Experimental evidence for slipped loop DNA, a novel folding type for polynucleotide chain

DNA regions with short direct repeats (5-7bp) with a spacer in between, when under super-helical stress, are known to become susceptible to single-strand specific nuclease S1. This is in accord with formation of two shifted loops protruding from the opposite chains. Such type of folding could have been additionally stabilized by base pairing between the complementary parts of the loops that explains existence of the protected from S1 moieties of the loops. To test this possibility we designed and synthesized an oligonucleotide of 56 bases, so that it forms a hairpin with a stem which fails to acquire a traditional helix due to a special sequence but may favor the formation of the proposed Slipped Loop Structure (SLS). The oligonucleotide folding was studied by a chemical modification method at one nucleotide level resolution. Three zones, protected from the used probes were found: the one that forms the stem, and the others that are located within the two by-loops in those moieties which have the base pairing potential. Proceeding from the data obtained and stereochemical analysis a 3-D scheme for the SLS form of DNA is suggested.