Triple-helical DNA pairing intermediates formed by recA protein.

RecA protein aligns homologous single- and double-stranded DNA molecules in three-stranded joints that can extend over thousands of base pairs. When cross-linked by 4'-amino-4,5',8-trimethyl-psoralen the joint structure observed in nonuniform and divided into multiple substructures each a few hundred base pairs long. Two paired substructures are observed; at least one, and possibly both, are right-handed triple helices. Sites of homologous contact are interspersed with regions where the DNA molecules are arranged side-by-side without contact. These substructures alternate in all combinations. The length and frequency of joints is much greater when one of the DNA substrates is linear, and interwinding is unrestricted, than when there are topological restrictions between the pairing partners. The results are consistent with the idea that recA protein facilitates the formation of a right-handed triple-helical DNA pairing intermediate during strand exchange. The results further suggest that recA filaments do not promote the formation of structures that provide efficient topological compensation for right-handed interwinding of two paired DNA molecules.