Nick-free formation of reciprocal heteroduplexes: a simple solution to the topological problem

Proc Natl Acad Sci U S A. 1979 Aug;76(8):3641-5. doi: 10.1073/pnas.76.8.3641.

Abstract

Because the individual strands of DNA are intertwined, formation of heteroduplex structures between duplexes--as in presumed recombination intermediates--presents a topological puzzle, known as the winding problem. Previous approaches to this problem have assumed that single-strand breaks are required to permit formation of fully coiled heteroduplexes. This paper describes a simple, nick-free solution to the winding problem that satisfies all topological constraints. Homologous duplexes associated by their minor-groove surfaces can switch strand pairing to form reciprocal heteroduplexes that coil together into a compact, four-stranded helix throughout the region of pairing. Model building shows that this fused heteroduplex structure is plausible, being composed entirely of right-handed primary helices with Watson-Crick base pairing throughout. Its simplicity of formation, structural symmetry, and high degree of specificity are suggestive of a natural mechanism for alignment by base pairing between intact homologous duplexes. Implications for genetic recombination are discussed.

MeSH terms

  • Base Sequence
  • DNA*
  • Hydrogen Bonding
  • Models, Molecular
  • Models, Structural
  • Nucleic Acid Conformation*
  • Recombination, Genetic*

Substances

  • DNA