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Structural Basis for the KlenTaq DNA Polymerase Catalysed Incorporation of Alkene- versus Alkyne-Modified Nucleotides.

Hottin A, Betz K, Diederichs K, Marx A
Chemistry 23 2109-2118 (2017)
Cited: 17 times
EuropePMC logo PMID: 27901305

Abstract

Efficient incorporation of modified nucleotides by DNA polymerases is essential for many cutting-edge biomolecular technologies. The present study compares the acceptance of either alkene- or alkyne-modified nucleotides by KlenTaq DNA polymerase and provides structural insights into how 7-deaza-adenosine and deoxyuridine with attached alkene-modifications are incorporated into the growing DNA strand. Thereby, we identified modified nucleotides that prove to be superior substrates for KlenTaq DNA polymerase compared with their natural analogues. The knowledge can be used to guide future design of functionalized nucleotide building blocks.

Reviews - 5szt mentioned but not cited (1)

  1. Recent progress in dissecting molecular recognition by DNA polymerases with non-native substrates. Pugliese KM, Weiss GA. Curr Opin Chem Biol 41 43-49 (2017)

Articles - 5szt mentioned but not cited (1)

  1. Non-Covalent Interactions between dUTP C5-Substituents and DNA Polymerase Decrease PCR Efficiency. Zasedateleva OA, Surzhikov SA, Kuznetsova VE, Shershov VE, Barsky VE, Zasedatelev AS, Chudinov AV. Int J Mol Sci 24 13643 (2023)


Reviews citing this publication (3)

  1. Labelling of DNA and RNA in the cellular environment by means of bioorthogonal cycloaddition chemistry. Ganz D, Harijan D, Wagenknecht HA. RSC Chem Biol 1 86-97 (2020)
  2. The Structural Basis for Processing of Unnatural Base Pairs by DNA Polymerases. Marx A, Betz K. Chemistry 26 3446-3463 (2020)
  3. Applications of Ruthenium Complexes Covalently Linked to Nucleic Acid Derivatives. Flamme M, Clarke E, Gasser G, Hollenstein M. Molecules 23 E1515 (2018)

Articles citing this publication (12)

  1. De novo DNA synthesis using polymerase-nucleotide conjugates. Palluk S, Arlow DH, de Rond T, Barthel S, Kang JS, Bector R, Baghdassarian HM, Truong AN, Kim PW, Singh AK, Hillson NJ, Keasling JD. Nat Biotechnol 36 645-650 (2018)
  2. Crystal structures of ternary complexes of archaeal B-family DNA polymerases. Kropp HM, Betz K, Wirth J, Diederichs K, Marx A. PLoS One 12 e0188005 (2017)
  3. Expanding the Scope of RNA Metabolic Labeling with Vinyl Nucleosides and Inverse Electron-Demand Diels-Alder Chemistry. Kubota M, Nainar S, Parker SM, England W, Furche F, Spitale RC. ACS Chem Biol 14 1698-1707 (2019)
  4. Snapshots of a modified nucleotide moving through the confines of a DNA polymerase. Kropp HM, Dürr SL, Peter C, Diederichs K, Marx A. Proc Natl Acad Sci U S A 115 9992-9997 (2018)
  5. Structural Basis for Expansion of the Genetic Alphabet with an Artificial Nucleobase Pair. Betz K, Kimoto M, Diederichs K, Hirao I, Marx A. Angew Chem Int Ed Engl 56 12000-12003 (2017)
  6. 1,2,4-Triazine-Modified 2'-Deoxyuridine Triphosphate for Efficient Bioorthogonal Fluorescent Labeling of DNA. Peewasan K, Wagenknecht HA. Chembiochem 18 1473-1476 (2017)
  7. Enzymatic synthesis of hypermodified DNA polymers for sequence-specific display of four different hydrophobic groups. Ondruš M, Sýkorová V, Bednárová L, Pohl R, Hocek M. Nucleic Acids Res 48 11982-11993 (2020)
  8. 2-Allyl- and Propargylamino-dATPs for Site-Specific Enzymatic Introduction of a Single Modification in the Minor Groove of DNA. Matyašovský J, Pohl R, Hocek M. Chemistry 24 14938-14941 (2018)
  9. Modified nucleoside triphosphates in bacterial research for in vitro and live-cell applications. Espinasse A, Lembke HK, Cao AA, Carlson EE. RSC Chem Biol 1 333-351 (2020)
  10. Epigenetic Pyrimidine Nucleotides in Competition with Natural dNTPs as Substrates for Diverse DNA Polymerases. Pospíšil Š, Panattoni A, Gracias F, Sýkorová V, Hausnerová VV, Vítovská D, Šanderová H, Krásný L, Hocek M. ACS Chem Biol 17 2781-2788 (2022)
  11. Phenothiazine-linked nucleosides and nucleotides for redox labelling of DNA. Simonova A, Havran L, Pohl R, Fojta M, Hocek M. Org Biomol Chem 15 6984-6996 (2017)
  12. Superanionic DNA: enzymatic synthesis of hypermodified DNA bearing four different anionic substituents at all four nucleobases. Kuprikova N, Ondruš M, Bednárová L, Riopedre-Fernandez M, Slavětínská LP, Sýkorová V, Hocek M. Nucleic Acids Res 51 11428-11438 (2023)


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