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Title

 

 

 

 

 

Targeting pseudoknots in H5N1 hemagglutinin using designed aptamers

Authors

 

Priyanka Dhar1,*, 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.