Structural heterogeneity of pyrimidine/purine-biased DNA sequence analyzed by atomic force microscopy

Mikio Kato; Chad J. McAllister; Shingo Hokabe; Nobuyoshi Shimizu; Yuri L. Lyubchenko

doi:10.1046/j.1432-1033.2002.03063.x

Structural heterogeneity of pyrimidine/purine-biased DNA sequence analyzed by atomic force microscopy

Mikio Kato, Chad J. McAllister, Shingo Hokabe, Nobuyoshi Shimizu, Yuri L. Lyubchenko

Research output: Contribution to journal › Article › peer-review

16 Scopus citations

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.

Original language	English (US)
Pages (from-to)	3632-3636
Number of pages	5
Journal	European Journal of Biochemistry
Volume	269
Issue number	15
DOIs	https://doi.org/10.1046/j.1432-1033.2002.03063.x
State	Published - 2002

Keywords

Alternative DNA structure
Atomic force microscopy (AFM)
H-DNA
Intramolecular triplex DNA
Polypyrimidine/polypurine sequence

ASJC Scopus subject areas

Biochemistry

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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.",

keywords = "Alternative DNA structure, Atomic force microscopy (AFM), H-DNA, Intramolecular triplex DNA, Polypyrimidine/polypurine sequence",

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AU - Kato, Mikio

AU - McAllister, Chad J.

AU - Hokabe, Shingo

AU - Shimizu, Nobuyoshi

AU - Lyubchenko, Yuri L.

PY - 2002

Y1 - 2002

N2 - 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.

AB - 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.

KW - Alternative DNA structure

KW - Atomic force microscopy (AFM)

KW - H-DNA

KW - Intramolecular triplex DNA

KW - Polypyrimidine/polypurine sequence

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