title: Cruciform extrusion facilitates intramolecular triplex formation between distal oligopurine.oligopyrimidine tracts: long range effects.
abstract: Two short d(AG)n tracts separated by either of two 40-base pair (bp) inverted repeats adopt a triple-stranded conformation (H-DNA) at the bottom of an extruded cruciform stem in negatively supercoiled plasmids at pH 4.5. Plasmids containing one d(AG)n adjacent to the inverted repeat or containing two d(AG)n tracts separated by a random sequence did not form the triplex structures. These conclusions were derived from chemical modification patterns and UV-sensitivity studies. Two-dimensional agarose gel electrophoresis revealed that the entire insert containing the cruciform and the triplex is locally unlinked. Moreover, a long range structural effect (over 40 bp of random sequence) of one (AG)7 block on the behavior of a second (AG)7 sequence was detected. This effect cannot be transmitted throughout a 50-bp segment of random sequence. A GenBank search revealed the frequent occurrence of short oligopurine blocks with an intervening random sequence of 17-40 bp.
authors.affiliation: Department of Biochemistry, School of Medicine, University of Alabama, Birmingham 35294.
authors.forename: J
authors.initials: J
authors.lastname: Klysik
mesh_terms: D001483:Base Sequence; D004278:DNA, Superhelical / Q000737:chemistry* / Q000302:isolation & purification / Q000528:radiation effects; D004587:Electrophoresis, Agar Gel; D006863:Hydrogen-Ion Concentration; D008961:Models, Structural; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009838:Oligodeoxyribonucleotides / Q000737:chemistry*; D010957:Plasmids / Q000528:radiation effects; D011687:Purines; D014466:Ultraviolet Rays
chemical_list: D004278:DNA, Superhelical; D009838:Oligodeoxyribonucleotides; D011687:Purines