Letter: Filamentous bacterial viruses. X. X-ray diffraction studies of the R4-protein mutant

Eukaryotic DNA fragments that are totally denatured by alkali swiftly re-form duplex regions that are several hundred up to several thousand nucleotide pairs in length. A combination of sedimentation and electron microscopic studies demonstrate that they arise by the folding-back of a single linear chain, and not from cross-linking between the two complementary chains. Thus these “hairpin”-like structures must come from inverted repetitions of the type A B C t C′B′A′ that are located at intervals along the chromatid. Electron microscopic studies, reveal no unpaired single-chain regions in the “turn-around” t. The resistance of these hairpins to single-chain specific nucleases indicates that t must only consist of a few nucleotides. Therefore we call these regions in double-chain DNA palindromes, because, given the antiparallel arrangement of the polynucleotide chains, these sequences read the same both backwards and forwards. The thermal stability profile of these hairpins is nearly identical to that of sonicated duplex fragments of comparable length. Since these hairpins have the same average base composition as bulk DNA, the palindromes are nearly perfect. By studying the fraction of DNA retained on hydroxyapatite as a function of chain length, one may determine the distribution of palindromes along the DNA. These experiments are best explained by clusters of palindromes located at intervals of 10 to 80 /gm depending on the species. The presence of such long, well-matched palindromes suggests that the linear double helix may sometimes adopt an alternative configuration, the cruciform, in which mismatches that may occur are eliminated by excision and repair.