Thermodynamic behavior of short oligonucleotides in microarray hybridizations can be described using Gibbs free energy in a nearest-neighbor model

The effect of well-defined mismatches on hybridization specificity is examined and the relation between hybridization intensity and Gibbs free energy is analyzed. The correlation between intensity and Gibbs free energy is used in quality control of microarray hybridizations by designing probes and corresponding RNA spikes with a range of Gibbs free energy values.