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

• Published in: Biomolecules (Basel, Switzerland) Vol. 10; no. 1; p. 119
• Main Authors: Novoseltseva, Anastasia A, Ivanov, Nikita M, Novikov, Roman A, Tkachev, Yaroslav V, Bunin, Dmitry A, Gambaryan, Alexandra S, Tashlitsky, Vadim N, Arutyunyan, Alexander M, Kopylov, Alexey M, Zavyalova, Elena G
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 10.01.2020; MDPI
• Subjects: Affinity; Annealing; Aptamers; Aptamers, Nucleotide - chemistry; Aptamers, Nucleotide - pharmacology; Avian flu; Base Sequence; Circular dichroism; dna aptamer; Experiments; g-quadruplex; G-Quadruplexes; hemagglutinin; Hemagglutinin Glycoproteins, Influenza Virus - genetics; Hemagglutinin Glycoproteins, Influenza Virus - metabolism; Hemagglutinins; Humans; Influenza A; Influenza A virus - drug effects; Influenza A virus - genetics; Influenza A virus - metabolism; influenza virus; Influenza, Human - drug therapy; Influenza, Human - virology; NMR; Nuclear magnetic resonance; Nucleotides; Oligonucleotides; Phylogeny; Potassium; Protein Binding; Sodium; Spectroscopy; Spectrum analysis; Structure-function relationships; structure–activity relationship; Surface plasmon resonance; Viruses; Sweden; Vietnam; United Kingdom > UK; United States > US; England; Germany; Russia; influenza virus; structure–activity relationship; DNA aptamer; hemagglutinin; G-quadruplex; affinity
• ISSN: 2218-273X; 2218-273X
• DOI: 10.3390/biom10010119

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.