The effect of topology on the structure and free energy landscape of DNA kissing complexes

TL;DR

This study uses a coarse-grained DNA model to explore how topology influences the structure and stability of DNA kissing complexes, revealing that linking number affects base pairing and thermodynamic stability.

Contribution

It demonstrates the impact of topological constraints on DNA kissing complexes' structure and stability using a novel coarse-grained modeling approach.

Findings

Higher base pairing with favorable topology

Decreased stability with increasing linking number

Structures involve coaxially stacked helices at junctions

Abstract

We use a recently developed coarse-grained model for DNA to study kissing complexes formed by hybridization of complementary hairpin loops. The binding of the loops is topologically constrained because their linking number must remain constant. By studying systems with linking numbers -1, 0 or 1 we show that the average number of interstrand base pairs is larger when the topology is more favourable for the right-handed wrapping of strands around each other. The thermodynamic stability of the kissing complex also decreases when the linking number changes from -1 to 0 to 1. The structures of the kissing complexes typically involve two intermolecular helices that coaxially stack with the hairpin stems at a parallel four-way junction.