I want to perform MTT. cell cycle, apoptosis and soft agar assays afters ASO (antisense oligonucleotides) based knockdown of lncRNAs, but I'm not sure how long last the effect of ASOs compare to siRNAs and if is possible to perform these type of experiments to see a phenotype as with siRNAs. I am using ASOs since I already try to knock down the lncRNA with siRNA but it didn't work
Dear Miguel, from own experience I know that it can be quite difficult to knock down lncRNAs with siRNAs and you may have to test a whole bunch to identify one that shows some knock down efficacy. For a few lncRNAs that have been tested so called siPOOLs have been proven quite potent, at least compared to normal siRNAs. A siPOOL is a complex pool of selected siRNAs that will target the lncRNA on multiple sites - so if one sequence stretch is involved in protein interaction or stem loop – and such is not available for interacting with your siRNA, then there is still a multitude of others, that will access your lncRNA target and mediate knock down. SiPOOls are generated on request – the company is called siTOOLs Biotech and they are located Germany. People known in the field like Sven Diederichs have successfully tested siPOOLs - so there seems to be something about the approach and may be worthwhile testing. I have not heard that antisense oligos are very potent in knocking down lncRNAs. You are talking about GAPmers – right? Again, you will have to test quite a few to find one that does the job. Maybe the siPOOLs can help you to move forward with your project. Good luck
stef
Thank you Stefan, antisense oligonucleotides or ASOs are from IDT (integrated DNA technologies), Kim Lennox is an expert on knocking down lncRNAs with these kind of molecules. Anyway I will check teh siPOOls thak you so much for your help
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