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[AVeen]

Hi everyone,

I'd like some advice on adapter design. I'm wanting to clone a ~550 piece of very structured RNA produced upon viral infection and I want to clone from mosquito and mammalian derived cell-lines. I'm looking to follow the standard protocol used for cloning of small RNAs, my only question is regarding the size of the oligo adapters. How big should they be? How can I check that the oligo is not complementary to the host genome? I think, ultimately this is sort of impossible, but how much % of complementarity of the adapter agaisnt the genome is acceptable and still get good ligation with your fragments? I was also thinking that I could use the standard adaptors (Hafner, Bartel, etc, etc)and add more nt if needed but I'm not sure exactly how many extra nt I need (seeing the size of adapters is the same lenght as small RNA and I can't afford to have a 500 nt adapter!).

Any help would be greatly appreciated it! I'm going nuts trying to work this out.

Thanks in advance,

AVeen