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Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases
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SYSNO ASEP 0577106 Document Type J - Journal Article R&D Document Type Journal Article Subsidiary J Článek ve WOS Title Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases Author(s) Kuprikova, Natalia (UOCHB-X)
Ondruš, Marek (UOCHB-X) ORCID, RID
Bednárová, Lucie (UOCHB-X) RID, ORCID
Riopedre Fernández, Miguel (UOCHB-X) ORCID, SAI
Poštová Slavětínská, Lenka (UOCHB-X) RID
Sýkorová, Veronika (UOCHB-X) ORCID, RID
Hocek, Michal (UOCHB-X) RID, ORCIDSource Title Nucleic Acids Research. - : Oxford University Press - ISSN 0305-1048
Roč. 51, č. 21 (2023), s. 11428-11438Number of pages 11 s. Language eng - English Country US - United States Keywords polymerase-catalyzed incorporation ; functionalized DNA ; primer extension OECD category Organic chemistry R&D Projects GX20-00885X GA ČR - Czech Science Foundation (CSF) Method of publishing Open access Institutional support UOCHB-X - RVO:61388963 UT WOS 001090289000001 EID SCOPUS 85178500386 DOI 10.1093/nar/gkad893 Annotation We designed and synthesized a set of four 2′-deoxyribonucleoside 5′-O-triphosphates (dNTPs) derived from 5-substituted pyrimidines and 7-substituted 7-deazapurines bearing anionic substituents (carboxylate, sulfonate, phosphonate, and phosphate). The anion-linked dNTPs were used for enzymatic synthesis of modified and hypermodified DNA using KOD XL DNA polymerase containing one, two, three, or four modified nucleotides. The polymerase was able to synthesize even long sequences of >100 modified nucleotides in a row by primer extension (PEX). We also successfully combined two anionic and two hydrophobic dNTPs bearing phenyl and indole moieties. In PCR, the combinations of one or two modified dNTPs gave exponential amplification, while most of the combinations of three or four modified dNTPs gave only linear amplification in asymmetric PCR. The hypermodified ONs were successfully re-PCRed and sequenced by Sanger sequencing. Biophysical studies including hybridization, denaturation, CD spectroscopy and molecular modelling and dynamics suggest that the presence of anionic modifications in one strand decreases the stability of duplexes while still preserving the B-DNA conformation, whilst the DNA hypermodified in both strands adopts a different secondary structure. Workplace Institute of Organic Chemistry and Biochemistry Contact asep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Jana Procházková, Tel.: 220 183 418 Year of Publishing 2024 Electronic address https://doi.org/10.1093/nar/gkad893
Number of the records: 1