Location of Homologous DNA Sequences Interspersed at Five Regions in the Baculovirus AcMNPV Genome

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Abstract
An examination of Autographa californica nuclear polyhedrosis virus DNA revealed the presence of 5 interspersed regions, rich in EcoRI restriction sites, which shared homologous sequences. These homologous regions (hr), designated hr1 to hr5, occur at or near the following EcoRI fragment junctions: hr1 EcoRI-B-EcoRI-I (0.0 map units); hr2, EcoRI-A-EcoRI-J (19.8 map units); hr3, EcoRI-C-EcoRI-G (52.9 map units); hr4, EcoRI-Q-EcoRI-L (69.8 map units); and hr5, EcoRI-S-EcoRI-X (88.0 map units). Four of these regions were identified, by cross-blot hybridization of Hind III-restricted A. californica nuclear polyhedrosis virus DNA, to be within the HindIII-A/B, -F, -L and -Q fragments. The location of these regions and the identification of a 5th homologous region were confirmed, and their characterization was facilitated, by using 2 plasmids with HindIII-L or -Q fragment insertions, which contained the homologous regions hr2 and hr5, respectively. The sizes of the homologous regions were .apprx. 800 base pairs for hr2, 500 base pairs for hr5, and < 500 base pairs for hr1, hr3 and hr4. A set of small EcoRI fragments (EcoRI minifragments) which ranged in size from 225 to 73 base pairs were detected in A. californica nuclear polyhedrosis virus DNA and HindIII-L and -Q fragments by polyacrylamide gel analysis. Some of the minifragments in viral DNA were present in extramolar amounts and corresponded in size to some of the minifragments present in HindIII-L and -Q. Clones of some of the EcoRI minifragments were used as probes in hybridizations to digests of viral DNA and of HindIII-L and -Q. The hybridization data, obtained under various levels of stringency, suggested that there was a degree of mismatching between the sequences which were responsible for the homology.