Structural determination of DNA using residual dipolar couplings

The molecular interactions between proteins and DNA are being categorized at a rapid rate. However the solution structure of the DNA prior to complex formation is still a void. Is the DNA a uniform structure or does the site of action at the DNA and its flanking sequences exhibit a defined structural target? Structural analysis of DNA by x-ray crystallography has been ambiguous. Structural determination by solution NMR spectroscopy has been limited due to the lack of long-range restraints available from the Nuclear Overhauser Effect and J coupling data. Recently a method to obtain long-range angular information in solution NMR spectroscopy was introduced. The measurement of residual dipolar couplings (RDCs) in a slightly orientating solution has the promise to offer a route to determine high-resolution solution structures of DNA sequences that are protein targets. We solved the solution structure of an A-tract DNA bend along with a control sequence using RDCs. Unlike several x-ray diffraction structures the solution structures are consistent with all previous twenty years of biochemical experiments on A-tracts. Having demonstrated the validity of RDCs for nucleic acid structural determination we have used these couplings to gather structural information from promoter DNA sequences. Initial results suggest that the Adenovirus Major Late Promoter (AdMLP) has local structural deviations in its TATA box