The 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 have built a model for the SLS. Presently, we are undertaking a high resolution NMR study of the SLS-DNA in solution using a specially designed oligonucleotide sequence. We will use experimental NMR data as restraints for the structural refinement. We are planning to use the interactive computer graphics software developed at the CGL at all stages of the refinement: firstly, to examine the self-consistency of the experimental restraints, then, to monitor the course of the refinement, and finally, to visualize and analyze the final structure. At the present stage of the project, we have obtained the proton resonance assignments and are working on determination of experimental inter-proton distance restraints.
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