(Q28757627)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18281386%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

title

Formation of the open complex by bacterial RNA polymerase--a quantitative model (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18281386%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

0 references

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18281386%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

author name string

Marko Djordjevic

series ordinal

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18281386%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

language of work or name

English

0 references

publication date

15 February 2008

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18281386%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

number of pages

16

1 reference

inferred from page(s)

published in

Biophysical Journal

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18281386%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

volume

94

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18281386%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

issue

11

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18281386%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

page(s)

4233-4248

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18281386%20AND%20SRC:MED&resulttype=core&format=json

RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions

2 January 2020

cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

A novel method for prokaryotic promoter prediction based on DNA stability

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Mfold web server for nucleic acid folding and hybridization prediction

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

The sigma70 family of sigma factors

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Structural basis of transcription initiation: an RNA polymerase holoenzyme-DNA complex

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Structural basis of transcription initiation: RNA polymerase holoenzyme at 4 A resolution

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Crystal structure of a bacterial RNA polymerase holoenzyme at 2.6 A resolution

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

DNA binding sites: representation and discovery

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

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

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

The complete genome sequence of Escherichia coli K-12

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Analysis of E. coli promoter sequences

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Detecting subtle sequence signals: a Gibbs sampling strategy for multiple alignment

16 March 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Specific recognition of the -10 promoter element by the free RNA polymerase sigma subunit

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

SELEX experiments: new prospects, applications and data analysis in inferring regulatory pathways

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Spontaneous sharp bending of DNA: role of melting bubbles

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Quantitative modeling and data analysis of SELEX experiments

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Solute probes of conformational changes in open complex (RPo) formation by Escherichia coli RNA polymerase at the lambdaPR promoter: evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding in the subse

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Escherichia coli RNA polymerase contacts outside the -10 promoter element are not essential for promoter melting

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Real-time characterization of intermediates in the pathway to open complex formation by Escherichia coli RNA polymerase at the T7A1 promoter

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Stress-induced DNA duplex destabilization (SIDD) in the E. coli genome: SIDD sites are closely associated with promoters

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Promoter unwinding and promoter clearance by RNA polymerase: detection by single-molecule DNA nanomanipulation.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

A biophysical approach to transcription factor binding site discovery

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Gibbs Recursive Sampler: finding transcription factor binding sites

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

RNA polymerase holoenzyme: structure, function and biological implications

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Bacterial RNA polymerases: the wholo story

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Role of the RNA polymerase sigma subunit in transcription initiation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Additivity in protein-DNA interactions: how good an approximation is it?

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Physical constraints and functional characteristics of transcription factor-DNA interaction.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Function of the bacterial TATAAT -10 element as single-stranded DNA during RNA polymerase isomerization

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

RNA polymerase: structural similarities between bacterial RNA polymerase and eukaryotic RNA polymerase II.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

The G+C-rich discriminator region of the tyrT promoter antagonises the formation of stable preinitiation complexes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Protein-nucleic acid interactions during open complex formation investigated by systematic alteration of the protein and DNA binding partners

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Promoter recognition by Escherichia coli RNA polymerase: effects of the UP element on open complex formation and promoter clearance

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

RNA polymerase-promoter interactions: the comings and goings of RNA polymerase

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Specificity, free energy and information content in protein-DNA interactions

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

In vitro comparison of initiation properties of bacteriophage lambda wild-type PR and x3 mutant promoters

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Kinetic measurements of Escherichia coli RNA polymerase association with bacteriophage T7 early promoters

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Rate-limiting steps in RNA chain initiation

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Mechanism and control of transcription initiation in prokaryotes

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Topological unwinding of strong and weak promoters by RNA polymerase. A comparison between the lac wild-type and the UV5 sites of Escherichia coli

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

The 0 degree C closed complexes between Escherichia coli RNA polymerase and two promoters, T7-A3 and lacUV5.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

KMnO4 as a probe for lac promoter DNA melting and mechanism in vivo

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

The transition between transcriptional initiation and elongation in E. coli is highly variable and often rate limiting.

3 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

A consensus adenine at position -11 of the nontemplate strand of bacterial promoter is important for nucleation of promoter melting

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Sequence-dependent base pair opening in DNA double helix

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Minimal machinery of RNA polymerase holoenzyme sufficient for promoter melting

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Sigma70 promoters in Escherichia coli: specific transcription in dense regions of overlapping promoter-like signals.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Bubble Dynamics in Double-Stranded DNA

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Statistical mechanical simulation of polymeric DNA melting with MELTSIM.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Selective binding of Escherichia coli RNA polymerase to topoisomers of minicircles carrying the TAC16 and TAC17 promoters.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

Functional and physical characterization of transcription initiation complexes in the bacteriophage lambda OR region.

27 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2480673

The OR control system of bacteriophage lambda. A physical-chemical model for gene regulation

27 November 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18281386

12 December 2020

inferred from PubMed ID database lookup

Studies of base pair kinetics by NMR measurement of proton exchange

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18281386

12 December 2020

inferred from PubMed ID database lookup

Do sigma factors need help with a meltdown?

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/18281386

12 December 2020

inferred from PubMed ID database lookup

Identifiers

DOI

10.1529/BIOPHYSJ.107.116970

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18281386%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:18281386%20AND%20SRC:MED&resulttype=core&format=json

2 January 2020

PubMed publication ID

18281386

1 reference