Solution structure of (rGGC(AG)under-bar-GCC)(2) by two-dimensional NMR and 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 iterative relaxation matrix approach. Each GA mismatch forms two hydrogen bonds: A-NH6 to G-O6 and A-N1 to G-NH1 (imino). This GA structure differs from the sheared tandem GA structure in [GRAPHICS] which also has two 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 only difference between the two sequences is the order of the two GA mismatches. Inspection of three-dimensional structures indicates that substituting [GRAPHICS] for [GRAPHICS] makes GA mismatches unable to have stable sheared conformations. This may explain why the [GRAPHICS] motif is rarely observed in nature, whereas [GRAPHICS] is common.