Damha. Mapping the Affinity Landscape of Thrombin-binding Aptamers on 2'F-ANA/DNA Chimeric G-Quadruplex Microarrays

Swiss National Science Foundation [PBBEP2-146174 to J.L.]; Natural Sciences and Engineering Research Council of Canada [to M.J.D.]; Austrian Science Fund [FWF P23797 and FWF P27275 to J.L. and M.M.S.]; Spanish MINECO [BFU2014-52864-R to C.G.]. Funding for open access charge: Austrian Science Fund [FWF P23797 and FWF P27275 to J.L. and M.M.S.].Peer Reviewe

Mapping the affinity landscape of Thrombin-binding aptamers on 2′F-ANA/DNA chimeric G-Quadruplex microarrays

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.© The Author(s) 201