An adsorption model of hybridization behaviour on oligonucleotide microarrays
Abstract
A physical model of the hybridization of labelled target cRNA to short oligonucleotide probes at the surface of microarray chips is presented. The model is based on competing processes of chemical adsorption and desorption and includes the effects of non-specific hybridization. The adsorption process is modelled as a rate determining nucleation step involving a small number of base pairs, followed by a rapid `zipping up' in which remaining base pairs bind. The model correctly predicts a hyperbolic Langmuir isotherm, consistent with data from the Affymetrix HG-U95A Latin Square spike-in experiment, and explains the differing responses of perfect match and mismatch features at saturation concentrations. A formula relating perfect match and mismatch responses in terms of duplex binding energies is also given.Keywords
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