title: Bulge defects do not destabilize negatively supercoiled DNA.
abstract: The conformational properties of DNA lesions such as extrahelical bulges are presumed to be essential for recognition of defects in DNA structure by a cell's genomic repair machinery. Efficient recognition and repair of lesions by DNA-repair systems occurs despite the wide range of normal heterogeneities in DNA structure, including features such as sequence-dependent bends. The effects of global negative supercoiling on the structure of DNA lesions have been largely unexplored. We have investigated the behavior of several plasmid DNAs containing bulge defects with up to five extrahelical adenine residues. Using two-dimensional agarose-gel electrophoresis, we show that there is no spontaneous cooperative unwinding of these bulge loci up to native levels of negative supercoiling (sigma = -0.055) under our conditions.
authors.affiliation: Department of Molecular and Cell Biology, and Institute of Biomedical Sciences and Technology, The University of Texas at Dallas, Richardson, TX, USA.
authors.forename: Lijing
authors.initials: L
authors.lastname: You
authors.forename: Stephen D
authors.initials: SD
authors.lastname: Levene
mesh_terms: D000225:Adenine / Q000737:chemistry; D001435:Bacteriophages / Q000737:chemistry; D001483:Base Sequence; D004247:DNA / Q000737:chemistry; D004278:DNA, Superhelical / Q000737:chemistry*; D004587:Electrophoresis, Agar Gel; D015180:Electrophoresis, Gel, Two-Dimensional; D004926:Escherichia coli / Q000378:metabolism; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000378:metabolism; D012492:Salts / Q000737:chemistry
chemical_list: D004278:DNA, Superhelical; D012492:Salts; D004247:DNA; D000225:Adenine