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Old 03-13-2012, 09:14 AM   #1
DrDTonge
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Location: MRC

Join Date: May 2011
Posts: 23
Question Pippin Prep - cDNA musings...

Dear all,

We've purchased a Pippin Prep and are awaiting training to use the 3% for size selecting our small RNA libraries. Briefly, these comprise of 18 - 38nt inserts with adapters making a total of 60 -80nt following reverse transcription.

We're informed that we can use the Pippin to size select straight from the cDNA reaction although I have a query about this...

Our usual method is to run the cDNA down a denaturing gel (TBE-UREA) and excise the cDNA fragments in line with a denatured DNA ladder. Therefore both reference and sample are denatured.

Unless I'm missing something obvious, I can't work out how the native gels in the Pippin Prep can achieve this against a native DNA ladder...the first strand cDNA would be ss, whilst the reference ladder would be ds.

What am I missing???

D :-)
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