DNA nanotweezers studied with a coarse-grained model of DNA

TL;DR

This paper presents a coarse-grained DNA model that accurately captures thermodynamic and structural properties, enabling detailed analysis of DNA nanodevices like DNA tweezers and their free-energy landscapes.

Contribution

The study introduces a novel coarse-grained DNA model that reproduces key thermodynamic and structural features, facilitating the analysis of DNA nanomachines.

Findings

Model accurately reproduces DNA duplex hybridization and hairpin formation.

Successfully calculates free-energy landscape of DNA tweezers.

Captures DNA helical pitch, persistence length, and flexibility.

Abstract

We introduce a coarse-grained rigid nucleotide model of DNA that reproduces the basic thermodynamics of short strands: duplex hybridization, single-stranded stacking and hairpin formation, and also captures the essential structural properties of DNA: the helical pitch, persistence length and torsional stiffness of double-stranded molecules, as well as the comparative flexibility of unstacked single strands. We apply the model to calculate the detailed free-energy landscape of one full cycle of DNA 'tweezers', a simple machine driven by hybridization and strand displacement.