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Biophys. J. BioFAST: First Published November 11, 2005. doi:10.1529/biophysj.105.072314
© 2005 by the Biophysical Society.

A more recent version of this article appeared on February 1, 2006.
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Justin A Bishop
Steve M Blair
Alexander M Chagovetz
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BIOPHYSICAL THEORY AND MODELING

A competitive kinetic model of nucleic acid surface hybridization in the presence of point mutants

Justin A Bishop 1*, Steve M Blair 1 and Alexander M Chagovetz 1

1 University of Utah

* To whom correspondence should be addressed. E-mail: jabishop{at}ece.utah.edu.

Submitted on August 9, 2005
Revised on September 15, 2005
Accepted on 18 October 2005


  Abstract
Microarray analysis has become increasingly complex due to the growing size of arrays and the inherent cross-binding of targets. In this work we explore the effects of matched and mismatched target species concentrations, temperature, and the time of hybridization on sensing specificity in two component systems. A finite element software is used to simulate the diffusion of DNA through a microfluidic chamber to the sensing surface where hybridization of DNA is modeled using the corresponding kinetic equation. Comparison between a single component system, where only one target is allowed to bind to a specific zone, and a two component system, where more than one target can hybridize in a sensing zone, uncovers significant kinetic disparities during the transitory state; however, at thermodynamic equilibrium a modified Langmuir isotherm governs the bound amount of both species. The results presented suggest that it may be more appropriate to consider collective rather than quasi-independent interaction of targets in multi-component systems.

Key Words: Association kinetics, Dissociation kinetics, Thermodynamic equilibrium




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Copyright © 2005 by the Biophysical Society.