(Q35649514)

9 August 2017

title

A kinetic zipper model with intrachain interactions applied to nucleic acid hairpin folding kinetics (English)

1 reference

9 August 2017

Serguei V Kuznetsov

1

1 reference

9 August 2017

Anjum Ansari

series ordinal

2

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9 August 2017

language of work or name

English

0 references

publication date

3 January 2012

1 reference

9 August 2017

number of pages

11

1 reference

inferred from page(s)

published in

Biophysical Journal

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9 August 2017

volume

102

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9 August 2017

issue

1

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9 August 2017

page(s)

101-111

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Loop and stem dynamics during RNA hairpin folding and unfolding

9 August 2017

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Free energy profile of RNA hairpins: a molecular dynamics simulation study

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Constructing multi-resolution Markov State Models (MSMs) to elucidate RNA hairpin folding mechanisms

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Fast folding of an RNA tetraloop on a rugged energy landscape detected by a stacking-sensitive probe

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Rearrangement of partially ordered stacked conformations contributes to the rugged energy landscape of a small RNA hairpin

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Structural insight into RNA hairpin folding intermediates

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Salt dependence of nucleic acid hairpin stability

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Loop dependence of the stability and dynamics of nucleic acid hairpins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Structures, kinetics, thermodynamics, and biological functions of RNA hairpins.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

DNA folding and melting observed in real time redefine the energy landscape

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Direct measurement of the full, sequence-dependent folding landscape of a nucleic acid

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Is hairpin formation in single-stranded polynucleotide diffusion-controlled?

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

The initial step of DNA hairpin folding: a kinetic analysis using fluorescence correlation spectroscopy

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Effects of denaturants on the dynamics of loop formation in polypeptides

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Nanomechanical measurements of the sequence-dependent folding landscapes of single nucleic acid hairpins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Mechanical unfolding of RNA hairpins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Stacked-unstacked equilibrium at the nick site of DNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Evidence that folding of an RNA tetraloop hairpin is less cooperative than its DNA counterpart

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Slow nucleic acid unzipping kinetics from sequence-defined barriers

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Conformational energetics of stable and metastable states formed by DNA triplet repeat oligonucleotides: implications for triplet expansion diseases

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

RNA hairpin-folding kinetics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

A semiflexible polymer model applied to loop formation in DNA hairpins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Monitoring the conformational fluctuations of DNA hairpins using single-pair fluorescence resonance energy transfer

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Configurational diffusion down a folding funnel describes the dynamics of DNA hairpins

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Early events in RNA folding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Non-Arrhenius kinetics for the loop closure of a DNA hairpin.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Replication by a single DNA polymerase of a stretched single-stranded DNA

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Measuring the rate of intramolecular contact formation in polypeptides

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

RNA folding energy landscapes.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Themes in RNA-protein recognition.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Kinetics of conformational fluctuations in DNA hairpin-loops

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Funnels, pathways, and the energy landscape of protein folding: a synthesis

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Hairpins are formed by the single DNA strands of the fragile X triplet repeats: structure and biological implications

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Thermodynamics and kinetics of G·C base pairing in the isolated extra arm of serine-specific transfer RNA from yeast

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Free energy of imperfect nucleic acid helices. II. Small hairpin loops

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

A direct measurement of the unzippering rate of a nucleic acid double helix.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Diffusion in a rough potential

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Analysis of melting transitions of the DNA hairpins formed from the oligomer sequences d[GGATAC(X)4GTATCC] (X = A, T, G, C).

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Dominant forces in protein folding

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Studies of DNA dumbbells. III. Theoretical analysis of optical melting curves of dumbbells with a 16 base-pair duplex stem and Tn end loops (n = 2, 3, 4, 6, 8, 10, 14)

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Probing the complete folding trajectory of a DNA hairpin using dual beam fluorescence fluctuation spectroscopy.

12 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Kinetics of end-to-end collision in short single-stranded nucleic acids

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Folding of a stable DNA motif involves a highly cooperative network of interactions.

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

RNA simulations: probing hairpin unfolding and the dynamics of a GNRA tetraloop

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Reversible unfolding of single RNA molecules by mechanical force

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Single-molecule studies of DNA mechanics

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Kinetics of Loop Formation in Polymer Chains†

25 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

Multiple Probes are Required to Explore and Control the Rugged Energy Landscape of RNA Hairpins

15 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3250679

V(D)J recombination: broken DNA molecules with covalently sealed (hairpin) coding ends in scid mouse thymocytes

15 November 2018

1 reference

12 December 2020

Misfolded loops decrease the effective rate of DNA hairpin formation

1 reference

12 December 2020

Slippery DNA and diseases

1 reference

12 December 2020

Predicting thermodynamic properties of RNA

1 reference

12 December 2020

Tn10 transposition via a DNA hairpin intermediate

1 reference

12 December 2020

A three-state mechanism for DNA hairpin folding characterized by multiparameter fluorescence fluctuation spectroscopy

1 reference

12 December 2020

Exploring the energy landscape of a small RNA hairpin

1 reference

12 December 2020

Simulation of the pressure and temperature folding/unfolding equilibrium of a small RNA hairpin

1 reference

12 December 2020

Thermodynamic and kinetic parameters of an oligonucleotide hairpin helix

1 reference

12 December 2020

Sequence dependent rigidity of single stranded DNA

1 reference

12 December 2020

All-atom Monte Carlo simulation of GCAA RNA folding

1 reference

12 December 2020

10.1016/J.BPJ.2011.11.4017

Identifiers

DOI

1 reference

release_te63hdabmfe4xptwcapo6jekha

9 August 2017

Fatcat ID

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/te63hdabmfe4xptwcapo6jekha

24 November 2022

mapped directly with Wikidata item

PMC publication ID

3250679

1 reference

9 August 2017

1 reference