Metal ion-dependent hydrolysis of RNA phosphodiester bonds within hairpin loops. A comparative kinetic study on chimeric ribo/2'-O-methylribo oligonucleotides

Abstract

Several chimeric ribo/2'- O -methylribo oligonucleotides were synthesized and their hydrolytic cleavage studied in the presence of Mg2+, Zn2+, Pb2+and the 1,4,9-triaza-cyclododecane chelate of Zn2+(Zn2+[12]aneN3) to evaluate the importance of RNA secondary structure as a factor determining the reactivity of phosphodiester bonds. In all the cases studied, a phosphodiester bond within a 4-7 nt loop was hydrolytically more stable than a similar bond within a linear single strand, but markedly less stable than that in a double helix. With Zn2+and Zn2+[12]aneN3, the hydrolytic stability of a phosphodiester bond within a hairpin loop gradually decreased on increasing the distance from the stem. A similar but less systematic trend was observed with Pb2+. Zn2+- and Pb2+-promoted cleavage was observed to be considerably more sensitive to the secondary structure of the chain than that induced by Zn2+[12]aneN3. This difference in behaviour may be attributed to bidentate binding of uncomplexed aquo ions to two different phosphodiester bonds. Mg2+was observed to be catalytically virtually inactive compared with the other cleaving agents studied.

Hydrolysis of Phosphodiester Bonds within RNA Hairpin Loops in Buffer Solutions: the Effect of Secondary Structure on the Inherent Reactivity of RNA Phosphodiester Bonds

“…As for the metal-ionpromoted cleavage, it has been suggested that bending of an RNA strand at an RNA bulge may create strong metal-ion coordination sites that are favorable for the catalysis [11]. In contrast, our previous results show that, in the presence of metal-ion catalysts, phosphodiester bonds within hairpin loops are clearly less reactive than those within linear oligonucleotides [9]. This difference was also attributed to the coordination of metal ions.…”

“…As the most striking example, the phosphodiester bonds within RNA-RNA or RNA-DNA duplexes are relatively stable, their cleavage being very slow compared to the cleavage of phosphodiester bonds within single-stranded regions [6] ± [9]. This is true in both the absence and the presence of metal ion catalysts.…”

“…It is believed that the duplex structure forces phosphodiester bonds into a conformation unfavorable for the cleavage. Phosphodiester bonds within bulges or hairpin loops, in contrast, are known to be cleaved by metal ion catalysts [6] [8] [9].…”

“…We have previously studied the effects of the secondary structure on metal-ion catalysis by studying the cleavage of phosphodiester bonds within small RNA hairpins [9]. In this paper, we set out to study the inherent reactivity of phosphodiester bonds within bent RNA strands.…”

Characterization of Metal Ion-Nucleic Acid Interactions in Solution

“…Conclusions, however, are not straightforward because different factors determine the sites of cleavage. Firstly, favorable backbone geometries for cleavage are more common in single-stranded and loop regions than in double-stranded helices [128,138]. On the other hand, strong relevant binding sites in a more rigid environment with an unfavorable geometry for inline attack might be missed.…”