Crystal structure of an RNA 16-mer duplex R(GCAGAGUUAAAUCUGC)2 with nonadjacent G(syn).A+(anti) mispairs.
G.A mispairs are one of the most common noncanonical structural motifs of RNA. The 1.9 A resolution crystal structure of the RNA 16-mer r(GCAGAGUUAAAUCUGC)2 has been determined with two isolated or nonadjacent G.A mispairs. The molecule crystallizes with one duplex in the asymmetric unit in space group R3 and unit cell dimensions a = b = c = 49.24 A and alpha = beta = gamma = 51.2 degrees. It is the longest known oligonucleotide duplex at this resolution and isomorphous to the 16-mer duplex with the C.A+ mispairs [Pan, et al., (1998) J. Mol. Biol. 283, 977-984]. The C.A+ mispair behaves like a wobble pair while the G.A+ does not. The G.A mispairs are protonated at N1 of the adenines as in the C.A+ mispairs, and two hydrogen bonds in the G(syn).A+(anti) conformation are formed. The syn guanine is stabilized by an intranucleotide hydrogen bond between the 2-amino and the 5'-phosphate groups. The G(syn).A+(anti) conformation can provide a different surface for recognition in the grooves compared to other G.A hydrogen bonding schemes. The major groove is widened between the two mispairs allowing access to ligands. One of the 3-fold axes is occupied by a sodium ion and a water molecule, while a second is occupied by another water molecule.
Pan
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Biological Macromolecular Structure Center, Department of Chemistry, The Ohio State University, Columbus 43210-1002, USA.
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Sundaralingam
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D000227:Adenine Nucleotides / Q000737:chemistry*; D020137:Base Pair Mismatch; D003460:Crystallization; D003597:Cytosine Nucleotides / Q000737:chemistry; D006150:Guanine Nucleotides / Q000737:chemistry*; D008670:Metals / Q000737:chemistry; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry*; D009838:Oligodeoxyribonucleotides / Q000737:chemistry; D011687:Purines / Q000737:chemistry; D012313:RNA / Q000737:chemistry*; D012997:Solvents
D000227:Adenine Nucleotides; D003597:Cytosine Nucleotides; D006150:Guanine Nucleotides; D008670:Metals; D009692:Nucleic Acid Heteroduplexes; D009838:Oligodeoxyribonucleotides; D011687:Purines; D012997:Solvents; D012313:RNA