title: Non-B right-handed DNA conformations of homopurine.homopyrimidine sequences in the murine immunoglobulin C alpha switch region.
abstract: The switch region of IgA immunoglobulin in mice cloned into a recombinant plasmid contains a supercoil-dependent S1 nuclease hypersensitive site, indicative of a non-B-DNA secondary structure. This site maps to the (AGGAG)28 direct repeat (DR2) of the alpha switch region and appears at a negative superhelical density of greater than 0.02. Studies with P1 nuclease and bromoacetaldehyde indicate that this structure is also present at neutral pH. S1 nuclease sensitivity is retained for the shorter repeat (AGGAG)6GA in a recombinant plasmid but is not seen for the repeat (CTGAG)6, corresponding to the DR1 repeat of the alpha switch region, or in a sequence corresponding to a portion of the consensus sequence which contains a short stretch of alternating pyrine-pyrimidine residues. Fine mapping of the (AGGAG)6GA and flanking sequences with dimethyl sulfate, bromoacetaldehyde, osmium tetroxide, and diethyl pyrocarbonate reveals an asymmetric pattern of modification dependent on both pH and supercoiling. Two-dimensional gel electrophoresis at low pH shows the relaxation of 3 superhelical turns on formation of this structure by the (AGGAG)6GA repeat. These results are most consistent with the formation of an intramolecular triple-strand.
authors: Department of Biochemistry, University of Alabama School of Medicine, Birmingham 35294.
authors: D A
authors: DA
authors: Collier
authors: J A
authors: JA
authors: Griffin
authors: R D
authors: RD
authors: Wells
mesh_terms: D000818:Animals; D001483:Base Sequence; D004247:DNA / Q000235:genetics* / Q000648:ultrastructure; D004278:DNA, Superhelical / Q000235:genetics; D005803:Genes, Immunoglobulin; D007070:Immunoglobulin A / Q000235:genetics*; D007127:Immunoglobulin Constant Regions / Q000235:genetics*; D051379:Mice; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010957:Plasmids; D011743:Pyrimidines
chemical_list: D004278:DNA, Superhelical; D007070:Immunoglobulin A; D007127:Immunoglobulin Constant Regions; D011743:Pyrimidines; D004247:DNA