Hemagglutinin aptamer

May 1, 2024 • Jiali Wang, Bo Fu

Description

In 2005, Misono TS and Kumar PK used Surface Plasma Resonance (SPR) technology, also known as Biocore technology, to select and analyze RNA aptamers with high affinity for human influenza virus hemagglutinin (HA). The Kd value of wild-type aptamer clone A for HA is approximately 200 pM, while the newly discovered sequence clone B has a Kd value of 115 ± 23 pM for HA^[1].

SELEX

In 2005, Misono TS and Kumar PK started with an RNA library containing approximately 10¹³ sequences, and after five rounds of screening, multiple high-affinity RNA aptamers clone sequences were ultimately obtained. Approximately 50% of these sequences exhibit high affinity binding to the target protein. Among these sequences, approximately 35% are wild-type sequences and 16% are newly discovered sequences^[1].
Detailed information are accessible on SELEX page.

Structure

The 2D structure of the figure is based on the article by ribodraw tool to draw. Clone B aptamer binds to Hemagglutinin influenza virus (HA influenza virus)^[1].

5'-GGGAGAAUUCCGACCAGAAGGGUUAGCGGUCGUCUUAAGUAGUUUUUGGUCCUUUCCUCUCUCCUUCCUCUUCU-3'

Ligand information

SELEX ligand

Haemagglutinin (HA) is one of two main surface fusion glycoproteins embedded in the envelope of influenza viruses, the other being neuraminidase (NA). There are sixteen known HA subtypes (H1-H16) and nine NA subtypes (N1-N9), which together are used to classify influenza viruses (e.g. H5N1). The antigenic variations in HA and NA enable the virus to evade host antibodies made to previous influenza strains, accounting for recurrent influenza epidemics. The HA glycoprotein is present in the viral membrane as a single polypeptide (HA0), which must be cleaved by the host's trypsin-like proteases to produce two peptides (HA1 and HA2) in order for the virus to be infectious. Once HA0 is cleaved, the newly exposed N-terminal of the HA2 peptide then acts to fuse the viral envelope to the cellular membrane of the host cell, which allows the viral negative-stranded RNA to infect the host cell. The type of host protease can influence the infectivity and pathogenicity of the virus.-----From Pfam

Name	Uniprot ID	Pfam	MW	Amino acids sequences	PDB	Gene ID
Hemagglutinin (HA)	A0A097PF13	IPR000149	63.635 kDa	MKTIIALSYILCLVFAQKLPGNDNSTATLCLGHHAVSNGTLVKTITNDQIEVTNATELVQSSSTGRICDSPHQILDGENCTLIDALLGDPHCDGFQNKEWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVAQNGTSSACKRRSNKSFFSRLNWLHQLNYKYPALNVTMPNNEKFDKLYIWGVLHPSTDSDQISLYAQASGRVTVSTKRSQQTVIPNIGSRPWVRGVSSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQINGKLNRLIEKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVVLLGFIMWACQKGNIRCNICI	NA	AY832929.1

Some isolated sequences bind to the affinity of the protein.

Name	Sequence	Ligand	Affinity
clone A	5'-GGGAGAAUUCCGACCAGAAGGGUUAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU-3'	HA	200 pM
clone B	5'-GGGAGAAUUCCGACCAGAAGGGUUAGCGGUCGUCUUAAGUAGUUUUUGGUCCUUUCCUCUCUCCUUCCUCUUCU-3'	HA	115 ± 23 pM

References

[1] Selection of RNA aptamers against human influenza virus hemagglutinin using surface plasmon resonance.
Misono, T. S., & Kumar, P. K.
Analytical biochemistry, 342(2), 312–317. (2005)