Back
SiRNA sequence model: redesign algorithm based on available genome-wide libraries.
Journal article

SiRNA sequence model: redesign algorithm based on available genome-wide libraries.

  • Kozak K a LMSC, ETH Zurich , Schafmattstr, 18 CH-8093 , Zurich , Switzerland .
  • 2012-12-21
Published in:
  • Journal of biomolecular structure & dynamics. - 2013
Algorithms
Base Sequence
Blood Coagulation Factors
Gene Library
Genome, Human
Green Fluorescent Proteins
HeLa Cells
Humans
Microscopy, Fluorescence
Models, Genetic
Molecular Biology
RNA Interference
RNA, Small Interfering
English The evolution of RNA interference (RNAi) and the development of technologies exploiting its biology have enabled scientists to rapidly examine the consequences of depleting a particular gene product in cells. Design tools have been developed based on experimental data to increase the knockdown efficiency of siRNAs. Not all siRNAs that are developed to a given target mRNA are equally effective. Currently available design algorithms take an accession, identify conserved regions among their transcript space, find accessible regions within the mRNA, design all possible siRNAs for these regions, filter them based on multi-scores thresholds, and then perform off-target filtration. These different criteria are used by commercial suppliers to produce siRNA genome-wide libraries for different organisms. In this article, we analyze existing siRNA design algorithms and evaluate weight of design parameters for libraries produced in the last decade. We proved that not all essential parameters are currently applied by siRNA vendors. Based on our evaluation results, we were able to suggest an siRNA sequence pattern. The findings in our study can be useful for commercial vendors improving the design of RNAi constructs, by addressing both the issue of potency and the issue of specificity.
Language
  • English
Open access status
closed
Identifiers
Persistent URL
https://fredi.hepvs.ch/global/documents/143410
Statistics
Document views: 2 File downloads: