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 superhelical stress, are known to become susceptible to s ingle-strand specific nuclease S1. This is in accord with formation of two shifted loops protruding from the opposite chains. Such type of f olding could have been additionally stabilized by base pairing between the complementary parts of the loops that explains existence of the p rotected from S1 moieties of the loops. To test this possibility we de signed and synthesized an oligonucleotide of 56 bases, so that it form s 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 Sli pped Loop Structure (SLS). The oligonucleotide folding was studied by a chemical modification method at one nucleotide level resolution. Thr ee zones, protected from the used probes were found: the one that form s 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 SL S form of DNA is suggested.