Anomalous dynamics of DNA hairpin folding

Abstract

By means of computer simulations of a coarse-grained DNA model we show that the DNA hairpin zippering dynamics is anomalous, i.e. the characteristic time T scales non-linearly with N, the hairpin length: T ~ N^a with a>1. This is in sharp contrast with the prediction of the zipper model for which T ~ N. We show that the anomalous dynamics originates from an increase in the friction during zippering due to the tension built in the closing strands. From a simple polymer model we get a = 1+ nu = 1.59 with nu the Flory exponent, a result which is in agreement with the simulations. We discuss transition path times data where such effects should be detected.

arXiv comment5 pages, 6 figures; watch video abstract at http://youtu.be/QLotNZaz76c

References in corpus (12)

• Structural, mechanical and thermodynamic properties of a coarse-grained DNA model
• Slow nucleic acid unzipping kinetics from sequence-defined barriers
• Scaling theory of driven polymer translocation
• Through the Eye of the Needle: Recent Advances in Understanding Biopolymer Translocation
• Splitting probabilities as a test of reaction coordinate choice in single-molecule experiments
• Dragging a polymer in a viscous fluid: steady-state and transient
• Propagation of Tension along a Polymer Chain
• Non-Equilibrium Dynamics of Single polymer Adsorption to Solid Surfaces
• Adsorption Kinetics of a Single Polymer on a Solid Plane
• Thermal and mechanical denaturation properties of a DNA model with three sites per nucleotide
• Unwinding relaxation dynamics of polymers
• Anomalous zipping dynamics and forced polymer translocation

Cited by in corpus (16)

• Kinetics of polymer looping with macromolecular crowding: effects of volume fraction and crowder size
• Physics of base-pairing dynamics in DNA
• The mean shape of transition and first-passage paths
• Transition path time distributions
• Length scale dependent elasticity in DNA from coarse-grained and all-atom models
• The role of loop stacking in the dynamics of DNA hairpin formation
• Overtwisting induces polygonal shapes in bent DNA
• The influence of absorbing boundary conditions on the transition path times statistics
• Non-Markovian dynamics of reaction coordinate in polymer folding
• Unwinding Dynamics of a Helically Wrapped Polymer
• Insights into elastic properties of coarse-grained DNA models: q-stiffness of cgDNA vs. cgDNA+
• Torque-Induced Rotational Dynamics in Polymers: Torsional Blobs and Thinning
• Role of helicity in DNA hairping folding dynamics
• First-passage times in conical varying-width channels biased by a transverse gravitational force: Comparison of analytical and numerical results
• Rotational dynamics of entangled polymers
• Hotter isn't faster for a melting RNA hairpin