Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate

Marie Flamme; Pascal Röthlisberger; Fabienne Levi-Acobas; Mohit Chawla; Romina Oliva; Luigi Cavallo; Gilles Gasser; Philippe Marlière; Piet Herdewijn; Marcel Hollenstein

doi:10.1021/acschembio.0c00396

Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate

Marie Flamme, Pascal Röthlisberger, Fabienne Levi-Acobas, Mohit Chawla, Romina Oliva, Luigi Cavallo, Gilles Gasser, Philippe Marlière, Piet Herdewijn, Marcel Hollenstein

Research output: Contribution to journal › Article › peer-review

24 Scopus citations

Abstract

The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC-AgI-dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC-AgI-dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.

Original language	English (US)
Journal	ACS Chemical Biology
DOIs	https://doi.org/10.1021/acschembio.0c00396
State	Published - Oct 22 2020

Bibliographical note

KAUST Repository Item: Exported on 2020-10-30
Acknowledgements: M.F. gratefully acknowledges a fellowship from the doctoral school MTCI University of Paris Descartes. The authors gratefully acknowledge financial support from Institut Pasteur. We thank Mr. Germain Niogret for his help for the preparation of the cover picture featuring this article. The start-up company DNA Script is acknowledged for help in the UPLC-MS analysis of the oligonucleotides. L.C. and M.C.
acknowledge King Abdullah University of Science and Technology (KAUST) for support and the KAUST Supercomputing Laboratory for providing computational resources of the supercomputer Shaheen II. R.O. thanks MIUR-FFABR (Fondo per il Finanziamento Attività Base di Ricerca) for funding. This work was financially supported by an ERC Consolidator Grant PhotoMedMet to G.G. (GA 681679) and has received support under the program “Investissements d’ Avenir” launched by the French Government and implemented by the ANR with the reference ANR-10-IDEX-0001-02 PSL (G.G.).

Access to Document

10.1021/acschembio.0c00396

Cite this

@article{1d8510a0697a43069a8d436157cb6840,

title = "Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate",

abstract = "The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC-AgI-dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC-AgI-dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.",

author = "Marie Flamme and Pascal R{\"o}thlisberger and Fabienne Levi-Acobas and Mohit Chawla and Romina Oliva and Luigi Cavallo and Gilles Gasser and Philippe Marli{\`e}re and Piet Herdewijn and Marcel Hollenstein",

note = "KAUST Repository Item: Exported on 2020-10-30 Acknowledgements: M.F. gratefully acknowledges a fellowship from the doctoral school MTCI University of Paris Descartes. The authors gratefully acknowledge financial support from Institut Pasteur. We thank Mr. Germain Niogret for his help for the preparation of the cover picture featuring this article. The start-up company DNA Script is acknowledged for help in the UPLC-MS analysis of the oligonucleotides. L.C. and M.C. acknowledge King Abdullah University of Science and Technology (KAUST) for support and the KAUST Supercomputing Laboratory for providing computational resources of the supercomputer Shaheen II. R.O. thanks MIUR-FFABR (Fondo per il Finanziamento Attivit{\`a} Base di Ricerca) for funding. This work was financially supported by an ERC Consolidator Grant PhotoMedMet to G.G. (GA 681679) and has received support under the program “Investissements d{\textquoteright} Avenir” launched by the French Government and implemented by the ANR with the reference ANR-10-IDEX-0001-02 PSL (G.G.).",

year = "2020",

month = oct,

day = "22",

doi = "10.1021/acschembio.0c00396",

language = "English (US)",

journal = "ACS Chemical Biology",

issn = "1554-8929",

publisher = "American Chemical Society",

}

TY - JOUR

T1 - Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate

AU - Flamme, Marie

AU - Röthlisberger, Pascal

AU - Levi-Acobas, Fabienne

AU - Chawla, Mohit

AU - Oliva, Romina

AU - Cavallo, Luigi

AU - Gasser, Gilles

AU - Marlière, Philippe

AU - Herdewijn, Piet

AU - Hollenstein, Marcel

N1 - KAUST Repository Item: Exported on 2020-10-30 Acknowledgements: M.F. gratefully acknowledges a fellowship from the doctoral school MTCI University of Paris Descartes. The authors gratefully acknowledge financial support from Institut Pasteur. We thank Mr. Germain Niogret for his help for the preparation of the cover picture featuring this article. The start-up company DNA Script is acknowledged for help in the UPLC-MS analysis of the oligonucleotides. L.C. and M.C. acknowledge King Abdullah University of Science and Technology (KAUST) for support and the KAUST Supercomputing Laboratory for providing computational resources of the supercomputer Shaheen II. R.O. thanks MIUR-FFABR (Fondo per il Finanziamento Attività Base di Ricerca) for funding. This work was financially supported by an ERC Consolidator Grant PhotoMedMet to G.G. (GA 681679) and has received support under the program “Investissements d’ Avenir” launched by the French Government and implemented by the ANR with the reference ANR-10-IDEX-0001-02 PSL (G.G.).

PY - 2020/10/22

Y1 - 2020/10/22

N2 - The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC-AgI-dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC-AgI-dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.

AB - The expansion of the genetic alphabet with additional, unnatural base pairs (UBPs) is an important and long-standing goal in synthetic biology. Nucleotides acting as ligands for the coordination of metal cations have advanced as promising candidates for such an expansion of the genetic alphabet. However, the inclusion of artificial metal base pairs in nucleic acids mainly relies on solid-phase synthesis approaches, and very little is known about polymerase-mediated synthesis. Herein, we report the selective and high yielding enzymatic construction of a silver-mediated base pair (dImC-AgI-dPurP) as well as a two-step protocol for the synthesis of DNA duplexes containing such an artificial metal base pair. Guided by DFT calculations, we also shed light into the mechanism of formation of this artificial base pair as well as into the structural and energetic preferences. The enzymatic synthesis of the dImC-AgI-dPurP artificial metal base pair provides valuable insights for the design of future, more potent systems aiming at expanding the genetic alphabet.

UR - http://hdl.handle.net/10754/665713

UR - https://pubs.acs.org/doi/10.1021/acschembio.0c00396

U2 - 10.1021/acschembio.0c00396

DO - 10.1021/acschembio.0c00396

M3 - Article

C2 - 33090769

SN - 1554-8929

JO - ACS Chemical Biology

JF - ACS Chemical Biology

ER -

Enzymatic Formation of an Artificial Base Pair Using a Modified Purine Nucleoside Triphosphate

Abstract

Bibliographical note

Access to Document

Other files and links

Fingerprint

Cite this