Hi Chitti Raju Khandavalli . If you plan to do imaging with a microscope, you should use YFP (or any other fluorescent protein or label) since you want to measure fluorescence intensity. Luciferase is a bioluminescent reporter that requires cofactors (e.g. ATP and metal ions) as well as a chemical substrate to facilitate an enzymatic reaction to produce quantifiable light signal.

Building off of what Johanna Marie Dela Cruz said, luciferase assays are far more sensitive than YFP. Luciferase is commonly employed when testing promoter regions or 3' UTR regulation.

Johanna Marie Dela Cruz ,John Hardy Lockhart thanks for your suggestions ,I am planning to test the 3 UTRs for Wild Type and Mutant whether I can do quantification or not

I agree with Johanna Marie Dela Cruz and John Hardy Lockhart. Detection/Imaging systems used for capturing the signals (bioluminescence or YFP) have software packages included which can be used for quantification. You can also use ImageJ (NIH, USA) for quantitating signals/images. ImageJ is free and quite easy to use for different analyses. Once downloaded and installed, you can access "help" and get detailed information and resources about how to use all features.

If you plan on using YFP, I'd encourage you to use flow cytometry to supplement fluorescence microscopy, particularly if you are introducing the reporters using transfection. You can also use Western blotting as more direct measure of the YFP expression level.

John Hardy Lockhart yeah that can be done. Thanks for the helpful advice!