If the bait and prey interact, which component is activated?
The readout of yeast two-hybrid depends on reconstitution of a functional transcription factor at the reporter locus. Bait-DNA-binding domain fusion and prey-activation domain fusion individually cannot activate transcription. Interaction bridges them, positioning the activation domain at upstream activating sequences of reporter genes such as HIS3, ADE2, or lacZ. This triggers recruitment of Mediator and RNA polymerase II, leading to measurable transcription. Reporter activation therefore serves as indirect but powerful evidence of protein-protein association inside living yeast nuclei under physiological conditions.
Ref: NCERT Biology Class XII Principles on Klenow fill-in labeling, Lehninger Chapter 9 DNA cloning techniques, and Molecular Cloning by Sambrook Chapter 10 documenting end-labeling of cohesive termini.