A nuclear magnetic resonance study of thermal effects upon base stacking in oligonucleotides. ApA--p

Nuclear-magnetic-resonance study of the conformation of a dinucleotide in solution using the lanthanide probe method

The conformation of the dinucleotide adenylyl(3'-5')adenosine 2'-phosphate (ApA2'p) in aqueous solution at different pH values and temperatures has been studied using the lanthanide(III) ethylenodiaminetetraacetate(EDTA) 1:1 complexes as shift and relaxation probes. The conformational analysis, based on mixing different conformations in fast exchange within the nuclear magnetic resonance time scale, agrees well with the results from vicinal coupling constants and dimerization shifts obtained for the metal-free system. The dinucleotide exists in a temperature-dependent and pH-dependent conformational equilibrium between unstacked and base-stacked forms. At neutral pH and low temperature, the stacked form predominates, and it is a predominantly right helical structure, characterized as an anti, 3E, g-, g- g-, g'g', gg, 3E, anti conformation. This situation contrasts with adenylyl(3'-5')adenosine (ApA), where both right and left helices contribute to the stacked form. The nucleotidyl units of the unstacked form of ApA2'p have average conformations which are very similar to those of the corresponding mononucleotides in similar conditions.