(Q36228471)

12 August 2017

Sequence dependence of transcription factor-mediated DNA looping (English)

1 reference

12 August 2017

Stephanie Johnson

1

1 reference

12 August 2017

Martin Lindén

series ordinal

2

1 reference

12 August 2017

Rob Phillips

series ordinal

3

1 reference

12 August 2017

language of work or name

English

0 references

publication date

19 June 2012

1 reference

12 August 2017

11

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inferred from page(s)

published in

Nucleic Acids Research

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12 August 2017

40

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12 August 2017

16

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12 August 2017

7728-7738

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Creative Commons Attribution-NonCommercial 3.0 Unported

12 August 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

DNA modeling reveals an extended lac repressor conformation in classic in vitro binding assays

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Working the kinks out of nucleosomal DNA

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Sequence dependence of DNA bending rigidity

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

DNA curvature and flexibility in vitro and in vivo

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Tetramer opening in LacI-mediated DNA looping.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

First-principles calculation of DNA looping in tethered particle experiments

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Concentration and length dependence of DNA looping in transcriptional regulation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Flexibility in the inducer binding region is crucial for allostery in the Escherichia coli lactose repressor

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Interconvertible lac repressor-DNA loops revealed by single-molecule experiments

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Biological consequences of tightly bent DNA: the other life of a macromolecular celebrity

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

The architectural role of nucleoid-associated proteins in the organization of bacterial chromatin: a molecular perspective.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Lac repressor hinge flexibility and DNA looping: single molecule kinetics by tethered particle motion

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Volume-Exclusion Effects in Tethered-Particle Experiments: Bead Size Matters

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Single-molecule spectroscopic determination of lac repressor-DNA loop conformation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Structural dynamics of the lac repressor-DNA complex revealed by a multiscale simulation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Cyclization of short DNA fragments and bending fluctuations of the double helix

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Fluorescence resonance energy transfer over approximately 130 basepairs in hyperstable lac repressor-DNA loops

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Looping and interaction between hypersensitive sites in the active beta-globin locus

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Role of DNA sequence in nucleosome stability and dynamics

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Crystal structure of the nucleosome core particle at 2.8 A resolution

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Action at a distance: DNA-looping and initiation of transcription

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

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

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Tethered particle motion method for studying transcript elongation by a single RNA polymerase molecule

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

lac repressor forms loops with linear DNA carrying two suitably spaced lac operators

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Gene regulation by proteins acting nearby and at a distance

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Stable DNA loops in vivo and in vitro: roles in gene regulation at a distance and in biophysical characterization of DNA.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Nucleoprotein structures initiating DNA replication, transcription, and site-specific recombination

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Transcription by single molecules of RNA polymerase observed by light microscopy

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Deletion of lactose repressor carboxyl-terminal domain affects tetramer formation

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Molecular parameters characterizing the interaction of Escherichia coli lac repressor with non-operator DNA and inducer

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Thermodynamic analysis of unfolding and dissociation in lactose repressor protein.

1 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

DNA bending and its relation to nucleosome positioning.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Dissociation of the lactose repressor-operator DNA complex: effects of size and sequence context of operator-containing DNA.

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Bead size effects on protein-mediated DNA looping in tethered-particle motion experiments

29 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Functional impact of polar and acidic substitutions in the lactose repressor hydrophobic monomer.monomer interface with a buried lysine

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Spontaneous sharp bending of double-stranded DNA.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Thermodynamics of the interactions of lac repressor with variants of the symmetric lac operator: effects of converting a consensus site to a non-specific site.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Subunit dissociation affects DNA binding in a dimeric lac repressor produced by C-terminal deletion.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Dependence of DNA helix flexibility on base composition.

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

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

22 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3439888

Influence of sequence and distance between two operators on interaction with the lac repressor

22 September 2018

1 reference

12 December 2020

DNA-binding properties of a lac repressor mutant incapable of forming tetramers

1 reference

12 December 2020

1 reference

12 December 2020

Measurement of lactose repressor-mediated loop formation and breakdown in single DNA molecules

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

New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning

1 reference

12 December 2020

Designed hyperstable Lac repressor.DNA loop topologies suggest alternative loop geometries

1 reference

12 December 2020

Alternative geometries of DNA looping: an analysis using the SfiI endonuclease

1 reference

12 December 2020

Thermodynamic analysis of the lactose repressor-operator DNA interaction

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKS473

1 reference

release_np2emycdbfb6pkcwjmdyk6bboa

12 August 2017

1 reference

1 reference

Fatcat

https://api.fatcat.wiki/v0/release/np2emycdbfb6pkcwjmdyk6bboa

24 November 2022

mapped directly with Wikidata item

1 reference

12 August 2017

1 reference