5mjx: Difference between revisions

<tr id='resources'><td class="sblockLbl"><b>Resources:</b></td><td class="sblockDat"><span class='plainlinks'>[http://oca.weizmann.ac.il/oca-docs/fgij/fg.htm?mol=5mjx FirstGlance], [http://oca.weizmann.ac.il/oca-bin/ocaids?id=5mjx OCA], [http://pdbe.org/5mjx PDBe], [http://www.rcsb.org/pdb/explore.do?structureId=5mjx RCSB], [http://www.ebi.ac.uk/pdbsum/5mjx PDBsum], [http://prosat.h-its.org/prosat/prosatexe?pdbcode=5mjx ProSAT]</span></td></tr>

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.

Mapping the affinity landscape of Thrombin-binding aptamers on 2'F-ANA/DNA chimeric G-Quadruplex microarrays.,Lietard J, Abou Assi H, Gomez-Pinto I, Gonzalez C, Somoza MM, Damha MJ Nucleic Acids Res. 2017 Jan 18. pii: gkw1357. doi: 10.1093/nar/gkw1357. PMID:28100695<ref>PMID:28100695</ref>

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</StructureSection>

[[Category: Damha, M J]]

[[Category: Somoza, M M]]

[[Category: 2'f-ana/dna tba structure]]

[[Category: Dna]]

[[Category: Structure from molmol]]