Probing allostery through DNA (Q36652321)

15 August 2017

Probing allostery through DNA (English)

1 reference

15 August 2017

Sangjin Kim

1

1 reference

15 August 2017

Erik Broströmer

2

1 reference

15 August 2017

Dong Xing

3

1 reference

15 August 2017

Jianshi Jin

4

1 reference

15 August 2017

Shasha Chong

5

1 reference

15 August 2017

Hao Ge

6

1 reference

15 August 2017

Siyuan Wang

7

1 reference

15 August 2017

Chan Gu

8

1 reference

15 August 2017

Lijiang Yang

9

1 reference

15 August 2017

Yi Qin Gao

10

1 reference

15 August 2017

Xiao-dong Su

11

1 reference

15 August 2017

Yujie Sun

12

1 reference

15 August 2017

X Sunney Xie

13

1 reference

15 August 2017

language of work or name

English

0 references

publication date

1 February 2013

1 reference

15 August 2017

1 reference

15 August 2017

339

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15 August 2017

6121

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15 August 2017

816-819

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Operator sequence alters gene expression independently of transcription factor occupancy in bacteria

15 August 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Inferring gene regulatory logic from high-throughput measurements of thousands of systematically designed promoters

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Chromatin accessibility pre-determines glucocorticoid receptor binding patterns.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Crystal structures of nucleosome core particles containing the '601' strong positioning sequence

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Origins of specificity in protein-DNA recognition.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Bacterial nucleoid-associated proteins, nucleoid structure and gene expression

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Specificity and affinity of Lac repressor for the auxiliary operators O2 and O3 are explained by the structures of their protein-DNA complexes

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

DNA Binding Site Sequence Directs Glucocorticoid Receptor Structure and Activity

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

The structure of a transcribing T7 RNA polymerase in transition from initiation to elongation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

A high-resolution atlas of nucleosome occupancy in yeast

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Single-molecule and ensemble fluorescence assays for a functionally important conformational change in T7 DNA polymerase

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

An Atomic Model of the Interferon-β Enhanceosome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Structural analysis of lac repressor bound to allosteric effectors

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Probing transcription factor dynamics at the single-molecule level in a living cell

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Refinement of the AMBER force field for nucleic acids: improving the description of alpha/gamma conformers

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Isolation of the lac repressor

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

A base-excision DNA-repair protein finds intrahelical lesion bases by fast sliding in contact with DNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Mechanochemical analysis of DNA gyrase using rotor bead tracking

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Very fast empirical prediction and rationalization of protein pKa values

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Coot: model-building tools for molecular graphics

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

ON THE NATURE OF ALLOSTERIC TRANSITIONS: A PLAUSIBLE MODEL

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Structural transitions and elasticity from torque measurements on DNA.

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Type II restriction endonucleases

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Structural basis for the transition from initiation to elongation transcription in T7 RNA polymerase

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Plasticity in protein-DNA recognition: lac repressor interacts with its natural operator 01 through alternative conformations of its DNA-binding domain

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Salt dependence of the elasticity and overstretching transition of single DNA molecules

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Electrostatics of nanosystems: application to microtubules and the ribosome

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

A highly efficient Escherichia coli-based chromosome engineering system adapted for recombinogenic targeting and subcloning of BAC DNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Operator DNA sequence variation enhances high affinity binding by hinge helix mutants of lactose repressor protein

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Crystallographic snapshots along a protein-induced DNA-bending pathway

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Closing the ring: links between SMC proteins and chromosome partitioning, condensation, and supercoiling

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Structural basis for initiation of transcription from an RNA polymerase-promoter complex

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

DNA-protein cooperative binding through variable-range elastic coupling

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

The role of metals in catalysis by the restriction endonuclease BamHI

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Ionic effects on the elasticity of single DNA molecules

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

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

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Transcriptional activation by protein-induced DNA bending: evidence for a DNA structural transmission model

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

The crystal structure of EcoRV endonuclease and of its complexes with cognate and non-cognate DNA fragments

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Structure of Bam HI endonuclease bound to DNA: partial folding and unfolding on DNA binding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Comparison of Experimental Binding Data and Theoretical Models in Proteins Containing Subunits*

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Ethidium Bromide as a Cooperative Effector of a DNA Structure

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

A DNA sequence of 15 base pairs is sufficient to mediate both glucocorticoid and progesterone induction of gene expression

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

DNA conformation and protein binding

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

The three operators of the lac operon cooperate in repression

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Crystallographic analysis of the interaction of the glucocorticoid receptor with DNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Deletion of lactose repressor carboxyl-terminal domain affects tetramer formation

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Direct mechanical measurements of the elasticity of single DNA molecules by using magnetic beads

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Transmission of allosteric effects in DNA

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Probing cellular protein complexes using single-molecule pull-down

30 September 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Mechanical properties of high-G.C content DNA with a-type base-stacking

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Targeted chemical wedges reveal the role of allosteric DNA modulation in protein-DNA assembly

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Multiplexed single-molecule assay for enzymatic activity on flow-stretched DNA.

28 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Extended upstream A-T sequence increases T7 promoter strength

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Sequence-specific recognition of DNA in the nucleosome by pyrrole-imidazole polyamides

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

Divalent metal ions at the active sites of the EcoRV and EcoRI restriction endonucleases.

20 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3586787

The missing term in effective pair potentials

20 September 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1229223

Numerical integration of the cartesian equations of motion of a system with constraints: molecular dynamics of n-alkanes

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1229223

Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1229223

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1126%2FSCIENCE.1229223

Equilibrium and stopped-flow kinetic studies of interaction between T7 RNA polymerase and its promoters measured by protein and 2-aminopurine fluorescence changes

21 January 2018

1 reference

12 December 2020

T7 RNA polymerase-induced bending of promoter DNA is coupled to DNA opening

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

New DNA sequence rules for high affinity binding to histone octamer and sequence-directed nucleosome positioning

1 reference

12 December 2020

lac repressor forms stable loops in vitro with supercoiled wild-type lac DNA containing all three natural lac operators

1 reference

12 December 2020

Twist- and tension-mediated elastic coupling between DNA-binding proteins

1 reference

12 December 2020

Rod models of DNA: sequence-dependent anisotropic elastic modelling of local bending phenomena

1 reference

12 December 2020

Evidence for DNA bending at the T7 RNA polymerase promoter

1 reference

12 December 2020

Identifiers

DOI

10.1126/SCIENCE.1229223

1 reference

15 August 2017

1 reference

15 August 2017

1 reference