Site-specific inversion sequence of the herpes simplex virus genome: Domain and structural features

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Abstract
The genome of herpes simplex virus-l consists of 2 covalently linked components, L [long] and S [short], that invert relative to each other. The L and S components consist of unique DNA sequences bracketed by inverted repeats. The inverted repeats of the L component are designated 4b and b''a'', and those of the S component are designated a''c'' and ca. The number of a sequences at the termini and at the L-S component junction varies from 1 to several copies. Insertion into the middle of the L component of a DNA fragment consisting of 156 base pairs (bp) of the b sequence, an entire a sequence of 501 bp and 618 bp of the c sequence created a new site through which ddditional inversions in the genome occurred. Comparison of the nucleotide sequences of DNA fragments containing 1 and 2 a sequences defined the domain of the a sequence. The single a sequence consists of 2 20-bp direct repeats (designated as DR1) bracketing a region that contains 19 tandem direct repeats of a 12-bp sequence (DR2) adjacent to 3 direct repeats of a 37-bp sequence (DR4), in addition to short stretches of unique sequences. The fragment with 2 tandem a sequences contained 3 copies of DR1, i.e., the intervening DR1 was shared by the 2 a sequences. One a sequence contained 22 copies of DR2 and 2 copies of DR4, the 2nd a sequence contained 19 copies of DR2 and 2 copies of DR4. Evidently, amplication of the number of terminal and internal a sequences is the consequence of intramolecular or intermolecular recombination through DR1, the number of copies of DR2 and DR4 within the a sequence is not fixed and may vary as a consequence of unequal crossing over or slippage and inversion results from intramolecular recombination between terminal and inverted a sequences.