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A computational analysis of antisense off-targets in prokaryotic organisms

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Date
2015-01-01
Authors
Worley-Morse, Thomas O
Gunsch, Claudia K
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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 article
Permalink
https://hdl.handle.net/10161/11463
Published Version (Please cite this version)
10.1016/j.ygeno.2014.11.010
Publication 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.
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Scholars@Duke

Gunsch

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
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