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

Abstract

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 (H₀ = –0.2 to pH 9) at 363.2 K. The buffer-independent pH-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 β_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 β_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.