DNA hairpins primarily promote duplex melting rather than inhibiting hybridization

Abstract

The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good agreement with experiment. By contrast, melting rates are accelerated by factors of ~100 and ~2000. This surprisingly large speed-up occurs because hairpins form during the melting process, stabilizing partially melted states, and facilitating dissociation. These results may help guide the design of DNA devices that use hairpins to modulate hybridization and dissociation pathways and rates.

5 pages + 14 pages of appendices

References in corpus (4)

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• Coarse-graining DNA for simulations of DNA nanotechnology
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• The effect of topology on the structure and free energy landscape of DNA kissing complexes

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• Coarse-grained modelling of DNA-RNA hybrids
• Multi-scale coarse-graining for the study of assembly pathways in DNA-brick self assembly
• Measuring internal forces in single-stranded DNA: Application to a DNA force clamp
• Free-energy landscapes of DNA and its assemblies: Perspectives from coarse-grained modelling