The Functional Role of Loops and Flanking Sequences of G-Quadruplex Aptamer to the Hemagglutinin of Influenza a Virus

Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is the G-quadruple...

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Published in:	International journal of molecular sciences Vol. 22; no. 5; p. 2409
Main Authors:	Bizyaeva, Anastasia A, Bunin, Dmitry A, Moiseenko, Valeria L, Gambaryan, Alexandra S, Balk, Sonja, Tashlitsky, Vadim N, Arutyunyan, Alexander M, Kopylov, Alexey M, Zavyalova, Elena G
Format:	Journal Article
Language:	English
Published:	Switzerland MDPI AG 27-02-2021 MDPI
Subjects:	Affinity Amino acid sequence Animals Aptamers Aptamers, Nucleotide - chemistry Aptamers, Nucleotide - metabolism Avian flu Binding Biomolecules Chickens Cricetinae DNA aptamer Enzymes G-quadruplex G-Quadruplexes hemagglutinin Hemagglutinin Glycoproteins, Influenza Virus - chemistry Hemagglutinin Glycoproteins, Influenza Virus - metabolism Hemagglutinins Homology Influenza A Influenza A virus - metabolism influenza virus Nucleic acids Nucleotides Orthomyxoviridae Infections - metabolism Orthomyxoviridae Infections - virology Proteins Sensors structure−activity relationship Virions Viruses influenza virus structure−activity relationship DNA aptamer hemagglutinin G-quadruplex affinity
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Summary:	Nucleic acid aptamers are generally accepted as promising elements for the specific and high-affinity binding of various biomolecules. It has been shown for a number of aptamers that the complexes with several related proteins may possess a similar affinity. An outstanding example is the G-quadruplex DNA aptamer RHA0385, which binds to the hemagglutinins of various influenza A virus strains. These hemagglutinins have homologous tertiary structures but moderate-to-low amino acid sequence identities. Here, the experiment was inverted, targeting the same protein using a set of related, parallel G-quadruplexes. The 5'- and 3'-flanking sequences of RHA0385 were truncated to yield parallel G-quadruplex with three propeller loops that were 7, 1, and 1 nucleotides in length. Next, a set of minimal, parallel G-quadruplexes with three single-nucleotide loops was tested. These G-quadruplexes were characterized both structurally and functionally. All parallel G-quadruplexes had affinities for both recombinant hemagglutinin and influenza virions. In summary, the parallel G-quadruplex represents a minimal core structure with functional activity that binds influenza A hemagglutinin. The flanking sequences and loops represent additional features that can be used to modulate the affinity. Thus, the RHA0385-hemagglutinin complex serves as an excellent example of the hypothesis of a core structure that is decorated with additional recognizing elements capable of improving the binding properties of the aptamer.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1422-0067 1661-6596 1422-0067
DOI:	10.3390/ijms22052409