Title

Targeting pseudoknots in H5N1 hemagglutinin using designed aptamers

Authors

Priyanka Dhar^1,*, Sayak Ganguli², Abhijit Datta²

Affiliation

¹Defence Institute of High Altitude Research, DRDO, C/o 56 APO, Pin- 901205, India; ²Bioinformatics Centre, Presidency College, Kolkata 700073, India

Email

priyanko_8@yahoo.co.in

Article Type

Hypothesis

Date

Received June 23, 2009; Revised July 07, 2009; Accepted September 09, 2009; Published October 25, 2009

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.
 

Keywords

H5N1, hemagglutinin, pseudoknot, ribosomal frameshifting, RNA aptamers

Citation

Dhar et al., Bioinformation 4(5): 193-196 (2009)

Edited by

P. Kangueane

ISSN

0973-2063

Publisher

Biomedical Informatics

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.