Nanodrop vs Picogreen to quantify post-PCR product - (Mar/03/2014 )

Dear all,

I wonder if it is the right subforum to ask, but since it has something to do with PCR product, I'm gonna ask here.

I purified my PCR product (excised the single band, and using column from roche kit to purify it) and I want to use this product as standard for the absolute quantification real-time PCR project. Thing is, I have to know the exact concentration of this purified PCR product, so that I can convert the concentration (ng/ul) to copy molecules/ul using Avogadro equation. From the journal, the researchers use picogreen to quantify that purified PCR product, but since I don't have such the equipment nor the reagen, I wonder if it is okay to quantify the purification product's concentration with Nanodrop?

I really hope you guys can help me with my question.

Thank you.

Cheers,

Dee

It's probably ok to use the Nanodrop after purification. Picogreen is good because it is less sensitive to ssDNA or nucleotides.  But you have eliminated most of those with gel purification.

You have to consider that you also lose DNA during the purification.

Thank you :)