siRNA / RNAi /miRNA transfection Rat IEC-6

Short hairpin or small hairpin RNA (shRNA) is artificial RNA, which has a hairpin loop structure, and uses inherent microRNA (miRNA) machinery to silence target gene expression. This is called RNA interference (RNAi). These can be delivered via plasmids or viral/bacterial vectors. Challenges in shRNA-mediated gene silencing include 1. Off-target silencing, 2. Packaging shRNA encoding lentivirus, and 3. Stable transduction in cells. RNAi has been designed to have anywhere from 19-27 bs, but the most effective design has 19 bp. In case commercial shRNAs are not available, potential target sites can be chosen within exon, 5’- or 3’ UTR, depending on which splice variants of the gene are desired. One should use the latest algorithms and choose at least two different sequences, targeting different regions, in order to have confidence in overcoming off-target effects. A BLAST search after selecting potential design will eliminate potential off-target sequences. For the second challenge, sequencing the vector using primers for either strand (50-100 bp upstream) is suggested, along with using enzymatic digestion on agarose gel for the vector. Next, once the shRNA-containing vector is packaged in a virus, it is important to check the viral titer before transduction. Finally, using a marker in the lentiviral vector (fluorescent protein or antibiotic resistance), along with qPCR for target gene expression can help in determining the efficacy of transduction and shRNA on its target site.

Get tips on using PU.1 siRNA (m) to perform siRNA / miRNA gene silencing Mouse - RAW264.7 PU.1

Get tips on using ADAMTS13 siRNA to perform siRNA / miRNA gene silencing Human - HUVEC ADAMTS-13

Get tips on using siRNA SKIL to perform siRNA / miRNA gene silencing Human - LuCaP-77 SKIL

Get tips on using siRNA FOXS1 to perform siRNA / miRNA gene silencing Human - rh-36 FOXS1

Get tips on using siRNA FOXO1 to perform siRNA / miRNA gene silencing Human - CRL-5915 FOXO1

Get tips on using siRNA FOXO1 to perform siRNA / miRNA gene silencing Human - ACC-MESO1 FOXO1

Get tips on using siRNA RUNX3 to perform siRNA / miRNA gene silencing Human - KLM-1 RUNX3

Get tips on using siRNA RUNX3 to perform siRNA / miRNA gene silencing Human - SUIT-2 RUNX3

Get tips on using siRNA MMP2 to perform siRNA / miRNA gene silencing Human - SKOV-3 MMP2