How do I quantitate how much duplex product I have obtained?

Probably the best way would be to run an aliquot of the annealed product alongside unannealed material on a non-denaturing polyacrylamide gel. You could end label your oligos in order to visualize the material or back-shadow the gel with a UV light, the advantage to labeling would be that you could use a very small fraction of your material in the analysis.

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