SOLUTION STRUCTURE OF (RGGC(AG)UNDER-BAR-GCC)(2) BY 2-DIMENSIONAL NMRAND THE ITERATIVE RELAXATION MATRIX APPROACH

The three-dimensional solution structure of the RNA self-complementary duplex [GRAPHICS] was derived from two-dimensional NMR and the iterat ive relaxation matrix approach. Each GA mismatch forms two hydrogen bo nds: A-NH6 to G-O6 and A-N1 to G-NH1 (imino). This GA structure differ s from the sheared tandem GA structure in [GRAPHICS] which also has tw o hydrogen bonds: A-N7 to G-NH2 and A-NH6 to G-N3 [SantaLucia, J., Jr. , & Turner, D. H. (1993) Biochemistry 32, 12612-12623], although the o nly difference between the two sequences is the order of the two GA mi smatches. Inspection of three-dimensional structures indicates that su bstituting [GRAPHICS] for [GRAPHICS] makes GA mismatches unable to hav e stable sheared conformations. This may explain why the [GRAPHICS] mo tif is rarely observed in nature, whereas [GRAPHICS] is common.