Physics of base-pairing dynamics in DNA

TL;DR

This paper reviews the physical mechanisms and theoretical models describing DNA base-pairing dynamics, emphasizing the coupling with polymer behavior and the influence of supercoiling, with insights relevant to biological and biotechnological processes.

Contribution

It provides a comprehensive review of theoretical developments in DNA base-pairing dynamics, highlighting the role of chain degrees of freedom and various physical mechanisms involved.

Findings

Quantitative insights into DNA denaturation and renaturation processes.

Categorization of mechanisms based on timescales and degrees of freedom.

Emphasis on the role of supercoiling and external forces in DNA dynamics.

Abstract

As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have brought quantitative insights into DNA base-pairing dynamics that we review in this Report, putting emphasis on theoretical developments. We discuss the dynamics at the base-pair scale and its pivotal coupling with the polymer one, with a polymerization index running from a few nucleotides to tens of kilo-bases. This includes opening and closure of short hairpins and oligomers as well as zipping and unwinding of long macromolecules. We review how different physical mechanisms are either used by Nature or utilized in biotechnological processes to separate the two intertwined DNA strands, by insisting on quantitative results. They go from thermally-assisted denaturation bubble nucleation to force- or torque- driven mechanisms. We show that the helical character of the molecule, possibly supercoiled, can play a key role in many denaturation and renaturation processes. We categorize the mechanisms according to the relative timescales associated with base-pairing and chain degrees of freedom such as bending and torsional elastic ones. In some specific situations, these chain degrees of freedom can be integrated out, and the quasi- static approximation is valid. The complex dynamics then reduces to the diffusion in a low-dimensional free-energy landscape. In contrast, some important cases of experimental interest necessarily appeal to far-from-equilibrium statistical mechanics and hydrodynamics.