PMID: 11333021May 3, 2001Paper

X-ray crystallographic observation of "in-line" and "adjacent" conformations in a bulged self-cleaving RNA/DNA hybrid

RNA
V TereshkoM Egli

Abstract

The RNA strand in an RNA/DNA duplex with unpaired ribonucleotides can undergo self-cleavage at bulge sites in the presence of a variety of divalent metal ions (Hüsken et al., Biochemistry, 1996, 35:16591-16600). Transesterification proceeds via an in-line mechanism, with the 2'-OH of the bulged nucleotide attacking the 3'-adjacent phosphate group. The site-specificity of the reaction is most likely a consequence of the greater local conformational freedom of the RNA backbone in the bulge region. A standard A-form backbone geometry prohibits formation of an in-line arrangement between 2'-oxygen and phosphate. However, the backbone in the region of an unpaired nucleotide appears to be conducive to an in-line approach. Therefore, the bulge-mediated phosphoryl transfer reaction represents one of the simplest RNA self-cleavage systems. Here we focus on the conformational features of the RNA that underlie site-specific cleavage. The structures of an RNA/DNA duplex with single ribo-adenosyl bulges were analyzed in two crystal forms, permitting observation of 10 individual conformations of the RNA bulge moiety. The bulge geometries cover a range of relative arrangements between the 2'-oxygen of the bulged nucleotide and the P-O5' bond ...Continue Reading

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Citations

Mar 17, 2004·Journal of Molecular Biology·Deborah M JohnKevin M Weeks
Nov 20, 2002·Journal of Biomolecular Structure & Dynamics·Nagarajan PattabiramanBruce A Shapiro
Apr 15, 2011·Nucleosides, Nucleotides & Nucleic Acids·Anthony D Saleh, Paul S Miller
Feb 24, 2006·Proceedings of the National Academy of Sciences of the United States of America·Baocheng PanMuttaiya Sundaralingam
Aug 9, 2011·Journal of Nucleic Acids·Shu-Ichi NakanoNaoki Sugimoto
Nov 15, 2012·Journal of Nucleic Acids·Dan-Andrei CatanaJean-Marc Escudier
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Oct 17, 2002·Journal of the American Chemical Society·Phillip Ordoukhanian, Gerald F Joyce
Jan 13, 2005·Journal of the American Chemical Society·Shu-ichi NakanoNaoki Sugimoto

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