title: New strategies for exploring RNA's 2'-OH expose the importance of solvent during group II intron catalysis.
abstract: 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.
authors.affiliation: Department of Biochemistry and Molecular Biology, The University of Chicago, 5841 South Maryland Avenue, MC1028, Chicago, IL 60637, USA.
authors.forename: Peter M
authors.initials: PM
authors.lastname: Gordon
authors.forename: Robert
authors.initials: R
authors.lastname: Fong
authors.forename: Shirshendu K
authors.initials: SK
authors.lastname: Deb
authors.forename: Nan-Sheng
authors.initials: NS
authors.lastname: Li
authors.forename: Jason P
authors.initials: JP
authors.lastname: Schwans
authors.forename: Jing-Dong
authors.initials: JD
authors.lastname: Ye
authors.forename: Joseph A
authors.initials: JA
authors.lastname: Piccirilli
mesh_terms: D002384:Catalysis; D002453:Cell Cycle; D045744:Cell Line, Tumor; D000431:Ethanol / Q000494:pharmacology; D006801:Humans; D006860:Hydrogen Bonding; D017665:Hydroxyl Radical / Q000737:chemistry; D007438:Introns; D021281:Quantitative Structure-Activity Relationship; D012313:RNA / Q000737:chemistry*; D022821:RNA Splice Sites / Q000502:physiology; D012326:RNA Splicing; D012266:Ribose / Q000737:chemistry; D012997:Solvents / Q000737:chemistry* / Q000378:metabolism; D014867:Water / Q000737:chemistry*
chemical_list: D022821:RNA Splice Sites; D012997:Solvents; D014867:Water; D017665:Hydroxyl Radical; D000431:Ethanol; D012313:RNA; D012266:Ribose