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.

Thermodynamic relations for DNA phase transitions

“…In fact only other system that shows similar thermodynamic relations is a superconductor with the Meissner phase not allowing the external magnetic field to penetrate [50]. In that analogy, a parallel scenario for DNA would be the case where the force penetrates for an intermediate range of force, leading to a continuous transition [49].…”

“…4, with the known exact solutions in certain class of models. Although all theoretical studies based on simple coarse-grained models predict a first-order unzipping transition, there is a proposal that local penetration of forces may lead to a continuous transition [49]. Thermodynamics does not rule out any continuous unzipping transition, but, instead, allows a different phase with partial penetration of force.…”

Hysteresis and nonequilibrium work theorem for DNA unzipping

“…Some aspects of interfaces in DNA have been discussed in Ref. [6]. Near the phase boundary there is a region of metastability where the system can stay in its previous phase * rkapri@iisermohali.ac.in even after crossing the phase boundary.…”

Elasticity of a DNA chain dotted with bubbles under force

“…We estimate the Helmholtz free energy F = −β −1 ln Z where Z is the partition function estimate directly from the PERM simulations and plot the Gibbs free energies for the two cases in Fig. 9 the hypothesis of the impenetrability of force, thermodynamics does not rule out the possibility of an unzipping continuous transition in case there are sources, that allow for the force to penetrate [64,65].…”