pH- and buffer-independent cleavage and mutual isomerization of uridine 2 '- and 3 '-alkyl phosphodiesters: implications for the buffer catalyzed cleavage of RNA



: Kosonen M, Yousefi-Salakdeh E, Stromberg R, Lonnberg H

Publisher: ROYAL SOC CHEMISTRY

: 1998

Royal Society of Chemistry. Journal: Perkin Transactions 2

JOURNAL OF THE CHEMICAL SOCIETY-PERKIN TRANSACTIONS 2

: J CHEM SOC PERK T 2

: 7

: 1589

: 1595

: 7

: 0300-9580

DOI: https://doi.org/10.1039/a801670d


Concurrent isomerization of the ethyl, 2-ethoxyethyl, 2,2-dichloroethyl and 2,2,2-trichloroethyl esters of uridine 3'-phosphate to their 2'-counterparts and cleavage to uridine 2',3'-cyclic phosphate have been studied over a wide pH-range (H-0 -0.2 to pH 9) at 363.2 K, The buffer-independent pa-rate profiles obtained show involvement of four distinct kinetic terms in the cleavage reaction, viz. dependence of rate on [H+][SH], [SH], [S-] and [S-][H+](-1) (S- denotes the diester monoanion). The beta(lg) values (lg = leaving group) for the partial reactions are -0.04 +/- 0.04, -0.19 +/- 0.12, -0.59 +/- 0.12 and -1.10 +/- 0.05, respectively. The isomerization, in turn, shows dependence of rate on [H+][SH], [SH] and [S-], the beta(rg) values (rg = remnant group) being -0.23 +/- 0.04, -0.23 +/- 0.11 and -0.03 +/- 0.01. The mechanisms of various partial reactions are evaluated by comparing these values with those of specific and buffer catalyzed reactions of the corresponding 3'-phosphotriesters, regarded as mimetics of the neutral ionic form of diesters, Furthermore, the mechanistic significance of the dissimilar competition between the cleavage and isomerization with diesters and triesters is discussed.



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