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During progeny assembly, viruses selectively package virion genomes from a nucleic acid pool that includes host nucleic acids. For large dsDNA viruses, including tailed bacteriophages and herpesviruses, immature viral DNA is recognized and translocated into a preformed icosahedral shell, the prohead. Recognition involves specific interactions between the viral packaging enzyme, terminase, and viral DNA recognition sites. Generally, viral DNA is recognized by terminase’s small subunit (TerS). The large terminase subunit (TerL) contains translocation ATPase and endonuclease domains. In phage lambda, TerS binds a sequence repeated three times in  cosB , the recognition site. TerS binding to  cosB  positions TerL to cut the concatemeric DNA at the adjacent nicking site,  cosN . TerL introduces staggered nicks in  cosN , generating twelve bp cohesive ends. Terminase separates the cohesive ends and remains bound to the  cosB -containing end, in a nucleoprotein structure called Complex I. Complex I docks on the prohead’s portal vertex and translocation ensues. DNA topology plays a role in the TerS λ - cosB   λ   interaction. Here we show that a site,  I2 , located between  cosN  and  cosB , is critically important for an early DNA packaging step.  I2  contains a complex static bend.  I2  mutations block DNA packaging.  I2  mutant DNA is cut by terminase at  cosN in vitro , but  in vivo , no  cos  cleavage is detected, nor is there evidence for Complex I. Models for what packaging step might be blocked by  I2  mutations are presented.

DNA Topology and the Initiation of Virus DNA Packaging