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We study the dynamics of DNA hairpin formation using oxDNA, anucleotide-level coarse-grained model of DNA. In particular, we explore theeffects of the loop stacking interactions and non-native base pairing on thehairpin closing times. We find a non-monotonic variation of the hairpin closingtime with temperature, in agreement with the experimental work of Wallace etal. [Proc. Nat. Acad. Sci. USA 2001, 98, 5584-5589]. The hairpin closingprocess involves the formation of an initial nucleus of one or two bondsbetween the stems followed by a rapid zippering of the stem. At hightemperatures, typically above the hairpin melting temperature, an effectivenegative activation enthalpy is observed because the nucleus has a lowerenthalpy than the open state. By contrast, at low temperatures, the activationenthalpy becomes positive mainly due to the increasing energetic cost ofbending a loop that becomes increasingly highly stacked as the temperaturedecreases. We show that stacking must be very strong to induce thisexperimentally observed behavior, and that the existence of just a few weakstacking points along the loop can substantially suppress it. Non-native basepairs are observed to have only a small effect, slightly accelerating hairpinformation.

The role of loop stacking in the dynamics of DNA hairpin formation