DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization

John S. Schreck, Thomas E. Ouldridge, Flavio Romano, Petr Šulc, Liam P. Shaw, Ard A. Louis, Jonathan P.K. Doye

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

Abstract

The effect of secondary structure on DNA duplex formation is poorly understood. Using oxDNA, a nucleotide level coarse-grained model of DNA, we study how hairpins influence the rate and reaction pathways of DNA hybridzation. We compare to experimental systems studied by Gao et al. (1) and find that 3-base pair hairpins reduce the hybridization rate by a factor of 2, and 4-base pair hairpins by a factor of 10, compared to DNA with limited secondary structure, which is in good agreement with experiments. 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, and significantly lower the free energy barrier for dissociation. These results should assist experimentalists in designing sequences to be used in DNA nanotechnology, by putting limits on the suppression of hybridization reaction rates through the use of hairpins and offering the possibility of deliberately increasing dissociation rates by incorporating hairpins into single strands.

Original languageEnglish (US)
Pages (from-to)6181-6190
Number of pages10
JournalNucleic acids research
Volume43
Issue number13
DOIs
StatePublished - May 22 2015
Externally publishedYes

ASJC Scopus subject areas

  • Genetics

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