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Sirna duplex oligonucleotides

Manufactured by Thermo Fisher Scientific
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SiRNA duplex oligonucleotides are synthetic RNA molecules that are used to induce RNA interference (RNAi) in cells. They consist of a double-stranded RNA structure designed to target and silence specific genes by binding to and degrading the corresponding messenger RNA (mRNA) molecules. These oligonucleotides are a key tool for studying gene function and can be used in a variety of cell-based applications.

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6 protocols using sirna duplex oligonucleotides

1

Silencing LSR and Tricellulin in Sawano Cells

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siRNA duplex oligonucleotides against LSR and tricellulin were synthesized by Thermo Fisher Scientific (Waltham, MA). At 24h after plating, Sawano cells were transfected with siRNAs of LSR and tricellulin using Lipofectamine™ RNAiMAX Reagent (Invitrogen).
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2

Silencing LSR, AREG, YAP, and AMOT in Sawano Cells

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siRNA duplex oligonucleotides against LSR (forward sense 5′-CCCACGCAACCCAUCGUCAUCUGGA-3′, reverse sense 5′-UCCAGAUGACGAUGGGUUGCGUGGG-3′) were synthesized by Thermo Fisher Scientific (Waltham, MA). siRNA duplex oligonucleotides against AMOT (sc-72489), YAP (sc-38637) and AREG (sc-39412) were synthesized by SantaCruz Biotechnology, Inc. (Santa Cruz, CA). A scrambled siRNA sequence (BLOCK-iT Alexa Fluor fluorescent, Invitrogen) was employed as control siRNA. At 24 h after plating, Sawano cells were transfected with 100 nM siRNAs of LSR, AREG, YAP and AMOT using LipofectamineTM RNAiMAX Reagent (Invitrogen). Some cells were transfected with 100 nM siRNA of LSR with or without 10 μM dobutamine, 500 μM 2-DG and glucose-free medium (Glucose free MEM, Sigma-Aldrich).
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3

FLAG-tagged Kinase Expression Vectors

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The expression vectors for FLAG-tagged MEKK1, FLAG-MEKK2, V5-tagged STK38, and V5-ΔN STK38 were previously described26 (link). Site-directed mutagenesis was performed using a Prime STAR Mutagenesis kit (Takara Bio). The sequences of the ORFs in the constructed plasmids were confirmed by DNA sequencing. The mammalian STK38 shRNA expression vector was described previously26 (link). Synthetic siRNA duplex oligonucleotides specific for regions in human MEKK2 (MAP3K2) mRNA were designed and synthesised by Invitrogen (Carlsbad, CA). The target sequences were as follows (only the antisense sequence is shown).
Stealth siRNA MEKK2 #662: 5′-GGAACUGCUGGAUCGUAGUAUUCAU-3′.
Stealth siRNA MEKK2 #663: 5′-CCAAUAACGAGUUGGUAAUUCCAUU-3′.
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4

Luciferase Reporter Assay with siRNA

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Cells were transfected with plasmids or siRNA oligonucleotides using Lipofectamine2000 (Invitrogen). For Luciferase reporter assays, the pRL-TK renilla luciferase was served as a normalizing control. One day after transfection, cells were treated with MG132 for an additional 2 h, and cell lysates were subjected to dual luciferase assays (Promega). For RNA interference, siRNA duplex oligonucleotides or scramble oligonucleotides were synthesized (Invitrogen). In total, 100 pmol siRNA was added in one well from a six-wells plate. The siRNA sequences are provided in Supplementary Table 3.
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5

Targeted siRNA Silencing of ChREBP in Caco-2 Cells

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The small interfering RNA (siRNA) duplex oligonucleotides targeting human ChREBP were selected and synthesized by Invitrogen (StealthTM RNAi, Carlsbad, CA, USA). The control siRNA oligonucleotides were purchased from Genolution (Seoul, Republic of Korea). The siRNA sequences were as follows: siChREBP forward 5′-CCAAGUGGAAGAAUUUCAAAGGCCU-3′, reverse 5′-AGGCCUUUGAAAUUCUUCCACUUGG-3′; siC forward 5′-CCUCGUGCCGUUCCAUCAGGUAGUU-3′; reverse 5′-CUACCUGAUGGAACGGCACGAGGUU-3′. For gene silencing or overexpression, Caco-2BBE cells were transfected with siRNAs or plasmids containing human ChREBP, Mlx, and β-galactosidase. The proximal region of Glut5 (–2165/+0) was amplified from mouse genomic DNA using PCR and inserted into the pGL4 basic vector (mGlut5-2165) [8]. All transfections were performed using reverse transfection. RNAiMAX (Thermo Fisher Carlsbad, CA, USA) and X-tremeGENE HP DNA transfection (Roche Diagnostics, Indianapolis, IN, USA) reagents were used for gene silencing and overexpression, respectively. Following 24 h of transfection, fresh DMEM containing 10% fetal bovine serum with 1% non-essential amino acids was added into individual wells of 24-well plates, followed by Dex treatment 24 h after media addition.
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6

Plasmid Transfection and siRNA Knockdown

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The full-length Epas1 plasmid was purchased from Youbio (Hunan, China). The pCMV-FLAG-FLCN plasmid was constructed as previously reported, using the following primer set. The above constructs were confirmed via DNA sequencing. The cells were seeded in a six-well plate, cultured to 80–90% confluence, and then transfected with Epas1 and pCMV-FLAG-FLCN plasmids, respectively, by using FuGENE HD Transfection Reagent (Promega Corporation, Madison, WI, USA).
The non-specific control siRNA and siRNAs for FLCN and EPAS1 were purchased from GenePharma (Shanghai, China). The cells were transfected with siRNA Duplex oligonucleotides using Lipofectamine 2000 (Invitrogen), according to the transfection method provided by the manufacturer. The siRNAs are listed in Table 1.
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