The role of loop stacking in the dynamics of DNA hairpin formation
arXiv:1410.1218 · doi:10.1021/jp510061f
Abstract
We study the dynamics of DNA hairpin formation using oxDNA, a nucleotide-level coarse-grained model of DNA. In particular, we explore the effects of the loop stacking interactions and non-native base pairing on the hairpin closing times. We find a non-monotonic variation of the hairpin closing time with temperature, in agreement with the experimental work of Wallace et al. [Proc. Nat. Acad. Sci. USA 2001, 98, 5584-5589]. The hairpin closing process involves the formation of an initial nucleus of one or two bonds between the stems followed by a rapid zippering of the stem. At high temperatures, typically above the hairpin melting temperature, an effective negative activation enthalpy is observed because the nucleus has a lower enthalpy than the open state. By contrast, at low temperatures, the activation enthalpy becomes positive mainly due to the increasing energetic cost of bending a loop that becomes increasingly highly stacked as the temperature decreases. We show that stacking must be very strong to induce this experimentally observed behavior, and that the existence of just a few weak stacking points along the loop can substantially suppress it. Non-native base pairs are observed to have only a small effect, slightly accelerating hairpin formation.
arXiv comment24 pages, 9 figures
References in corpus (14)
- Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
- Sampling rare switching events in biochemical networks
- Sequence-dependent thermodynamics of a coarse-grained DNA model
- DNA hybridization kinetics: zippering, internal displacement and sequence dependence
- Mechanical unfolding of RNA hairpins
- Coarse-graining DNA for simulations of DNA nanotechnology
- DNA nanotweezers studied with a coarse-grained model of DNA
- Avoiding unphysical kinetic traps in Monte Carlo simulations of strongly attractive particles
- A nucleotide-level coarse-grained model of RNA
- Plectoneme tip bubbles: Coupled denaturation and writhing in supercoiled DNA
- Coarse-grained simulations of DNA overstretching
- DNA hairpins primarily promote duplex melting rather than inhibiting hybridization
- Mesoscopic modeling for nucleic acid chain dynamics
- Anomalous dynamics of DNA hairpin folding
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