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doing it on a gel is painful and the gel extraction yield is low. does Pippin do ssRNA or ssDNA size selection?
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Pippin for ssRNA and ssDNA
Sage is working on ssDNA for the Pippin as I write this. ssRNA is much harder.
If you have a Pippin Prep, and if you have enough RNA to play with, you might try experimenting with timed cuts to estimate the the run parameters for the ssRNA you are interested in. It might work. If you would like to try it, then I can send some free cassettes.
You may want to look into the new Sage ELF (Electrophoretic Lateral Fractionator), which electrophoreses a gel lane, then automatically cross elutes the contents of the entire lane into 12 micro elution modules that are off the side and run the length of the lane. It should work well for ssDNA and ssRNA. There is a blurb about how it works on the Sage website (sage science.com).
Because the ELF cassettes also do not contain denaturants, there will be secondary structure effects, such that the rate of migration may change. Unlike Pippin, all of the fractions from a given sample are retained in the ELF, so the trick is figuring out which fraction holds the ssRNA of interest. A lot of secondary structure might land an otherwise lengthy ssRNA into a #9 elution module, whereas little secondary structure might land it #5.
Best, -
Gary
PS. Sage Science really tries to steer clear of promoting our products in forums, so as to keep the forums about science and clear of commercialization. I therefore apologize to everyone for the seemingly shameless Sage ELF plug above. I noted it only because I think it really is a potentially good solution and worth noting. -
Hi Gary,
Do you know if it would be possible to use a denaturing loading dye to denature the samples prior to running on the Pippin Prep or ELF? I frequently denature RNA with a formalin-based loading dye and heating at 65 for a while, then run on a standard pre-cast agarose gel. The RNA stays denatured for runs of up to 1 hour or so. I know that this would mess with the fraction collection on the Pippin, but shouldn't matter on the ELF.
Any word on when the ELF will be available?
Thanks,
BrettComment
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