Prediction of nucleic acid hybridization: Parameters and algorithms

The thermodynamic contributions to duplex stability of DNA structural motifs were studied by monitoring the thermal denaturation of model DNA oligonugonucleotide duplexes by UV spectroscopy. The motifs studied included single symmetric mismatches, dangling ends, and coaxially stacked helices. The study of these motifs is a step toward the completion of a DNA thermodynamic database to predict DNA hybridization and folding. The thermodynamic parameters obtained for the motifs studied were implemented in the MFOLD secondary-structure prediction algorithm and in a novel hybridization prediction algorithm, HYT HER.;HYTHER, was developed to predict nucleic acid hybridization using thermodynamic data. The algorithm, rigorously calculates the most efficient primers or probes complementary to a target. HY THER accounts for folding of probe and target as well as competitive mismatch binding sites on the target, probe or target dimerization, and probe dimer or target dimer interactions. Moreover, HYT HER uses a novel numerical procedure to simulate the temperature dependence of the concentration of all the species involved in the hybridization process. This algorithm should be invaluable to optimize probes for PCR, FISH, and the design molecular beacons and DNA oligonucleotide arrays.