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Book of Abstracts: Albany 2007

category image Albany 2007
Conversation 15
June 19-23 2007

Molecular Modelling Studies of Peptide Nucleic Acids

Peptide Nucleic Acids (PNA) bind sequence specifically to DNA/RNA and are of major interest for all fields of molecular biology and could form the basis for gene-targeted drugs. Modifications are introduced in PNA to overcome ambiguity in binding, to restrict conformational flexibility of backbone and to impart features for either DNA or RNA binding specificity. The addition of geometrical isomers (1R,2S/1S,2R)-aminocyclohexylglycyl in the backbone of PNA could be interesting and overcome the problems of PNA. The molecular dynamics (MD) simulations carried out to understand the effect of backbone modification on the structure and dynamics along with the stability of the resulting 10mer triplexes/duplexes of PNA with DNA/RNA of homologues/mixed sequence. A detailed study of MD simulation for all the mixed duplex systems to study structural and internal dynamics was carried out for 10 nanoseconds each. Such studies can help pharmaceutical companies to design novel molecules targeted towards DNA or RNA. Molecular Dynamics trajectories have been analyzed to probe and characterize the possible structures and internal dynamics involved in the PNA and (1R,2S/1S,2R)-aminocyclohexylglycyl PNAs.

References and Footnotes
  1. Nielson, P. E., Berg, R. Science 254, 163 (1991).
  2. Ray, A., Norden, B. FASEB J 14, 1041 (2000).
  3. Govindraju, T., Ganesh, K. N. Org Lett 5, 3013 (2003).

Smriti Sharma
Uddhavesh B Sonavane
Rajendra R Joshi*

Bioinformatics Team
Scientific Engineering and Computing Group
Centre for Development of Advanced Computing
Ganeshkhind, Pune University Campus
Pune ? 411007

Phone: +91-20-25704188
Fax: +91-20-25694081
Email: uddhaveshs@cdac.in
rajendra@cdac.in