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ACS Chem Biol. 2019 Oct 7. doi: 10.1021/acschembio.9b00237. [Epub ahead of print]

Selection of 2'-Deoxy-2'-Fluoroarabino Nucleic Acid (FANA) Aptamers That Bind HIV-1 Integrase with Picomolar Affinity.

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Cell Biology and Molecular Genetics, Bioscience Research Building , University of Maryland , College Park , Maryland 20742 , United States.
Laboratory of Molecular Biology, NIDDK , National Institutes of Health , Bethesda , Maryland 20892 , United States.
Exobiology Branch, Space Science and Astrobiology Division , NASA Ames Research Center , Moffett Field , California 94035 , United States.
MRC Laboratory of Molecular Biology , Francis Crick Avenue, Cambridge Biomedical Campus , Cambridge CB2 0QH , United Kingdom.
Maryland Pathogen Research Institute (MPRI) , College Park , Maryland 20742 , United States.


Systematic Evolution of Ligands by Exponential Enrichment (SELEX) is the iterative process by which nucleic acids that can bind with high affinity and specificity (termed aptamers) to specific protein targets are selected. Using a SELEX protocol adapted for Xeno-Nucleic Acid (XNA) as a suitable substrate for aptamer generation, 2'-fluoroarabinonucleic acid (FANA) was used to select several related aptamers to HIV-1 integrase (IN). IN bound FANA aptamers with equilibrium dissociation constants (KD,app) of ∼50-100 pM in a buffer with 200 mM NaCl and 6 mM MgCl2. Comparisons to published HIV-1 IN RNA and DNA aptamers as well as IN genomic binding partners indicated that FANA aptamers bound more than 2 orders of magnitude more tightly to IN. Using a combination of RNA folding algorithms and covariation analysis, all strong binding aptamers demonstrated a common four-way junction structure, despite significant sequence variation. IN aptamers were selected from the same starting library as FA1, a FANA aptamer that binds with pM affinity to HIV-1 Reverse Transcriptase (RT). It contains a 20-nucleotide 5' DNA sequence followed by 59 FANA nucleotides. IN-1.1 (one of the selected aptamers) potently inhibited IN activity and intasome formation in vitro. Replacing the FANA nucleotides of IN-1.1 with 2'-fluororibonucleic acid (F-RNA), which has the same chemical formula but with a ribose rather than arabinose sugar conformation, dramatically reduced binding, suggesting that FANA adopts unique structural conformations that promote binding to HIV-1 IN.


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