The mode of Mg++ binding to oligonucleotides. Inner sphere complexes as markers for recognition?

Large changes of UV absorbance and CD spectra as well as specific relaxation processes with time constants around 50 μs are found for the association of Mg++ with A(pA)n. The Mg++ binding constants strongly increase with increasing n. The relaxation data dmionstrate that a large fraction of Mg++ bound to short A(pA)n forms inner sphere complexes (ISC), with H2O molecules from the inner hydration sphere of Mg++ exchanged against some site(s) of the oligomer. This fraction decreases from about 85% for A(pA)4 to less than 10% for A(pA)17. A parallel decrease is observed in the relative change of CD spectrum upon Mg++ binding from 77.5% for A(pA)4 to 13.4% for A(pA)17. The rate of ISC formation decreases with increasing n suggesting some (probably sterical) hindrance effect at high n. The data support the conclusion that Mg++ favours the formation of outer sphere complexes with linear polynucleotides and require a special chain folding for ISC. Measurements of Mg++ binding to C(pC)5, U(pU)5, I(pI)5 and d{A(pA)5} did not give evidence for the formation of ISC, indicating that both specific base and sugar residues are required for ISC. These results suggest the possibility that Mg++ ISC are used for specific recognition of nucleic acid sequences.