title: Asymmetric structure of a three-arm DNA junction.
abstract: We present here experimental evidence that three-arm branched DNA molecules form an asymmetric structure in the presence of Mg2+. Electrophoretic mobility and chemical and enzymatic footprinting experiments on a three-arm branched DNA molecule formed from three 16-mer strands are described. The electrophoretic mobilities of three species of a three-arm junction in which pairs of arms are extended are found to differ in the presence of Mg2+: one combination of elongated arms migrates significantly faster than the other two. This effect is eliminated in the absence of Mg2+, leading us to suggest that the three-arm DNA junction forms an asymmetric structure due to preferential stacking of two of the arms at the junction in the presence of Mg2+. The pattern of self-protection of each 16-mer strand of the core complex exposed to Fe(II).EDTA and DNase I scission is unique, consistent with formation of an asymmetric structure in the presence of Mg2+. We conclude that three-arm junctions resemble four-arm junctions in showing preferential stacking effects at the branch site. Comparison of the scission patterns of linear duplexes and the branched trimer by the reactive probes methidiumpropyl-EDTA.Fe(II) [MPE.Fe(II)] and Cu(I)-[o-phenanthroline]2 [(OP)2CuI] further indicates that the branch point represents a site of enhanced binding for drugs, as it does in the four-arm case. Reaction with diethyl pyrocarbonate (DEPC), a purine-specific probe sensitive to conformation, is enhanced at the branch site, consistent with loosening of base pairing or unpairing at this point.(ABSTRACT TRUNCATED AT 250 WORDS)
authors.affiliation: Department of Chemistry, New York University, New York 10003.
authors.forename: Q
authors.initials: Q
authors.lastname: Guo
authors.forename: M
authors.initials: M
authors.lastname: Lu
authors.forename: M E
authors.initials: ME
authors.lastname: Churchill
authors.forename: T D
authors.initials: TD
authors.lastname: Tullius
authors.forename: N R
authors.initials: NR
authors.lastname: Kallenbach
mesh_terms: D001483:Base Sequence; D003300:Copper; D004247:DNA / Q000737:chemistry / Q000648:ultrastructure; D003850:Deoxyribonuclease I / Q000494:pharmacology; D004047:Diethyl Pyrocarbonate / Q000737:chemistry; D004587:Electrophoresis, Agar Gel; D004720:Endonucleases / Q000378:metabolism; D005609:Free Radicals; D006878:Hydroxides; D007501:Iron; D008274:Magnesium; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D011687:Purines / Q000737:chemistry
chemical_list: D005609:Free Radicals; D006878:Hydroxides; D011687:Purines; D003300:Copper; D004247:DNA; D007501:Iron; D004720:Endonucleases; D003850:Deoxyribonuclease I; D008274:Magnesium; D004047:Diethyl Pyrocarbonate