ChipCheckA Program Predicting Total Hybridization Equilibria for DNA Binding to Small Oligonucleotide Microarrays

Presented here is the program ChipCheck that allows the computation of total hybridization equilibria for
hybridization experiments involving small oligonucleotide arrays. The calculation requires the free energies
of binding for all pairs of probes and targets as well as total strand concentrations and probe molecule
numbers. ChipCheck has been tested computationally on microarrays with up to 100 spots and 42 target
strands (4200 binding equilibria). It arrives at solutions through iterations employing the multidimensional
Newton method. While currently running in simulation mode only, an extension of the approach to the
exhaustive analysis of chip results is being outlined and may be implemented in the future. The output
displays the extent of correct and cross hybridization both graphically and numerically. In principle, calculating
total hybridization equilibria allows for eliminating noise from DNA chip results and thus an improvement
in sensitivity and accuracy.