Construction of a genome-scale structural map at single-nucleotide resolution (Q33287631)

25 July 2017

Construction of a genome-scale structural map at single-nucleotide resolution (English)

1 reference

25 July 2017

Thomas D Tullius

3

0 references

author name string

Jason A Greenbaum

series ordinal

1

1 reference

PubMed ID

17568010

25 July 2017

Bo Pang

series ordinal

2

1 reference

25 July 2017

1 June 2007

1 reference

25 July 2017

1 reference

25 July 2017

17

1 reference

25 July 2017

6

1 reference

25 July 2017

947-953

1 reference

Detection of DNA structural motifs in functional genomic elements.

25 July 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

A new generation of JASPAR, the open-access repository for transcription factor binding site profiles

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

TRANSFAC and its module TRANSCompel: transcriptional gene regulation in eukaryotes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

How sequence defines structure: a crystallographic map of DNA structure and conformation.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

The ENCODE (ENCyclopedia Of DNA Elements) Project

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Structural origins of adenine-tract bending

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Matrix2png: a utility for visualizing matrix data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

The UCSC Genome Browser Database

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Transcription initiation in vivo without classical transactivators: DNA kinks flanking the core promoter of the housekeeping yeast adenylate kinase gene, AKY2, position nucleosomes and constitutively activate transcription

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Incorporating residual dipolar couplings into the NMR solution structure determination of nucleic acids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Mildly eccentric 'E-DNA'.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

A new crystal form for the dodecamer C-G-C-G-A-A-T-T-C-G-C-G: symmetry effects on sequence-dependent DNA structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Sequence-dependent DNA structure: tetranucleotide conformational maps

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

21 June 2018

The Protein Data Bank

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

DNA strand breaking by the hydroxyl radical is governed by the accessible surface areas of the hydrogen atoms of the DNA backbone

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Crystal studies of B-DNA: the answers and the questions

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Quantitative analysis of electrophoresis data: novel curve fitting methodology and its application to the determination of a protein-DNA binding constant

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Sequence-dependent structural variation in B-DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

A DNA dodecamer containing an adenine tract crystallizes in a unique lattice and exhibits a new bend

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

The structure of an oligo(dA).oligo(dT) tract and its biological implications

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Principles of sequence-dependent flexure of DNA.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

The influence of exocyclic substituents of purine bases on DNA curvature

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Crystal lattice packing is important in determining the bend of a DNA dodecamer containing an adenine tract

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Synthetic curved DNA sequences can act as transcriptional activators in Escherichia coli

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

The effect of crystal packing on oligonucleotide double helix structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Local variability and base sequence effects in DNA crystal structures.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Analysis of local helix geometry in three B-DNA decamers and eight dodecamers

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

DNA structure from A to Z.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

The nucleic acid database. A comprehensive relational database of three-dimensional structures of nucleic acids

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Using hydroxyl radical to probe DNA structure

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Sequence-dependent DNA structure: a database of octamer structural parameters.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1891353

Structural features of B-DNA dodecamer crystal structures: influence of crystal packing versus base sequence

31 October 2018

1 reference

12 December 2020

Structure of a B-DNA dodecamer. II. Influence of base sequence on helix structure

1 reference

12 December 2020

Mechanics of sequence-dependent stacking of bases in B-DNA

1 reference

12 December 2020

Base sequence and helix structure variation in B and A DNA

1 reference

12 December 2020

Chemical determinants of DNA bending at adenine-thymine tracts

1 reference

12 December 2020

Sequence-dependent helix deformability in the recognition of B-DNA

1 reference

12 December 2020

Intrinsically bent DNA in a eukaryotic transcription factor recognition sequence potentiates transcription activation

1 reference

12 December 2020

The organic crystallizing agent 2-methyl-2,4-pentanediol reduces DNA curvature by means of structural changes in A-tracts

1 reference

12 December 2020

Effect of the crystallizing agent 2-methyl-2,4-pentanediol on the structure of adenine tract DNA in solution

1 reference

12 December 2020

Sequence-dependent DNA structure: dinucleotide conformational maps

1 reference

12 December 2020

Identifiers

DOI

10.1101/GR.6073107

1 reference

25 July 2017

1 reference

25 July 2017

1 reference

PubMed ID

17568010