Hi  Pallabi, 

You can first cut the  gel segments of interest. Then use commercially available kits (I am using Qiagen gel extraction and purification kit) to extract DNA. This  extracted DNA can then be quantified using Qubit pico green assay method (or any other available methods to quantify DNA)

Thank you

Thank you for the answer..

I am aware of the assay you mentioned. I was looking for a simpler way because the no. of samples are many. And also I have already performed all the RT-PCRs. For Qubit pico assay, I need to redo all the experiments that will be time-consuming too. That's why I have mentioned the details of the PCR experiment. My query is if I could determine the concentration with the help of these primary information of PCR experiment.

Thank you.

Dear Pallabi,

I think only in an ideal PCR where you have exponential growth of the DNA concentration, it could be possible to calculate the resulting concentration of the DNA depending on the number of cycles and the initial concentration. Typically, in a "real" PCR the growth the DNA concentration is not exponential.

Did you run a DNA quantification ladder on your gel? Did you take a photo of the gel? Depending on the ladder volume that you transferred into the well, you can calculate the DNA mass of each ladder band. Using a software like ImageJ (free), you can plot the intensity of each ladder band depending on its mass/concentration and create a calibration lane for you gel. You can use this line to calculate, or at least to estimate, the DNA mass/concentration of a certain band of your PCR sample.

Best regards,

Emanuel