NMR STUDY OF SLIPPED LOOP DNA STRUCTURE

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Slipped Loop DNA Structure (SLS-DNA) is a novel hypothetical type of folding for nucleic acids. It may form for DNA sequences with short direct repeats (about 5-6 base pairs long), when one strand of DNA is shifted relative to another. Two loops, formed as a result of such a shift, have a potential to form tertiary base pairs. Using a combination of the DNAminiCarlo program and interactive work with the MidasPlus molecular graphics, we built a model for the SLS. We carried out a high resolution NMR study of a model 25-nucleotide DNA sequence, which was designed to form an immobile SLS as a homodimer. However, we showed that this molecule folds in a distinct, albeit SLS-related topology. This is a novel tertiary fold of nucleic acids, which we call a Pseudosquare Knot (PSQ). We calculated a high-resolution structure for the DNA Pseudosquare Knot in solution, based on nuclear Overhauser effect data. Both SLS and PSQ sequence motifs are frequent in single-stranded DNA and RNA genomes; they may play structural and/or functional roles. Presently we are identifying such motifs from viral RNA genomes suitable for high-resolution structural studies. The interactive computer graphics software developed at the Computer Graphics Laboratory is used at all stages of the refinement: to examine the self-consistency of the experimental restraints, to monitor the course of the refinement, and finally, to visualize and analyze the final structure.