Hybridisation thermodynamic parameters allow accurate detection of point mutations with DNA microarrays

Abstract

We consider mixtures of two DNA sequences t and t' differing by a single nucleotide, which are analyzed by an Agilent custom DNA microarray. In particular we focus on the case in which t, the " wild type" , is predominantly abundant and t' the " mutant" is at very low concentrations compared to t. We show that by using appropriately designed arrays it is possible to accurately quantify the presence of t' even at low relative concentrations (≈1%). The detection method is based on thermodynamic models of DNA hybridisation and on the analysis of a large number of hybridisation intensities from probes containing one or two mismatches with respect to t and t'. © 2010 Elsevier B.V.