Singh, A;
Mishra, A;
Khosravi, A;
Khandelwal, G;
Jayaram, B;
(2017)
Physico-chemical fingerprinting of RNA genes.
Nucleic Acids Research
, 45
(7)
, Article e47. 10.1093/nar/gkw1236.
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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.
| Type: | Article |
|---|---|
| Title: | Physico-chemical fingerprinting of RNA genes |
| Open access status: | An open access version is available from UCL Discovery |
| DOI: | 10.1093/nar/gkw1236 |
| Publisher version: | http://dx.doi.org/10.1093/nar/gkw1236 |
| Language: | English |
| Additional information: | Copyright © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com. |
| Keywords: | Nucleic acid structure, Computational Methods |
| UCL classification: | UCL UCL > Provost and Vice Provost Offices UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute UCL > Provost and Vice Provost Offices > School of Life and Medical Sciences > Faculty of Medical Sciences > Cancer Institute > Research Department of Cancer Bio |
| URI: | https://discovery.ucl.ac.uk/id/eprint/10048596 |
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