity in base pairing. However, it has not been explored as much as DNA in self-assembling functional nanostructures or nanoelectronic devices. We report here for the first time the metallization of PNA with platinum (Pt) nanoparticles via chemical binding, reduction and deposition. Pt ions from a precursor salt solution are allowed to bind over the PNA fragments followed by a reduction and then growth into metal nanoparticles. PNA-Pt complexes form chains several hundred nanometres in length and by varying the duration of chemical reduction step, the dimension of the Pt nanoparticles can be controlled. The structural features and chemical composition of PNA-Pt nanoparticles have been characterized via scanning electron microscopy, transmission electron microscopy and Fourier transform-infrared spectroscopy. These results are also supported by modelling and analysis of the nature of high-lying molecular orbitals on PNA using density functional theory (DFT) method.

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

2006-03-01

432

Electrochemical microfluidic biosensor for the detection of nucleic acid sequences.  

PubMed

A microfluidic biosensor with electrochemical detection for the quantification of nucleic acid sequences was developed. In contrast to most microbiosensors that are based on fluorescence for signal generation, it takes advantage of the simplicity and high sensitivity provided by an amperometric and coulorimetric detection system. An interdigitated ultramicroelectrode array (IDUA) was fabricated in a glass chip and integrated directly with microchannels made of poly(dimethylsiloxane) (PDMS). The assembly was packaged into a Plexiglas housing providing fluid and electrical connections. IDUAs were characterized amperometrically and using cyclic voltammetry with respect to static and dynamic responses for the presence of a reversible redox couple-potassium hexacyanoferrate (ii)/hexacyanoferrate (iii) (ferri/ferrocyanide). A combined concentration of 0.5 microM of ferro/ferricyanide was determined as lower limit of detection with a dynamic range of 5 orders of magnitude. Background signals were negligible and the IDUA responded in a highly reversible manner to the injection of various volumes and various concentrations of the electrochemical marker. For the detection of nucleic acid sequences, liposomes entrapping the electrochemical marker were tagged with a DNA probe, and superparamagnetic beads were coated with a second DNA probe. A single stranded DNA target sequence hybridized with both probes. The sandwich was captured in the microfluidic channel just upstream of the IDUA via a magnet located in the outside housing. Liposomes were lysed using a detergent and the amount of released ferro/ferricyanide was quantified while passing by the IDUA. Optimal location of the magnet with respect to the IDUA was investigated, the effect of dextran sulfate on the hybridization reaction was studied and the amount of magnetic beads used in the assay was optimized. A dose response curve using varying concentrations of target DNA molecules was carried out demonstrating a limit of detection at 1 fmol assay(-1) and a dynamic range between 1 and 50 fmol. The overall assay took 6 min to complete, plus 15-20 min of pre-incubation and required only a simple potentiostat for signal recording and interpretation. PMID:16511625

Goral, Vasiliy N; Zaytseva, Natalya V; Baeumner, Antje J

2006-03-01

433

Two-dimensional infrared spectroscopy of nucleic acids : application to tautomerism and DNA aptamer unfolding dynamics  

E-print Network

The structural dynamics of nucleic acids are intimately related to their biological functions; however, our ability to study these molecular dynamics has been largely impeded by the lack of techniques that possess both ...

Peng, Chunte Sam

2014-01-01

434

Studies toward biomimetic claisen condensation using nucleic acid templates and ribozyme catalysis  

E-print Network

Many different experimental approaches were attempted to achieve carbon-carbon bond formation by nucleic acid template-directed reactions and ribozyme catalysis as potential lipid synthesizing machineries in the RNA world. A novel biomimetic...

Ryu, Youngha

2005-08-29

435

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

436

Evaluation of DNA/RNAshells for Room Temperature Nucleic Acids Storage.  

PubMed

Traditional nucleic acids preservation methods rely on maintaining samples in cold environments, which are costly to operate and time sensitive. Recent work validated that using room temperature for the storage of nucleic acids is possible if the samples are completely protected from water and oxygen. Here, we conducted accelerated aging and real-time degradation studies to evaluate the new technology DNAshell and RNAshell, which preserves DNA and RNA at room temperature, including the DNA and RNA yield, purity, and integrity. DNA and RNA solutions are dried in the presence of stabilizers in stainless steel minicapsules, then redissolved after different time points of heating and storing at room temperature. Results show that DNAshell and RNAshell ensure the safe storage of nucleic acids at room temperature for long periods of time, and that the quality of these nucleic acids is suitable for common downstream analysis. PMID:25686048

Liu, Xiaopan; Li, Qiyuan; Wang, Xian; Zhou, Xiaolin; He, Xuheng; Liao, Qiuyan; Zhu, Fengqin; Cheng, Le; Zhang, Yong

2015-02-01

437

Nucleic Acids Research, 2007, 112 doi:10.1093/nar/gkm603  

E-print Network

Nucleic Acids Research, 2007, 1­12 doi:10.1093/nar/gkm603 Does distance matter? Variations in alternative 3' splicing regulation Martin Akerman and Yael Mandel-Gutfreund* The Faculty of Biology, Technion

Mandel-Gutfreund, Yael

438

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

439

Neighbouring group participation in the unblocking of phosphotriesters of nucleic acids.  

PubMed Central

Two examples of neighbouring group participation during the removal of protecting groups from phosphotriesters of partially or fully protected intermediates of nucleic acids are presented. The first example shows that ammonolysis of aryl groups from phosphotriesters of partially protected - 5'- hydroxy free - nucleic acids (e.g., 4b approximately to; Ar=2C1C 6H4) gives rise to the formation of unnatural nucleic acids (e.g., 7 approximately to and 8 approximately to). The second one illustrates that fluoride ion promoted hydrolysis of 2,2,2-trichloroethyl groups from phosphotriesters of fully protected nucleic acids (e.g., 18a approximately to), having t-butyldimethylsilyl groups at the 2'-positions, leads to the formation of a considerable amount of side-products (e.g., 20 approximately to and 21 approximately to). PMID:461188

de Rooij, J F; Wille-Hazeleger, G; Burgers, P M; van Boom, J H

1979-01-01

440

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

441

Peptide nucleic acid-encoded libraries for microarray-based high-throughput screening   

E-print Network

Peptide nucleic acids (PNAs) were used as encoding tags to enable the analysis of peptide libraries by PNA/DNA hybridisation onto DNA microarrays. This allowed entire peptide libraries to be organised and sorted in a two ...

Planonth, Songsak

2012-06-22

442

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

443

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

444

Nucleic Acid Extraction, Amplification, and Detection on Si-Based Microfluidic Platforms  

Microsoft Academic Search

This paper gives a brief overview of silicon-based microfluidic platforms developed over the years by our group for the extraction, amplification, and detection of nucleic acids. Extraction of both genomic and viral nucleic acids from whole blood has been demonstrated on Si-based microfluidics. Rapid amplification has been achieved by polymerase chain reaction in Si-based thermal reactors (micro-PCR). Detection has been

Levent Yobas; Hongmiao Ji; Wing-Cheong Hui; Yu Chen; Tit-Meng Lim; Chew-Kiat Heng; Dim-Lee Kwong

2007-01-01

445

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

Microsoft Academic Search

Plasmacytoid dendritic cells (pDCs) are important mediators of antiviral immunity through their ability to produce large amounts of type I interferons (IFNs) on viral infection. This function of pDCs is linked to their expression of Toll-like receptor 7 (TLR7) and TLR9, which sense viral nucleic acids within the early endosomes. Exclusion of self nucleic acids from TLR-containing early endosomes normally

Michel Gilliet; Wei Cao; Yong-Jun Liu

2008-01-01

446

RNA Sequences Complementary to Citrus Exocortis Viroid in Nucleic Acid Preparations from Infected Gynura aurantiaca  

Microsoft Academic Search

Molecular hybridization with 125I-labeled citrus exocortis viroid RNA has been used to survey nucleic acid preparations from Gynura aurantiaca for viroid complementary molecules. A differential hybridization effect was detected between nucleic acid extracts from healthy and infected tissue in which significant RNase-resistant 125I-labeled citrus exocortis viroid resulted in hybridization studies with the infected tissue extracts. Subsequent characterization indicated that RNA

L. K. Grill; J. S. Semancik

1978-01-01

447

Effect of brassinosteroids on nucleic acids and protein content in cultured cells of Chlorella vulgaris  

Microsoft Academic Search

This study was conducted to investigate changes of nucleic acids and protein levels in response to brassinosteroid (BR) effect in the green alga Chlorella vulgaris Beijerinck. BRs had the greatest effect on growth and metabolism of algae between 24 and 36 h after treatment in the range from 10–12 to 10–8 M. The highest growth of the content of nucleic acids and

Andrzej Bajguz

2000-01-01

448

Affinity Purification of DNA and RNA from Environmental Samples with Peptide Nucleic Acid Clamps  

Microsoft Academic Search

Bispeptide nucleic acids (bis-PNAs; PNA clamps), PNA oligomers, and DNA oligonucleotides were evaluated as affinity purification reagents for subfemtomolar 16S ribosomal DNA (rDNA) and rRNA targets in soil, sed- iment, and industrial air filter nucleic acid extracts. Under low-salt hybridization conditions (10 mM NaPO4, 5 mM disodium EDTA, and 0.025% sodium dodecyl sulfate (SDS)) a PNA clamp recovered significantly more

DARRELL P. CHANDLER; JENNIE R. STULTS; SHARON CEBULA; BEATRICE L. SCHUCK; DEREK W. WEAVER; KEVIN K. ANDERSON; MICHAEL EGHOLM; FRED J. BROCKMAN

2000-01-01

449

Inhibition of the bovine papillomavirus E2 protein activity by peptide nucleic acid  

Microsoft Academic Search

The bovine papillomavirus type-1 E2 protein is the master regulator of the papillomavirus transcription and replication, the activity of which is regulated through sequence-specific DNA binding. Peptide nucleic acid (PNA) is a nucleic acid analogue, which associates with high affinity to complementary DNA, RNA or PNA, yielding in formation of stable complexes. The potential use of PNA as a sequence-specific

Reet Kurg; Ülo Langel; Mart Ustav

2000-01-01

450

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

451

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

452

Site-specific incorporation of nitroxide spin-labels into 2?-positions of nucleic acids  

Microsoft Academic Search

A protocol is described for the incorporation of nitroxide spin-labels into specific 2?-sites within nucleic acids. This labeling strategy facilitates the investigation of nucleic acid structure and dynamics using electron paramagnetic resonance (EPR) spectroscopy and macromolecular complex formation using paramagnetic relaxation enhancement NMR spectroscopy. A spin-labeling reagent, 4-isocyanato TEMPO, which can be prepared in one facile step or obtained commercially,

Thomas E Edwards; Snorri Th Sigurdsson

2007-01-01

453

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

454

Polymerization and nucleic acid-binding properties of human L1 ORF1 protein  

PubMed Central

The L1 (LINE 1) retrotransposable element encodes two proteins, ORF1p and ORF2p. ORF2p is the L1 replicase, but the role of ORF1p is unknown. Mouse ORF1p, a coiled-coil-mediated trimer of ?42-kDa monomers, binds nucleic acids and has nucleic acid chaperone activity. We purified human L1 ORF1p expressed in insect cells and made two findings that significantly advance our knowledge of the protein. First, in the absence of nucleic acids, the protein polymerizes under the very conditions (0.05?M NaCl) that are optimal for high (?1?nM)-affinity nucleic acid binding. The non-coiled-coil C-terminal half mediates formation of the polymer, an active conformer that is instantly resolved to trimers, or multimers thereof, by nucleic acid. Second, the protein has a biphasic effect on mismatched double-stranded DNA, a proxy chaperone substrate. It protects the duplex from dissociation at 37°C before eventually melting it when largely polymeric. Therefore, polymerization of ORF1p seemingly affects its interaction with nucleic acids. Additionally, polymerization of ORF1p at its translation site could explain the heretofore-inexplicable phenomenon of cis preference—the favored retrotransposition of the actively translated L1 transcript, which is essential for L1 survival. PMID:21937507

Callahan, Kathryn E.; Hickman, Alison B.; Jones, Charles E.; Ghirlando, Rodolfo; Furano, Anthony V.

2012-01-01

455

Comparative Evaluation of Three Commercial Systems for Nucleic Acid Extraction from Urine Specimens  

PubMed Central

A nucleic acid extraction system that can handle small numbers of specimens with a short test turnaround time and short hands-on time is desirable for emergent testing. We performed a comparative validation on three systems: the MagNA Pure compact system (Compact), the NucliSens miniMAG extraction instrument (miniMAG), and the BioRobot EZ1 system (EZ1). A total of 75 urine specimens submitted for polyomavirus BK virus detection were used. The human ?-actin gene was detected on 75 (100%), 75 (100%), and 72 (96%) nucleic acid extracts prepared by the miniMAG, EZ1, and Compact, respectively. The miniMAG produced the highest quantity of nucleic acids and the best precision among the three systems. The agreement rate was 100% for BKV detection on nucleic acid extracts prepared by the three extraction systems. When a full panel of specimens was run, the hands-on time and test turnaround time were 105.7 and 121.1 min for miniMAG, 6.1 and 22.6 min for EZ1, and 7.4 and 33.7 min for Compact, respectively. The EZ1 and Compact systems processed automatic nucleic acid extraction properly, providing a good solution to the need for sporadic but emergent specimen detection. The miniMAG yielded the highest quantity of nucleic acids, suggesting that this system would be the best for specimens containing a low number of microorganisms of interest. PMID:16145151

Tang, Yi-Wei; Sefers, Susan E.; Li, Haijing; Kohn, Debra J.; Procop, Gary W.

2005-01-01

456

Improved assay-dependent searching of nucleic acid sequence databases  

PubMed Central

Nucleic acid-based biochemical assays are crucial to modern biology. Key applications, such as detection of bacterial, viral and fungal pathogens, require detailed knowledge of assay sensitivity and specificity to obtain reliable results. Improved methods to predict assay performance are needed for exploiting the exponentially growing amount of DNA sequence data and for reducing the experimental effort required to develop robust detection assays. Toward this goal, we present an algorithm for the calculation of sequence similarity based on DNA thermodynamics. In our approach, search queries consist of one to three oligonucleotide sequences representing either a hybridization probe, a pair of Padlock probes or a pair of PCR primers with an optional TaqMan™ probe (i.e. in silico or ‘virtual’ PCR). Matches are reported if the query and target satisfy both the thermodynamics of the assay (binding at a specified hybridization temperature and/or change in free energy) and the relevant biological constraints (assay sequences binding to the correct target duplex strands in the required orientations). The sensitivity and specificity of our method is evaluated by comparing predicted to known sequence tagged sites in the human genome. Free energy is shown to be a more sensitive and specific match criterion than hybridization temperature. PMID:18515842

Gans, Jason D.

2008-01-01

457

Nucleic acid aptamers: clinical applications and promising new horizons  

PubMed Central

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, Xiaohua; Castanares, Mark; Mukherjee, Amarnath; Lupold, Shawn E.

2011-01-01

458

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

459

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

460

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

461

Peptide nucleic acids: versatile tools for gene therapy strategies  

PubMed Central

Peptide nucleic acids, or PNAs, are oligonucleotide analogs in which the phosphodiester backbone is replaced with a polyamide structure. First synthesized less than 10 years ago, they have received great attention due to their several favorable properties, including resistance to nuclease and protease digestion, stability in serum and cell extracts, and their high affinity for RNA and single and double-stranded DNA targets. Although initially designed and demonstrated to function as antisense and antigene reagents that inhibit both transcription and translation by steric hindrance, more recent applications have included gene activation by synthetic promoter formation and mutagenesis of chromosomal targets. Most notably for gene delivery, they have been used to specifically label plasmids and act as adapters to link synthetic peptides or ligands to the DNA. Thus, their great potential lies in the ability to attach specific targeting peptides to plasmids to circumvent such barriers to gene transfer as cell-targeting or nuclear localization, thereby increasing the efficacy of gene therapy. PMID:11072107

Dean, David A.

2015-01-01

462

Nucleic acid metabolism during cytokinin induced cellular differentiation.  

PubMed

Edstrom's microphoresis technique has been employed to determine the quantitative alterations in nucleic acid content and base composition of individual cells associated with the initiation of bud primordia in Funaria hygrometrica. The filamentous protonema of this moss initiates bud cells which through repeated divisions form the leafy gametophores. The cytokinin, 6-furfurylaminopurine (kinetin), was used to induce the differentiation of bud cells from protonematal cells. The total RNA content of kinetin-induced bud cells (22.0 mumug/cell) was nearly 15 times that of protonematal cells (1.6 mumug/cell). The same dramatic increase in total RNA was apparent in bud cells which developed spontaneously in older cultures. As would be predicted, the adenine (A) to guanine (G) ratio for DNA from bud and protonematal cells was identical (0.7). The A:G ratio for RNA from bud cells (1.0) was much lower than that from protonematal cells (1.7). Thus, kinetin-induced differentiation in this system involves a dramatic increase in total RNA, the base composition of which approaches that of DNA. The base composition (A:G ratio) of DNA remains constant. PMID:5379105

Schneider, M J; Lin, J C; Skoog, F

1969-09-01

463

Reticuloendotheliosis Virus Nucleic Acid Sequences in Cellular DNA  

PubMed Central

Reticuloendotheliosis virus 60S RNA labeled with 125I, or reticuloendotheliosis virus complementary DNA labeled with 3H, were hybridized to DNAs from infected chicken and pheasant cells. Most of the sequences of the viral RNA were found in the infected cell DNAs. The reticuloendotheliosis viruses, therefore, replicate through a DNA intermediate. The same labeled nucleic acids were hybridized to DNA of uninfected chicken, pheasant, quail, turkey, and duck. About 10% of the sequences of reticuloendotheliosis virus RNA were present in the DNA of uninfected chicken, pheasant, quail, and turkey. None were detected in DNA of duck. The specificity of the hybridization was shown by competition between unlabeled and 125I-labeled viral RNAs and by determination of melting temperatures. In contrast, 125I-labeled RNA of Rous-associated virus-O, an avian leukosis-sarcoma virus, hybridized 55% to DNA of uninfected chicken, 20% to DNA of uninfected pheasant, 15% to DNA of uninfected quail, 10% to DNA of uninfected turkey, and less than 1% to DNA of uninfected duck. PMID:4372393

Kang, Chil-Yong; Temin, Howard M.

1974-01-01

464

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

465

What controls the hybridization thermodynamics of spherical nucleic acids?  

PubMed

The hybridization of free oligonucleotides to densely packed, oriented arrays of DNA modifying the surfaces of spherical nucleic acid (SNA)-gold nanoparticle conjugates occurs with negative cooperativity; i.e., each binding event destabilizes subsequent binding events. DNA hybridization is thus an ever-changing function of the number of strands already hybridized to the particle. Thermodynamic quantification of this behavior reveals a 3 orders of magnitude decrease in the binding constant for the capture of a free oligonucleotide by an SNA conjugate as the fraction of pre-hybridized strands increases from 0 to ?30%. Increasing the number of pre-hybridized strands imparts an increasing enthalpic penalty to hybridization that makes binding more difficult, while simultaneously decreasing the entropic penalty to hybridization, which makes binding more favorable. Hybridization of free DNA to an SNA is thus governed by both an electrostatic barrier as the SNA accumulates charge with additional binding events and an effect consistent with allostery, where hybridization at certain sites on an SNA modify the binding affinity at a distal site through conformational changes to the remaining single strands. Leveraging these insights allows for the design of conjugates that hybridize free strands with significantly higher efficiencies, some of which approach 100%. PMID:25738968

Randeria, Pratik S; Jones, Matthew R; Kohlstedt, Kevin L; Banga, Resham J; Olvera de la Cruz, Monica; Schatz, George C; Mirkin, Chad A

2015-03-18

466

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

467

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

468

DNA binding proteins that alter nucleic acid flexibility  

NASA Astrophysics Data System (ADS)

Dual - beam optical tweezers experiments subject single molecules of DNA to high forces (~ 300 pN) with 0.1 pN accuracy, probing the energy and specificity of nucleic acid - ligand structures. Stretching phage ?-DNA reveals an increase in the applied force up to a critical force known as the overstretching transition. In this region, base pairing and stacking are disrupted as double stranded DNA (dsDNA) is melted. Proteins that bind to the double strand will tend to stabilize dsDNA, and melting will occur at higher forces. Proteins that bind to single stranded DNA (ssDNA) destabilize melting, provided that the rate of association is comparable to the pulling rate of the experiment. Many proteins, however, exhibit some affinity for both dsDNA and ssDNA. We describe experiments upon DNA + HMGB2 (box A), a nuclear protein that is believed to facilitate transcription. By characterizing changes in the structure of dsDNA with a polymer model of elasticity, we have determined the equilibrium association constant for HMGB2 to be K ds = 0.15 +/- 0.7 10 9 M -1 for dsDNA binding. Analysis of the melting transition reveals an equilibrium association constant for HMGB2 to ssDNA to be K ss = 0.039 +/- 0.019 10 9 M -1 for ssDNA binding.

McCauley, Micah; Hardwidge, Philip R.; Maher, L. J., III; Williams, Mark C.

2007-09-01

469

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

470

Oxidative Stress and Nucleic Acid Oxidation in Patients with Chronic Kidney Disease  

PubMed Central

Patients with chronic kidney disease (CKD) have high cardiovascular mortality and morbidity and a high risk for developing malignancy. Excessive oxidative stress is thought to play a major role in elevating these risks by increasing oxidative nucleic acid damage. Oxidative stress results from an imbalance between reactive oxygen/nitrogen species (RONS) production and antioxidant defense mechanisms and can cause vascular and tissue injuries as well as nucleic acid damage in CKD patients. The increased production of RONS, impaired nonenzymatic or enzymatic antioxidant defense mechanisms, and other risk factors including gene polymorphisms, uremic toxins (indoxyl sulfate), deficiency of arylesterase/paraoxonase, hyperhomocysteinemia, dialysis-associated membrane bioincompatibility, and endotoxin in patients with CKD can inhibit normal cell function by damaging cell lipids, arachidonic acid derivatives, carbohydrates, proteins, amino acids, and nucleic acids. Several clinical biomarkers and techniques have been used to detect the antioxidant status and oxidative stress/oxidative nucleic acid damage associated with long-term complications such as inflammation, atherosclerosis, amyloidosis, and malignancy in CKD patients. Antioxidant therapies have been studied to reduce the oxidative stress and nucleic acid oxidation in patients with CKD, including alpha-tocopherol, N-acetylcysteine, ascorbic acid, glutathione, folic acid, bardoxolone methyl, angiotensin-converting enzyme inhibitor, and providing better dialysis strategies. This paper provides an overview of radical production, antioxidant defence, pathogenesis and biomarkers of oxidative stress in patients with CKD, and possible antioxidant therapies. PMID:24058721

Sung, Chih-Chien; Hsu, Yu-Chuan; Lin, Yuh-Feng

2013-01-01

471

Brnsted Acids The Strongest Isolable Acid**  

E-print Network

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

Reed, Christopher A.

472

The Effects of Borate Minerals on the Synthesis of Nucleic Acid Bases, Amino Acids and Biogenic Carboxylic Acids from Formamide  

Microsoft Academic Search

The thermal condensation of formamide in the presence of mineral borates is reported. The products afforded are precursors\\u000a of nucleic acids, amino acids derivatives and carboxylic acids. The efficiency and the selectivity of the reaction was studied\\u000a in relation to the elemental composition of the 18 minerals analyzed. The possibility of synthesizing at the same time building\\u000a blocks of both

Raffaele Saladino; Maurizio Barontini; Cristina Cossetti; Ernesto Di Mauro; Claudia Crestini

2011-01-01

473

Circulating nucleic acids damage DNA of healthy cells by integrating into their genomes.  

PubMed

Whether nucleic acids that circulate in blood have any patho-physiological functions in the host have not been explored.We report here that far from being inert molecules, circulating nucleic acids have significant biological activities of their own that are deleterious to healthy cells of the body. Fragmented DNA and chromatin (DNAfs and Cfs) isolated from blood of cancer patients and healthy volunteers are readily taken up by a variety of cells in culture to be localized in their nuclei within a few minutes. The intra-nuclear DNAfs and Cfs associate themselves with host cell chromosomes to evoke a cellular DNA-damage-repair-response (DDR) followed by their incorporation into the host cell genomes. Whole genome sequencing detected the presence of tens of thousands of human sequence reads in the recipient mouse cells. Genomic incorporation of DNAfs and Cfs leads to dsDNA breaks and activation of apoptotic pathways in the treated cells. When injected intravenously into Balb/C mice, DNAfs and Cfs undergo genomic integration into cells of their vital organs resulting in activation of DDR and apoptotic proteins in the recipient cells. Cfs have significantly greater activity than DNAfs with respect to all parameters examined, while both DNAfs and Cfs isolated from cancer patients are more active than those from normal volunteers. All the above pathological actions of DNAfs and Cfs described above can be abrogated by concurrent treatment with DNase I and/or anti-histone antibody complexed nanoparticles both in vitro and in vivo. Taken together, our results suggest that circulating DNAfs and Cfs are physiological, continuously arising, endogenous DNA damaging agents with implications to ageing and a multitude of human pathologies including initiation of cancer. PMID:25740145

Mittra, Indraneel; Khare, Naveen Kumar; Raghuram, Gorantla Venkata; Chaubal, Rohan; Khambatti, Fatema; Gupta, Deepika; Gaikwad, Ashwini; Prasannan, Preeti; Singh, Akshita; Iyer, Aishwarya; Singh, Ankita; Upadhyay, Pawan; Nair, Naveen Kumar; Mishra, Pradyumna Kumar; Dutt, Amit

2015-03-01

474

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

475

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

476

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.

477

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 com