3D reconstruction and comparison of shapes of DNA minicircles observed by cryo-electron microscopy (Q24674491)

Jason D Kahn

6

0 references

Mathews Jacob

Mathews Jacob

3

0 references

Michael A. Unser

4

Michael Unser

0 references

Andrzej Stasiak

8

Andrzej Stasiak

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author name string

Arnaud Amzallag

1

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Cédric Vaillant

2

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Jan Bednar

5

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John H Maddocks

A-tract clusters may facilitate DNA packaging in bacterial nucleoid

9

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language of work or name

English

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publication date

2006

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published in

Nucleic Acids Research

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volume

34

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page(s)

e125

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issue

18

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cites work

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Curved DNA without A-A: experimental estimation of all 16 DNA wedge angles

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Crystal structure of the nucleosome core particle at 2.8 A resolution

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

How proteins recognize the TATA box

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Crystal structure of a yeast TBP/TATA-box complex

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Crystal structure at 1.7 A of the bovine papillomavirus-1 E2 DNA-binding domain bound to its DNA target

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

VMD: visual molecular dynamics

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Using quaternions to calculate RMSD

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Cryo-electron microscopy of vitrified specimens

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

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

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Sorting points into neighborhoods (SPIN): data analysis and visualization by ordering distance matrices

7 April 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Predicting indirect readout effects in protein-DNA interactions

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

The structure of DNA in the nucleosome core

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

DNA rings with multiple energy minima

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

DNA flexibility studied by covalent closure of short fragments into circles

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Cyclic AMP receptor protein of E. coli: its role in the synthesis of inducible enzymes

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Direct visualization of supercoiled DNA molecules in solution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Cryoelectron microscopy of DNA molecules in solution

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Protein-induced bending and DNA cyclization

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

3-D shape estimation of DNA molecules from stereo cryo-electron micro-graphs using a projection-steerable snake

28 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Determination of DNA persistence length by cryo-electron microscopy. Separation of the static and dynamic contributions to the apparent persistence length of DNA.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

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

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

DNA sequence determinants of CAP-induced bending and protein binding affinity.

30 May 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

The influence of DNA stiffness upon nucleosome formation

19 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Analyzing protein-DNA recognition mechanisms.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

DNA looping and physical constraints on transcription regulation.

28 November 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1635295

Spatial visualization of DNA in solution

28 November 2018

1 reference

12 December 2020

1 reference

12 December 2020

CRP-DNA complexes: inducing the A-like form in the binding sites with an extended central spacer

1 reference

12 December 2020

Pre-bending of a promoter sequence enhances affinity for the TATA-binding factor

1 reference

12 December 2020

Identification and characterization of genomic nucleosome-positioning sequences

1 reference

12 December 2020

Sequence and position-dependence of the equilibrium accessibility of nucleosomal DNA target sites

1 reference

12 December 2020

TATA box DNA deformation with and without the TATA box-binding protein

1 reference

12 December 2020

Identifiers

DOI

10.1093/NAR/GKL675

1 reference

3389508

3389508

1 reference

1 reference

1 reference