Folding of a DNA hairpin loop structure in explicit solvent using replica-exchange molecular dynamics simulations (Q36069622)

12 August 2017

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

1 reference

12 August 2017

2

Martin Zacharias

1 reference

12 August 2017

Srinivasaraghavan Kannan

series ordinal

1

1 reference

12 August 2017

language of work or name

English

0 references

publication date

27 July 2007

1 reference

12 August 2017

11

1 reference

inferred from page(s)

published in

Biophysical Journal

1 reference

12 August 2017

93

1 reference

12 August 2017

9

1 reference

12 August 2017

3218-3228

1 reference

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

12 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Does water play a structural role in the folding of small nucleic acids?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Single-Stranded Adenine-Rich DNA and RNA Retain Structural Characteristics of Their Respective Double-Stranded Conformations and Show Directional Differences in Stacking Pattern †

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

MMTSB Tool Set: enhanced sampling and multiscale modeling methods for applications in structural biology.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Insights into nucleic acid conformational dynamics from massively parallel stochastic simulations

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Unusual DNA duplex and hairpin motifs.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Selection for thermodynamically stable DNA tetraloops using temperature gradient gel electrophoresis reveals four motifs: d(cGNNAg), d(cGNABg),d(cCNNGg), and d(gCNNGc).

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Can a continuum solvent model reproduce the free energy landscape of a beta -hairpin folding in water?

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

V(D)J recombination: RAG proteins, repair factors, and regulation

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Conformational analysis of DNA-trinucleotide-hairpin-loop structures using a continuum solvent model

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

The crystal structure of UUCG tetraloop

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Stable sheared A.C pair in DNA hairpins.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Hairpin loops consisting of single adenine residues closed by sheared A.A and G.G pairs formed by the DNA triplets AAA and GAG: solution structure of the d(GTACAAAGTAC) hairpin

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

VMD: visual molecular dynamics

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Most compact hairpin-turn structure exerted by a short DNA fragment, d(GCGAAGC) in solution: an extraordinarily stable structure resistant to nucleases and heat

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Trinucleotide repeats that expand in human disease form hairpin structures in vitro

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Structure of a single-cytidine hairpin loop formed by the DNA triplet GCA

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

The purine-rich trinucleotide repeat sequences d(CAG)15 and d(GAC)15 form hairpins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

A thermodynamic study of unusually stable RNA and DNA hairpins

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Thermodynamic parameters for loop formation in RNA and DNA hairpin tetraloops

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Solution structure of an unusually stable RNA hairpin, 5GGAC(UUCG)GUCC

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Influence of sequence context and length on the structure and stability of triplet repeat DNA oligomers

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Structural and energetic consequences of expanding a highly cooperative stable DNA hairpin loop

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Exploring the protein folding free energy landscape: coupling replica exchange method with P3ME/RESPA algorithm

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Does native state topology determine the RNA folding mechanism?

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

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

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Thermodynamic coupling of the loop and stem in unusually stable DNA hairpins closed by CG base pairs

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Structure of Met-enkephalin in explicit aqueous solution using replica exchange molecular dynamics

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Replica Monte Carlo simulation of spin glasses.

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Specific sequences and a hairpin structure in the template strand are required for N4 virion RNA polymerase promoter recognition

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Stable formation of a pyrimidine-rich loop hairpin in a cruciform promoter

23 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2025651

Flexibility of single-stranded DNA: use of gapped duplex helices to determine the persistence lengths of poly(dT) and poly(dA)

21 October 2018

1 reference

12 December 2020

SUTURE TRANSITIONS OBSERVED IN DNA AND POLY A IN SOLUTION AS A FUNCTION OF TEMPERATURE AND PH

1 reference

12 December 2020

GNA trinucleotide loop sequences producing extraordinarily stable DNA minihairpins

1 reference

12 December 2020

The hairpin structure of a topoisomerase II site DNA strand analyzed by combined NMR and energy minimization methods

1 reference

12 December 2020

E. coli SSB activates N4 virion RNA polymerase promoters by stabilizing a DNA hairpin required for promoter recognition

1 reference

12 December 2020

Triplet repeat instability and DNA topology: an expansion model based on statistical mechanics

1 reference

12 December 2020

Base interactions of nucleotide polymers in aqueous solution

1 reference

12 December 2020

The trinucleotide repeat sequence d(CGG)15 forms a heat-stable hairpin containing Gsyn. Ganti base pairs

1 reference

12 December 2020

Efficient search on energy minima for structure prediction of nucleic acid motifs

1 reference

12 December 2020

10.1529/BIOPHYSJ.107.108019

Identifiers

DOI

1 reference

release_etzz6i2ifneznpbk6h6jwimm7q

12 August 2017

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/etzz6i2ifneznpbk6h6jwimm7q

24 November 2022

mapped directly with Wikidata item

1 reference

12 August 2017

PubMed publication ID

17660316

1 reference