Computing Molecular Devices in L.major through Transcriptome Analysis: Structured Simulation Approach

PloS One
Pruthvi Raj Bejugam, Shailza Singh

Abstract

In the modern era of post genomics and transcriptomics, non-coding RNAs and non-coding regions of many RNAs are a big puzzle when we try deciphering their role in specific gene function. Gene function assessment is a main task wherein high throughput technologies provide an impressive body of data that enables the design of hypotheses linking genes to phenotypes. Gene knockdown technologies and RNA-dependent gene silencing are the most frequent approaches to assess the role of key effectors in a particular scenario. Ribozymes are effective modulators of gene expression because of their simple structure, site-specific cleavage activity, and catalytic potential. In our study, after an extensive transcriptomic search of Leishmania major transcriptome we found a Putative ATP dependent DNA helicase (Lmjf_09_0590) 3' UTR which has a structural signature similar to well-known HDV hammerhead ribozyme, even though they have variable sequence motifs. Henceforth, to determine their structural stability and sustainability we analyzed our predicted structural model of this 3'UTR with a 30ns MD simulation, further confirmed with 100ns MD simulation in presence of 5mM MgCl2 ionic environment. In this environment, structural stability was sign...Continue Reading

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Citations

Apr 16, 2018·International Journal of Biological Macromolecules·Pruthvi Raj Bejugam, Shailza Singh

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Methods Mentioned

BETA
MDS
in
ribozyme

Software Mentioned

Desmond
MC Cons
Deformation Profile ( DP )
Ligplot
Interactive Network Fidelity ( INF )
PHENIX
LigPlot +
Viparr
RegRNA
Sym

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