Investigation of the energetics of C-H center dot center dot center dot O hydrogen bonds in the DNA i-motif via the equilibrium between alternative intercalation topologies

The existence of C-(HO)-O-. . . hydrogen bonds in organic and biological mo lecules is suggested by the observation in crystal structures of short hydr ogen-to-oxygen distances (<0.27 nm) and of the approximate alignment of the C-H and (HO)-O-... segments. However, the associated free energy is rarely known. Here, we determine the free energy of C-(HO)-O-. . . bonds in the i -motif, a four-stranded intercalated structure of DNA strands carrying a st retch of at least two cytidines. It includes narrow grooves that bring the phosphate groups of two anti-parallel strands in close proximity, thus enha ncing electrostatic repulsion. But the sugar moieties are also close, and m ay form pairs suitable for C-H1'(. . .)O4' hydrogen bonds across the groove . It has been suggested that such bonds could explain the narrowness of the grooves and the stability of the i-motif. An opportunity for the evaluatio n of the free energy of such hydrogen bonds comes from the observation that the oligo-deoxynucleotides d(C-n) (n = 2 to 6) form two i-motif structures with different intercalation topologies. The most conspicuous difference b etween them is that one forms two more sugar pairs than the other. In high salt, where electrostatic effects of the phosphate charge distribution are reduced, the free energy difference between the two structures should come mostly from the corresponding C-(HO)-O-. . . bonds, whose free energy could then be determined. The model can be tested by its prediction that the equ ilibrium constant between the two structures should be independent of n in high salt, and this is supported by NMR measurements, except for the quite short strand d(C-2). The equilibrium constant corresponds to a free energy difference of -5.2 kJ mol(-1). This is assigned to the difference (two) in the number of sugar pairs. The geometry derived from solution structures in dicates a single C-(HO)-O-. . . bond within each pair, for a free energy pe r bond of 2.6 kJ mol(-1). This is much less than values commonly quoted for C-(HO)-O-. . . bonds (e.g. 7.5 kJ mol(-1)), probably because the C-(HO)-O- . . . bonds of sugar pairs are not formed anew in one structure, but replac e C-(HO)-O-. . . bonds to water in the other structure. Given the small val ue of the associated free energy, it seems difficult to single out C-(HO)-O -. . . bonds as a structural determinant of the formation and stability of the i-motif. Copyright (C) 2001 John Wiley & Sons, Ltd.