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

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′.