title: Double-stranded DNA homology produces a physical signature.
abstract: DNA is found in the cell largely as a negatively supercoiled molecule. This high-energy form of the genetic material can engender sequence-dependent structures, such as cruciforms, Z-DNA, or H-DNA, even though they are not favored by conventional conditions in relaxed DNA. A key feature of DNA in living systems is the presence of homology. We have sought homology-dependent structural phenomena based on topological relaxation. Using two-dimensional electrophoresis, we demonstrate a structural transition in supercoiled plasmid molecules containing homologous segments. Atomic force microscopy (AFM) reveals a dumbbell structure in molecules whose linking difference is beyond the transition point. The position of the dumbbell shaft is a function of the site of homology, and its extent is proportional to the linking difference. Second-site-reversion electrophoresis data support the notion that the shaft contains PX-DNA. Predicted cross-linking patterns generated in vivo suggest that homology-dependent structures can occur within the cell.
authors.affiliation: Department of Chemistry, New York University, New York, NY 10003, USA.
authors.forename: Xing
authors.initials: X
authors.lastname: Wang
authors.forename: Xiaoping
authors.initials: X
authors.lastname: Zhang
authors.forename: Chengde
authors.initials: C
authors.lastname: Mao
authors.forename: Nadrian C
authors.initials: NC
authors.lastname: Seeman
mesh_terms: D000818:Animals; D001483:Base Sequence; D004247:DNA; D043542:DNA, Z-Form; D004586:Electrophoresis; D018625:Microscopy, Atomic Force / Q000379:methods; D010957:Plasmids
chemical_list: D043542:DNA, Z-Form; C051802:triplex DNA; D004247:DNA