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Front Bioeng Biotechnol. 2014 Dec 11;2:65. doi: 10.3389/fbioe.2014.00065. eCollection 2014.

Synthetic RNAs for Gene Regulation: Design Principles and Computational Tools.

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Department of Molecular Virology, Immunology and Medical Genetics, Comprehensive Cancer Center, The Ohio State University , Columbus, OH , USA.
Courant Institute of Mathematical Sciences, New York University , New York, NY , USA.


The use of synthetic non-coding RNAs for post-transcriptional regulation of gene expression has not only become a standard laboratory tool for gene functional studies but it has also opened up new perspectives in the design of new and potentially promising therapeutic strategies. Bioinformatics has provided researchers with a variety of tools for the design, the analysis, and the evaluation of RNAi agents such as small-interfering RNA (siRNA), short-hairpin RNA (shRNA), artificial microRNA (a-miR), and microRNA sponges. More recently, a new system for genome engineering based on the bacterial CRISPR-Cas9 system (Clustered Regularly Interspaced Short Palindromic Repeats), was shown to have the potential to also regulate gene expression at both transcriptional and post-transcriptional level in a more specific way. In this mini review, we present RNAi and CRISPRi design principles and discuss the advantages and limitations of the current design approaches.


AntagomiR; CRISPRi; RNAi; Sponge; a-miR; miRNA; siRNA

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