Abstract
Dynamical features of solitary excitations in DNA are studied under the assumption that the most relevant modes to lead a locally open state are nonlinear collective modes of base rotations. Some remarks and reconsiderations are given about the expression of the H-bonding potential between complementary bases. Extended Hamiltonian is formulated by introducing the coupling interactions between rotational motions and longitudinal and transverse vibrational motions into a plane base-rotator model. In the continuum limit the double sine-Gordon equations and the soliton solutions which can be attributed to the open state are obtained. The energy and the length of the open configuration theoretically estimated are in same order with the values inferred from H-D exchange measurements. Number of solitons in a DNA with length of 10 5 base pairs is estimated to be about 4 at physiological temperatures.
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