Role of helicity in DNA hairping folding dynamics

Abstract

We study hairpin folding dynamics by means of extensive computer simulations, with particular attention paid to the influence of helicity on the folding time $\tau$. We find that the dynamical exponent $\alpha$ of the anomalous scaling $\tau \sim N^{\alpha }$ for a hairpin with length N changes from 1.6 ($1+\nu$) to 1.2 ($2\nu$) in three dimensions, when duplex helicity is removed. The relation $\alpha =2\nu$ in rotationless hairpin folding is further verified in two dimensions ($\nu =0.75$), and for a ghost-chain ($\nu =0.5$). This, to our knowledge, is the first observation of the theoretical lower bound on $\alpha$, which was predicted earlier on the basis of energy conservation for polymer translocation through a pore. 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 $\alpha =1+\nu$ in helical chains, assuming that duplex relaxation required for orientational positioning of the next pair of bases is the rate-limiting process.

arXiv comment4 pages, 5 figures, submitted for publication

References in corpus (13)

• Anomalous Dynamics of Forced Translocation
• Nonequilibrium dynamics of polymer translocation and straightening
• Driven polymer translocation through nanopores: slow versus fast dynamics
• Pore-blockade Times for Field-Driven Polymer Translocation
• Slow nucleic acid unzipping kinetics from sequence-defined barriers
• Poland-Scheraga models and the DNA denaturation transition
• Physics of base-pairing dynamics in DNA
• Scaling theory of driven polymer translocation
• Anomalous dynamics of DNA hairpin folding
• Anomalous zipping dynamics and forced polymer translocation
• Non-Markovian dynamics of reaction coordinate in polymer folding
• Unwinding Dynamics of a Helically Wrapped Polymer
• Unwinding dynamics of double-stranded polymers

Cited by in corpus (4)

• Length scale dependent elasticity in DNA from coarse-grained and all-atom models
• Overtwisting induces polygonal shapes in bent DNA
• Transient helix formation in semiflexible polymers without confinement effects
• Hotter isn't faster for a melting RNA hairpin