Mapping of the functional phosphate groups in the catalytic core of deoxyribozyme 10–23

Abstract

The RNA-cleaving DNA enzymes, like most ribozymes, require a divalent metal cation for their cleavage activity [1]. Among metal ion-dependent DNA enzymes, deoxyribozyme 10-23, first selected and characterized by Santoro & Joyce [1,2], has been examined most extensively both in vitro and in vivo [3][4][5]. This enzyme consists of a 15-nucleotide conserved catalytic core and variable substrate recognition arms (Fig. 1A). Cleavage of an RNA substrate is highly sequence-specific, and occurs between the bulged 5¢-purine and paired 3¢-pyrimidine nucleosides, resulting in the formation of the two products, a 5¢-terminal product with a 2¢,3¢-cyclic phosphate, and a 3¢-terminal product containing an OH group at its 5¢-end. The enzyme preferentially uses Mg 2+ for its activity, although other divalent metal ions are accepted as cofactors [1,2,6]. To date, the structure of the substrate-deoxyribozyme 10-23 active complex remains unknown [7,8], and the mechanistic details of the catalytic reaction are not fully understood. Therefore, much effort has been devoted to determine the role of individual nucleotides in the 10-23 catalytic core, as well as their relative importance [9-13]. Despite numerous studies performed on a mutant deoxyribozyme 10-23 containing chemical modifications inserted into the catalytic core, the role of particular phosphates within this domain has not been investigated in detail. We have studied this issue by systematic modification of each phosphate of the core with phosphorothioate (PS) analogs, in which one of the two nonbridging oxygen atoms of the phosphate group was replaced with a sulfur atom. The RNA phosphodiester bond cleavage activity of a series of 16 thio-deoxyribozymes 10-23, containing a P-stereorandom single phosphorothioate linkage in predetermined positions of the catalytic core from P1 to P16, was evaluated under single-turnover conditions in the presence of either 3 mm Mg 2+ or 3 mm Mn 2+. A metal-specificity switch approach permitted the identification of nonbridging phosphate oxygens (proR P or proS P ) located at seven positions of the core (P2, P4 and P9-13) involved in direct coordination with a divalent metal ion(s). By contrast, phosphorothioates at positions P3, P6, P7 and P14-16 displayed no functional relevance in the deoxyribozyme-mediated catalysis. Interestingly, phosphorothioate modifications at positions P1 or P8 enhanced the catalytic efficiency of the enzyme. Among the tested deoxyribozymes, thio-substitution at position P5 had the largest deleterious effect on the catalytic rate in the presence of Mg 2+ , and this was reversed in the presence of Mn 2+. Further experiments with thio-deoxyribozymes of stereodefined P-chirality suggested direct involvement of both oxygens of the P5 phosphate and the proR P oxygen at P9 in the metal ion coordination. In addition, it was found that the oxygen atom at C6 of G 6 contributes to metal ion binding and that this interaction is essential for 10-23 deoxyribozyme catalytic activity.Abbreviations AP, 2-aminopurine; DNAzyme, RNA-...

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