Affiliation
Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi-110016, IndiaIssue Date
2016-12-08
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We advance here a novel concept for characterizing different classes of RNA genes on the basis of physico-chemical properties of DNA sequences. As knowledge-based approaches could yield unsatisfactory outcomes due to limitations of training on available experimental data sets, alternative approaches that 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, 255 524 tRNA, 40 649 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 physico-chemical properties of different functional units on genomic DNA differ in their signatures.Citation
Physico-chemical fingerprinting of RNA genes. 2016, Nucleic Acids ResJournal
Nucleic Acids ResearchDOI
10.1093/nar/gkw1236PubMed ID
27932456Type
ArticleLanguage
enISSN
1362-4962ae974a485f413a2113503eed53cd6c53
10.1093/nar/gkw1236
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