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Biophys. J. BioFAST: First Published October 20, 2006. doi:10.1529/biophysj.106.097121
© 2006 by the Biophysical Society.

A more recent version of this article appeared on January 1, 2007.
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BIOPHYSICAL LETTERS

Competitive Displacement of DNA during Surface Hybridization

Justin Bishop 1*, Colby Wilson 1, Alex M Chagovetz 1 and Steve Blair 2

1 University of Utah
2 Univerity of Utah

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

Submitted on September 8, 2006
Revised on October 17, 2006
Accepted on 18 October 2006


  Abstract
Using real-time dual-color fluorescence detection, we have experimentally tracked individual target species during competitive DNA surface hybridization in a two-component sample. Our experimental results demonstrate displacement of the lower affinity species by the higher affinity species and corroborate recent theoretical models describing competitive DNA surface hybridization. Competition at probe sites complementary to one of the two DNA species was monitored in separate experiments for two different target pairs. Each pair differs in sequence by a SNP, and one pair includes a folding target. Fluorescently labeled control sites were used to normalize the individual signals from each target species, such that total bound probe fraction could be quantified. We propose a mechanistic interpretation of the differences between hybridization curves of targets in multi-component and single component experiments, which are relevant for the analysis of DNA microarray data.


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Copyright © 2006 by the Biophysical Society.