Towards the enzymatic formation of artificial metal base pairs with a carboxy-imidazole-modified nucleotide

The identification of synthetic nucleotides that sustain the formation of orthogonal, unnatural base pairs is an important goal in synthetic biology. Such artificial synthons have been used for the generation of semi-synthetic organisms as well as functional nucleic acids with enhanced binding properties. The enzymatic formation of artificial metal-base pairs is a vastly underexplored and alluring alternative to existing systems. Here, we report the synthesis and biochemical characterization of 1-(2-deoxy-beta-D-ribofuranosyl) imidazole-4-carboxylate nucleoside triphosphate (dIm (TP)-T-C) which is equipped with a carboxylic acid moiety on the imidazole moiety in order to increase the coordination environment to [2 + 2] and [2 + 1]. A clear metal dependence was observed for the single incorporation of the modified nucleotide into DNA by the DNA polymerase from Therms aquaticus (Taq). The presence of Ag-I in primer extension reactions conducted with combinations of 1-(2-deoxy-beta-D-ribofuranosyl) imidazole nucleoside triphosphate (dImTP) and dIm (TP)-T-C supported the unusual [2 + 1] coordination pattern. The efficiency of the tailing reactions mediated by the terminal deoxynucleotidyl transferase (TdT) was markedly improved when using dIm (TP)-T-c instead of dImTP. Even though products with multiple modified nucleotides were not observed, the appendage of additional metal binding ligands on the imidazole nucleobase appears to be a valid approach to improve the biochemical properties of modified triphosphates in the context of an expansion of the genetic alphabet with metal base pairs.