Journal of Proteomics & Bioinformatics
Open Access

Design and characterization of symmetric nucleic acids via molecular dynamics simulations

9^th International Conference on Structural Biology

September 18-20, 2017 Zurich, Switzerland

Pradeep Pant and B Jayaram

Indian Institute of Technology Delhi, India

Posters & Accepted Abstracts: J Proteomics Bioinform

Abstract :

Directionality (5��?��?3��?) is so fundamental to the nucleic acid architecture and is essential for replication and transcription. We observed that this asymmetry can be manipulated either by breaking (C3��? to C2��?) or making (C5��? to C2��?) chemical bond in each nucleotide unit leading to symmetric nucleic acids. Keeping their potential synthetic and therapeutic interest in mind, we designed a few novel symmetric nucleic acids. We investigated their conformational stability and flexibility via detailed all atom explicit solvent 100-ns long molecular dynamics simulations and compared the resulting structures with that of regular B-DNA. Quite interestingly, some of the symmetric nucleic acids retain the overall double helical structure indicating their potential for integration in physiological DNA without causing major structural perturbations.

Biography :

Pradeep Pant has done his Master’s in Chemistry from Indian Institute of Technology Delhi. He joined in the Department of Chemistry as a PhD scholar under the supervision of Prof. B. Jayaram in 2014. Currently, he is focusing on theoretical studies on the structure, dynamics and energetics of nucleic acid-protein/ligand interactions.