Type II DNA: When the interfacial energy becomes negative

Abstract

An important step in transcription of a DNA base sequence to a protein is the initiation from the exact starting point, called promoter region. We propose a physical mechanism for identification of the promoter region, which relies on a new classification of DNAs into two types, Type I and Type II, like superconductors, depending on the sign of the energy of the interface separating the zipped and the unzipped phases. This is determined by the energies of helical ordering and stretching over two independent length scales. The negative interfacial energy in Type II DNA leads to domains of helically ordered state separated by defect regions, or blobs, enclosed by the interfaces. The defect blobs, pinned by non-coding promoter regions, would be physically distinct from all other types of bubbles. We also show that the order of the melting transition under a force is different for Type I and Type II.