What does a clear plaque indicate when using lambda CI gene as a marker?
Bacteriophage lambda cI gene encodes repressor protein maintaining lysogenic state by inhibiting lytic promoters pL and pR. Vectors containing intact cI form lysogens, producing turbid plaques as host cells survive within plaque area. Insertional inactivation of cI by foreign DNA abolishes repressor synthesis, forcing the phage into lytic cycle, leading to complete cell lysis and formation of clear plaques lacking surviving bacteria. Thus clear plaque morphology serves as direct positive selection for recombinant phage, distinguishing them from non-recombinant turbid plaques.
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.