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Structural and Functional Aspects of G-Quadruplex Aptamers Which Bind a Broad Range of Influenza A Viruses

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Chemistry Department, Lomonosov Moscow State University, 119991 Moscow, Russia
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Engelhardt Institute of Molecular Biology RAS, 119991 Moscow, Russia
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Chumakov Federal Scientific Centre for Research and Development of Immune and Biological Products RAS, 108819 Moscow, Russia
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Belozersky Research Institute of Physical Chemical Biology, Lomonosov Moscow State University, 119991 Moscow, Russia
*
Author to whom correspondence should be addressed.
Biomolecules 2020, 10(1), 119; https://doi.org/10.3390/biom10010119
Received: 13 December 2019 / Revised: 5 January 2020 / Accepted: 7 January 2020 / Published: 10 January 2020
An aptamer is a synthetic oligonucleotide with a unique spatial structure that provides specific binding to a target. To date, several aptamers to hemagglutinin of the influenza A virus have been described, which vary in affinity and strain specificity. Among them, the DNA aptamer RHA0385 is able to recognize influenza hemagglutinins with highly variable sequences. In this paper, the structure of RHA0385 was studied by circular dichroism spectroscopy, nuclear magnetic resonance, and size-exclusion chromatography, demonstrating the formation of a parallel G-quadruplex structure. Three derivatives of RHA0385 were designed in order to determine the contribution of the major loop to affinity. Shortening of the major loop from seven to three nucleotides led to stabilization of the scaffold. The affinities of the derivatives were studied by surface plasmon resonance and an enzyme-linked aptamer assay on recombinant hemagglutinins and viral particles, respectively. The alterations in the loop affected the binding to influenza hemagglutinin, but did not abolish it. Contrary to aptamer RHA0385, two of the designed aptamers were shown to be conformationally homogeneous, retaining high affinities and broad binding abilities for both recombinant hemagglutinins and whole influenza A viruses. View Full-Text
Keywords: DNA aptamer; G-quadruplex; influenza virus; hemagglutinin; affinity; structure–activity relationship DNA aptamer; G-quadruplex; influenza virus; hemagglutinin; affinity; structure–activity relationship
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Novoseltseva, A.A.; Ivanov, N.M.; Novikov, R.A.; Tkachev, Y.V.; Bunin, D.A.; Gambaryan, A.S.; Tashlitsky, V.N.; Arutyunyan, A.M.; Kopylov, A.M.; Zavyalova, E.G. Structural and Functional Aspects of G-Quadruplex Aptamers Which Bind a Broad Range of Influenza A Viruses. Biomolecules 2020, 10, 119.

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