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RNA INTERFERENCE 7
psiRNA System
InvivoGen provides a plasmid-based system developed to knockdown efficiently the expression of a wide variety
of mammalian genes. This system represents a simple and affordable method to generate short hairpin RNAs
(shRNAs) by eliminating the need to synthesize RNA oligonucleotides.
The psiRNA System is designed to assist you in all the steps necessary to obtain efficient silencing of a gene of
interest from the selection of an effective siRNA/shRNA to its prevalidation.
• Selection of Candidate siRNA/shRNA and Design of Hairpin Insert:
siRNA Wizard Software - www.sirnawizard.com
The design of siRNAs and short hairpin RNAs (shRNAs) remains an empirical process since the
molecular mechanisms underlying RNAi are not yet sufficiently understood to allow for their
rational design. However, based on the research from various laboratories including our own,
InvivoGen has been able to develop siRNA Wizard, a free software accessible online from our
homepage, that will help you do the following:
➥ Select Candidate siRNA/shRNAs
The siRNA Wizard algorithm allows to select effective and specific siRNAs/shRNAs against your
gene of interest based on thermodynamic and sequence-related criteria. Two search options are
available:
- Standard Search
“Standard Search” uses default criteria described in the “siRNA/shRNA Design Guidelines”
paragraph to select several candidate siRNAs/shRNAs against your gene of interest.
- Advanced Search
“Advanced Search” lets you manually set the selection criteria.
➥ Design Hairpin Insert
Using your selected siRNA/shRNA sequence, this tool will design two complementary
oligonucleotides necessary to create the hairpin insert for psiRNA cloning vectors and let you
choose the sequence of the loop.
➥ Generate siRNA/shRNA Scramble Sequence
This tool will return a scramble sequence with no match with any mRNA of the selected species
database. This scramble sequence that serves as a negative control contains the same nucleotide
composition as the selected siRNA/shRNA sequence.
• Cloning of siRNA/shRNA Insert: psiRNA-h7SK Plasmids
InvivoGen provides psiRNA-h7SK, a family of cloning vectors featuring the human 7SK RNA
polymerase III promoter and a choice of selection markers (see page 144). psiRNA-h7SK plasmids
exploit the white/blue selection system to facilitate the screening of recombinant bacterial clones.
Furthermore, they feature a GFP::Zeo fusion gene that allows to evaluate transfection efficiency
and normalize silencing experiments.
psiRNA-h7SK plasmids are provided in a kit that contains, in addition to the cloning vector, two
control vectors, and a set of tools designed to facilitate the cloning of shRNAs in the plasmid. The
psiRNA-h7SK tools are the following:
- E. coli GT116 & GT115
- Sequencing Primers
- Fast-Media ® X-Gal & X-Gluc
142 www.invivogen.com/psirna-system
“Standard Search” Selection Criteria
Target gene trimming
> > > > > > > > >
Thermodynamic analysis
GC content analysis
Termination signal exclusion
Secondary structure avoidance
Immunostimulatory motif exclusion
BLAST search
3’ UTR/seed region analysis
(optional)
siRNAs/shRNAs failing the selection
are rejected
Effective and specific
siRNAs/shRNAs