title: Nick-free formation of reciprocal heteroduplexes: a simple solution to the topological problem.
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: D001483:Base Sequence; D004247:DNA; D006860:Hydrogen Bonding; D008958:Models, Molecular; D008961:Models, Structural; D009690:Nucleic Acid Conformation; D011995:Recombination, Genetic
chemical_list: D004247:DNA