Simulation of electrophoretic stretching of DNA in a microcontraction using an obstacle array for conformational preconditioning

Recently our group has reported experiments using an obstacle array to precondition the conformations of DNA molecules to facilitate their stretch in a microcontraction. Based upon previous successes simulating electrophoretic stretching in microcontractions without obstacles, we use our simulation...

Full description

Saved in:
Bibliographic Details
Published in:Biomicrofluidics 2009-01, Vol.3 (1), p.12803-12803
Main Authors: Trahan, Daniel W., Doyle, Patrick S.
Format: Article
Language:English
Subjects:
Special Topic: Papers from the 82nd American Chemical Society Colloid and Surface Science Symposium, Raleigh, North Carolina, 2008 (Guest Editors: Dimiter Petsev and Patrick S. Doyle)
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
Description
Summary:Recently our group has reported experiments using an obstacle array to precondition the conformations of DNA molecules to facilitate their stretch in a microcontraction. Based upon previous successes simulating electrophoretic stretching in microcontractions without obstacles, we use our simulation model to study the deformation of DNA chains in a microcontraction preceded by an array of cylindrical obstacles. We compare our data to the experimental results and find good qualitative, and even quantitative, agreement concerning the behavior of the chains in the array; however, the simulations overpredict the mean stretch of the chains as they leave the contraction. We examine the amount of stretch gained between leaving the array and reaching the end of the contraction and speculate that the differences seen are caused by nonlinear electrokinetic effects that become important in the contraction due to a combination of field gradients and high field strengths.
ISSN:1932-1058
1932-1058
DOI:10.1063/1.3055275