Recognition of G-U mismatches by tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III).
The coordination complex tris(4,7-diphenyl-1,10-phenanthroline)rhodium(III) [Rh(DIP)3(3+)], which promotes RNA cleavage upon photoactivation, has been shown to target specifically guanine-uracil (G-U) mismatches in double-helical regions of folded RNAs. Photoactivated cleavage by Rh(DIP)3(3+) has been examined on a series of RNAs that contain G-U mismatches, yeast tRNA(Phe) and yeast tRNA(Asp), as well as on 5S rRNAs from Xenopus oocytes and Escherichia coli. In addition, a "microhelix" was synthesized, which consists of seven base pairs of the acceptor stem of yeast tRNA(Phe) connected by a six-nucleotide loop and contains a mismatch involving residues G4 and U69. A U4.G69 variant of this sequence was also constructed, and cleavage by Rh(DIP)3(3+) was examined. In each of these cases, specific cleavage is observed at the residue which lies to the 3'-side of the wobble-paired U; some cleavage by the rhodium complex is also evident in several structured RNA loops. The remarkable site selectivity for G-U mismatches within double-helical regions is attributed to shape-selective binding by the rhodium complex. This binding furthermore depends upon the orientation of the G-U mismatch, which produces different stacking interactions between the G-U base pair with the Watson-Crick base pair following it on the 5'-side of U compared to the Watson-Crick pair preceding it on the 3'-side of U. Rh(DIP)3(3+) therefore serves as a unique probe of G-U mismatches and may be useful both as a model and in probing RNA-protein interactions as well as in identifying G-U mismatches within double-helical regions of folded RNAs.
Chow
C S
CS
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena 91125.
Barton
J K
JK
D006150:Guanine Nucleotides / Q000737:chemistry; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009942:Organometallic Compounds / Q000737:chemistry*; D010618:Phenanthrolines / Q000737:chemistry*; D012329:RNA, Bacterial / Q000737:chemistry; D012330:RNA, Double-Stranded / Q000737:chemistry*; D012341:RNA, Ribosomal, 5S / Q000737:chemistry; D012343:RNA, Transfer / Q000737:chemistry; D014500:Uracil Nucleotides / Q000737:chemistry
D006150:Guanine Nucleotides; D009942:Organometallic Compounds; D010618:Phenanthrolines; D012329:RNA, Bacterial; D012330:RNA, Double-Stranded; D012341:RNA, Ribosomal, 5S; D014500:Uracil Nucleotides; D012343:RNA, Transfer; C057118:tris(4,7-diphenyl-1,10-phenanthroline)-rhodium (III)