Helical chirality: a link between local interactions and global topology in DNA (Q33670305)

28 July 2017

title

Helical chirality: a link between local interactions and global topology in DNA (English)

1 reference

28 July 2017

1 reference

Youri Timsit

1 reference

28 July 2017

Péter Várnai

series ordinal

1 reference

28 July 2017

language of work or name

English

0 references

publication date

19 February 2010

1 reference

28 July 2017

1 reference

28 July 2017

1 reference

28 July 2017

1 reference

28 July 2017

page(s)

e9326

1 reference

Creative Commons Attribution 4.0 International

28 July 2017

start time

19 February 2010

1 reference

April 2022 Public Data File from Crossref

copyrighted

0 references

cites work

Differential stability of DNA crossovers in solution mediated by divalent cations

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Mechanisms of chiral discrimination by topoisomerase IV

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Phylogenomics of DNA topoisomerases: their origin and putative roles in the emergence of modern organisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

How do type II topoisomerases use ATP hydrolysis to simplify DNA topology beyond equilibrium? Investigating the relaxation reaction of nonsupercoiling type II topoisomerases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Structural basis for gate-DNA recognition and bending by type IIA topoisomerases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

An all-atom model of the chromatin fiber containing linker histones reveals a versatile structure tuned by the nucleosomal repeat length

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Holoenzyme assembly and ATP-mediated conformational dynamics of topoisomerase VI

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Widespread distribution of archaeal reverse gyrase in thermophilic bacteria suggests a complex history of vertical inheritance and lateral gene transfers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

A common topology for bacterial and eukaryotic transcription initiation?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Electrostatic free energy landscapes for nucleic acid helix assembly

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Unexpected twist: harnessing the energy in positive supercoils to control telomere 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=2824830

Structure of the '30 nm' chromatin fibre: a key role for the linker histone

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

X-ray structure of a tetranucleosome and its implications for the chromatin fibre

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

The structural basis of DNA flexibility

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Reverse gyrase has heat-protective DNA chaperone activity independent of supercoiling

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

DNA axial rotation and the merge of oppositely supercoiled DNA domains in Escherichia coli: effects of DNA bends

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Information content and complexity in the high-order organization of 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=2824830

Untangling intracellular DNA topology.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Single-molecule study of DNA unlinking by eukaryotic and prokaryotic type-II topoisomerases.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Chirality sensing by Escherichia coli topoisomerase IV and the mechanism of type II topoisomerases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Intersegmental interactions in supercoiled DNA: atomic force microscope 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=2824830

The inherent properties of DNA four-way junctions: comparing the crystal structures of 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=2824830

Dimensions of plectonemically supercoiled 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=2824830

Cellular roles of dna topoisomerases: a molecular perspective

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Topological challenges to DNA replication: conformations at the fork

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

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=2824830

Preferential relaxation of positively supercoiled DNA by E. coli topoisomerase IV in single-molecule and ensemble measurements.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Plasmid pGS5 from the hyperthermophilic archaeon Archaeoglobus profundus is negatively supercoiled.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

DNA supercoiling and temperature adaptation: A clue to early diversification of life?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Behavior of supercoiled 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=2824830

Both DNA gyrase and reverse gyrase are present in the hyperthermophilic bacterium Thermotoga maritima

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Winding of the DNA helix by divalent metal ions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Simplification of DNA topology below equilibrium values by type II topoisomerases

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Cruciform structures and functions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Chirality of DNA trefoils: implications in intramolecular synapsis of distant DNA segments

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

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=2824830

Effect of supercoiling on the juxtaposition and relative orientation of DNA sites

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

DNA stability at temperatures typical for hyperthermophiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

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=2824830

Comparison of plasmid DNA topology among mesophilic and thermophilic eubacteria and archaebacteria

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

DNA self-fitting: the double helix directs the geometry of its supramolecular assembly

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Conformational and thermodynamic properties of supercoiled 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=2824830

Supercoiling of the DNA template during transcription

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Unusual helical packing in crystals of DNA bearing a mutation hot spot

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

The definition of generalized helicoidal parameters and of axis curvature for irregular 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=2824830

Eukaryotic topoisomerases recognize nucleic acid topology by preferentially interacting with DNA crossovers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Base-pairing shift in the major groove of (CA)n tracts by B-DNA crystal structures

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2824830

Groove-backbone interaction in B-DNA. Implication for DNA condensation and 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=2824830

Trefoil knotting revealed by molecular dynamics simulations of supercoiled 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=2824830

The nucleic acid database. A comprehensive relational database of three-dimensional structures 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=2824830

Sticky DNA: effect of the polypurine.polypyrimidine sequence.

21 June 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

Of topo and Maxwell's dream.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

Multiple modes of Escherichia coli DNA gyrase activity revealed by force and torque

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

Human topoisomerase IIalpha rapidly relaxes positively supercoiled DNA: implications for enzyme action ahead of replication forks

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

The structural basis for substrate specificity in DNA topoisomerase IV.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

Left-handed DNA crossovers. Implications for DNA-DNA recognition and structural alterations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

Inter-DNA attraction mediated by divalent counterions.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

Self-assembly of double-stranded DNA molecules at nanomolar concentrations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

The packing of α-helices: simple coiled-coils

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

Geometry and physics of knots

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

Electrophoretic mobility of DNA knots

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

A kinetic proofreading mechanism for disentanglement of DNA by topoisomerases

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0009326

Asymmetric removal of supercoils suggests how topoisomerase II simplifies DNA topology

21 January 2018

1 reference

12 December 2020

Statistical mechanics of supercoiled DNA

1 reference

12 December 2020

A cruciform structural transition provides a molecular switch for chromosome structure and dynamics

1 reference

12 December 2020

Topological information embodied in local juxtaposition geometry provides a statistical mechanical basis for unknotting by type-2 DNA topoisomerases

1 reference

12 December 2020

A hot story from comparative genomics: reverse gyrase is the only hyperthermophile-specific protein

1 reference

12 December 2020

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

1 reference

12 December 2020

Modeling DNA deformations

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0009326

Identifiers

DOI

1 reference

28 July 2017

0 references

1 reference

28 July 2017

1 reference