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Site Directed Mutagenesis (SDM) Human

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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 have 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 efficacy of transduction and shRNA on its target site.

RNA shRNA gene silencing Human Islets of langerhans SOX6 lentiviral particles

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.

RNA shRNA gene silencing Human Neuroblastoma cells (SH-SY5Y) Beclin 1

Get tips on using siGENOME Human PDCD1LG2 (80380) siRNA - SMARTpool to perform siRNA / miRNA gene silencing Human - M244 PD-L2

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Get tips on using siGENOME Human PPARD (5467) siRNA - SMARTpool to perform siRNA / miRNA gene silencing Human - DU145 PPAR-delta

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Get tips on using siGENOME Human ATG12 (9140) siRNA - SMARTpool to perform siRNA / miRNA gene silencing Human - BT-20 Atg12

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Get tips on using siGENOME Human RAB5A (5868) siRNA - SMARTpool to perform siRNA / miRNA gene silencing Human - BT-20 Rab5a

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Wound healing assay can be challenging due to inconsistencies and variations while making a wound on the confluent cell monolayer, consequently leads to wounds of varying sizes and widths. Moreover, this assay causes damage to the cells that are at the edge of the wound, which can prevent cell migration into the wound site and healing. The best solution is to use the standard wound healing assay kits using either combs or inserts to make a defined wound field or gap and prevent the well-to-well variation in these assays.

Cellular assays Wound healing assay cell type human MDA-MB-231

Get tips on using siGENOME Human ATG7 (10533) siRNA - SMARTpool to perform siRNA / miRNA gene silencing Human - LN-18 ATG-7

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Get tips on using siGENOME Human MAPKAPK2 (9261) siRNA - SMARTpool to perform siRNA / miRNA gene silencing Human - LN-18 MK2/MAPKAPK2

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Get tips on using siGENOME Human RIPK3 (11035) siRNA - SMARTpool to perform siRNA / miRNA gene silencing Human - LN-18 RIP3/RIPK3

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