Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations (Q43131308)

14 November 2017

Effects of the nucleoid protein HU on the structure, flexibility, and ring-closure properties of DNA deduced from Monte Carlo simulations (English)

1 reference

14 November 2017

Luke Czapla

1

1 reference

PMC publication ID

2679585

14 November 2017

David Swigon

series ordinal

2

1 reference

PMC publication ID

2679585

14 November 2017

Wilma K Olson

series ordinal

3

1 reference

PMC publication ID

2679585

14 November 2017

language of work or name

English

0 references

publication date

19 June 2008

1 reference

Journal of Molecular Biology

14 November 2017

1 reference

14 November 2017

382

1 reference

14 November 2017

2

1 reference

14 November 2017

353-370

1 reference

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

14 November 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Effects of nucleoid proteins on DNA repression loop formation in Escherichia coli

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Multilevel deconstruction of the In vivo behavior of looped DNA-protein complexes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Structure-based analysis of HU-DNA binding

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Moments of the End-to-End Vector of a Chain Molecule, Its Persistence and Distribution

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Modulation of DNA conformations through the formation of alternative high-order HU-DNA complexes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Dual architectural roles of HU: formation of flexible hinges and rigid filaments

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

IHF and HU: flexible architects of bent DNA.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

3DNA: a software package for the analysis, rebuilding and visualization of three-dimensional nucleic acid structures

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Flexible DNA bending in HU-DNA cocrystal structures

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

HU binding to bent DNA: a fluorescence resonance energy transfer and anisotropy study

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Multimerization-cyclization of DNA fragments as a method of conformational analysis

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

DNA bending and twisting properties of integration host factor determined by DNA cyclization

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Growth phase-dependent variation in protein composition of the Escherichia coli nucleoid

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

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

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

The elastic rod model for DNA and its application to the tertiary structure of DNA minicircles in mononucleosomes

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

The complete genome sequence of Escherichia coli K-12

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Scanning force microscopy of DNA deposited onto mica: equilibration versus kinetic trapping studied by statistical polymer chain analysis.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Crystal structure of the lactose operon repressor and its complexes with DNA and inducer

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

The nonspecific DNA-binding and -bending proteins HMG1 and HMG2 promote the assembly of complex nucleoprotein structures

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Quality and position of the three lac operators of E. coli define efficiency of repression.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Theoretical aspects of DNA-protein interactions: co-operative and non-co-operative binding of large ligands to a one-dimensional homogeneous lattice.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Ring closure probabilities for DNA fragments by Monte Carlo simulation.

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Protein-induced bending and DNA cyclization

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Anisotropic flexibility of DNA and the nucleosomal structure

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Bacterial protein HU dictates the morphology of DNA condensates produced by crowding agents and polyamines

25 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Bacterial repression loops require enhanced DNA flexibility.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Spontaneous sharp bending of double-stranded DNA.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

In vivo thermodynamic analysis of repression with and without looping in lac constructs. Estimates of free and local lac repressor concentrations and of physical properties of a region of supercoiled plasmid DNA in vivo.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Influence of fluctuations on DNA curvature. A comparison of flexible and static wedge models of intrinsically bent DNA.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Configurational statistics of the DNA duplex: extended generator matrices to treat the rotations and translations of adjacent residues.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme.

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Physical properties of DNA in vivo as probed by the length dependence of the lac operator looping process

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Polymer chain statistics and conformational analysis of DNA molecules with bends or sections of different flexibility

15 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2679585

Supercoiling-dependent site-specific binding of HU to naked Mu DNA

1 December 2018

1 reference

12 December 2020

Effects of DNA-distorting proteins on DNA elastic response

1 reference

12 December 2020

Structural perturbations induced in linear and circular DNA by the architectural protein HU from Bacillus stearothermophilus

1 reference

12 December 2020

Sequence-Dependent Effects in the Cyclization of Short DNA.

1 reference

12 December 2020

DNA ring closure mediated by protein HU

1 reference

12 December 2020

Base sequence effects in double-helical DNA. II. Configurational statistics of rodlike chains

1 reference

12 December 2020

Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor

1 reference

12 December 2020

Repression of lac promoter as a function of distance, phase and quality of an auxiliary lac operator

1 reference

12 December 2020

Dimeric lac repressors exhibit phase-dependent co-operativity

1 reference

12 December 2020

10.1016/J.JMB.2008.05.088

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DOI

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30 July 2022

release_g6oy3p7i4vb3jdpptev6mnq62u

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Fatcat

https://api.fatcat.wiki/v0/release/g6oy3p7i4vb3jdpptev6mnq62u

30 July 2022

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30 July 2022

https://api.fatcat.wiki/v0/release/g6oy3p7i4vb3jdpptev6mnq62u

PubMed publication ID

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30 July 2022