(Q41772110)

9 October 2017

Nearest-neighbor non-additivity versus long-range non-additivity in TATA-box structure and its implications for TBP-binding mechanism (English)

1 reference

nearest neighbour algorithm

9 October 2017

1 reference

Tali E Haran

3

0 references

author name string

Hana Faiger

series ordinal

1

1 reference

PMC publication ID

1935006

9 October 2017

Marina Ivanchenko

series ordinal

2

1 reference

9 October 2017

18 June 2007

1 reference

9 October 2017

Nucleic Acids Research

1 reference

9 October 2017

35

1 reference

9 October 2017

13

1 reference

9 October 2017

4409-4419

1 reference

A systems approach to measuring the binding energy landscapes of transcription factors

9 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Analysis of sequence specificities of DNA-binding proteins with protein binding microarrays

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

DNA microarray technologies for measuring protein-DNA interactions

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Application of a Theory of Enzyme Specificity to Protein Synthesis

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

TBP flanking sequences: asymmetry of binding, long-range effects and consensus sequences

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Quantitative modeling of DNA-protein interactions: effects of amino acid substitutions on binding specificity of the Mnt repressor

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

The Eukaryotic Promoter Database EPD: the impact of in silico primer extension

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

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

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Nucleotides of transcription factor binding sites exert interdependent effects on the binding affinities of transcription factors

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Comparison of TATA-binding protein recognition of a variant and consensus DNA promoters

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Signals for TBP/TATA box recognition

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

DNA binding sites: representation and discovery

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Sequence-dependent DNA structure: tetranucleotide conformational maps

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

TATA element recognition by the TATA box-binding protein has been conserved throughout evolution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

The eukaryotic promoter database (EPD).

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Crystal structure of the nucleosome core particle at 2.8 A resolution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Dynamic interplay of TFIIA, TBP and TATA DNA.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Repressor assembly at trp binding sites is dependent on the identity of the intervening dinucleotide between the binding half sites.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

How proteins recognize the TATA box

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Crystal structure of a human TATA box-binding protein/TATA element complex

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Co-crystal structure of TBP recognizing the minor groove of a TATA element

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Crystal structure of a yeast TBP/TATA-box complex

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

"...the tyranny of the lattice...".

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

1.9 A resolution refined structure of TBP recognizing the minor groove of TATAAAAG

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Fitting a mixture model by expectation maximization to discover motifs in biopolymers

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

The flexibility of alternating dA-dT sequences

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters.

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Selection of DNA binding sites by regulatory proteins. II. The binding specificity of cyclic AMP receptor protein to recognition sites

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Structural basis for DNA bending

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Defining the structure of irregular nucleic acids: conventions and principles

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Weight matrix descriptions of four eukaryotic RNA polymerase II promoter elements derived from 502 unrelated promoter sequences

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

6 June 2018

Intrinsically bent DNA.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Kinetic analysis of yeast TFIID-TATA box complex formation suggests a multi-step pathway

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Alternative structures for alternating poly(dA-dT) tracts: the structure of the B-DNA decamer C-G-A-T-A-T-A-T-C-G

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Helical repeat of DNA in solution

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Non-additivity in protein-DNA binding

6 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

Affinity, stability and polarity of binding of the TATA binding protein governed by flexure at the TATA Box.

18 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1935006

DNA bending is an important component of site-specific recognition by the TATA binding protein

18 August 2018

1 reference

12 December 2020

A-Tract Polarity Dominate the Curvature in Flanking Sequences†

1 reference

12 December 2020

Contributions of the TATA box sequence to rate-limiting steps in transcription initiation by RNA polymerase II

1 reference

12 December 2020

DNA bends in TATA-binding protein-TATA complexes in solution are DNA sequence-dependent

1 reference

12 December 2020

Marked stepwise differences within a common kinetic mechanism characterize TATA-binding protein interactions with two consensus promoters

1 reference

12 December 2020

Sequence-dependent DNA structure: dinucleotide conformational maps

1 reference

12 December 2020

DNA sequence-dependent differences in TATA-binding protein-induced DNA bending in solution are highly sensitive to osmolytes

1 reference

12 December 2020

Cooperativity in A-tract structure and the bending properties of composite TnAn blocks

1 reference

12 December 2020

Evidence for functional binding and stable sliding of the TATA binding protein on nonspecific DNA

1 reference

12 December 2020

DNA bending by Fos and Jun: the flexible hinge model

1 reference

12 December 2020

Intermediate species possessing bent DNA are present along the pathway to formation of a final TBP-TATA complex

1 reference

12 December 2020

Direct versus indirect readout in the interaction of the trp repressor with non-canonical binding sites

1 reference

12 December 2020

Sequence Elements Responsible for DNA Curvature

1 reference

12 December 2020

Sequence-directed curvature of DNA

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKM451

1 reference

9 October 2017

1 reference

PMC publication ID

1935006

9 October 2017

PubMed publication ID

17576671

1 reference

PMC publication ID

1935006