Anomalous reaction-diffusion as a model of nonexponential DNA escape kinetics

Chatterjee, Debarati and Cherayil, Binny J (2010) Anomalous reaction-diffusion as a model of nonexponential DNA escape kinetics. In: JOURNAL OF CHEMICAL PHYSICS, 132 (2).

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Abstract

We show that data from recent experiments carried out on the kinetics of DNA escape from alpha-hemolysin nanopores [M. Wiggin, C. Tropini, C. T. Cossa, N. N. Jetha, and A. Marziali, Biophys. J. 95, 5317 (2008)] may be rationalized by a model of chain dynamics based on the anomalous diffusion of a particle moving in a harmonic well in the presence of a delta function sink. The experiments of Wiggin found, among other things, that the occasional occurrence of unusually long escape times in the distribution of chain trapping events led to nonexponential decays in the survival probability, S(t), of the DNA molecules within the nanopore. Wiggin ascribed this nonexponentiality to the existence of a distribution of trapping potentials, which they suggested was theresult of stochastic interactions between the bases of the DNA and the amino acids located on the surface of the nanopore. Based on this idea, they showed that the experimentally determined S(t) could be well fit in both the short and long time regimes by a function of the form (1+t/tau)(-alpha) (the so called Becquerel function). In our model, S(t) is found to be given by a Mittag-Leffler function at short times and by a generalized Mittag-Leffler function at long times. By suitable choice of certain parameter values, these functions are found to fit the experimental S(t) even better than the Becquerel function. Anomalous diffusion of DNA within the trap prior to escape over a barrier of fixed height may therefore provide a second, plausible explanation of the data, and may offer fresh perspectives on similar trapping and escape problems.

Item Type:	Journal Article
Publication:	JOURNAL OF CHEMICAL PHYSICS
Publisher:	American Institute of Physics
Additional Information:	Copyright for this article belongs to American Institute of Physics.
Keywords:	biochemistry; biodiffusion; DNA; molecular biophysics; proteins; reaction-diffusion systems; stochastic processes
Department/Centre:	Division of Chemical Sciences > Inorganic & Physical Chemistry
Date Deposited:	09 Feb 2010 11:31
Last Modified:	19 Sep 2010 05:54
URI:	http://eprints.iisc.ac.in/id/eprint/25516

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