5MJX

2'F-ANA/DNA Chimeric TBA Quadruplex structure

Summary for 5MJX

• Entry DOI: 10.2210/pdb5mjx/pdb
• NMR Information: BMRB: 34071
• Descriptor: DNA (5'-D(*GP*GP*(FT)P*TP*GP*GP*TP*GP*TP*GP*GP*TP*TP*GP*G)-3') (1 entity in total)
• Functional Keywords: 2'f-ana/dna tba structure, structure from molmol, dna
• Biological source: synthetic construct
• Total number of polymer chains: 1
• Total formula weight: 4761.04

Authors

Lietard, J.,Abou Assi, H.,Gomez-Pinto, I.,Gonzalez, C.,Somoza, M.M.,Damha, M.J. (deposition date: 2016-12-02, release date: 2017-02-01, Last modification date: 2024-06-19)

Primary citation

Lietard, J.,Abou Assi, H.,Gomez-Pinto, I.,Gonzalez, C.,Somoza, M.M.,Damha, M.J.
Mapping the affinity landscape of Thrombin-binding aptamers on 2 F-ANA/DNA chimeric G-Quadruplex microarrays.
Nucleic Acids Res., 45:1619-1632, 2017

PubMed 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.

PubMed: 28100695
DOI: 10.1093/nar/gkw1357

Experimental method

SOLUTION NMR