Molecular dynamics simulations of the 136 unique tetranucleotide sequences of DNA oligonucleotides. I. Research design and results on d(CpG) steps (Q34188047)

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

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31 December 2019

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

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31 December 2019

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David L Beveridge

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Gabriela Barreiro

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K Suzie Byun

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David A Case

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Surjit B Dixit

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Emmanuel Giudice

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Filip Lankas

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John H Maddocks

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Roman Osman

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Eleanore Seibert

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Heinz Sklenar

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Kelly M Thayer

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Péter Varnai

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Thomas E Cheatham

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31 December 2019

Biophysical Journal

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3799-3813

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31 December 2019

describes a project that uses

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Ion motions in molecular dynamics simulations on DNA.

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DNA Basepair Step Deformability Inferred from Molecular Dynamics Simulations

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Structural origins of adenine-tract bending

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A refined prediction method for gel retardation of DNA oligonucleotides from dinucleotide step parameters: reconciliation of DNA bending models with crystal structure data

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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

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Effect of artificial periodicity in simulations of biomolecules under Ewald boundary conditions: a continuum electrostatics study

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Sequence-dependent DNA structure: dinucleotide conformational maps

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1 reference

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

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Structure of a B-DNA dodecamer. III. Geometry of hydration

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The unusual conformation adopted by the adenine tracts in kinetoplast DNA

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10.1529/BIOPHYSJ.104.045252

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