HENRY M. SOBELL

THE PREMELTON AS A (LOW ENERGY) BREATHER SOLITON IN DNA

Conceptually, the lowest energy kink-antikink bound state in DNA structure (termed, the premelton) contains a central hyperflexible beta-DNA core region modulated into B-DNA on either side through kink and antikink boundaries. Kink and antikink correspond to frictionless molecular boundaries and, as such, are able to move in and out in a concerted fashion with minimal energy loss (see animation).

As kink and antikink move together, for example, the energy density in the central beta-DNA core region rises. This energy is used first to enhance (alternate) base pair unstacking, and next, to stretch and to eventually break hydrogen-bonds connecting base-pairs. As kink and antikink move apart, the reverse happens. Energy within this central core region falls, allowing hydrogen bonds to reform, and (alternate) base pairs to partially restack. Isoenergetic breather-motions such as these facilitate the intercalation of drugs and dyes into DNA, and allow tritium exchange to occur at temperatures well below the melting temperature. These motions demonstrate the collective effect, an effect well known in many areas of physics. Small movements of atoms in sugar residues within kink and antikink boundaries combine together to give larger movements of atoms within base pairs in the central beta-DNA core (i.e., 0.025 Angstroms versus 2 to 3 Angstroms). This effect explains how energy is transiently focused within the centers of premeltons to do the work required for DNA breathing.

Premeltons nucleate DNA melting and give rise to other types of DNA phase transitions. To understand this, we next review the structure and properties of beta-DNA.