Nature of the open state in long polynucleotide double helices: possibility of soliton excitations.

Abstract

The existence of transiently open states in DNA and synthetic polynucleotide double helices as been demonstrated by hydrogen exchange measurements; base pairs reversibly separate and reclose, exposing nucleotide protons to exchange with solvent protons. Recently it has been possible to define the equilibrium kinetic, and activation parameters of the major open state tdat determines base pair hydrogen exchange. However, there is no direct information at the moment about the conformation of the open form. Here we consider the possibility that the low energy and slow opening and closing rates observed reflect a deformation involving several adjacent base pairs. Assuming a mobile open unit capable of diffusing along the double helix, we find that available data are consistent with structures of 10 or so adjacent open pairs. It is further suggested that these structures correspond to thermally induced so on excitations of the double helix, which retain coherence by sharing the energy of a twist deformation among several base tairs. Solitons

On the DNA Kink Motion Under the Action of Constant Torque

“…Для математического описания вращательной динамики ДНК часто используют простую модель Инглэндера [9], основанную на уравнении синус-Гордона:…”

“…которые Инглэндер [9] и многие другие авторы [10][11][12][13][14][15][16][17][18][19] интерпретируют как открытые состояния ДНК. Такие открытые состояния представляют собой небольшие (около 10 и более пар оснований) области в двойной цепи ДНК, внутри которых водородные связи между комплементарными основаниями разорваны.…”

Composite model for DNA torsion dynamics

“…in [17,61], whose estimate is based on the evaluation of the free energy of superhelical winding; this fixes the range for the total torsional energy to be…”

“…The possibility that nonlinear excitations -in particular, kink solitons or breathers -in DNA chains play a functional role has attracted the attention of biophysicists as well as nonlinear scientists since the pioneering paper of Englander et al [17], and the works by Davydov on solitons in biological systems [14].…”

“…The latter is a "bubble" of about 20 bases, to which RNA Polymerase (RNAP) binds in order to read the base sequence and produce the RNA Messenger; the RNAP travels along the DNA double chain, and so does the unwound region. The proposal of Englander et al [17] was that if the nonlinear excitations are not created or forced by the RNAP but are anyway present due to the nonlinear dynamics of the DNA double helix itself, a number of questions -in particular, concerning energy flows -receive a simple explanation.…”