(Q40161732)

8 January 2018

title

Influence of DNA sequence on the structure of minicircles under torsional stress (English)

1 reference

8 January 2018

3

Wah Chiu

1 reference

8 January 2018

Qian Wang

1

1 reference

8 January 2018

Rossitza N Irobalieva

2

1 reference

8 January 2018

Michael F Schmid

4

1 reference

8 January 2018

Jonathan M Fogg

5

1 reference

8 January 2018

Lynn Zechiedrich

6

1 reference

8 January 2018

B Montgomery Pettitt

7

1 reference

8 January 2018

publication date

13 June 2017

1 reference

8 January 2018

published in

Nucleic Acids Research

1 reference

8 January 2018

volume

45

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8 January 2018

issue

13

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8 January 2018

page(s)

7633-7642

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8 January 2018

Creative Commons Attribution-NonCommercial 4.0 International

copyright license

start time

13 June 2017

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

Effects of Replication and Transcription on DNA Structure-Related Genetic Instability

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Effects of Circular DNA Length on Transfection Efficiency by Electroporation into HeLa Cells

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Sequence Affects the Cyclization of DNA Minicircles

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

DNA topology confers sequence specificity to nonspecific architectural proteins

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

DNA supercoiling: a regulatory signal for the λ repressor

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Modeling DNA thermodynamics under torsional stress

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Bullied no more: when and how DNA shoves proteins around

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Cooperative kinking at distant sites in mechanically stressed DNA.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Transfection of shRNA-encoding Minivector DNA of a few hundred base pairs to regulate gene expression in lymphoma cells

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

DNA supercoiling and its role in DNA decatenation and unknotting

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Exploring writhe in supercoiled minicircle DNA.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Flexible fitting of atomic structures into electron microscopy maps using molecular dynamics

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

B-DNA under stress: over- and untwisting of DNA during molecular dynamics simulations

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Decomposition of the linking number of a closed ribbon: A problem from molecular biology

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Genomic transcriptional response to loss of chromosomal supercoiling in Escherichia coli

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Plasmid DNA size does not affect the physicochemical properties of lipoplexes but modulates gene transfer efficiency

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

A unified view of polymer, dumbbell, and oligonucleotide DNA nearest-neighbor thermodynamics

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

VMD: visual molecular dynamics

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Analysis of the structure of dimeric DNA catenanes by electron microscopy

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

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

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

The twisted circular form of polyoma viral DNA

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Replication and supercoiling of simian virus 40 DNA in cell extracts from human cells

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Supercoiling of the DNA template during transcription

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Structure of plectonemically supercoiled DNA.

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Direct visualization of supercoiled DNA molecules in solution

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Superhelical torsion in cellular DNA responds directly to environmental and genetic factors

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

The level of supercoiling affects the regulation of DNA replication in Escherichia coli

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Twist-induced defects of the P-SSP7 genome revealed by modeling the cryo-EM density

15 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Supercoiled Minivector DNA resists shear forces associated with gene therapy delivery

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

State-of-the-art gene-based therapies: the road ahead

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Topoisomerase IV, not gyrase, decatenates products of site-specific recombination in Escherichia coli

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Thermodynamics of writhe in DNA minicircles from molecular dynamics simulations.

17 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Sequence-dependent thermodynamics of a coarse-grained DNA model.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Plasmid DNA size does affect nonviral gene delivery efficiency in stem cells

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

The functional response of upstream DNA to dynamic supercoiling in vivo

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Minicircle DNA vectors devoid of bacterial DNA result in persistent and high-level transgene expression in vivo

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Computation of writhe in modeling of supercoiled DNA.

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Protein folding by restrained energy minimization and molecular dynamics

20 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5737869

Advances in Non-Viral DNA Vectors for Gene Therapy

20 August 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKX516

Molecular dynamics simulations at constant pressure and/or temperature

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKX516

Rapid transcriptome responses of maize (Zea mays) to UV-B in irradiated and shielded tissues

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKX516

Exact method for numerically analyzing a model of local denaturation in superhelically stressed DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FNAR%2FGKX516

Statistical mechanics of a nonlinear model for DNA denaturation

21 January 2018

1 reference

12 December 2020

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

1 reference

12 December 2020

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

1 reference

12 December 2020

Supercoiling induces denaturation bubbles in circular DNA

1 reference

12 December 2020

Torsional tension in the DNA double helix measured with trimethylpsoralen in living E. coli cells: analogous measurements in insect and human cells

1 reference

12 December 2020

Structural, mechanical, and thermodynamic properties of a coarse-grained DNA model

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKX516

1 reference

8 January 2018

PMC publication ID

5737869

1 reference

8 January 2018

PubMed publication ID

28609782

1 reference

8 January 2018