Mercury(II)-Catalyzed Cleavage, Isomerization and Depurination of RNA and DNA Model Compounds and Desulfurization of Their Phosphoromonothioate Analogs

Abstract

The potential of Hg(II), a metal ion so-far overlooked in the development of artificial nucleases, to cleave RNA and DNA has been assessed. Accordingly, Hg(II)-promoted cleavage and isomerization of the RNA model compound adenylyl-3′,5′-(2′,3′-O-methyleneadenosine) and depurination of 2′-deoxyadenosine were followed by HPLC as a function of pH (5.0–6.0) and the desulfurization of both diastereomers of the phosphoromonothioate analog of adenylyl-3′,5′-(2′,3′-O-methyleneadenosine) at a single pH (6.9). At 5 mM [Hg(II)], cleavage of the RNA model compound was accelerated by two orders of magnitude at the low and by one order of magnitude at the high end of the pH range. Between 0 and 5 mM [Hg(II)], the cleavage rate showed a sigmoidal dependence on [Hg(II)], suggesting the participation of more than one Hg(II) in the reaction. Isomerization and depurination were also facilitated by Hg(II), but much more modestly than cleavage, less than 2-fold over the entire pH range studied. Phosphoromonothioate desulfurization was by far the most susceptible reaction to Hg(II) catalysis, being accelerated by more than four orders of magnitude.

Cleavage of an RNA Model Compound by an Arylmercury Complex

“…Over the concentration range studied, the reaction was first-order in and the rate acceleration ranged from three-to 17-fold [1-Hg] (Figure 2). In contrast to the previous report on the catalysis of the same reaction by Hg II , [15] the plot was essentially linear, indicating that the association constant for the reactive complex between 4 (or 5) and 1-Hg is too low to be determined given the limited solubility of 1-Hg. In line with this result, the association constant of MeHg II has been found to be more than an order of magnitude lower than that of Hg II with both adenine ring nitrogens as well as with oxygen donors.…”

“…Cleavage of adenylyl‐3′,5′‐(2′,3′‐ O ‐methyleneadenosine) [15] ( 4 ) was followed as a function of pH (3.0–8.5) in the absence and presence of 1 ‐Hg (1 mM) at 90 °C by analyzing the composition of the aliquots withdrawn from the reaction mixture by RP‐HPLC. The improved aqueous solubility of compound 1 ‐Hg, featuring a hydrophilic penta(ethylene glycol) tail, allowed considerable expansion of the pH range compared to the previous study with Hg II , as evidenced by both visual inspection of the clarity of the reaction solutions as well as the fact that catalysis by 1 ‐Hg prevailed under conditions where catalysis by Hg II could not be detected.…”

“…For reference, a 17-fold rate enhancement by free Hg II has been reported under the same conditions. [15] The rate of mutual isomerization of 4 and 5 was not appreciably affected by the presence of 1-Hg.…”

“…We have recently tested the catalytic effect of a free metal ion, Hg II , on the cleavage of RNA with a simple dinucleoside monophosphate model compound as well as its phosphoromonothioate analogs. [15] The solubility of Hg II limited the studies to a relatively narrow pH range excluding physiological conditions. At pH 5.0, a more than 100-fold acceleration of the cleavage of an RNA phosphodiester linkage could be attained, comparable to many other divalent metal ions.…”

Organomercury Nucleic Acids: Past, Present and Future

“…As discussed above, direct mercuration of oligonucleotides by electrophilic aromatic substitution is a feasible strategy when the aromatic ring to be mercurated is sufficiently electron‐rich. With less reactive systems, the conditions required can be so harsh that competing reactions, such as RNA cleavage, [17] become a problem. In such cases, the organomercury moiety can first be synthesized separately using whatever conditions necessary and then introduced to the oligonucleotide by suitable conjugation chemistry.…”