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. 2005 Dec;31(3-4):323–337. doi: 10.1007/s10867-005-1284-3

Modeling B–A Transformations of the DNA Double Helix

S N Volkov 1,✉
PMCID: PMC3456325  PMID: 23345901

Abstract

An approach to the description of DNA conformational transformations of B–A type is presented. Due to the consideration of joint motions of DNA structural elements the model for DNA transformation is constructed in the two-component form. One component is the degree of freedom of the elastic rod, and another component – the effective coordinate of the conformational transformation. In the model the internal and external components are interrelated, as it is characteristic for DNA B–A rearrangements. It is demonstrated that kinetic energy of the double helix transformations of heterogeneous DNA can be put in homogeneous form. In the frame of the developed approach the possible localized excitations in a static state are found to compare with the experiments on DNA B–A deformability. The comparison shows good qualitative agreement between theory and experiment. The conclusion is made that the found excitations in the DNA structure may be classified as static conformational solitons, and that such localized excitations may play the key role in the mechanisms of DNA intrinsic bending.

Key words: DNA, conformational transformations, localized excitations, deformability

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