A computational analysis of antisense off-targets in prokaryotic organisms
Abstract
© 2014 .The adoption of antisense gene silencing as a novel disinfectant for prokaryotic
organisms is hindered by poor silencing efficiencies. Few studies have considered
the effects of off-targets on silencing efficiencies, especially in prokaryotic organisms.
In this computational study, a novel algorithm was developed that determined and sorted
the number of off-targets as a function of alignment length in Escherichia coli K-12
MG1655 and Mycobacterium tuberculosis H37Rv. The mean number of off-targets per a
single location was calculated to be 14.1. ±. 13.3 and 36.1. ±. 58.5 for the genomes
of E. coli K-12 MG1655 and M. tuberculosis H37Rv, respectively. Furthermore, when
the entire transcriptome was analyzed, it was found that there was no general gene
location that could be targeted to minimize or maximize the number of off-targets.
In an effort to determine the effects of off-targets on silencing efficiencies, previously
published studies were used. Analyses with acpP, ino1, and marORAB revealed a statistically
significant relationship between the number of short alignment length off-targets
hybrids and the efficacy of the antisense gene silencing, suggesting that the minimization
of off-targets may be beneficial for antisense gene silencing in prokaryotic organisms.
Type
Journal articlePermalink
https://hdl.handle.net/10161/11463Published Version (Please cite this version)
10.1016/j.ygeno.2014.11.010Publication Info
Worley-Morse, Thomas O; & Gunsch, Claudia K (2015). A computational analysis of antisense off-targets in prokaryotic organisms. Genomics, 105(2). pp. 123-130. 10.1016/j.ygeno.2014.11.010. Retrieved from https://hdl.handle.net/10161/11463.This is constructed from limited available data and may be imprecise. To cite this
article, please review & use the official citation provided by the journal.
Collections
More Info
Show full item recordScholars@Duke
Claudia K. Gunsch
Professor in the Department of Civil and Environmental Engineering
Claudia Gunsch is a Professor of Civil and Environmental Engineering and holds secondary
appointments in the Nicholas School of the Environment and the Department of Biomedical
Engineering. She joined the Duke Faculty in 2004 after obtaining her PhD from the
University of Texas at Austin, her MS from Clemson University and her BS from Purdue
University. Currently, she serves as the Director for PreMiEr, the National Science
Foundation Engineering Research Center for Precis

Articles written by Duke faculty are made available through the campus open access policy. For more information see: Duke Open Access Policy
Rights for Collection: Scholarly Articles
Works are deposited here by their authors, and represent their research and opinions, not that of Duke University. Some materials and descriptions may include offensive content. More info