Compatibility of 5-ethynyl-2'F-ANA UTP with in vitro selection for the generation of base-modified, nuclease resistant aptamers

Fabienne Levi-Acobas; Adam Katolik; Pascal Röthlisberger; Thomas Cokelaer; Ivo Sarac; Masad J Damha; Christian J Leumann; Marcel Hollenstein

doi:10.1039/c9ob01515a

Compatibility of 5-ethynyl-2'F-ANA UTP with in vitro selection for the generation of base-modified, nuclease resistant aptamers

Org Biomol Chem. 2019 Sep 21;17(35):8083-8087. doi: 10.1039/c9ob01515a. Epub 2019 Aug 28.

Authors

Fabienne Levi-Acobas¹, Adam Katolik², Pascal Röthlisberger¹, Thomas Cokelaer³, Ivo Sarac¹, Masad J Damha⁴, Christian J Leumann⁵, Marcel Hollenstein¹

Affiliations

¹ Institut Pasteur, Department of Structural Biology and Chemistry, Laboratory for Bioorganic Chemistry of Nucleic Acids, CNRS UMR 3523, 28, rue du Docteur Roux, 75724 Paris Cedex 15, France. marcel.hollenstein@pasteur.fr and Institut Pasteur, Department of Genome and Genetics, Paris, France.
² Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland and Department of Chemistry, McGill University, 801 Rue Sherbrooke Street West, Montréal, QC H3A 0B8, Canada.
³ Institut Pasteur, Bioinformatics and Biostatistics Hub, Department of Computational Biology, Institut Pasteur, USR 3756 CNRS, Paris, France and Institut Pasteur, Biomics Platform, C2RT, Paris, France.
⁴ Department of Chemistry, McGill University, 801 Rue Sherbrooke Street West, Montréal, QC H3A 0B8, Canada.
⁵ Department of Chemistry and Biochemistry, University of Bern, Freiestrasse 3, CH-3012 Bern, Switzerland.

PMID: 31460550
DOI: 10.1039/c9ob01515a

Abstract

A modified nucleoside triphosphate bearing two modifications based on a 2'-deoxy-2'-fluoro-arabinofuranose sugar and a uracil nucleobase equipped with a C5-ethynyl moiety (5-ethynyl-2'F-ANA UTP) was synthesized. This nucleotide analog could enzymatically be incorporated into DNA oligonucleotides by primer extension and reverse transcribed to unmodified DNA. This nucleotide could be used in SELEX for the identification of high binding affinity and nuclease resistant aptamers.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Aptamers, Nucleotide / chemistry*
Arabinose / analogs & derivatives*
Arabinose / chemistry
Binding Sites
Carbohydrate Conformation
DNA / chemistry
DNA / genetics
Uridine Triphosphate / chemistry*

Substances

Aptamers, Nucleotide
arabinofuranose
DNA
Arabinose
Uridine Triphosphate