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

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.

References in corpus (2)

• The role of collective motion in examples of coarsening and self-assembly
• Self-assembly of short DNA duplexes: from a coarse-grained model to experiments through a theoretical link

Cited by in corpus (5)

• Sequence-dependent thermodynamics of a coarse-grained DNA model
• A nucleotide-level coarse-grained model of RNA
• A primer on the oxDNA model of DNA: When to use it, how to simulate it and how to interpret the results
• Characterizing the bending and flexibility induced by bulges in DNA duplexes
• Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling