Gel electrophoresis of linear and star-branched DNA

Henry W. Lau and Lynden A. Archer
Phys. Rev. E 84, 061916 – Published 22 December 2011

Abstract

The electrophoretic mobility of double-stranded DNA in polyacrylamide gel is investigated using an activated hopping model for the transport of a charged object within a heterogeneous medium. The model is premised upon a representation of the DNA path through the gel matrix as a series of traps with alternating large and small cross sections. Calculations of the trap dimensions from gel data show that the path imposes varying degrees of confinement upon migrating analytes, which retard their forward motion in a size-dependent manner. An expression derived for DNA mobility is shown to provide accurate predictions for the dynamics of linear DNA (67–622 bp) in gels of multiple concentrations. For star-branched DNA, the incorporation within the model of a length scale previously proposed to account for analyte architecture [Yuan et al., Anal. Chem. 78, 6179 (2006)] leads to mobility predictions that compare well with experimental results for a wide range of DNA shapes and molecular weights.

  • Figure
  • Figure
  • Figure
  • Figure
  • Figure
  • Figure
  • Received 5 May 2011

DOI:https://doi.org/10.1103/PhysRevE.84.061916

©2011 American Physical Society

Authors & Affiliations

Henry W. Lau and Lynden A. Archer*

  • School of Chemical and Biomolecular Engineering, Cornell University, Ithaca, New York 14853, USA

  • *laa25@cornell.edu

Article Text (Subscription Required)

Click to Expand

References (Subscription Required)

Click to Expand
Issue

Vol. 84, Iss. 6 — December 2011

Reuse & Permissions
Access Options
CHORUS

Article Available via CHORUS

Download Accepted Manuscript
Author publication services for translation and copyediting assistance advertisement

Authorization Required


×
×

Images

×

Sign up to receive regular email alerts from Physical Review E

Log In

Cancel
×

Search


Article Lookup

Paste a citation or DOI

Enter a citation
×