title: DNA hairpins destabilize duplexes primarily by promoting melting rather than by inhibiting hybridization.
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.
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK john.schreck@chem.ox.ac.uk.
authors.forename: John S
authors.initials: JS
authors.lastname: Schreck
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK Department of Mathematics, Imperial College, 180 Queen's Gate, London, SW7 2AZ, UK t.ouldridge@imperial.ac.uk.
authors.forename: Thomas E
authors.initials: TE
authors.lastname: Ouldridge
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK.
authors.forename: Flavio
authors.initials: F
authors.lastname: Romano
authors.affiliation: Center for Studies in Physics and Biology, The Rockefeller University, 1230 York Avenue, New York, NY 10065, USA.
authors.forename: Petr
authors.initials: P
authors.lastname: Šulc
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK.
authors.forename: Liam P
authors.initials: LP
authors.lastname: Shaw
authors.affiliation: Rudolf Peierls Centre for Theoretical Physics, University of Oxford, 1 Keble Road, Oxford OX1 3NP, UK.
authors.forename: Ard A
authors.initials: AA
authors.lastname: Louis
authors.affiliation: Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, UK jonathan.doye@chem.ox.ac.uk.
authors.forename: Jonathan P K
authors.initials: JP
authors.lastname: Doye
mesh_terms: D020029:Base Pairing; D004247:DNA / Q000737:chemistry*; D007700:Kinetics; D009690:Nucleic Acid Conformation; D009691:Nucleic Acid Denaturation; D009693:Nucleic Acid Hybridization; D013816:Thermodynamics
chemical_list: D004247:DNA