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

• Published in: Journal of inorganic biochemistry 2019-02, Vol.191, p.154-163
• Main Authors: Röthlisberger, Pascal, Levi-Acobas, Fabienne, Sarac, Ivo, Marlière, Philippe, Herdewijn, Piet, Hollenstein, Marcel
• Format: Article
• Language: English
• Subjects: Base Pairing; Chemical Sciences; Coordination Complexes - chemistry; DNA; DNA polymerases; DNA-Directed DNA Polymerase - metabolism; Enzymatic synthesis; Imidazoles - chemistry; Inorganic chemistry; Ligands; Metal-mediated base pairs; Metals - chemistry; Nucleoside triphosphate; Nucleotides - chemistry; Organic chemistry; Silver
• ISSN: 0162-0134; 1873-3344
• DOI: 10.1016/j.jinorgbio.2018.11.009

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‑β‑d‑ribofuranosyl) imidazole‑4‑carboxylate nucleoside triphosphate (dImCTP) 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 Thermus aquaticus (Taq). The presence of AgI in primer extension reactions conducted with combinations of 1‑(2‑deoxy‑β‑d‑ribofuranosyl) imidazole nucleoside triphosphate (dImTP) and dImCTP 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 dImCTP 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. The synthesis of a 4-carboxyimidazole containing nucleotide is presented. The acceptance of this nucleotide by various polymerases was then evaluated in the context of the enzymatic construction of metal base pairs for an expansion of the genetic code. [Display omitted] •Synthesis of nucleotide 1‑(2‑deoxy‑β‑d‑ribofuranosyl) imidazole‑4‑carboxylate (dImCTP).•The additional ligand imparts metal dependence to incorporation by DNA polymerases.•A [2 + 1] coordination environment was observed with a combination of modified nucleotides.•dImCTP is an excellent substrate for the terminal deoxynucleotidyl transferase (TdT).•The additional ligand enhances the biochemical properties of imidazole-based nucleotides.