title: Physico-chemical fingerprinting of RNA genes.
abstract: 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.
authors.affiliation: Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
authors.forename: Ankita
authors.initials: A
authors.lastname: Singh
authors.affiliation: Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.|Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
authors.forename: Akhilesh
authors.initials: A
authors.lastname: Mishra
authors.affiliation: Ale-Taha Institute of Higher Education, Tehran, Iran.
authors.forename: Ali
authors.initials: A
authors.lastname: Khosravi
authors.affiliation: Cancer Research UK Manchester Institute, The University of Manchester, Wilmslow Road, Manchester M20 4BX, UK.
authors.forename: Garima
authors.initials: G
authors.lastname: Khandelwal
authors.affiliation: Supercomputing Facility for Bioinformatics & Computational Biology, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.|Kusuma School of Biological Sciences, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.|Department of Chemistry, Indian Institute of Technology, Hauz Khas, New Delhi-110016, India.
authors.forename: B
authors.initials: B
authors.lastname: Jayaram
mesh_terms: D004247:DNA / Q000737:chemistry; D005796:Genes; D006860:Hydrogen Bonding; D056004:Molecular Dynamics Simulation; D012333:RNA, Messenger / Q000235:genetics*; D022661:RNA, Untranslated / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D012333:RNA, Messenger; D022661:RNA, Untranslated; D004247:DNA