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Dharmafect 3

Manufactured by Horizon Discovery
Sourced in United States, United Kingdom

DharmaFECT 3 is a transfection reagent designed for the efficient delivery of small interfering RNA (siRNA) and other nucleic acids into a variety of mammalian cell types. It facilitates the uptake of nucleic acids by cells, enabling gene silencing and other applications. The product specifications and performance characteristics are available from the manufacturer.

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27 protocols using dharmafect 3

1

Bladder Cancer Cell Knockdown

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Cells were transfected with the indicated siRNAs in the presence of DharmaFECT 1 (#T-2001-03, Horizon Discovery, Cambridge, UK) (HT-1376, UM-UC-6, VM-CUB-1, T24, JON, and TCC-SUP-G), DharmaFECT 3 (#T-2003-03, Horizon Discovery, Cambridge, UK) (5637 and UM-UC-10), DharmaFECT 4 (#T-2004-03, Horizon Discovery, Cambridge, UK) (UM-UC-3) or RNAiMAX (#13778150, Thermo Fisher Scientific (Waltham, MA, USA)) (CAL-29, J82, and RT-112); according to the manufacturer’s instruction with a final siRNA concentration of 90 nM (DharmaFECT 1, 3 and 4) or 50 nM (RNAiMAX). The sequences of the siRNAs (Stealth RNAi™ siRNAs; Life Technologies) used in the experiments are as follows: siCtrl: 5′-GAAAGUCCUAGAUCCACACGCAAAU-3′; siKMT9α#1: 5′-ACGCUGUAACAAAGUUCACAUUCAA-3′; and siKMT9α#2: 5′-CACGCUGUAACAAAGUUCACAUUCA-3′.
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2

Targeted Knockdown of EP300 and CREBBP

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SMARTPool EP300 siGENOME siRNA (M-003486-04-0010) and SMARTPool CREBBP ON-TARGETplus siRNA (L-003477-00-0010) were purchased from Horizon Discovery/Dharmacon. siRNA transfection in HDFs were performed using DharmaFECT 3 (Horizon Discovery/Dharmacon) according to the manufacturer’s instructions.
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3

Efficient Knockdown of Target Genes

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Cells were transfected with 50nM siRNA using Dharmafect 3 (Dharmacon) as per the manufacturer’s instructions in Gibco™ Opti-MEM™ Reduced Serum Media supplemented with 10% FCS. Cells were maintained for 48 hrs for full knock-down before harvesting for further experiments. siRNA sequences are as follows: siTFAP2C 1: CACAGAACUUCUCAGCCAA, siTFAP2C 2:GCUAUUGGCGGCCCAGCAA, siRnd3 1: GACAAAGGAATCTAGTGTA, siRnd3 2:CAGATTGGAGCAGCTACTT, siMKX 1:GAAACCACUCGGGAUCUUU, siMKX 2:CAAGCAAGGAUGACACGUA, siMKX 3:CAAGCAAGGAUGACACGUA.
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4

Modulation of Myotube Signaling Pathways

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Where pharmacological inhibitors were used, myotubes were pre-treated for 1 h with 1 μM SB203580 and 0.1 μM BIRB796, 1 μM JNK V inhibitor, or vehicle (DMSO), before being treated with CM containing the same substances for 16 h. Where siRNA was employed, C2C12s were transfected with 50 nM nonsense or p38α MAPK-targeting siRNA pool using Dharmafect 3 (Dharmacon, Fisher Scientific, Loughborough, UK) on day 2 of differentiation and then left for 72 h before treatment with CM. Where TNFα blockade was undertaken, half of the CM for each treatment group contained 10 μg/ml of blocking antibody (eBioscience, Hatfield, UK), added before and during myotube incubation with control, palmitic acid or LPS-treated macrophage-CM for 16 h.
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5

ARNT Knockdown Effect on HUVEC Glucose Response

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ARNT knockdown was induced by small interfering RNA (siRNA) directed against ARNT (Ambion, Carlsbad, CA, United States) in HUVECs. HUVECs were transfected with 25 nM of non-targeted or ARNT siRNA mixed with the siRNA transfection reagent Dharma FECT 3 (GE Healthcare Dharmacon). The mixtures were incubated in serum-free medium for 20 min at room temperature before being added to the HUVECs. siRNA transfection was allowed to proceed for 48 h before harvesting whole cells for RNA isolation for real-time PCR. Cells were treated with high glucose followed by 12 h of starvation. Cells in the high glucose (HG) group were cultured in 35 mmol/L D-glucose media (Sigma). Identical concentrations of medium containing 5.5 mmol/L D-glucose plus 29.5 mmol/L mannitol served as the normal glucose (NG) control group. To test whether reactive oxygen species (ROS) inhibitors have a role in the rescue of cell death, MMVECs were pretreated with PBS or mito-TEMPO (Sigma-Aldrich) at 0.5 μM for 30 min before HG was added.
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6

Silencing Cyclophilin B and Cell Cycle Regulators

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The fluorescently labelled siRNA targeting cyclophilin B (siGLO) was selected as this did not influence the phenotype of either EP or DS cultures (Figure S12). HMECs were transfected with 60 nM siGLO siRNA (Dharmacon) or p16 siRNA (Qiagen) in 384‐well plates using Dharmafect 3 (Dharmacon). HMFs were transfected with 30 nM siGLO siRNA or p16 siRNA or p21 siRNA (Dharmacon) in 384‐well plates or 6‐well plates using Dharmafect 2 (Dharmacon). DS + siGLO, DS + p16 siRNA, DS + p21 siRNA or DS + p16 + p21 siRNA cells were harvested for RTqPCR, Western blotting or immunofluorescence as detailed below.
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7

Cell Culture Conditions for HEK-293, U2OS, and HeLa

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HEK-293, U2OS, and HeLa cells were grown in high-glucose DMEM (Gibco) supplemented with 10% (vol/vol) FCS (Sigma-Aldrich) and penicillin-streptomycin (Gibco) and maintained in an incubator at 37°C and 5% CO2. Cell lines were regularly tested for mycoplasma contamination. For siRNA transfection, Dharmafect-3 (Dharmacon) was used for U2OS cells, while Lipofectamine 2000 (Life Technologies) was used for HeLa cells. All siRNAs were made by Dharmacon or MWG. For DNA transfection, Fugene 6 and Fugene HD (Promega) were used according to the manufacturers’ guidelines.
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8

Silencing Bovine Chondrocyte Sox9 Expression

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Bovine sox9 siRNA (ON-TARGETplus Custom SMARTpool) was synthesized by Dharmacon (Table I). To determine whether this sox9 siRNA efficiently silences sox9 expression, adult bovine articular chondrocytes were transfected with sox9 siRNA or non-targeting siRNA (Dharmacon) according to manufacturer’s instructions. After 3 days in culture, the medium was replaced with 2ml complete medium and cells were transfected using 4 µl/well DharmaFECT3 (Dharmacon) and 10 µl of 20 µM sox9 siRNA. ON-TARGETplus non-targeting siRNA was used for mock-transfection. After 16 h, siRNA transfection was stopped by replacing the medium with 4ml of fresh complete medium supplemented with the designated growth factor(s), 50 ng/ml FGF-2 or the combination of 200 ng/ml IGF-I with 100 ng/ml BMP-2 and 100 ng/ml BMP-7. Fresh complete medium without growth factors was used as control. On days 2 and 4 after transfection, conditioned medium was harvested and replaced with basal medium containing 0.1% BSA and the designated growth factor(s) as described above. Basal medium containing 0.1% BSA without growth factors was used as control. On day 6 after transfection, conditioned medium and cell layer were harvested separately.
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9

Modulating MYC and RAD17 in Cells

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Control siRNA A (Santa Cruz Biotechnology #sc 37007), RAD17 siRNA (Santa Cruz Biotechnology # sc 36358) or MYC siRNA (Santa Cruz Biotechnology #sc-29226) was transfected into cells using DharmaFECT 3 (Dharmacon #T-2003-01).
pcDNA3-EV, pcDNA3-MYC (from the Jianjun Chen lab in the Department of Systems Biology at the Beckman Research Institute of City of Hope) and pCMV6-RAD17 (ORIGENE CAT#: RC215866) constructs were transfected into the cells using Lipofectamine 2000 (ThermoFisher Scientific Invitrogen #11668030).
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10

Silencing Pja1 and Ezh2 in C2C12 and Satellite Cells

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Down-regulation of Pja1 and Ezh2 expression in C2C12 and satellite cells was achieved by siRNA using ON-TARGETplus SMARTpool - mouse PJA1, SMARTpool- mouse EZH2 or ON-TARGETplus Non-targeting Pool (Dharmacon) as a control. RNA interference was performed according to Dharmafect3 (Dharmacon) transfection protocol.
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