Hybridization of phosphate-methylated DNA and natural oligonucleotides. Implications for protein-induced DNA duplex destabilization

Duplex stabilities have been determined for several hybrids of phosphate-methylated oligonucleotides and natural DNA or RNA using UV hyperchromicity experiments. These hybrids have a higher stability than the corresponding natural duplexes, due to the absence of interstrand electrostatic repulsions. Comparison with stability data for hybrids of other neutral oligonucleotides (with phosphate-ethylated and methyl phosphonate linkages) and natural DNA or RNA revealed that differences in stability could be attributed mainly to steric and stereoelectronic factors. For phosphate-ethylated oligonucleotides, hybridization with a natural strand is strongly influenced by steric interactions of the ethyl group. Hybridization with RNA, which requires a tight A-type conformation, is therefore difficult and the ethyl orientation (inward or outward, depending on the phosphorus configuration) determines the strength of the association with natural DNA. In methyl phosphonate systems, it appears that the presence of a PC bond disturbs the helix conformation for stereoelectronic reasons. This leads to a weaker hybridization with DNA and RNA for longer strands. Phosphate-methylated oligonucleotides are found to have an optimal combination of steric and stereoelectronic factors and form the strongest hybrids with natural DNA. Absence of intrastrand phosphate-phosphate repulsions causes a slightly different conformation for phosphate-methylated DNA, which is evident in the cooperative character of the hybridization with natural DNA. A thermodynamic model for this cooperativity is presented and the model studies are extended to protein-DNA complexes in which phosphate charges are also shielded. The preliminary results suggest that protein association can destabilize a DNA duplex, thus providing a possible mechanism for the action of DNA unwinding enzymes.