Structural diversity of supercoiled DNA. (Q22122088)

26 June 2017

Structural diversity of supercoiled DNA. (English)

1 reference

Understanding supercoiling-dependent DNA recognition: a combined experimental and computational approach

26 June 2017

1 reference

Gateway to Research Project ID

Gateway to Research

BB/I019472/1

Erratum: Structural diversity of supercoiled DNA

27 April 2019

corrigendum / erratum

0 references

Thana Sutthibutpong

4

Thana

Sutthibutpong

1 reference

Dimensions

6 February 2023

Anna K Barker

6

Anna K.

Barker

1 reference

Dimensions

6 February 2023

10

Wah Chiu

Wah

Chiu

2 references

26 June 2017

6 February 2023

8

Sarah A Harris

Sarah A.

Harris

2 references

26 June 2017

6 February 2023

7

Steven J Ludtke

Steven J.

Ludtke

2 references

26 June 2017

6 February 2023

author name string

Rossitza N Irobalieva

1

Rossitza N.

Irobalieva

2 references

26 June 2017

6 February 2023

Jonathan M Fogg

2

Jonathan M.

Fogg

2 references

26 June 2017

6 February 2023

Daniel J Catanese

3

Daniel J.

Catanese

2 references

26 June 2017

6 February 2023

Muyuan Chen

5

Muyuan

Chen

2 references

26 June 2017

6 February 2023

Michael F Schmid

9

Michael F.

Schmid

2 references

26 June 2017

6 February 2023

Lynn Zechiedrich

11

Lynn

Zechiedrich

2 references

26 June 2017

6 February 2023

language of work or name

English

0 references

publication date

12 October 2015

1 reference

PubMed ID

26455586

full work available at URL

26 June 2017

http://eprints.whiterose.ac.uk/100232

content deliverer

White Rose Research Online

copyright license

Creative Commons Attribution 4.0 International

object has role

published version

1 reference

White Rose Research Online

15 December 2018

published in

Nature Communications

1 reference

26 June 2017

6

1 reference

26 June 2017

8440

1 reference

Extrachromosomal microDNAs and chromosomal microdeletions in normal tissues

26 June 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Molecular Structure of Nucleic Acids: A Structure for Deoxyribose Nucleic Acid

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Stretched and overwound DNA forms a Pauling-like structure with exposed bases

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

EMAN2: an extensible image processing suite for electron microscopy

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

UCSF Chimera--a visualization system for exploratory research and analysis

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Computer visualization of three-dimensional image data using IMOD

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Cryo-electron microscopy of vitrified specimens

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Dynamic, structural, and regulatory aspects of lambda site-specific recombination

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

GROMACS 4.5: a high-throughput and highly parallel open source molecular simulation toolkit

19 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Automated electron microscope tomography using robust prediction of specimen movements

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Clustering Molecular Dynamics Trajectories: 1. Characterizing the Performance of Different Clustering Algorithms

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Mechanism of transcriptional bursting in bacteria

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Transcription-dependent dynamic supercoiling is a short-range genomic force

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Reference simulations of noncanonical nucleic acids with different χ variants of the AMBER force field: quadruplex DNA, quadruplex RNA and Z-DNA.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Bullied no more: when and how DNA shoves proteins around

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

The importance of being supercoiled: how DNA mechanics regulate dynamic processes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Cooperative kinking at distant sites in mechanically stressed DNA.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Gene repression by minimal lac loops in vivo.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

DNA curvature and flexibility in vitro and in vivo

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

In the absence of writhe, DNA relieves torsional stress with localized, sequence-dependent structural failure to preserve B-form

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Kinking the double helix by bending deformation

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Mapping the phase diagram of the writhe of DNA nanocircles using atomistic molecular dynamics simulations

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

DNA twisting flexibility and the formation of sharply looped protein-DNA complexes

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

WebSIDD: server for predicting stress-induced duplex destabilized (SIDD) sites in superhelical DNA.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Supercoil-induced extrusion of a regulatory DNA hairpin

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Analysis of the structure of dimeric DNA catenanes by electron microscopy

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Growth-phase-dependent synthesis of histones in the archaeon Methanothermus fervidus.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Direct visualization of supercoiled DNA molecules in solution

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Extracellular nucleases of Alteromonas espejiana BAL 31.IV. The single strand-specific deoxyriboendonuclease activity as a probe for regions of altered secondary structure in negatively and positively supercoiled closed circular DNA

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Conformational fluctuations of DNA helix

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Gel mobilities of linking-number topoisomers and their dependence on DNA helical repeat and elasticity.

12 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

The effect of ionic conditions on DNA helical repeat, effective diameter and free energy of supercoiling

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

BAL 31 nuclease as a probe in concentrated salt for the B-Z DNA junction

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Measurement of unrestrained negative supercoiling and topological domain size in living human cells

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Atomistic simulations reveal bubbles, kinks and wrinkles in supercoiled DNA.

27 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Exploring writhe in supercoiled minicircle DNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

The twist, writhe and overall shape of supercoiled DNA change during counterion-induced transition from a loosely to a tightly interwound superhelix. Possible implications for DNA structure in vivo

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Curved helix segments can uniquely orient the topology of supertwisted DNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Structure of plectonemically supercoiled DNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=4608029

Spontaneous sharp bending of double-stranded DNA.

30 May 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS9440

Kinking occurs during molecular dynamics simulations of small DNA minicircles.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS9440

The analysis of stress-induced duplex destabilization in long genomic DNA sequences

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS9440

Comparison of recombination in vitro and in E. coli cells: measure of the effective concentration of DNA in vivo.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS9440

Histone release during transcription: displacement of the two H2A-H2B dimers in the nucleosome is dependent on different levels of transcription-induced positive stress.

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS9440

The functional response of upstream DNA to dynamic supercoiling in vivo

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS9440

A modified TIP3P water potential for simulation with Ewald summation

21 January 2018

1 reference

https://api.crossref.org/works/10.1038%2FNCOMMS9440

Theory and applications of the generalized Born solvation model in macromolecular simulations

21 January 2018

1 reference

12 December 2020

Use of site-specific recombination as a probe of DNA structure and metabolism in vivo

1 reference

12 December 2020

Anomalous electrophoretic mobility of restriction fragments containing the att region

1 reference

12 December 2020

Energetics of the strand separation transition in superhelical DNA

1 reference

12 December 2020

Understanding the rates and molecular mechanism of water-exchange around aqueous ions using molecular simulations

1 reference

12 December 2020

Electron and scanning force microscopy studies of alterations in supercoiled DNA tertiary structure

1 reference

12 December 2020

Supercoiling-induced DNA bending

1 reference

12 December 2020

Identifiers

DOI

10.1038/NCOMMS9440

1 reference

26 June 2017

0 references

0 references

release_cgzo76ve7fekxjty3zakehqhwa

0 references

Fatcat ID

0 references

OpenCitations bibliographic resource ID

308247

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

Consolidated OpenCitations Corpus – April 2017

OpenCitations bibliographic resource ID

1 reference

PubMed ID

26455586