(Q30990709)

28 June 2017

title

Sequence preference for BI/BII conformations in DNA: MD and crystal structure data analysis (English)

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28 June 2017

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28 June 2017

Manju Bansal

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28 June 2017

publication date

1 August 2005

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Journal of Biomolecular Structure and Dynamics

28 June 2017

published in

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28 June 2017

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28 June 2017

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28 June 2017

page(s)

13-27

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Comprehensive analysis of hydrogen bonds in regulatory protein DNA-complexes: in search of common principles

28 June 2017

cites work

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https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Crystal structure of trp repressor/operator complex at atomic resolution

21 January 2018

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Probing contacts to the DNA backbone in the trp repressor-operator sequence-specific protein-nucleic acid complex using diastereomeric methylphosphonate analogues

21 January 2018

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https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Indirect readout of the trp-repressor-operator complex by B-DNA's backbone conformation transitions

21 January 2018

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Refined 1.8 A crystal structure of the lambda repressor-operator complex

21 January 2018

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31P NMR spectra of oligodeoxyribonucleotide duplex lac operator-repressor headpiece complexes: importance of phosphate ester backbone flexibility in protein-DNA recognition

21 January 2018

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Operator recognition by the phage 434 cI repressor: MD simulations of free and bound 50-bp DNA reveal important differences between the OR1 and OR2 sites

21 January 2018

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Stepwise induced fit in the pico- to nanosecond time scale governs the complexation of the even-skipped transcriptional repressor homeodomain to DNA.

21 January 2018

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https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Probing the indirect readout of the restriction enzyme EcoRV. Mutational analysis of contacts to the DNA backbone

21 January 2018

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Resonance Raman spectroscopy of 4-thiothymidine and oligodeoxynucleotides containing this base both free in solution and bound to the restriction endonuclease EcoRV.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Alpha/gamma transitions in the B-DNA backbone

21 January 2018

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https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Conformational flexibility of DNA: polymorphism and handedness

21 January 2018

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https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Helix geometry, hydration, and G.A mismatch in a B-DNA decamer

21 January 2018

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https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

BI-BII transitions in B-DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Flexibility of the B-DNA backbone: effects of local and neighbouring sequences on pyrimidine-purine steps

21 January 2018

1 reference

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Molecular dynamics simulations of A. T-rich oligomers: sequence-specific binding of Na+ in the minor groove of B-DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

DNA fine structure and dynamics in crystals and in solution: the impact of BI/BII backbone conformations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Conformational Characteristics and Correlations in Crystal Structures of Nucleic Acid Oligonucleotides: Evidence for Sub-states

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Solution structure of a non-palindromic 16 base-pair DNA related to the HIV-1 kappa B site: evidence for BI-BII equilibrium inducing a global dynamic curvature of the duplex

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

NF-kappa B binding mechanism: a nuclear magnetic resonance and modeling study of a GGG --> CTC mutation

21 January 2018

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Polyamine-nucleic acid interactions and the effects on structure in oriented DNA fibers

21 January 2018

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Complex of B-DNA with polyamides freezes DNA backbone flexibility

21 January 2018

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Activation of nuclear factor kappaB by polyamines in breast cancer cells

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Solution structure of the CpG containing d(CTTCGAAG)2 oligonucleotide: NMR data and energy calculations are compatible with a BI/BII equilibrium at CpG.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Impact of CpG methylation on structure, dynamics and solvation of cAMP DNA responsive element

21 January 2018

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https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Structural effects of cytosine methylation on DNA sugar pucker studied by FTIR.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

The role of DNA structure and dynamics in the recognition of bovine papillomavirus E2 protein target sequences

21 January 2018

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Conformations and dynamics of Ets-1 ETS domain-DNA complexes

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

BII nucleotides in the B and C forms of natural-sequence polymeric DNA: A new model for the C form of DNA

21 January 2018

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https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

21 January 2018

Internal motions in DNA

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Effect of distortions in the deoxyribose phosphate backbone conformation of duplex oligodeoxyribonucleotide dodecamers containing GT, GG, GA, AC, and GU base-pair mismatches on 31P NMR spectra

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Structural insights into the effect of hydration and ions on A-tract DNA: a molecular dynamics study

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Molecular structure of the B-DNA dodecamer d(CGCAAATTTGCG)2. An examination of propeller twist and minor-groove water structure at 2.2 A resolution

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Structure of an alternating-B DNA helix and its relationship to A-tract DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Ion motions in molecular dynamics simulations on DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

NMR evidence for mechanical coupling of phosphate B(I)-B(II) transitions with deoxyribose conformational exchange in DNA.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Molecular dynamics simulations of the d(CCAACGTTGG)(2) decamer: influence of the crystal environment.

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

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

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

How NF-κB can be attracted by its cognate DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

Molecular dynamics with coupling to an external bath

21 January 2018

1 reference

https://api.crossref.org/works/10.1080%2F07391102.2005.10507043

10.1080/07391102.2005.10507043

21 January 2018

Identifiers

DOI

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release_5w3gegfwq5f5hpvydurbdygez4

28 June 2017

Fatcat ID

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Fatcat

https://api.fatcat.wiki/v0/release/5w3gegfwq5f5hpvydurbdygez4

mapped directly with Wikidata item

24 November 2022

based on heuristic

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