RNA Hydrolysis by Heterocyclic Amidines and Guanidines: Parameters Affecting Reactivity

Abstract

In memory of Klaus Hafner 2-Aminobenzimidazole 10, although a weak catalyst in the monomeric state, is a successful building block for effective artificial ribonucleases. In an effort to identify new building blocks with improved catalytic potential, RNA cleavage by a variety of heterocyclic amidines and guanidines has been studied. In addition to pK a values and steric effects, the energy difference between tautomeric forms seems to be another important parameter for catalysis. This information is available from quantum chemical calculations on higher levels, but semiempirical methods are sufficient to get a first estimate. According to this assumption, imidazoimidazol 18, characterized by isoenergetic tautomeric forms, is superior to 2-aminoimidazol 6, the best candidate among the simple compounds. By far the largest effects are seen with 2-aminoperimidine 24, which rapidly cleaves RNA even in the micromolar concentration range. The impressive reactivity, however, is related to a tendency of compound 24 to form polycationic aggregates which are the actual catalysts.

Structural Modifications as Tools in Mechanistic Studies of the Cleavage of RNA Phosphodiester Linkages

“…Guanidine derived compounds shown to cleave phosphodiester linkages typically contain two guanidine groups. The factors that are of importance for efficient proton shuttling, in addition to overall structure of the cleaving agent, include p K a value close to 7 of the guanidinium units, planar hydrophobic structure and small free energy difference between the tautomeric forms [93] . The pioneering study in the field of nonmetallic cleaving agents of RNA is the finding of Göbel's group [94,95] that tris‐guanidines derived from 2‐aminobenzimidazole units ( 3 ) are effective catalysts.…”

Quality Control of mRNA Vaccines by Synthetic Ribonucleases: Analysis of the Poly‐A‐Tail

“…In recent years, we have developed small-molecule catalysts for RNA hydrolysis based on heterocyclic guanidine analogs. [28,29] When attached to oligonucleotides, the resulting conjugates act as synthetic ribonucleases and reliably cut complementary RNA strands: hybridization between substrate and conjugate places the catalyst close to the duplex end and defines the cleavage site (see Figure 1). Cleavage has no sequence restrictions and is independent from Mg 2 + ions.…”