(Q33754154)

29 July 2017

Conformational model of the Holliday junction transition deduced from molecular dynamics simulations (English)

1 reference

29 July 2017

1

Jin Yu

1 reference

29 July 2017

3

Klaus Schulten

1 reference

29 July 2017

2

Taekjip Ha

1 reference

PubMed ID

15613597

29 July 2017

language of work or name

English

0 references

publication date

21 December 2004

1 reference

29 July 2017

Nucleic Acids Research

1 reference

29 July 2017

32

1 reference

29 July 2017

22

1 reference

29 July 2017

6683-6695

1 reference

Microscopic Kinetics of DNA Translocation through synthetic nanopores

29 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Sizing DNA using a nanometer-diameter pore

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Definitions and analysis of DNA Holliday junction geometry

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Structural insights by molecular dynamics simulations into specificity of the major human AP endonuclease toward the benzene-derived DNA adduct, pBQ-C.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

The structure of Escherichia coli RusA endonuclease reveals a new Holliday junction DNA binding fold

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Large scale simulation of protein mechanics and function

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

The complex between a four-way DNA junction and T7 endonuclease I.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Escaping free-energy minima

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Metal ions bound at the active site of the junction-resolving enzyme T7 endonuclease I

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

The effect of cytosine methylation on the structure and geometry of the Holliday junction: the structure of d(CCGGTACm5CGG) at 1.5 A resolution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Rapid grid-based construction of the molecular surface and the use of induced surface charge to calculate reaction field energies: applications to the molecular systems and geometric objects

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Brownian-dynamics simulations of metal-ion binding to four-way junctions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

The crystal structures of DNA Holliday junctions.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

The junction-resolving enzymes.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Structures of helical junctions in nucleic acids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Molecular dynamics simulation of nucleic acids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Alternative conformations of a nucleic acid four-way junction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

The Holliday junction in an inverted repeat DNA sequence: sequence effects on the structure of four-way junctions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Crystal structure of a DNA Holliday junction

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Probing the role of structural water in a duplex oligodeoxyribonucleotide containing a water-mimicking base analog

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Structure prediction of a complex between the chromosomal protein HMG-D and DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Binding of the estrogen receptor to DNA. The role of waters

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

VMD: visual molecular dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

The kinetics of spontaneous DNA branch migration

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

The solution structure of the four-way DNA junction at low-salt conditions: a fluorescence resonance energy transfer analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

A Holliday recombination intermediate is twofold symmetric

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Geometry of a branched DNA structure in solution

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

The stereochemistry of a four-way DNA junction: a theoretical study

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Modeling DNA structures: molecular mechanics and molecular dynamics

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

A general model for genetic recombination

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Structural dynamics of individual Holliday junctions.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Increasing temperature accelerates protein unfolding without changing the pathway of unfolding

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Exchange between stacking conformers in a four-Way DNA junction.

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Sequence dependence and direct measurement of crossover isomer distribution in model Holliday junctions using NMR spectroscopy

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=545448

Direct evidence for Holliday junction crossover isomerization

30 October 2018

1 reference

12 December 2020

Molecular dynamics investigation of the interaction between DNA and distamycin

1 reference

12 December 2020

The structure of the Holliday junction, and its resolution

1 reference

12 December 2020

Fluorescence energy transfer shows that the four-way DNA junction is a right-handed cross of antiparallel molecules

1 reference

12 December 2020

Exploring rare conformational species and ionic effects in DNA Holliday junctions using single-molecule spectroscopy

1 reference

12 December 2020

DNA bending induced by cruciform formation

1 reference

12 December 2020

NMR study of the exchange rate between two stacked conformers of a model Holliday junction

1 reference

12 December 2020

Molecular dynamics simulation study of DNA dodecamer d(CGCGAATTCGCG) in solution: conformation and hydration

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKH1006

1 reference

29 July 2017

1 reference

29 July 2017

1 reference

PubMed ID

15613597