Minor groove deformability of DNA: a molecular dynamics free energy simulation study (Q35023850)

5 August 2017

title

Minor groove deformability of DNA: a molecular dynamics free energy simulation study (English)

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5 August 2017

1

Martin Zacharias

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5 August 2017

language of work or name

English

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publication date

12 May 2006

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5 August 2017

number of pages

10

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inferred from page(s)

published in

Biophysical Journal

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5 August 2017

volume

91

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5 August 2017

issue

3

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5 August 2017

page(s)

882-891

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Base-stacking and base-pairing contributions into thermal stability of the DNA double helix

5 August 2017

cites work

1 reference

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

8 July 2018

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Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. II: sequence context effects on the dynamical structures of the 10 unique dinucleotide steps

8 July 2018

1 reference

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DNA adducts of the enantiomers of the Pt(II) complexes of the ahaz ligand (ahaz=3-aminohexahydroazepine) and recognition of these adducts by HMG domain proteins.

8 July 2018

1 reference

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Macromolecular recognition

8 July 2018

1 reference

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Structure of a repair enzyme interrogating undamaged DNA elucidates recognition of damaged DNA.

8 July 2018

1 reference

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Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps

8 July 2018

1 reference

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Nucleosomes facilitate their own invasion

8 July 2018

1 reference

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Simulation and modeling of nucleic acid structure, dynamics and interactions

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Recognition of the DNA minor groove by pyrrole-imidazole polyamides

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

The role of intercalating residues in chromosomal high-mobility-group protein DNA binding, bending and specificity

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

The structure of DNA in the nucleosome core

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Controlling the double helix

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

The S. cerevisiae architectural HMGB protein NHP6A complexed with DNA: DNA and protein conformational changes upon binding

8 July 2018

1 reference

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Critical effect of the N2 amino group on structure, dynamics, and elasticity of DNA polypurine tracts

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Structural basis for SRY-dependent 46-X,Y sex reversal: modulation of DNA bending by a naturally occurring point mutation

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Crystal structures of mismatch repair protein MutS and its complex with a substrate DNA

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

HMG-domain protein recognition of cisplatin 1,2-intrastrand d(GpG) cross-links in purine-rich sequence contexts

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Enhanced binding of the TATA-binding protein to TATA boxes containing flanking cisplatin 1,2-cross-links

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Signals for TBP/TATA box recognition

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Sequence-dependent DNA structure: tetranucleotide conformational maps

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

The structure of a chromosomal high mobility group protein-DNA complex reveals sequence-neutral mechanisms important for non-sequence-specific DNA recognition

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Basis for recognition of cisplatin-modified DNA by high-mobility-group proteins

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Sequence-dependent dynamics of TATA-Box binding sites

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Minor groove-binding architectural proteins: structure, function, and DNA recognition.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Modifying the helical structure of DNA by design: recruitment of an architecture-specific protein to an enforced DNA bend.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

DNA sequence context and protein composition modulate HMG-domain protein recognition of cisplatin-modified DNA.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Local DNA stretching mimics the distortion caused by the TATA box-binding protein

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Towards an understanding of protein-DNA recognition

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Modelling extreme stretching of DNA.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Overstretching B-DNA: the elastic response of individual double-stranded and single-stranded DNA molecules

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Crystal structure of a yeast TBP/TATA-box complex

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Crystal structure of LacI member, PurR, bound to DNA: minor groove binding by alpha helices

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Structural basis for DNA bending by the architectural transcription factor LEF-1

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Defining the structure of irregular nucleic acids: conventions and principles

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

The definition of generalized helicoidal parameters and of axis curvature for irregular nucleic acids

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Sequence-directed curvature of DNA.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

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

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

High-resolution structure of an extended A-tract: [d(CGCAAATTTGCG)]2.

8 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

DNA deformability at the base pair level.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

DNA deformation energetics and protein binding

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

DNA: an extensible molecule.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

The assessment of the geometry of dinucleotide steps in double-helical DNA; a new local calculation scheme.

25 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=1563752

Intercalating residues determine the mode of HMG1 domains A and B binding to cisplatin-modified DNA

25 October 2018

1 reference

12 December 2020

Looking into the grooves of DNA

1 reference

12 December 2020

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

1 reference

12 December 2020

Conformational properties of the TATA-box binding sequence of DNA

1 reference

12 December 2020

Binding of tsHMG, a mouse testis-specific HMG-domain protein, to cisplatin-DNA adducts

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

Modeling DNA deformations induced by minor groove binding proteins

1 reference

12 December 2020

DNA stretching and compression: large-scale simulations of double helical structures

1 reference

12 December 2020

Accurate Interaction Energies of Hydrogen-Bonded Nucleic Acid Base Pairs

1 reference

12 December 2020

10.1529/BIOPHYSJ.106.083816

Identifiers

DOI

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5 August 2017

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5 August 2017

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