Role of Helicity in DNA Hairpin Folding Dynamics

Phys Rev Lett. 2018 Sep 28;121(13):138101. doi: 10.1103/PhysRevLett.121.138101.


We study hairpin folding dynamics by means of extensive molecular dynamics simulations, with particular attention paid to the influence of helicity on the folding time. We find that the dynamical exponent α in the anomalous scaling n(t)∼t^{1/α} of the hairpin length n with time changes from 1.6 (≃1+ν, where ν is the Flory exponent) to 1.2 (≃2ν) in three dimensions, when duplex helicity is removed. The relation α=2ν in rotationless hairpin folding is further verified in two dimensions (ν=0.75) and for a ghost chain (ν=0.5). Our findings suggest that the folding dynamics in long helical chains is governed by the duplex dynamics, contrasting the earlier understanding based on the stem-flower picture of unpaired segments. We propose a scaling argument for α=1+ν in helical chains, assuming that duplex relaxation required for orientational positioning of the next pair of bases is the rate-limiting process.

MeSH terms

  • DNA / chemistry*
  • Models, Chemical*
  • Molecular Dynamics Simulation
  • Nucleic Acid Conformation*
  • Thermodynamics


  • DNA