Protein/DNA interactions in complex DNA topologies: expect the unexpected (Q28073043)

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

sponsor

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Gateway to Research Project ID

Gateway to Research

27 April 2019

Thana Sutthibutpong

2

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Agnes Noy

object named as

Agnes Noy

series ordinal

1

0 references

Sarah A Harris

series ordinal

3

object named as

Sarah A. Harris

1 reference

language of work or name

1 reference

2016

1 reference

full work available at URL

http://eprints.whiterose.ac.uk/106843

content deliverer

White Rose Research Online

object of statement has role

published version

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White Rose Research Online

http://eprints.whiterose.ac.uk/106843

15 December 2018

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8

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issue

3

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page(s)

233-243

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Creative Commons Attribution 4.0 International

copyright license

start time

8 August 2016

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April 2022 Public Data File from Crossref

copyright status

copyrighted

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cites work

Structural diversity of supercoiled DNA.

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Epigenetic regulatory functions of DNA modifications: 5-methylcytosine and beyond

20 March 2017

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DNA topology and transcription

20 March 2017

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Structural insight into the sequence dependence of nucleosome positioning

20 March 2017

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Spiral structure of Escherichia coli HU provides foundation for DNA supercoiling

20 March 2017

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

20 March 2017

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Single-cell Hi-C reveals cell-to-cell variability in chromosome structure

20 March 2017

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The Polycomb complex PRC2 and its mark in life

7 April 2017

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Spatial partitioning of the regulatory landscape of the X-inactivation centre

7 April 2017

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DNA sequence-dependent deformability deduced from protein-DNA crystal complexes

7 April 2017

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Supercoiling of the DNA template during transcription

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Long-range correlations in the mechanics of small DNA circles under topological stress revealed by multi-scale simulation

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

RNA Polymerase II Regulates Topoisomerase 1 Activity to Favor Efficient Transcription

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Genome scale patterns of supercoiling in a bacterial chromosome.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Transcription-coupled DNA supercoiling dictates the chromosomal arrangement of bacterial genes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

DNA supercoiling, a critical signal regulating the basal expression of the lac operon in Escherichia coli

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Comparison of molecular contours for measuring writhe in atomistic supercoiled DNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

The chromatin fiber: multiscale problems and approaches

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

High-resolution mapping of architectural DNA binding protein facilitation of a DNA repression loop in Escherichia coli

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Topological polymorphism of the two-start chromatin fiber.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Analyzing ion distributions around DNA: sequence-dependence of potassium ion distributions from microsecond molecular dynamics.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Which way up? Recognition of homologous DNA segments in parallel and antiparallel alignments.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

DNA topology confers sequence specificity to nonspecific architectural proteins

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Free-energy calculations for semi-flexible macromolecules: applications to DNA knotting and looping

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

DNA supercoiling: a regulatory signal for the λ repressor

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Simulations of DNA topoisomerase 1B bound to supercoiled DNA reveal changes in the flexibility pattern of the enzyme and a secondary protein-DNA binding site

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Mechanism of transcriptional bursting in bacteria

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

DNA torsion as a feedback mediator of transcription and chromatin dynamics.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Supercoiling in DNA and chromatin.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Pack, unpack, bend, twist, pull, push: the physical side of gene expression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Models that include supercoiling of topological domains reproduce several known features of interphase chromosomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Cohesin and CTCF differentially affect chromatin architecture and gene expression in human cells

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Understanding the connection between epigenetic DNA methylation and nucleosome positioning from computer simulations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

High-resolution mapping of the spatial organization of a bacterial chromosome

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Poly(dA:dT)-rich DNAs are highly flexible in the context of DNA looping

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

DNA supercoiling enhances cooperativity and efficiency of an epigenetic switch

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Nonspecific bridging-induced attraction drives clustering of DNA-binding proteins and genome organization.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Divergent RNA transcription: a role in promoter unwinding?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Helical structure determines different susceptibilities of dsDNA, dsRNA, and tsDNA to counterion-induced condensation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Exploring the three-dimensional organization of genomes: interpreting chromatin interaction data

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Small DNA circles as probes of DNA topology

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Genome architecture: domain organization of interphase chromosomes

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Interplay of protein and DNA structure revealed in simulations of the lac operon

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Transcription forms and remodels supercoiling domains unfolding large-scale chromatin structures

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Complexity of chromatin folding is captured by the strings and binders switch model

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Bullied no more: when and how DNA shoves proteins around

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

DNA information: from digital code to analogue structure

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Dividing a supercoiled DNA molecule into two independent topological domains

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Exploiting bacterial DNA gyrase as a drug target: current state and perspectives.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Enhancer function: new insights into the regulation of tissue-specific gene expression

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Cellular strategies for regulating DNA supercoiling: a single-molecule perspective

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Condensed DNA: condensing the concepts.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

DNA curvature and flexibility in vitro and in vivo

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Differential stability of DNA crossovers in solution mediated by divalent cations

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

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

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

The unique structure of A-tracts and intrinsic DNA bending

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Theoretical analysis of disruptions in DNA minicircles

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Single-molecule manipulation reveals supercoiling-dependent modulation of lac repressor-mediated DNA looping

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

A novel roll-and-slide mechanism of DNA folding in chromatin: implications for nucleosome positioning

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

A common topology for bacterial and eukaryotic transcription initiation?

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Modeling the Lac repressor-operator assembly: the influence of DNA looping on Lac repressor conformation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Structural plasticity of single chromatin fibers revealed by torsional manipulation

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

How sequence defines structure: a crystallographic map of DNA structure and conformation.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Polylysine-coated mica can be used to observe systematic changes in the supercoiled DNA conformation by scanning force microscopy in solution

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Supercoiling and denaturation in Gal repressor/heat unstable nucleoid protein (HU)-mediated DNA looping

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Intersegmental interactions in supercoiled DNA: atomic force microscope study

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

An architectural role of the Escherichia coli chromatin protein FIS in organising DNA.

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

The histone-like protein HU binds specifically to DNA recombination and repair intermediates

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Winding of the DNA helix by divalent metal ions

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Knotting of a DNA chain during ring closure

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

The influence of salt on the structure and energetics of supercoiled DNA

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Spatial genome organization: contrasting views from chromosome conformation capture and fluorescence in situ hybridization

29 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Impact of methylation on the physical properties of DNA.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Electrostatic Origin of Salt-Induced Nucleosome Array Compaction

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

Exploring writhe in supercoiled minicircle DNA.

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

FIS activates sequential steps during transcription initiation at a stable RNA promoter

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

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

2 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5039213

A systematic in vitro study of nucleoprotein complexes formed by bacterial nucleoid-associated proteins revealing novel types of DNA organization.

2 June 2018

1 reference

https://api.crossref.org/works/10.1007%2FS12551-016-0208-8

Thermodynamics of writhe in DNA minicircles from molecular dynamics simulations.

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS12551-016-0208-8

Bacterial chromosome organization and segregation

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS12551-016-0208-8

Dynamics of DNA Supercoils

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS12551-016-0208-8

Single-molecule study of the DNA denaturation phase transition in the force-torsion space

21 January 2018

1 reference

https://api.crossref.org/works/10.1007%2FS12551-016-0208-8

Roles of topoisomerases in maintaining steady-state DNA supercoiling in Escherichia coli

21 January 2018

1 reference

https://pubmed.ncbi.nlm.nih.gov/27738452

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Inter-DNA electrostatics from explicit solvent molecular dynamics simulations

1 reference

https://pubmed.ncbi.nlm.nih.gov/27738452

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

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

1 reference

https://pubmed.ncbi.nlm.nih.gov/27738452

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1007/S12551-016-0208-8

1 reference

10.1007/S12551-016-0208-8

Altmetric DOI

0 references

CORE ID

81183355

0 references

Dimensions Publication ID

1049488338

0 references

1 reference

1 reference

PubMed publication ID

27738452

1 reference