title: Unusual DNA structures in the adenovirus genome.
abstract: More than 80% (approximately 29 kilobase pairs) of the adenovirus serotype 2 genome was surveyed for the presence of unusual DNA conformations. Seven recombinant DNAs containing the largest HindIII fragments of AD2 DNA were analyzed for the presence of negative supercoil-dependent S1 nuclease-sensitive sites. Four plasmids each contained a specific site of S1 nuclease sensitivity whereas the other three showed no reaction. Further investigation was focused on a plasmid containing one of the positively reacting fragments (fragment C) which contained the major late promoter at coordinate 16.4 on the genome; three serotypes (Ad2, Ad7, Ad12) were studied. Fine mapping studies revealed the S1-sensitive sites to be a small region (approximately 6 base pairs) located at the TATA box of the major late promoter in all three cases. Other determinations (supercoil relaxation, T7 gene 3 product sensitivity, bromoacetaldehyde reactivity, anomalous gel mobility, the influence of negative superhelical density on nuclease sensitivity) led to the conclusion that the B-helix deformation was not due to a previously recognized DNA conformation (left-handed Z-DNA, cruciform, bent DNA), but may be accounted for by the homopurine X homopyrimidine nature of this region.
mesh_terms: D000079:Acetaldehyde / Q000031:analogs & derivatives / Q000494:pharmacology; D000256:Adenoviridae / Q000235:genetics*; D001483:Base Sequence; D004262:DNA Restriction Enzymes / Q000378:metabolism; D004279:DNA, Viral / Q000032:analysis*; D015247:Deoxyribonuclease HindIII; D004587:Electrophoresis, Agar Gel; D004720:Endonucleases / Q000378:metabolism; D009690:Nucleic Acid Conformation; D010957:Plasmids; D015719:Single-Strand Specific DNA and RNA Endonucleases
chemical_list: D004279:DNA, Viral; C038235:bromoacetaldehyde; D004720:Endonucleases; D004262:DNA Restriction Enzymes; D015247:Deoxyribonuclease HindIII; D015719:Single-Strand Specific DNA and RNA Endonucleases; D000079:Acetaldehyde