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Biophys. J. BioFAST: First Published May 20, 2005. doi:10.1529/biophysj.105.063479
© 2005 by the Biophysical Society.

A more recent version of this article appeared on August 1, 2005.
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BIOPHYSICAL THEORY AND MODELING

Brush Effects on DNA Chips: Thermodynamics, Kinetics and Design Guidlines

Avraham S Halperin 1*, Arnaud Buhot 2 and Ekaterina B. Zhulina 3

1 CNRS
2 CEA
3 Institut of Macromolecular Compounds

* To whom correspondence should be addressed. E-mail: ahalperin{at}cea.fr.

Submitted on March 25, 2005
Revised on April 27, 2005
Accepted on 2 May 2005


  Abstract
In biology experiments, oligonucleotide microarrays are contacted with a solution of long nucleic acid (NA) targets. The hybridized probes thus carry long tails. When the surface density of the oligonucleotide probes is high enough, the progress of hybridization leads to the formation of a polyelectrolyte brush due to mutual crowding of the NA tails. The free energy penalty associated with the brush modifies both the hybridization isotherms and the rate equations: the attainable hybridization is lowered significantly as is the hybridization rate. While the equilibrium hybridization fraction, xeq, is low, the hybridization follows a Langmuir type isotherm, xeq/(1-xeq)= ct K where ct is the target concentration and K is the equilibrium constant smaller than its bulk value by a factor (n/N)2/5 due to wall effects where n and N denote the number of bases in the probe and the target. At higher xeq, when the brush is formed, the leading correction is xeq/(1-xeq)= ct K exp[-const'(xeq)2/3) - xB2/3)] where xB corresponds to the onset of the brush regime. The denaturation rate constant in the two regimes are identical. However, the hybridization rate constant in the brush regime is lower, the leading correction being exp [- const'(xeq)2/3) - xB2/3)].

Key Words: DNA microarrays, Gene expression, Hybridization isotherm, Hybridization rate, Mutation detection, Polyelectrolyte brush




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Copyright © 2005 by the Biophysical Society.