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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.


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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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