Modeling DNA deformations

Recent developments have been made in modeling double-helical DNA at four levels of three-dimensional structure: the all-atom level, whereby an oligonucleotide duplex is surrounded by a shroud of solvent molecules; the base-pair level, with explicit backbone atoms; the mesoscopic level, that is, a f...

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Bibliographic Details
Published in:Current Opinion in Structural Biology 2000-06, Vol.10 (3), p.286-297
Main Authors: Olson, Wilma K, Zhurkin, Victor B
Format: Article
Language:English
Subjects:
Animals
Base sequence dependance
Conformational transitions
DNA - chemistry
DNA bending
DNA deformations
DNA folding
DNA solvation
DNA stretching
DNA twisting
Humans
Models, Molecular
Molecular simulation
Nucleic Acid Conformation
Protein–DNA complexes
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Summary:Recent developments have been made in modeling double-helical DNA at four levels of three-dimensional structure: the all-atom level, whereby an oligonucleotide duplex is surrounded by a shroud of solvent molecules; the base-pair level, with explicit backbone atoms; the mesoscopic level, that is, a few hundred base pairs, with the local duplex conformation described by knowledge-based harmonic energy functions; and the scale of several thousand nucleotides, with the duplex described as an ideal elastic rod. Predictions of the sequence-dependent bending and twisting of the double helix, as well as solvent- and force-induced B→A and over-stretching conformational transitions, are compared with experimental data. These subtle conformational changes are critical to the functioning of the double helix, including its packaging in the close confines of the cell, the mutual fit of DNA and protein in nucleoprotein complexes, and the effective recognition of base pairs in recombination and transcription.
ISSN:0959-440X
1879-033X
DOI:10.1016/S0959-440X(00)00086-5