To identify genetic contributions to alcoholism vulnerability, we have been using single-strand conformational polymorphism (SSCP) analysis. SSCP analysis identifies polymorphic alleles through the detection of altered single-strand DNA secondary structure. The altered secondary structure occurs due to nucleotide changes in DNA sequence. To aid in our understanding of the SSCP technique, we have devised a computer program, DNA-Fold Version 1, to emulate the folding of single-strand DNAs. The efficiency of the DNA-fold program is being evaluated for its predication of SSCP mobility of several hundred DNA molecules. In an effort to improve the efficiency of the DNA-fold program, the DNA thermodynamics for the dangle stacking energies are being determined. These dangle energies and improved thermodynamic measurements that have recently become available are being evaluated in the DNA-Fold program to see if the efficiency of the program will be improved. Parameters will be modified to increase predictive efficiency under various conditions.
