Synthesis and Behavior of DNA Oligomers Containing the Ambiguous Z-Nucleobase 5-Aminoimidazole-4-carboxamide

• Published in: Molecules (Basel, Switzerland) Vol. 28; no. 7; p. 3265
• Main Authors: Nogi, Yuhei, Saito-Tarashima, Noriko, Karanjit, Sangita, Minakawa, Noriaki
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 06-04-2023; MDPI
• Subjects: 5-aminoimidazole-4-carboxamide; Aminoimidazole Carboxamide; Antiviral agents; Base Pairing; base-pairing property; Biosynthesis; Carbon; Chemical properties; Chemical reactions; chemically modified oligonucleotide; Deoxyribonucleic acid; DNA; DNA biosynthesis; DNA polymerase; DNA-directed DNA polymerase; Hepatitis C; melting temperature; mutagenic nucleosides; Nucleoside analogs; Nucleosides; Nucleotides; Oligomers; Pharmaceutical research; Ribavirin; Ring opening; RNA polymerase; single nucleotide insertion; Thermal denaturation; Japan; chemically modified oligonucleotide; mutagenic nucleosides; base-pairing property; 5-aminoimidazole-4-carboxamide; melting temperature; single nucleotide insertion
• ISSN: 1420-3049; 1420-3049
• DOI: 10.3390/molecules28073265

5-Amino-1-β-D-ribofuranosylimidazole-4-carboxamide 5'-monophosphate (ZMP) is a central intermediate in de novo purine nucleotide biosynthesis. Its nucleobase moiety, 5-aminoimidazole-4-carboxamide (Z-base), is considered an ambiguous base that can pair with any canonical base owing to the rotatable nature of its 5-carboxamide group. This idea of ambiguous base pairing due to free rotation of the carboxamide has been applied to designing mutagenic antiviral nucleosides, such as ribavirin and T-705. However, the ambiguous base-pairing ability of Z-base has not been elucidated, because the synthesis of Z-base-containing oligomers is problematic. Herein, we propose a practical method for the synthesis of Z-base-containing DNA oligomers based on the ring-opening reaction of an
-dinitrophenylhypoxanthine (Hxa
) base. Thermal denaturation studies of the resulting oligomers revealed that the Z-base behaves physiologically as an A-like nucleobase, preferentially forming pairs with T. We tested the behavior of Z-base-containing DNA oligomers in enzyme-catalyzed reactions: in single nucleotide insertion, Klenow fragment DNA polymerase recognized Z-base as an A-like analog and incorporated dTTP as a complementary nucleotide to Z-base in the DNA template; in PCR amplification, Taq DNA polymerase similarly incorporated dTTP as a complementary nucleotide to Z-base. Our findings will contribute to the development of new mutagenic antiviral nucleoside analogs.