Presence of Nonlinear Excitations in DNA Structure and their Relationship to DNA Premelting and to Drug Intercalation

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Abstract
We propose that collectively localized nonlinear excitations (solitons) exist in DNA structure. These arise as a consequence of an intrinsic nonlinear ribose inversion instability that results in a modulated β alternation in sugar puckering along the polymer backbone. In their bound state, soliton-antisoliton pairs contain β premelted core regions capable of undergoing breathing motions that facilitate drug intercalation. We call such bound state structures—β premeltons. The stability of a β premelton is expected to reflect the collective properties of extended DNA regions and to be sensitive to temperature, pH, ionic strength and other thermodynamic factors. Its tendency to localize at specific nucleotide base sequences may serve to initiate site-specific DNA premelting and melting. We suggest that β premeltons provide nucleation centers important for RNA polymerase-promoter recognition. Such nucleation centers could also correspond to nuclease hypersensitive sites.