Polymerase Synthesis of Hypermodified DNA Displaying a Combination of Thiol, Hydroxyl, Carboxylate, and Imidazole Functional Groups in the Major Groove

2025/05/06 by Lukáš Kaiser, Marek Ondruš, Lenka Poštová Slavětínská +2 · 1 voice
Biochemistry, Genetics and Molecular Biology · #Advanced biosensing and bioanalysis techniques #DNA and Nucleic Acid Chemistry #RNA Interference and Gene Delivery

paper · pdf · doi:10.1002/chem.202501034

openalex publication_date 2025/05/06 · openalex created_date 2025/10/10 · openalex updated_date 2026/05/21

Abstract

We designed and synthesized a set of six 2'-deoxyribonucleoside 5'-O-triphosphates (dNTPs) bearing functional groups mimicking amino acid side chains in enzyme active sites (OH, SH, COOH, and imidazole) attached to position 5 of pyrimidines or position 7 of 7-deazapurines through different linkers. These modified dNTPs were studied as substrates in enzymatic synthesis of modified and hypermodified DNA using several DNA polymerases. In primer extension (PEX), all modified dNTPs provided DNA containing one, two, three, or, (all) four modified nucleotides each bearing a different modification, although the thiol-modified dNTPs were worse substrates compared to the others. In PCR, we observed exponential amplification for any combination of one, two, or three nonsulfur dNTPs but the thiol-modified dNTP did not work well in any combinations. Sequencing of the hypermodified DNA confirmed the good fidelity of the incorporation of all the modified nucleotides. This set of modified dNTPs extends the portfolio of building blocks for prospective use in selections of functional nucleic acids.

Citations

• Zwitterionic DNA: enzymatic synthesis of hypermodified DNA bearing four different cationic substituents at all four nucleobases
• Modified nucleic acid aptamers: development, characterization, and biological applications

Cited by

• Hydrophobic alkyl-linked base-modified pyrimidine and 7-deazapurine 2′-deoxyribonucleoside phosphoramidites: synthesis and application in solid-phase synthesis of modified and hypermodified oligonucleotides

Discussions

• Our newest paper on enzymatic synthesis of hypermodified DNA bearing functional groups mimicking amino acid side chains in enzyme active sites just published in ChemEurJ. doi.org/10.1002/chem... @iocb [bsky, 6 points, 0 comments]

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