TERTIARY BASE-PAIR INTERACTIONS IN SLIPPED LOOP-DNA - AN NMR AND MODEL-BUILDING STUDY

Short direct repeat sequences are often found in regulatory regions of various genes; in some cases they display hypersensitivity to S1 nucl ease cleavage in supercoiled plasmids. A non-standard DNA structure (S lipped Loop Structure, or SLS) has been proposed for these regions in order to explain the S1 cleavage data; the formation of this structure may be involved in the regulation of transcription. The structure can be generally classified as a particular type of pseudoknot To date, n o detailed stereochemical model has been developed. We have applied on e-dimensional H-1 NMR spectroscopy to study a synthetic DNA, 55 nucleo tides in length, which cannot fold as a standard hairpin but which may favor the SLS formation. AT base pairs were identified, consistent on ly with the formation of an additional, tertiary miniduplex in the SLS . An all-atom stereochemically sound model has been developed for the SLS with the use of conformational calculations. The model building st udies have demonstrated that the tertiary miniduplex can be formed for one of the plausible SLS isomers, but not for the other.