Thermodynamic properties of branched DNA complexes with full-matched and mismatched DNA strands

2006 ◽  
pp. 2329 ◽  
Author(s):  
Masayuki Endo ◽  
Tetsuro Majima
Keyword(s):  
Thermodynamic Properties ◽  
Dna Complexes ◽  
Mismatched Dna ◽  
Branched Dna ◽  
Dna Strands

scholarly journals DNA Ligase-Based Strategy for Quantifying Heterogeneous DNA Methylation without Sequencing

2015 ◽  
Vol 61 (1) ◽  
pp. 163-171 ◽  
Author(s):  
Eugene J H Wee ◽  
Sakandar Rauf ◽  
Muhammad J A Shiddiky ◽  
Alexander Dobrovic ◽  
Matt Trau
Keyword(s):  
Dna Methylation ◽  
Single Molecule ◽  
Region Of Interest ◽  
Suppressor Gene ◽  
Fluorescent Detection ◽  
Routine Practice ◽  
Dna Ligases ◽  
Mismatched Dna ◽  
Dna Strands ◽  
Analytical Accuracy

Abstract BACKGROUND DNA methylation is a potential source of disease biomarkers. Typically, methylation levels are measured at individual cytosine/guanine (CpG) sites or over a short region of interest. However, regions of interest often show heterogeneous methylation comprising multiple patterns of methylation (epialleles) on individual DNA strands. Heterogeneous methylation is largely ignored because digital methods are required to deconvolute these usually complex patterns of epialleles. Currently, only single-molecule approaches, such as next generation sequencing (NGS), can provide detailed epiallele information. Because NGS is not yet feasible for routine practice, we developed a single-molecule–like approach, named for epiallele quantification (EpiQ). METHODS EpiQ uses DNA ligases and the enhanced thermal instability of short (≤19 bases) mismatched DNA probes for the relative quantification of epialleles. The assay was developed using fluorescent detection on a gel and then adapted for electrochemical detection on a microfabricated device. NGS was used to validate the analytical accuracy of EpiQ. RESULTS In this proof of principle study, EpiQ detected with 90%–95% specificity each of the 8 possible epialleles for a 3-CpG cluster at the promoter region of the CDKN2B (p15) tumor suppressor gene. EpiQ successfully profiled heterogeneous methylation patterns in clinically derived samples, and the results were cross-validated with NGS. CONCLUSIONS EpiQ is a potential alternative tool for characterizing heterogeneous methylation, thus facilitating its use as a biomarker. EpiQ was developed on a gel-based assay but can also easily be adapted for miniaturized chip-based platforms.

scholarly journals DNA Hybridization Detection Based on Resonance Frequency Readout in Graphene on Au SPR Biosensor

2016 ◽  
Vol 2016 ◽  
pp. 1-7 ◽  
Author(s):  
Md. Biplob Hossain ◽  
Md. Masud Rana
Keyword(s):  
Resonance Frequency ◽  
Dna Hybridization ◽  
Biomolecular Recognition ◽  
Nucleotide Polymorphisms ◽  
Mismatched Dna ◽  
Spr Sensor ◽  
Spr Biosensor ◽  
Target Dna ◽  
Dna Strands ◽  
Recognition Elements

This paper demonstrates a numerical modeling of surface plasmon resonance (SPR) biosensor for detecting DNA hybridization by recording the resonance frequency characteristics (RFC). The proposed sensor is designed based on graphene material as biomolecular recognition elements (BRE) and the sharp SPR curve of gold (Au). Numerical analysis shows that the variation of RFC for mismatched DNA strands is quiet negligible whereas that for complementary DNA strands is considerably countable. Here, graphene is used to perform faster immobilization between target DNA and probe DNA. The usage of graphene also changes the RFC that ensure hybridization of DNA event by utilizing its optochemical property. In addition, proposed sensor successfully distinguishes between hybridization and single-nucleotide polymorphisms (SNP) by observing the variation level of RFC and maximum transmittance. Therefore, the proposed frequency readout based SPR sensor could potentially open a new window of detection for biomolecular interactions. We also highlight the advantage of using graphene sublayer by performing the sensitivity analysis. Sandwiching of each graphene sublayer enhances 95% sensitivity comparing with conventional SPR sensor.

Surfactant-free nanoparticle–DNA complexes with ultrahigh stability against salt for environmental and biological sensing

The Analyst ◽  
2014 ◽  
Vol 139 (22) ◽  
pp. 5936-5944 ◽  
Author(s):  
Jun Hyuk Heo ◽  
Hui Hun Cho ◽  
Jung Heon Lee
Keyword(s):  
Ionic Strength ◽  
High Ionic Strength ◽  
Biological Sensing ◽  
Dna Complexes ◽  
Dna Strands ◽  
Dna Complex ◽  
High Ionic Strength Media

A AuNP–DNA complex highly stable in extremely high ionic strength media, such as seawater, was obtained by inserting a few thymine bases into the DNA strands.

scholarly journals Sequence specificity, energetics and mechanism of mismatch recognition by DNA damage sensing protein Rad4/XPC

2020 ◽  
Vol 48 (5) ◽  
pp. 2246-2257 ◽  
Author(s):  
Abhinandan Panigrahi ◽  
Hemanth Vemuri ◽  
Madhur Aggarwal ◽  
Kartheek Pitta ◽  
Marimuthu Krishnan
Keyword(s):  
Molecular Basis ◽  
High Specificity ◽  
Umbrella Sampling ◽  
Dna Lesions ◽  
Sequence Specificity ◽  
Dna Complexes ◽  
Mismatched Dna ◽  
Damage Sensing ◽  
Molecular Events ◽  
Mismatch Recognition

Abstract The ultraviolet (UV) radiation-induced DNA lesions play a causal role in many prevalent genetic skin-related diseases and cancers. The damage sensing protein Rad4/XPC specifically recognizes and repairs these lesions with high fidelity and safeguards genome integrity. Despite considerable progress, the mechanistic details of the mode of action of Rad4/XPC in damage recognition remain obscure. The present study investigates the mechanism, energetics, dynamics, and the molecular basis for the sequence specificity of mismatch recognition by Rad4/XPC. We dissect the following three key molecular events that occur as Rad4/XPC tries to recognize and bind to DNA lesions/mismatches: (a) the association of Rad4/XPC with the damaged/mismatched DNA, (b) the insertion of a lesion-sensing β-hairpin of Rad4/XPC into the damage/mismatch site and (c) the flipping of a pair of nucleotide bases at the damage/mismatch site. Using suitable reaction coordinates, the free energy surfaces for these events are determined using molecular dynamics (MD) and umbrella sampling simulations on three mismatched (CCC/CCC, TTT/TTT and TAT/TAT mismatches) Rad4-DNA complexes. The study identifies the key determinants of the sequence-dependent specificity of Rad4 for the mismatches and explores the ramifications of specificity in the aforementioned events. The results unravel the molecular basis for the high specificity of Rad4 towards CCC/CCC mismatch and lower specificity for the TAT/TAT mismatch. A strong correlation between the depth of β-hairpin insertion into the DNA duplex and the degree of coupling between the hairpin insertion and the flipping of bases is also observed. The interplay of the conformational flexibility of mismatched bases, the depth of β-hairpin insertion, Rad4-DNA association energetics and the Rad4 specificity explored here complement recent experimental FRET studies on Rad4-DNA complexes.

Homogeneous enzyme-free and entropy-driven isothermal fluorescent assay for nucleic acids based on a dual-signal output amplification strategy

2018 ◽  
Vol 54 (89) ◽  
pp. 12594-12597 ◽  
Author(s):  
Erhu Xiong ◽  
Deshuai Zhen ◽  
Ling Jiang
Keyword(s):  
Nucleic Acids ◽  
Reaction Rate ◽  
Analytical Performance ◽  
Fluorescent Assay ◽  
Mismatched Dna ◽  
Fluorescent Biosensor ◽  
Dna Strands ◽  
Signal Output ◽  
Amplification Strategy

The proposed fluorescent biosensor improves the reaction rate, has excellent analytical performance (LOD 15.6 fM) and shows outstanding recognition toward mismatched DNA strands. This approach provides a potential universal platform for the determination of other nucleic acids.

scholarly journals Dynamics of MutS–Mismatched DNA Complexes Are Predictive of Their Repair Phenotypes

Biochemistry ◽  
2014 ◽  
Vol 53 (12) ◽  
pp. 2043-2052 ◽  
Author(s):  
Vanessa C. DeRocco ◽  
Lauryn E. Sass ◽  
Ruoyi Qiu ◽  
Keith R. Weninger ◽  
Dorothy A. Erie
Keyword(s):  
Dna Complexes ◽  
Mismatched Dna

Generic Technique to Generate Large Branched DNA Complexes

2006 ◽  
Vol 7 (3) ◽  
pp. 677-681 ◽  
Author(s):  
Paul Tosch ◽  
Christoph Wälti ◽  
Anton P. J. Middelberg ◽  
A. Giles Davies
Keyword(s):  
Dna Complexes ◽  
Branched Dna
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