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Treat with RNAse and spec at 260. A spec can definitely be used. The extinction coefficient (Beers Lamberts Law) will not be calculating measuring NTPs, just intact dsDNA.


Nanodrop may be fine for the volumes but as you rightly guessed it is not so easy to distinguish DNA from RNA (and primers). Qubit (invitrogen) is a sensitive, dye based quantification assay. You can use that for estimating cDNA yield. The kit contains different dyes for DNA, RNA and protein estimation.

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