TAILIEUCHUNG - Báo cáo Y học: Structural heterogeneity of pyrimidine/purine-biased DNA sequence analyzed by atomic force microscopy

We report here the direct evidence for the formation of alternative DNA structures in a plasmid DNA, termed pTIR10, containing a 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 ) was deposited on APS-modified mica, and after drying it was imaged with an atomic force microscope in air. . | Eur. J. Biochem. 269 322 636 22002 FEBS 2002 doi PRIORITY PAPER Structural heterogeneity of pyrimidine purine-biased DNA sequence analyzed by atomic force microscopy Mikio Kato1 2 Chad J. McAllister2 Shingo Hokabe1 Nobuyoshi Shimizu3 and Yuri L. Lyubchenko2 1 Department of Life Science Osaka Prefecture University College of Integrated Arts and Sciences Sakai Japan department of Microbiology Arizona State University Tempe USA 3Department of Molecular Biology Keio University School of Medicine Shinjuku-ku Tokyo Japan We report here the direct evidence for the formation of alternative DNA structures in a plasmid DNA termed pTIR10 containing a .234 b pyrimidina auOne-aiased Pyr Pur stretch isolated from the rat nenome. Lonn Pyr Pur sequences are abundant in eukaryotic nenomes and they may modulate the biolonical activity of nenes and nenomes via formation of various types of triplex-related structures. The plasmid DNA in sodium acetate buffer pH was deposited on APS-modified mica intel alter dryinn it was imaned with an atomic force microscope in air. Various types of thick protrusions have been observed on pTIR10 DNA. Structural parameters width and heinht of DNA molecules sunnest that the alternative structures observed here are variations on the theme of an intramolecular triplex. The biolonical relevance of the structural features within Pyr Pur stretches is discussed. Keywords alternative DNA structure atomic force microscopy AFM H-DNA intramolecular triplex DNA poly-pyrimidine polypurine sequence. There is a wealth of evidence indicatinn that short pyrimidine purine-biased Pyr Pur mirror symmetry sequences adopt an intramolecular triplex conformation H-DNA 1 2 . Intramolecular triplexes play important roles in nenome functions . triplex lormatinn causes pausinn of polymerases durinn replication 3 and transcription 4 and enhances homolonous recombination 5 6 . Structural transition between B-DNA and triplex DNA may provide

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