title: Structural heterogeneity of pyrimidine/purine-biased DNA sequence analyzed by atomic force microscopy.
abstract: We report here the direct evidence for the formation of alternative DNA structures in a plasmid DNA, termed pTIR10, containing a 0.23-kb pyrimidine/purine-biased (Pyr/Pur) stretch isolated from the rat genome. Long Pyr/Pur sequences are abundant in eukaryotic genomes, and they may modulate the biological activity of genes and genomes via formation of various types of triplex-related structures. The plasmid DNA in sodium acetate buffer (pH 4.35) was deposited on APS-modified mica, and after drying it was imaged with an atomic force microscope in air. Various types of thick protrusions have been observed on pTIR10 DNA. Structural parameters (width and height) of DNA molecules suggest that the alternative structures observed here are variations on the theme of an intramolecular triplex. The biological relevance of the structural features within Pyr/Pur stretches is discussed.
authors.affiliation: Department of Life Science, Osaka Prefecture University College of Integrated Arts and Sciences, Sakai, Japan. mikio_kato@mac.com
authors.forename: Mikio
authors.initials: M
authors.lastname: Kato
authors.forename: Chad J
authors.initials: CJ
authors.lastname: McAllister
authors.forename: Shingo
authors.initials: S
authors.lastname: Hokabe
authors.forename: Nobuyoshi
authors.initials: N
authors.lastname: Shimizu
authors.forename: Yuri L
authors.initials: YL
authors.lastname: Lyubchenko
mesh_terms: D004247:DNA / Q000737:chemistry*; D018625:Microscopy, Atomic Force / Q000379:methods; D009690:Nucleic Acid Conformation; D010957:Plasmids / Q000737:chemistry / Q000235:genetics; D011687:Purines / Q000737:chemistry*; D011743:Pyrimidines / Q000737:chemistry*
chemical_list: D011687:Purines; D011743:Pyrimidines; D004247:DNA; C030986:pyrimidine; C030985:purine