Synthesis of a Nonhydrolyzable Nucleotide Phosphoroimidazolide Analogue That Catalyzes Nonenzymatic RNA Primer Extension

• Published in: Journal of the American Chemical Society Vol. 140; no. 2; pp. 783 - 792
• Main Authors: Tam, Chun Pong, Zhou, Lijun, Fahrenbach, Albert C, Zhang, Wen, Walton, Travis, Szostak, Jack W
• Format: Journal Article
• Language: English
• Published: WASHINGTON American Chemical Society 17.01.2018; Amer Chemical Soc
• Subjects: Catalysis; Chemistry; Chemistry, Multidisciplinary; Cytidine Monophosphate - analogs & derivatives; Cytidine Monophosphate - chemistry; Hydrolysis; Imidazoles - chemistry; Nucleotides - chemistry; Physical Sciences; RNA - chemistry; Science & Technology; CONSTANTS; PREBIOTIC SYNTHESIS; LIGATION; MONOMER; TEMPLATE-DIRECTED SYNTHESIS; URIDINE; HAIRPIN OLIGONUCLEOTIDES; OLIGOMERIZATION; BINDING; DERIVATIVES
• ISSN: 0002-7863; 1520-5126
• DOI: 10.1021/jacs.7b11623

We report the synthesis of guanosine 5′-(4-methylimidazolyl)­phosphonate (ICG), the third member of a series of nonhydrolyzable nucleoside 5′-phosphoro-2-methylimidazolide (2-MeImpN) analogues designed for mechanistic studies of nonenzymatic RNA primer extension. The addition of a 2-MeImpN monomer to a primer is catalyzed by the presence of a downstream activated monomer, yet the three nonhydrolyzable analogues do not show catalytic effects under standard mildly basic primer extension conditions. Surprisingly, ICG, which has a pK a similar to that of 2-MeImpG, is a modest catalyst of nonenzymatic primer extension at acidic pH. Here we show that ICG reacts with 2-MeImpC to form a stable 5′–5′-imidazole-bridged guanosine-cytosine dinucleotide, with both a labile nitrogen–phosphorus and a stable carbon–phosphorus linkage flanking the central imidazole bridge. Cognate RNA primer–template complexes react with this GC-dinucleotide by attack of the primer 3′-hydroxyl on the activated N–P side of the 5′-5′-imidazole bridge. These observations support the hypothesis that 5′–5′-imidazole-bridged dinucleotides can bind to cognate RNA primer–template duplexes and adopt appropriate conformations for subsequent phosphodiester bond formation, consistent with our recent mechanistic proposal that the formation of activated 5′–5′-imidazolium-bridged dinucleotides is responsible for 2-MeImpN-driven primer extension.