Ankita Singh, Akhilesh Mishra, Ali Khosravi, Garima Khandelwa and B Jayaram
Supercomputing Facility for Bioinformatics & Computational Biology IIT Delhi, India
Kusuma School of Biological Sciences IIT Delhi, India
Al-Taha Institute of Higher Education, Iran
The University of Manchester, UK
Indian Institute of Technology Delhi, India
Posters & Accepted Abstracts: Biochem Anal Biochem
Over the years, various computational methods have displayed a potential for fast and accurate characterization of genes. Majority of these methods are knowledge-based and involve sophisticated statistical and mathematical techniques for training and prediction. An alternative approach to solve this complex challenge is based on the hypothesis that different functional units on genomic DNA differ in their physicochemical properties, which, in principle, can be extracted from atomic models of DNA. The present work encompasses elucidation of physicochemical fingerprints for different functional units in prokaryotic and eukaryotic genomes on the basis of atomic level descriptions of oligonucleotides derived from molecular simulations. We advance here a novel concept for characterizing different classes of RNA genes on the basis of physicochemical properties of DNA sequences. As knowledge-based approaches could yield unsatisfactory outcomes due to limitations of training on available experimental datasets, alternative approaches which utilize properties intrinsic to DNA are needed to supplement training based methods and to eventually provide molecular insights into genome organization. Based on a comprehensive series of molecular dynamics simulations of Ascona B-DNA consortium, we extracted hydrogen bonding, stacking and solvation energies of all combinations of DNA sequences at the dinucleotide level and calculated these properties for different types of RNA genes. Considering ~7.3 million mRNA, 255524 tRNA, 40649 rRNA (different subunits) and 5250 miRNA, 3747 snRNA, gene sequences from 9282 complete genome chromosomes of all prokaryotes and eukaryotes available at NCBI, we observed that physicochemical properties of different functional units on genomic DNA differ in their signatures.
Ankita Singh is currently pursuing PhD from Indian Institute of Technology Delhi, India. Her research interests centers around the development of protein structural database for malarial parasites and advancing the quality assessment methodologies. She has her expertise in scoring and assessing the predicted protein tertiary structures with different parameters to select best predicted model.