The article details the protocol for site-specific transfection of scrambled sequence of siRNA in an adherent mammalian cell culture using a microelectrode array (MEA).
The discovery of RNAi pathway in eukaryotes and the subsequent development of RNAi agents, such as siRNA and shRNA, have achieved a potent method for silencing specific genes1-8 for functional genomics and therapeutics. A major challenge involved in RNAi based studies is the delivery of RNAi agents to targeted cells. Traditional non-viral delivery techniques, such as bulk electroporation and chemical transfection methods often lack the necessary spatial control over delivery and afford poor transfection efficiencies9-12. Recent advances in chemical transfection methods such as cationic lipids, cationic polymers and nanoparticles have resulted in highly enhanced transfection efficiencies13. However, these techniques still fail to offer precise spatial control over delivery that can immensely benefit miniaturized high-throughput technologies, single cell studies and investigation of cell-cell interactions.
Recent technological advances in gene delivery have enabled high-throughput transfection of adherent cells14-23, a majority of which use microscale electroporation. Microscale electroporation offers precise spatio-temporal control over delivery (up to single cells) and has been shown to achieve high efficiencies19, 24-26. Additionally, electroporation based approaches do not require a prolonged period of incubation (typically 4 hours) with siRNA and DNA complexes as necessary in chemical based transfection methods and lead to direct entry of naked siRNA and DNA molecules into the cell cytoplasm. As a consequence gene expression can be achieved as early as six hours after transfection27. Our lab has previously demonstrated the use of microelectrode arrays (MEA) for site-specific transfection in adherent mammalian cell cultures17-19. In the MEA based approach, delivery of genetic payload is achieved via localized micro-scale electroporation of cells. An application of electric pulse to selected electrodes generates local electric field that leads to electroporation of cells present in the region of the stimulated electrodes. The independent control of the micro-electrodes provides spatial and temporal control over transfection and also enables multiple transfection based experiments to be performed on the same culture increasing the experimental throughput and reducing culture-to-culture variability.
Here we describe the experimental setup and the protocol for targeted transfection of adherent HeLa cells with a fluorescently tagged scrambled sequence siRNA using electroporation. The same protocol can also be used for transfection of plasmid vectors. Additionally, the protocol described here can be easily extended to a variety of mammalian cell lines with minor modifications. Commercial availability of MEAs with both pre-defined and custom electrode patterns make this technique accessible to most research labs with basic cell culture equipment.
1. MEA Preparation
2. Seeding Cells on the MEA
3. Site-specific Transfection of siRNA
4. Electroporation Parameter Optimization
5. Representative Results
Figure 1 shows the site-specific loading of HeLA cells with PI. It can be observed that only cells on the electrode demonstrate an uptake of PI (Figure 1B). A live assay performed post electroporation was used to assess the viability of cells (Figure 1A). The electroporation efficiency and cell viability for the example shown in Figure 1 are 81.8 % and 96.1 % respectively. High cell viability and electroporation efficiency can be achieved by optimizing the electroporation pulse parameters. Site-specific transfection of HeLA cells with fluorescently tagged siRNA for an optimized electroporation pulse (8 V, 1 msec) is shown in Figure 2. The electroporation efficiency for the siRNA at 8 V, 1 msec was found to be 74.4 ± 16.0 % and cell viability was found to be 87.9 ± 8.4 % (all data represented as mean ± standard deviation, N=5).
Figure 1. Site-specific delivery of PI in HeLa cells on a 200 μm electrode (6 V, 5 msec). A) Calcien based live assay performed 2 hr post electroporation. Alive cells are indicated by green fluorescence. B) Red fluorescence demonstrates the uptake of PI by cells on the electrode. C) A superimposed image of A and B. The white arrows indicate cells that are electroporated and alive. The black arrows indicate cells that are dead. The white circle in A, B and C indicates the outline of the electrode.
Figure 2. Transfection of HeLa cells with fluorescently tagged scramble sequence of siRNA. A) Image of HeLa cells on a 100 μm electrode transfected with Alexa 488 tagged siRNA (8 V, 1 msec). B) Image of cell nuclei stained with DAPI. The white circle marks the edge of the electrode.
In this video article we demonstrate the use of MEA for site-specific transfection of HeLa cells with scrambled sequence of siRNA. One of the advantages of this technology is its applicability to different cell lines including primary cell lines. Our lab has previously demonstrated the use of this technology for site-specific transfection of primary hippocampal neuronal culture from E18 day old rat and NIH-3T3 cells with scrambled siRNA sequences and GFP plasmid18, 19. We have also had success in delivering functional siRNA against an endogenous target in HeLa cells (unpublished data). A typical commercially available MEA is compatible with optical imaging (upright microscope), enabling quantitative assessment of functional impact of gene silencing, using fluorescent immunostaining techniques. Additionally, the microelectrodes in MEA can be used to monitor electrical activity of cells, such as primary neurons, in response to genetic perturbation. The unique nature of MEA enables simultaneous multiple experiments on a single cell culture, thereby increasing the experimental throughput. Currently a major limitation with the MEA based system is the large amount of siRNA needed for transfection (400 μl of 1μM siRNA), which is high compared to conventional chemical transfection based approaches and thus limits the cost effectiveness of the system. This can partly be overcome by incorporating mircofluidics with the MEA based system to decrease the total volume of siRNA electroporation solution to less than a few microliters. Additionally, the microfluidics can enable serial delivery of different siRNA molecules; thereby greatly enhancing the throughput of the MEA based technology. Alternatively, siRNA molecules can be spotted on the microelectrodes prior to cell seeding and then the siRNA molecules can be transfected into cells by reverse electroporation15, 23. Further development of this technology offers a novel high-throughput, efficient and low cost method for gene manipulation studies.
The authors have nothing to disclose.
Name of the reagent | Company | Catalogue number | Comments (optional) |
Cell media: Advanced MEM L-Glutamine 200 mM Penicillin/Streptomycin Fetal bovine serum |
Gibco/Invitrogen Himedia Laboratories/VWR Lonza group Ltd. Gibco/Invitrogen |
12492-013 95057-448 09-757F 16000-044 |
Cell media composition: 2% FBS, 2%L-glutamine and 2% Pennstrep in Advance MEM |
Trypsin EDTA | Mediatech, Inc. | 25-053-CL | |
PBS | Mediatech, Inc. | 21-040-CV | |
Alexa 488 and rhodamine tagged scrambled sequence siRNA | Qiagen, Inc. | 1027292 | |
Electroporation buffer | Biorad Laboratories | 165-2677 | |
Waveform generator | Pragmatic | 2414A | Any waveform/pulse generator that can deliver the desired pulses can be used. |