title: Mapping the affinity landscape of Thrombin-binding aptamers on 2΄F-ANA/DNA chimeric G-Quadruplex microarrays.
abstract: In situ fabricated nucleic acids microarrays are versatile and very high-throughput platforms for aptamer optimization and discovery, but the chemical space that can be probed against a given target has largely been confined to DNA, while RNA and non-natural nucleic acid microarrays are still an essentially uncharted territory. 2΄-Fluoroarabinonucleic acid (2΄F-ANA) is a prime candidate for such use in microarrays. Indeed, 2΄F-ANA chemistry is readily amenable to photolithographic microarray synthesis and its potential in high affinity aptamers has been recently discovered. We thus synthesized the first microarrays containing 2΄F-ANA and 2΄F-ANA/DNA chimeric sequences to fully map the binding affinity landscape of the TBA1 thrombin-binding G-quadruplex aptamer containing all 32 768 possible DNA-to-2΄F-ANA mutations. The resulting microarray was screened against thrombin to identify a series of promising 2΄F-ANA-modified aptamer candidates with Kds significantly lower than that of the unmodified control and which were found to adopt highly stable, antiparallel-folded G-quadruplex structures. The solution structure of the TBA1 aptamer modified with 2΄F-ANA at position T3 shows that fluorine substitution preorganizes the dinucleotide loop into the proper conformation for interaction with thrombin. Overall, our work strengthens the potential of 2΄F-ANA in aptamer research and further expands non-genomic applications of nucleic acids microarrays.
authors.affiliation: Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria.|Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada.
authors.forename: Jory
authors.initials: J
authors.lastname: Lietard
authors.affiliation: Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada.
authors.forename: Hala
authors.initials: H
authors.lastname: Abou Assi
authors.affiliation: Instituto de Química Física 'Rocasolano', CSIC, 28006 Madrid, Spain.
authors.forename: Irene
authors.initials: I
authors.lastname: Gómez-Pinto
authors.affiliation: Instituto de Química Física 'Rocasolano', CSIC, 28006 Madrid, Spain.
authors.forename: Carlos
authors.initials: C
authors.lastname: González
authors.affiliation: Institute of Inorganic Chemistry, Faculty of Chemistry, University of Vienna, Althanstraße 14 (UZA II), 1090 Vienna, Austria.
authors.forename: Mark M
authors.initials: MM
authors.lastname: Somoza
authors.affiliation: Department of Chemistry, McGill University, 801 Rue Sherbrooke O, Montréal, QC H3A 0B8, Canada.
authors.forename: Masad J
authors.initials: MJ
authors.lastname: Damha
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry*; D001088:Arabinonucleotides / Q000737:chemistry*; D001483:Base Sequence; D004247:DNA / Q000737:chemistry*; D054856:G-Quadruplexes; D009682:Magnetic Resonance Spectroscopy; D008958:Models, Molecular; D020411:Oligonucleotide Array Sequence Analysis; D009943:Organophosphorus Compounds / Q000737:chemistry
chemical_list: C507672:2'-deoxy-2'-fluoro-beta-D-arabinonucleic acid; D052157:Aptamers, Nucleotide; D001088:Arabinonucleotides; D009943:Organophosphorus Compounds; C434331:phosphoramidite; C081676:thrombin aptamer; D004247:DNA