Solution structure of (rGCGGACGC)2 by two-dimensional NMR and the iterative relaxation matrix approach.
The three-dimensional solution structure of the RNA self-complementary duplex [sequence: see 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 is the first three-dimensional RNA structure with imino hydrogen-bonded tandem GA mismatches. This GA structure is totally different from the sheared tandem GA structure in [sequence: see 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]. In particular, the sheared and imino GA mismatches produce a narrowing and widening of the backbone, respectively. The results show that substitutions of Watson-Crick base pairs can have dramatic effects on the three-dimensional structures of adjacent non-Watson-Crick paired regions; i.e., the structure depends on sequence context. Thus compensating substitutions in site-directed mutagenesis experiments may not always restore biological activities.
Wu
M
M
Department of Chemistry, University of Rochester, New York 14627-0216, USA.
Turner
D H
DH
D001483:Base Sequence; D006860:Hydrogen Bonding; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000138:chemical synthesis / Q000737:chemistry* / Q000302:isolation & purification; D012313:RNA / Q000737:chemistry*; D012996:Solutions
D009843:Oligoribonucleotides; D012996:Solutions; D012313:RNA