A build-up technique has been devised that permits prediction of DNA structure from sequence. No experimental information is employed other than the force field parameters. This strategy for dealing with the multiple minimum problem requires a supercomputer to make the necessary global searches. The number of energy minimization trials that were made for each of the 16 deoxydinucleoside monophosphate conformational building blocks of DNA was 1944. As a test case, the minimum energy conformations of d(GpC) and d(CpG) to 5.5 kcal/mole were then combined to generate energy-minimized structures for d(CpGpC). The number of trials that were made for d(CpGpC) was 3752. Minima for this single-stranded trimer to 15 kcal/mole were then employed to search for minimum energy conformations of the duplex d(CpGpC).d(GpCpG). The number of starting conformations that were utilized at this stage was 1514. The lowest energy duplex had a Z-II-DNA conformation, followed by a B-DNA form at 1.2 kcal/mole. The A- and Z-I-forms as well as many novel Watson-Crick base-paired structures were found at higher energy. Finally, energy-minimized structures of d(CG)6.d(CG)6 in Z-II and B-DNA conformations were computed using torsion angles from the analogous duplex trimer minima.

Two algorithms are introduced that show exceptional promise in finding molecular conformations using distance geometry on nuclear magnetic resonance data. The f i s t algorithm is a gradient version of the majorization algorithm from multidimensional scaling. The main contribution is a large decrease in CPU time. The second algorithm is an iterative algorithm between possible conformations obtained from the f i s t algorithm and permissible data points near the configuration. These ideas are similar to alternating least squares or alternating projections on convex sets. The iterations significantly improve the conformation from the first algorithm when applied to the small peptide E. coZi STh enterotoxin. 0 1993 by John Wiley & Sons, Inc.

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