In the large double-stranded DNA viruses, such as the herpes viruses and the tailed bacteriophages, viral DNA is recognized for packaging thru the interactions of a packaging enzyme, called terminase, and specific recognition sites in the viral DNA. In the lambda-like bacteriophages, these recognition sites are located in an approximately 200 bp-long DNA segment called cos. cos contains several subsites, including cosB, the terminase binding site, and cosN, the site where terminase cuts the DNA to make unit-length DNA molecules. This research investigates the function of a newly-discovered subsite located between cosN and cosB. The possibility that the new site includes a DNA bend will be determined. Whether the new site is needed at the start and/or the end of DNA packaging will be studied. The terminase binding site in the cos of the paradigm lambda-like bacteriophage, lambda, is large and complex, with three binding sites for terminase. Because of this complexity, the terminase of lambda forms a complicated DNA-protein complex on cos. Bacteriophage N15 is a lambda-like virus. The terminase binding site for N15 is very simple -- there is only one terminase binding site. A major question is whether N15 terminase forms a complicated DNA-protein complex, or whether N15 recognition differs fundamentally from lambda recognition. Experiments on how N15 terminase binds the cos of N15 will give important insights into DNA recognition in the dsDNA viruses. This research project will provide challenging research experiences to several undergraduates from diverse backgrounds. The work is of general significance for understanding how dsDNA viruses package viral DNA.
