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Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases

  1. 1.
    SYSNO ASEP0577106
    Document TypeJ - Journal Article
    R&D Document TypeJournal Article
    Subsidiary JČlánek ve WOS
    TitleSuperanionic 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, ORCID
    Source TitleNucleic Acids Research. - : Oxford University Press - ISSN 0305-1048
    Roč. 51, č. 21 (2023), s. 11428-11438
    Number of pages11 s.
    Languageeng - English
    CountryUS - United States
    Keywordspolymerase-catalyzed incorporation ; functionalized DNA ; primer extension
    OECD categoryOrganic chemistry
    R&D ProjectsGX20-00885X GA ČR - Czech Science Foundation (CSF)
    Method of publishingOpen access
    Institutional supportUOCHB-X - RVO:61388963
    UT WOS001090289000001
    EID SCOPUS85178500386
    DOI10.1093/nar/gkad893
    AnnotationWe 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.
    WorkplaceInstitute of Organic Chemistry and Biochemistry
    Contactasep@uochb.cas.cz ; Kateřina Šperková, Tel.: 232 002 584 ; Jana Procházková, Tel.: 220 183 418
    Year of Publishing2024
    Electronic addresshttps://doi.org/10.1093/nar/gkad893
Number of the records: 1  

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