Double-stranded DNA homology produces a physical signature

Xing Wang, Xiaoping Zhang, Chengde Mao, Nadrian C. Seeman

Research output: Contribution to journalArticlepeer-review


DNA is found in the cell largely as a negatively supercoiled molecule. This high-energy form of the genetic material can engender sequence-dependent structures, such as cruciforms, Z-DNA, or H-DNA, even though they are not favored by conventional conditions in relaxed DNA. A key feature of DNA in living systems is the presence of homology. We have sought homology-dependent structural phenomena based on topological relaxation. Using two-dimensional electrophoresis, we demonstrate a structural transition in supercoiled plasmid molecules containing homologous segments. Atomic force microscopy (AFM) reveals a dumbbell structure in molecules whose linking difference is beyond the transition point. The position of the dumbbell shaft is a function of the site of homology, and its extent is proportional to the linking difference. Second-site-reversion electrophoresis data support the notion that the shaft contains PX-DNA. Predicted cross-linking patterns generated in vivo suggest that homology-dependent structures can occur within the cell.

Original languageEnglish (US)
Pages (from-to)12547-12552
Number of pages6
JournalProceedings of the National Academy of Sciences of the United States of America
Issue number28
StatePublished - Jul 13 2010


  • Atomic force microscopy
  • Homology recognition
  • PX-DNA
  • Supercoiling relaxation
  • Unusual DNA motifs

ASJC Scopus subject areas

  • General


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