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  • Title: Intracomplex general acid/base catalyzed cleavage of RNA phosphodiester bonds: the leaving group effect.
    Author: Lönnberg T, Luomala M.
    Journal: Org Biomol Chem; 2012 Sep 07; 10(33):6785-91. PubMed ID: 22825538.
    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.
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