DNA–RNA hybrid duplexes with decreasing pyrimidine content in the DNA strand provide structural snapshots for the A- to B-form conformational transition of nucleic acids

2014 ◽  
Vol 16 (34) ◽  
pp. 18148-18155 ◽  
Author(s):  
Gorle Suresh ◽  
U. Deva Priyakumar
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Conformational Transition ◽  
Gradual Increase ◽  
Nuclease Activity ◽  
Dna Strand ◽  
Hybrid Duplexes

A gradual increase in the deoxypyrimidine content in DNA–RNA hybrids leads to B- to A-form nucleic acid transition. Possible factors that govern nuclease activity on hybrid duplexes are presented.

Mercury Electrodes in Nucleic Acid Electrochemistry: Sensitive Analytical Tools and Probes of DNA Structure. A Review

2004 ◽  
Vol 69 (4) ◽  
pp. 715-747 ◽  
Author(s):  
Miroslav Fojta
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Double Helix ◽  
Dna Structure ◽  
Electrochemical Analysis ◽  
Label Free ◽  
Helix Formation ◽  
Mercury Electrodes ◽  
Dna Strand ◽  
Dna Double Helix

This review is devoted to applications of mercury electrodes in the electrochemical analysis of nucleic acids and in studies of DNA structure and interactions. At the mercury electrodes, nucleic acids yield faradaic signals due to redox processes involving adenine, cytosine and guanine residues, and tensammetric signals due to adsorption/desorption of polynucleotide chains at the electrode surface. Some of these signals are highly sensitive to DNA structure, providing information about conformation changes of the DNA double helix, formation of DNA strand breaks as well as covalent or non-covalent DNA interactions with small molecules (including genotoxic agents, drugs, etc.). Measurements at mercury electrodes allow for determination of small quantities of unmodified or electrochemically labeled nucleic acids. DNA-modified mercury electrodes have been used as biodetectors for DNA damaging agents or as detection electrodes in DNA hybridization assays. Mercury film and solid amalgam electrodes possess similar features in the nucleic acid analysis to mercury drop electrodes. On the contrary, intrinsic (label-free) DNA electrochemical responses at other (non-mercury) solid electrodes cannot provide information about small changes of the DNA structure. A review with 188 references.

Nucleic Acid Molecules Prepared by Monolayer Techniques

1972 ◽  
Vol 30 ◽  
pp. 178-179
Author(s):  
Dimitrij Lang
Keyword(s):  
Electron Microscopy ◽  
Standard Deviation ◽  
Nucleic Acid ◽  
Cytochrome C ◽  
Nucleic Acids ◽  
Contour Length ◽  
Sample Standard Deviation ◽  
Molecular Weights ◽  
Length Measurements ◽  
Protein Monolayer

The success of the protein monolayer technique for electron microscopy of individual DNA molecules is based on the prevention of aggregation and orientation of the molecules during drying on specimen grids. DNA adsorbs first to a surface-denatured, insoluble cytochrome c monolayer which is then transferred to grids, without major distortion, by touching. Fig. 1 shows three basic procedures which, modified or not, permit the study of various important properties of nucleic acids, either in concert with other methods or exclusively:1) Molecular weights relative to DNA standards as well as number distributions of molecular weights can be obtained from contour length measurements with a sample standard deviation between 1 and 4%.

Snapshot blotting: The transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to EM grids

1992 ◽  
Vol 50 (1) ◽  
pp. 762-763
Author(s):  
Stephen D. Jett
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Nucleic Acid Binding ◽  
Mobility Shift ◽  
Carbon Coated ◽  
Nucleoprotein Complexes ◽  
Mobility Shift Assay ◽  
Protein Nucleic Acid ◽  
Gel Mobility Shift ◽  
Nucleic Acid Interactions

The electrophoresis gel mobility shift assay is a popular method for the study of protein-nucleic acid interactions. The binding of proteins to DNA is characterized by a reduction in the electrophoretic mobility of the nucleic acid. Binding affinity, stoichiometry, and kinetics can be obtained from such assays; however, it is often desirable to image the various species in the gel bands using TEM. Present methods for isolation of nucleoproteins from gel bands are inefficient and often destroy the native structure of the complexes. We have developed a technique, called “snapshot blotting,” by which nucleic acids and nucleoprotein complexes in electrophoresis gels can be electrophoretically transferred directly onto carbon-coated grids for TEM imaging.

Molecular insights on the dynamic stability of peptide nucleic acid functionalized carbon and boron nitride nanotubes

2021 ◽  
Vol 23 (1) ◽  
pp. 219-228
Author(s):  
Nabanita Saikia ◽  
Mohamed Taha ◽  
Ravindra Pandey
Keyword(s):  
Nucleic Acid ◽  
Boron Nitride ◽  
Nucleic Acids ◽  
Dynamic Stability ◽  
Peptide Nucleic Acid ◽  
Rational Design ◽  
Peptide Nucleic Acids ◽  
Boron Nitride Nanotubes ◽  
Molecular Hybrids ◽  
Single Wall Nanotubes

The rational design of self-assembled nanobio-molecular hybrids of peptide nucleic acids with single-wall nanotubes rely on understanding how biomolecules recognize and mediate intermolecular interactions with the nanomaterial's surface.

scholarly journals Kinetics of DNA Strand Displacement Systems with Locked Nucleic Acids

2017 ◽  
Vol 121 (12) ◽  
pp. 2594-2602 ◽  
Author(s):  
Xiaoping Olson ◽  
Shohei Kotani ◽  
Bernard Yurke ◽  
Elton Graugnard ◽  
William L. Hughes
Keyword(s):  
Nucleic Acids ◽  
Strand Displacement ◽  
Dna Strand Displacement ◽  
Locked Nucleic Acids ◽  
Dna Strand ◽  
Kinetics Of

Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors

The Analyst ◽  
2021 ◽  
Author(s):  
Qingteng Lai ◽  
Wei Chen ◽  
Yanke Zhang ◽  
Zheng-Chun Liu
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Peptide Nucleic Acids ◽  
Dna Probes ◽  
Highly Sensitive ◽  
Increased Sensitivity ◽  
Acid Sensors

Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensor due to their higher stability and increased sensitivity than common DNA probes....

scholarly journals Validating DNA Extraction Protocols for Bentonite Clay

mSphere ◽  
2019 ◽  
Vol 4 (5) ◽  
Author(s):  
Katja Engel ◽  
Sara Coyotzi ◽  
Melody A. Vachon ◽  
Jennifer R. McKelvie ◽  
Josh D. Neufeld
Keyword(s):  
Microbial Community ◽  
Nucleic Acid ◽  
Nucleic Acids ◽  
Dna Extraction ◽  
Genomic Dna ◽  
Bentonite Clay ◽  
Dna Recovery ◽  
Blocking Agents ◽  
Clay Matrix ◽  
Microbial Dna

ABSTRACT Bentonite clay is an integral component of the engineered barrier system of deep geological repositories (DGRs) that are planned for the long-term storage of high-level radioactive waste. Although nucleic acid extraction and analysis can provide powerful qualitative and quantitative data reflecting the presence, abundance, and functional potential of microorganisms within DGR materials, extraction of microbial DNA from bentonite clay is challenging due to the low biomass and adsorption of nucleic acids to the charged clay matrix. In this study, we used quantitative PCR, gel fingerprinting, and high-throughput sequencing of 16S rRNA gene amplicons to assess DNA extraction efficiency from natural MX-80 bentonite and the same material “spiked” with Escherichia coli genomic DNA. Extraction protocols were tested without additives and with casein and phosphate as blocking agents. Although we demonstrate improved DNA recovery by blocking agents at relatively high DNA spiking concentrations, at relatively low spiking concentrations, we detected a high proportion of contaminant nucleic acids from blocking agents that masked sample-specific microbial profile data. Because bacterial genomic DNA associated with casein preparations was insufficiently removed by UV treatment, casein is not recommended as an additive for DNA extractions from low-biomass samples. Instead, we recommend a kit-based extraction protocol for bentonite clay without additional blocking agents, as tested here and validated with multiple MX-80 bentonite samples, ensuring relatively high DNA recoveries with minimal contamination. IMPORTANCE Extraction of microbial DNA from MX-80 bentonite is challenging due to low biomass and adsorption of nucleic acid molecules to the charged clay matrix. Blocking agents improve DNA recovery, but their impact on microbial community profiles from low-biomass samples has not been characterized well. In this study, we evaluated the effect of casein and phosphate as blocking agents for quantitative recovery of nucleic acids from MX-80 bentonite. Our data justify a simplified framework for analyzing microbial community DNA associated with swelling MX-80 bentonite samples within the context of a deep geological repository for used nuclear fuel. This study is among the first to demonstrate successful extraction of DNA from Wyoming MX-80 bentonite.

scholarly journals Peptide Nucleic Acids: Applications in Biomedical Sciences

Molecules ◽  
2020 ◽  
Vol 25 (15) ◽  
pp. 3317
Author(s):  
Eylon Yavin
Keyword(s):  
Nucleic Acid ◽  
Nucleic Acids ◽  
Peptide Nucleic Acid ◽  
Peptide Nucleic Acids ◽  
Biomedical Sciences

The DNA mimic, PNA (peptide nucleic acid), has been with us now for almost 3 decades [...]

scholarly journals Tsetse Salivary Gland Proteins 1 and 2 Are High Affinity Nucleic Acid Binding Proteins with Residual Nuclease Activity

PLoS ONE ◽  
2012 ◽  
Vol 7 (10) ◽  
pp. e47233 ◽  
Author(s):  
Guy Caljon ◽  
Karin De Ridder ◽  
Benoît Stijlemans ◽  
Marc Coosemans ◽  
Stefan Magez ◽  
...  
Keyword(s):  
Salivary Gland ◽  
Nucleic Acid ◽  
Binding Proteins ◽  
Nuclease Activity ◽  
Nucleic Acid Binding ◽  
High Affinity ◽  
Nucleic Acid Binding Proteins
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