Adsorption models of hybridization and post-hybridization behaviour on oligonucleotide microarrays
Date
2006
Authors
Burden, Conrad
Pittelkow, Yvonne
Wilson, Susan
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Institute of Physics Publishing
Abstract
Analysis of data from an Affymetrix Latin Square spike-in experiment indicates that measured fluorescence intensities of features on an oligonucleotide microarray are related to spike-in RNA target concentrations via a hyperbolic response function, generally identified as a Langmuir adsorption isotherm. Furthermore, the asymptotic signal at high spike-in concentrations is almost invariably lower for a mismatch feature than for its partner perfect match feature. We survey a number of theoretical adsorption models of hybridization at the microarray surface and find that in general they are unable to explain the differing saturation responses of perfect and mismatch features. On the other hand, we find that a simple and consistent explanation can be found in a model in which equilibrium hybridization is followed by partial dissociation of duplexes during the post-hybridization washing phase.
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Keywords
Keywords: Adsorption; Dissociation; Fluorescence; RNA; Affymetrix Latin Square; Hyperbolic response function; Oligonucleotide microarray; Nucleic acids
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Source
Journal of Physics: Condensed Matter
Type
Journal article
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2037-12-31
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