Synthetic RNAs for gene regulation: Design principles and computational tools

Alessandro Laganà, Dennis Shasha, Carlo Maria Croce

Research output: Contribution to journalShort surveypeer-review


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.

Original languageEnglish (US)
Article number65
JournalFrontiers in Bioengineering and Biotechnology
Issue numberDEC
StatePublished - 2014


  • A-miR
  • AntagomiR
  • MiRNA
  • RNAi
  • SiRNA
  • Sponge

ASJC Scopus subject areas

  • Biotechnology
  • Bioengineering
  • Histology
  • Biomedical Engineering


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