Single DNA conformations and biological function

TL;DR

This review discusses how DNA's physical conformations, such as looping and knotting, influence biological functions like protein binding and transcription, highlighting recent biophysical insights and potential nanosensing applications.

Contribution

It summarizes recent findings on DNA conformations and their biological significance, emphasizing the role of DNA structure in cellular processes and nanotechnology.

Findings

DNA looping affects protein target search efficiency

DNA knots influence biological processes

DNA nanobubbles are important for transcription initiation

Abstract

From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA molecules, and the coupling of these reactions to the physical conformations of DNA. In this review, we summarise recent results on the following phenomena: We investigate the biophysical properties of DNA-looping and the equilibrium configurations of DNA-knots, whose relevance to biological processes are increasingly appreciated. We discuss how random DNA-looping may be related to the efficiency of the target search process of proteins for their specific binding site on the DNA molecule. And we dwell on the spontaneous formation of intermittent DNA nanobubbles and their importance for biological processes, such as transcription initiation. The physical properties of DNA may indeed turn out to be particularly suitable for the use of DNA in nanosensing applications.