Adsorption models of hybridization and post-hybridization behaviour on oligonucleotide microarrays

Adsorption models of hybridization and post-hybridisation behaviour on oligonucleotide microarrays

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...

Specific and nonspecific hybridization of oligonucleotide probes on microarrays.

Gene expression analysis by means of microarrays is based on the sequence-specific binding of RNA to DNA oligonucleotide probes and its measurement using fluorescent labels. The binding of RNA fragments involving sequences other than the intended target is problematic because it adds a chemical background to the signal, which is not related to the expression degree of the target gene. The artic...

Assessing Effect of Cross-hybridization on Oligonucleotide Microarrays

We introduce computational method, which allows estimating the input of non-specific binding into hybridization signal intensities on the oligonucleotide-based Affymetrix GeneChip arrays. We consider a simplified linear model of hybridization that should work well for microarray experiments with low DNA concentrations during hybridization, and use the quadratic programming technique to estimate...

Analysis of nucleic acids by tandem hybridization on oligonucleotide microarrays.

Limit Theorems for Hybridization Reactions on Oligonucleotide Microarrays

We derive herein the limiting laws for certain stationary distributions of birth-and-death processes related to the classical model of chemical adsorption-desorption reactions due to Langmuir. The model has been recently considered in the context of a hybridization reaction on an oligonucleotide DNA microarray. Our results imply that the truncated gammaand betatype distributions can be used as ...