A QUANTUM-MECHANICAL INVESTIGATION OF THE ANNEALING ENERGY FOR PHOSPHODIESTER, FORMACETAL, AND THIOFORMACETAL BACKBONES

The changes in the annealing properties of a DNA duplex upon replaceme nt of one phosphodiester linker by a formacetal or thioformacetal link er have been investigated using ab initio quantum mechanics. Potential energy as a function of torsional angle was evaluated using the 6-31G basis set. The detrimental effect of the formacetal linker on the T- m of the duplex (-3 degrees C) is attributed primarily to a much stron ger stereoelectronic effect for a COCO torsion than that for a COPO to rsion. The effects of the thioformacetal linkers on T-m can be rationa lized based on torsion angle potential and steric interactions. (C) 19 93 John Wiley & Sons, Inc.