Solution structure of (rGGCAGGCC)2 by two-dimensional NMR and the iterative relaxation matrix approach.
The three-dimensional solution structure of the RNA self-complementary duplex [formula in text] 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 [formula in text] 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 [formula in text] for [formula in text] makes GA mismatches unable to have stable sheared conformations. This may explain why the [formula in text] motif is rarely observed in nature, whereas [formula in text] common.
Wu
M
M
Department of Chemistry, University of Rochester, New York 14627-0216, USA.
SantaLucia
J
J
Turner
D H
DH
D018360:Crystallography, X-Ray; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D009841:Oligonucleotides / Q000138:chemical synthesis / Q000737:chemistry; D012313:RNA / Q000138:chemical synthesis / Q000737:chemistry*
D009692:Nucleic Acid Heteroduplexes; D009841:Oligonucleotides; D012313:RNA