Premium
Continuous‐time random walk models of DNA electrophoresis in a post array: Part I. Evaluation of existing models
Author(s) -
Olson Daniel W.,
Ou Jia,
Tian Mingwei,
Dorfman Kevin D.
Publication year - 2011
Publication title -
electrophoresis
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.666
H-Index - 158
eISSN - 1522-2683
pISSN - 0173-0835
DOI - 10.1002/elps.201000466
Subject(s) - random walk , continuous time random walk , statistical physics , brownian motion , series (stratigraphy) , exponential function , stochastic process , algorithm , physics , computer science , mathematics , statistics , quantum mechanics , paleontology , mathematical analysis , biology
Several continuous‐time random walk (CTRW) models exist to predict the dynamics of DNA in micropost arrays, but none of them quantitatively describes the separation seen in experiments or simulations. In Part I of this series, we examine the assumptions underlying these models by observing single molecules of λ DNA during electrophoresis in a regular, hexagonal array of oxidized silicon posts. Our analysis takes advantage of a combination of single‐molecule videomicroscopy and previous Brownian dynamics simulations. Using a custom‐tracking program, we automatically identify DNA‐post collisions and thus study a large ensemble of events. Our results show that the hold‐up time and the distance between collisions for consecutive collisions are uncorrelated. The distance between collisions is a random variable, but it can be smaller than the minimum value predicted by existing models of DNA transport in post arrays. The current CTRW models correctly predict the exponential decay in the probability density of the collision hold‐up times, but they fail to account for the influence of finite‐sized posts on short hold‐up times. The shortcomings of the existing models identified here motivate the development of a new CTRW approach, which is presented in Part II of this series.