Origins of the large differences in stability of DNA and RNA helices: C-5 methyl and 2'-hydroxyl effects.

Recent studies have shown that there can be large differences in the stability of double and triple helical nucleic acid complexes, depending on whether RNA or DNA strands are involved. These differences have been attributed to structural differences in the sugar-phosphate backbone of these two polymers. However, since there are in fact two structural features which distinguish DNA from RNA (the 2'-hydroxyl and C-5 methyl groups), the stability differences may arise from either or both of these factors. We have separated effects of the 2'-hydroxyl and C-5 methyl groups by synthesizing nucleic acid strands which contain all possible combinations with and without these groups. Studies of the stabilities of double and triple helices involving these strands show that in fact the C-5 methyl group of thymine and the 2'-OH group of ribose have equally large effects on stability. The two effects vary with secondary structure and can be reinforcing or even opposing in their influence on stability. Three types of complexes are specifically examined: bimolecular pyrimidine.purine duplexes, termolecular pyrimidine.purine.pyrimidine triplexes, and bimolecular triplexes formed from circular pyrimidine oligonucleotides with purine target strands. It is found in general that the two types of substitutional effects are independent of one another and that C-5 methyl groups are in all cases stabilizing, while 2'-OH groups can be stabilizing or destabilizing, depending on the type of complex. In addition, studies with partially methylated duplexes lend evidence that the largest contribution to stabilization by the methyl group arises from increased base stacking ability rather than from a favorable hydrophobic methyl-methyl contact.(ABSTRACT TRUNCATED AT 250 WORDS)