Aren't other methods suitable? Like the viral and the electroporation?
It depends on your purpose. For a clinician scientist like me without PhD tarining, Lipofectamine is easy to perform according to the protocol. I have tried electroporation in our primary endothelial cell culture for two years but never worked so we used and worked in one month. But, I will not say one method is better than the other. Whichever method work for me I will use it. Viral vector may be efficient but you will need to have higher level of protection for safety reason. Also, if you do not have the viral vector carried DNA or RNAS then you have to spend some time to do it.
I dont think Lipofectamine is someway specifically preferred for siRNAs. It works with some of the most difficult to transfect cells, which makes it popular choice (if money is not an issue!!).
We have very often used Hiperfect and Microporation with good success rate for siRNA transfection (Even though for the same cell lines, DNA transfection is better achieved with Lipofectamine!!).
I compared different lipoplex reagents to delivery an siRNA to inhibit the expression of our model gene EpCAM in SKOV-3 cells. In our hands SAINT-RED performed best under identical conditions (same amounts of siRNA) . The reagent is commercial available (see link). In the attached file more details about the experiment performed.
http://www.synvolux.com/sirna-transfection-reagent
We use nucleofector electroporation method to deliver siRNA and lentivirus for shRNA delivery. We do oligodendrocyte and neural stem cell primary culture from rodents, and at least for primary cultures, these methods are more efficient than lipid carrier for gene knockdown. We have not tried lipofectamine but used fugene HD. We only use it for delivering DNA into cell lines such as 293T.
Electroporation and virus both have their advantages and drawbacks. For electroporation in our system we usually get a 60%-70% knockdown rate. But you need a lot of cells for each electroporation experiment (about 5 million), or most cells will die. And you need to trypsinize the cells, and replate them after electroporation. The siRNA usually lasts for about 5 days so it is not permanent, same as lipid carriers. Virus delivery of shRNA is permanent and you may be able to make stable cell lines. And you can have a very efficient knockdown rate. You will also be able to identify if a particular cell is infected or not if your virus has GFP or antibiotic resistant gene. But virus production is time consuming (takes about a week for collection and concentration, and it is only enough for a few infections in my hands). If you need to subclone your shRNA into an empty backbone it takes another week or so. If you are new to the protocol, it may take a month to optimize everything. But you will be able to buy ready-to-use plasmids or virus particles if you prefer.
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