Bacteriophage lambda DNA packaging: scanning for the terminal cohesive end site during packaging.

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Abstract
Bacteriophage .lambda. packages the DNA of the related phage 21 poorly. To understand the nature of the packaging defect, the interaction of the cohesive end site (cos) specific for phage 21 (cos.vphi.21) with phage .lambda. terminase was investigated. The ability of .lambda. terminase to cleave cos.vphi.21 was studied in vitro; .lambda. terminase cleaved cos.vphi.21 only 1% as well as it cleaved the phage .lambda. cohesive end site (cos.lambda.). In vitro packaging experiments showed that the .lambda. and 21 packaging specificities observed in vivo are also found in vitro. The cos cleavage reaction was modified so that competition experiments could be performed; these experiments showed that cos.vphi.21 was unable to bind .lambda. terminase, thus identifying the nature of the defect. The base pairs giving .lambda. or 21 packaging specificity are at the left end of the chromosome, outside the 22 base pair symmetry region that includes the annealed cohesive ends. Therefore, terminase binding to cos requires interactions with base pairs to the Nu1 side of the cohesive end symmetry segment. cos apparently consists of adjacent sites for binding of terminase and for nicking by terminase. Because cos.vphi.21 can be cut by .lambda. terminase to terminate DNA packaging, the terminase that binds and nicks at the initial cos site appears to be brought into contact with the terminal cos site by the packaging process. Terminase recognizes and nicks the cohesive end sequence of the terminal cos without requiring the binding site.