Targeting pseudoknots in H5N1 hemagglutinin using designed aptamers |
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Authors: | Dhar Sayak Ganguli Abhijit Datta |
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Institution: | 1.Defence Institute of High Altitude Research, DRDO, C/o 56 APO, Pin- 901205, India;2.Bioinformatics Centre, Presidency College, Kolkata 700073, India |
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Abstract: | Influenza A virus subtype H5N1 is highly contagious among birds, causing high mortality among domestic poultry. The viral genome is
contained on eight single RNA strands of which HA encode the antigenic glycoprotein called hemagglutinin. Hemagglutinin found on the surface
of the influenza viruses and is responsible for binding the virus to the cell that is being infected. Among the most prevalent RNA structures the
pseudoknot motif represents an important piece of RNA architecture, as it provides a means for a single RNA strand to fold upon itself to produce
a globular structure capable of performing important biological functions. In this analysis we have identified the pseudoknot motifs in the
hemagglutinin gene of HPAI A (H5N1) Asian strains. Specific aptamers have been designed against these pseudoknots. These in-silico aptamers
can be used to hinder the ability of pseudoknots to facilitate ribosomal frameshifting. This may ultimately lead to reduce the coding efficiency of
the HA that encodes hemagglutinin and might be used as molecular medicine for H5N1. |
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Keywords: | H5N1 hemagglutinin pseudoknot ribosomal frameshifting RNA aptamers |
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