The 2′-hydroxyl group contributes inextricably to the functional behavior of many RNA molecules, fulfilling numerous essential chemical roles. To assess how hydroxyl groups impart functional behavior to RNA, we developed a series of experimental strategies using an array of nucleoside analogs. These strategies provide the means to investigate whether a hydroxyl group influences function directly (via hydrogen bonding or metal ion coordination), indirectly (via space-filling capacity, inductive effects, and sugar conformation), or through interactions with solvent. The nucleoside analogs span a broad range of chemical diversity, such that quantitative structure activity relationships (QSAR) now become possible in the exploration of RNA biology. We employed these strategies to investigate the spliced exons reopening (SER) reaction of the group II intron. Our results suggest that the cleavage site 2′-hydroxyl may mediate an interaction with a water molecule.
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We thank Professors Scott Silverman and Stephen Kent for comments on the manuscript. We also thank members of the Piccirilli lab for helpful discussions and comments on the manuscript. P.M.G. and J.-D.Y. are Research Associates; N.-S.L. is a Research Specialist; and J.A.P. is an Associate Investigator of the Howard Hughes Medical Institute. P.M.G. and R.F. were supported in part by the Medical Science Training Program (5 T32 GM07281) at the University of Chicago.