An intermediate phase in DNA melting

Abstract

We predict a novel temperature-driven phase transition of DNA below the melting transition. The additional, intermediate phase exists for repetitive sequences, when the two strands have different lengths. In this phase, the excess bases of the longer strand are completely absorbed as bulge loops inside the helical region. When the temperature is lowered, the excess bases desorb into overhanging ends, resulting in a contour length change. This continuous transition is in many aspects analogous to Bose Einstein condensation. Weak sequence disorder renders the transition discontinuous.