Excision of DNA fragments corresponding to the unit-length a sequence of herpes simplex virus type 1 and terminus variation predominate on one side of the excised fragment.

DNA fragments corresponding to the unit-length a sequence of herpes simplex virus type 1 (HSV-1) were identified in HSV-1 DNA preparations extracted by the method of Hirt. The DNA fragments were molecularly cloned, and nucleotide sequences were determined. Most termini of the fragments were at sites on DR1 corresponding to the termini of linear HSV-1 DNA generated by the cleavage-packaging system. In one-step growth experiments, DNA fragments of the unit-length a sequence appeared simultaneously with the termini of linear HSV-1 DNAs produced by cleavage of circular and concatemeric DNAs. Therefore, excision of the unit-length a sequence appeared closely related to the cleavage-packaging system. Termini of the excised DNA fragments of the variant a sequence with two DR2 arrays varied on the L-component side, while termini on the S-component side were at the site on DR1 corresponding to the authentic cleavage site. It is thus assumed that the cleavage-packaging system functions adequately on the DR1 second distal from the S component, and cleavages of other DR1 are rare and less accurate. If this notion is tenable, then most termini on the S-component side of the excised DNA fragments are derived from the second DR1 properly cleaved and should be constant, while termini on the L-component side are from regions on and around the DR1 third distal from the S component and may be variable. Cleavage of DR1 is likely to be affected by the topological relationship with the S component.