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DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization.
File(s)
Author(s)
Schreck, JS
Ouldridge, TE
Romano, F
Šulc, P
Shaw, LP
Type
Journal Article
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.
Date Issued
2015-06-08
Date Acceptance
2015-05-22
Citation
Nucleic Acids Research, 2015, 43 (13), pp.6181-6190
URI
DOI
ISSN
1362-4962
Publisher
Oxford University Press (OUP)
Start Page
6181
End Page
6190
Journal / Book Title
Nucleic Acids Research
Volume
43
Issue
13
Copyright Statement
© The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.
License URL
Identifier
http://www.ncbi.nlm.nih.gov/pubmed/26056172
Publication Status
Published