[SLS--a new type of polynucleotide chain folding]

Short tandem repeats (5-8 base pairs) are not uncommon in the prokaryotic and eukaryotic DNA. Regions with such sequence motifs, when under superhelical stress, manifest unusual sensitivity to single-strand specific nuclease. To explain this, it has been suggested that one DNA thread should be shifted relatively to another, so that they could form two single-stranded loops protruding from the opposite chains and separated on the DNA helix by the length of a direct repeat. The structure was proposed to play a role in the regulation of transcription, organization of chromatin and in the recombination. Such type of folding could have been extra-stabilized by base pairing between the loops. This attractive possibility of the interloop minihelix formation requires a delicate stereochemical analysis and direct experimental support. Formation of the interloop minihelix in the Slipped Loop Structure (SLS) was tested by a chemical modification method at one nucleotide level resolution. The results show that bases located within the proposed interloop helix are well protected from the probes used. This fact encourages us to publish a 3-D model for the SLS-form DNA (and RNA). The SLS is characterized by a remarkable symmetry having three mutually perpendicular dyad axes. Scanning the bank of nucleotide sequences has revealed more than 500 sites, the transcripts of which are capable of folding into the SLS form, which allow us to regard the SLS form as a novel universal structural form. Remarkably, the abundance of SLS in intrones three times exceeds that of the coding sequences. This may reflect a functional role (or roles) of the SLS conformation.