(Q30318361)

6 September 2017

Role of the closing base pair for d(GCA) hairpin stability: free energy analysis and folding simulations (English)

1 reference

6 September 2017

2

Martin Zacharias

1 reference

6 September 2017

Srinivasaraghavan Kannan

series ordinal

1

1 reference

PMC publication ID

3201870

6 September 2017

language of work or name

English

0 references

publication date

30 June 2011

1 reference

6 September 2017

Nucleic Acids Research

1 reference

6 September 2017

39

1 reference

6 September 2017

19

1 reference

6 September 2017

8271-8280

1 reference

Creative Commons Attribution-NonCommercial 3.0 Unported

6 September 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

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

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

Refinement of d(GCGAAGC) hairpin structure using one- and two-bond residual dipolar couplings

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

Structural and thermodynamic studies on mutant RNA motifs that impair the specificity between a viral replicase and its promoter

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

Stable sheared A.C pair in DNA hairpins.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

VMD: visual molecular dynamics

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

Multiple routes to characterize the folding of a small DNA hairpin

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

Portability of the GN(R)A hairpin loop motif between RNA and DNA.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

Contribution of the closing base pair to exceptional stability in RNA tetraloops: roles for molecular mimicry and electrostatic factors.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

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

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

Replica Monte Carlo simulation of spin glasses.

26 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3201870

GNA trinucleotide loop sequences producing extraordinarily stable DNA minihairpins

26 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21724608

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21724608

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKR541

1 reference

6 September 2017

1 reference

PMC publication ID

3201870

6 September 2017

PubMed publication ID

21724608

1 reference

PMC publication ID

3201870