A curved RNA helix incorporating an internal loop with G.A and A.A non-Watson-Crick base pairing.
The crystal structure of the RNA dodecamer 5'-GGCC(GAAA)GGCC-3' has been determined from x-ray diffraction data to 2.3-A resolution. In the crystal, these oligomers form double helices around twofold symmetry axes. Four consecutive non-Watson-Crick base pairs make up an internal loop in the middle of the duplex, including sheared G.A pairs and novel asymmetric A.A pairs. This internal loop sequence produces a significant curvature and narrowing of the double helix. The helix is curved by 34 degrees from end to end and the diameter is narrowed by 24% in the internal loop. A Mn2+ ion is bound directly to the N7 of the first guanine in the Watson-Crick region following the internal loop and the phosphate of the preceding residue. This Mn2+ location corresponds to a metal binding site observed in the hammerhead catalytic RNA.
Baeyens
K J
KJ
Structural Biology Division, Lawrence Berkeley National Laboratory, University of California, Berkeley 94720, USA.
De Bondt
H L
HL
Pardi
A
A
Holbrook
S R
SR
D000225:Adenine; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D018360:Crystallography, X-Ray; D006147:Guanine; D006860:Hydrogen Bonding; D008670:Metals; D008957:Models, Genetic; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009843:Oligoribonucleotides / Q000138:chemical synthesis / Q000737:chemistry*; D012313:RNA / Q000737:chemistry*
D008670:Metals; D009843:Oligoribonucleotides; D006147:Guanine; D012313:RNA; D000225:Adenine