TYPE II DNA: when the interfacial energy becomes negative

TL;DR

This paper introduces a physical classification of DNA into two types based on interfacial energy, revealing a novel mechanism for promoter region identification through domain formation and differing melting transition behaviors.

Contribution

It proposes a new classification of DNA into Type I and Type II based on interfacial energy, linking physical properties to biological promoter recognition.

Findings

Type II DNA has negative interfacial energy leading to domain formation.

Defect blobs are pinned by promoter regions, distinguishing them physically.

Melting transition behavior differs between Type I and Type II DNA.

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.