title: Structure of branched DNA molecules: gel retardation and atomic force microscopy studies.
abstract: DNA heteroduplexes as models for slipped strand DNA have been analyzed by polyacrylamide gel migration and atomic force microscopy (AFM). All heteroduplexes containing one hairpin or loop have reduced electrophoretic mobilities compared with that expected for their molecular weights. The retarded gel mobility correlates with the formation of a sharp kink detected by AFM. Increasing the hairpin length from 7 bp to 50 bp results in a monotonous decrease in gel mobility of heteroduplexes. This secondary retardation effect appears to depend only on the hairpin size since the AFM data show no dependence of the kink angle on the hairpin length. Heteroduplex isomers with a loop or hairpin in opposite strands migrate with distinct mobilities. Analysis of gel migration of heteroduplexes with altered hairpin orientations as well as of truncated heteroduplexes indicates that the difference in mobility is due to an inherent curvature in one of the long arms. This is confirmed by the end-to-end distance measurements from AFM images. In addition, significant variation of the end-to-end distances is consistent with a dynamic structure of heteroduplexes at the three-way junction. Double heteroduplexes containing one hairpin in each of the complementary strands also separate in a gel as two isomers. Their appearance in AFM showed a complicated pattern of flat representations of the three-dimensional structure and may indicate a certain degree of interaction between complementary parts of the hairpins that are several helical turns apart.
authors.affiliation: Institute of Biosciences and Technology, The Texas A&M University System Health Science Center, 2121 West Holcombe Blvd., Houston, TX 77030-3303, USA.
authors.forename: E A
authors.initials: EA
authors.lastname: Oussatcheva
authors.forename: L S
authors.initials: LS
authors.lastname: Shlyakhtenko
authors.forename: R
authors.initials: R
authors.lastname: Glass
authors.forename: R R
authors.initials: RR
authors.lastname: Sinden
authors.forename: Y L
authors.initials: YL
authors.lastname: Lyubchenko
authors.forename: V N
authors.initials: VN
authors.lastname: Potaman
mesh_terms: D001483:Base Sequence; D002850:Chromatography, Gel; D004262:DNA Restriction Enzymes / Q000378:metabolism; D007091:Image Processing, Computer-Assisted; D018625:Microscopy, Atomic Force; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000737:chemistry* / Q000648:ultrastructure; D010316:Particle Size
chemical_list: D009692:Nucleic Acid Heteroduplexes; D004262:DNA Restriction Enzymes