title: Intracomplex general acid/base catalyzed cleavage of RNA phosphodiester bonds: the leaving group effect.
abstract: The general acid/base catalyzed cleavage of a number of alkyl esters of uridine-3'- (and -5'-)phosphate has been studied by utilizing a cleaving agent, in which the catalytic moiety (a substituted 1,3,5-triazine) is tethered to an anchoring Zn(II):cyclen moiety. Around pH 7, formation of a strong ternary complex between uracil, Zn(II) and cyclen brings the general acid/base catalyst close to the scissile phosphodiester linkage, resulting in rate acceleration of 1-2 orders of magnitude with the uridine-3'-phosphodiesters. Curiously, no acceleration was observed with their 5'-counterparts. A β(lg) value of -0.7 has been determined for the general acid/base catalyzed cleavage, consistent with a proton transfer to the leaving group in the rate-limiting step.
authors: Department of Chemistry, University of Turku, Finland. tuanlo@utu.fi
authors: Tuomas
authors: T
authors: Lönnberg
authors: Mikko
authors: M
authors: Luomala
mesh_terms: D000143:Acids / Q000737:chemistry; D002384:Catalysis; D000080027:Cyclams; D004952:Esters; D006571:Heterocyclic Compounds / Q000737:chemistry*; D006863:Hydrogen-Ion Concentration; D012313:RNA / Q000737:chemistry*; D014227:Triazines / Q000737:chemistry; D014500:Uracil Nucleotides / Q000737:chemistry*; D015032:Zinc / Q000737:chemistry*
chemical_list: D000143:Acids; D000080027:Cyclams; D004952:Esters; D006571:Heterocyclic Compounds; D014227:Triazines; D014500:Uracil Nucleotides; D012313:RNA; C038072:cyclen; D015032:Zinc