Analysis of in-vivo LacR-mediated gene repression based on the mechanics of DNA looping (Q33268304)

24 July 2017

title

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

1 reference

24 July 2017

Stephen D Levene

4

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Donald Crothers

series ordinal

3

object named as

Donald M Crothers

1 reference

24 July 2017

2

Abbye E McEwen

1 reference

24 July 2017

Yongli Zhang

1

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24 July 2017

language of work or name

English

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publication date

27 December 2006

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24 July 2017

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24 July 2017

volume

1

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24 July 2017

page(s)

e136

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Creative Commons Attribution 4.0 International

24 July 2017

copyright license

start time

27 December 2006

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

cites work

DNA looping by two-site restriction endonucleases: heterogeneous probability distributions for loop size and unbinding force

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Real-time observation of DNA looping dynamics of Type IIE restriction enzymes NaeI and NarI.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Statistical-mechanical theory of DNA looping.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Inferring the in vivo looping properties of DNA.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

A new approach to DNA bending by polyamines and its implication in DNA condensation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

DNA looping in gene regulation: from the assembly of macromolecular complexes to the control of transcriptional noise.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Transcriptional regulation by the numbers: applications

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Transcriptional regulation by the numbers: models.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Predicting indirect readout effects in protein-DNA interactions

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Untangling intracellular DNA topology.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Structural transitions and elasticity from torque measurements on DNA.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

High-throughput approach for detection of DNA bending and flexibility based on cyclization

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Statistical mechanics of sequence-dependent circular DNA and its application for DNA cyclization

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

HMG proteins and DNA flexibility in transcription activation

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

The mechanism of CAP-lac repressor binding cooperativity at the E. coli lactose promoter.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

DNA looping and the helical repeat in vitro and in vivo: effect of HU protein and enhancer location on Hin invertasome assembly

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

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

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Crystal structure of lac repressor core tetramer and its implications for DNA looping

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Energetics of DNA twisting. I. Relation between twist and cyclization probability.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

DNA flexibility studied by covalent closure of short fragments into circles

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Upstream operators enhance repression of the lac promoter

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Probing co-operative DNA-binding in vivo. The lac O1:O3 interaction.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

DNA dynamic flexibility and protein recognition: differential stimulation by bacterial histone-like protein HU.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

The helical repeat of double-stranded DNA varies as a function of catenation and supercoiling

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

Supercoiling of the DNA template during transcription

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

In vivo DNA loops in araCBAD: size limits and helical repeat

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

DNA bending, flexibility, and helical repeat by cyclization kinetics.

28 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1762422

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.

28 July 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

Spontaneous sharp bending of double-stranded DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

Exact theory of kinkable elastic polymers.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

High flexibility of DNA on short length scales probed by atomic force microscopy.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

Bacterial repression loops require enhanced DNA flexibility.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

Making contacts on a nucleic acid polymer

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

Gal repressosome contains an antiparallel DNA loop

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

DNA looping and physical constraints on transcription regulation.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

Probing gene expression in live cells, one protein molecule at a time.

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

In vitro interaction of the Escherichia coli cyclic AMP receptor protein with the lactose repressor

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

The Affinity-Enhancing Roles of Flexible Linkers in Two-Domain DNA-Binding Proteins†

21 January 2018

1 reference

https://api.crossref.org/works/10.1371%2FJOURNAL.PONE.0000136

Use of site-specific recombination as a probe of DNA structure and metabolism in vivo

21 January 2018

1 reference

12 December 2020

DNA ring closure mediated by protein HU

1 reference

12 December 2020

Persistence length and bending dynamics of DNA from electrooptical measurements at high salt concentrations

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

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

Two types of localization of the DNA-binding proteins within the Escherichia coli nucleoid

1 reference

12 December 2020

Localized single-stranded bubble mechanism for cyclization of short double helix DNA

1 reference

12 December 2020

Micromechanical analysis of the binding of DNA-bending proteins HMGB1, NHP6A, and HU reveals their ability to form highly stable DNA-protein complexes

1 reference

12 December 2020

The influence of polyvalency on the binding properties of antibodies

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

Conformation of Lac repressor tetramer in solution, bound and unbound to operator DNA

1 reference

12 December 2020

Statistics of loop formation along double helix DNAs

1 reference

12 December 2020

Multiple DNA-protein interactions governing high-precision DNA transactions

1 reference

12 December 2020

10.1371/JOURNAL.PONE.0000136

Identifiers

DOI

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24 July 2017

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24 July 2017

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