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 journalArticlepeer-review

18 Scopus citations


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 languageEnglish (US)
Pages (from-to)3632-3636
Number of pages5
JournalEuropean Journal of Biochemistry
Issue number15
StatePublished - 2002
Externally publishedYes


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

ASJC Scopus subject areas

  • Biochemistry


Dive into the research topics of 'Structural heterogeneity of pyrimidine/purine-biased DNA sequence analyzed by atomic force microscopy'. Together they form a unique fingerprint.

Cite this