Protein–DNA Interactions

The recognition of specific DNA sequences by proteins and the coupling to signaling events are fundamental occurrences that lie at the root of many cellular processes. Many examples of tight control by protein–DNA interactions can be found in such dynamic processes as transcription, replication and repair. Mechanistic defects therein can be the cause of severe diseases and reduced lifespan. Therefore, the study of the interaction processes between proteins and DNA is of crucial importance not only for our basic understanding of molecular function, but also for a rational approach to drug design. In the involved complexes, both protein and DNA can adopt a variety of different conformations, as a result of external stimuli or as a part of the formation of the molecular complexes. Since NMR can characterize the molecular structures of the different components, their complexes, as well as the formation and dynamics of these complexes, and the steps that occur during the various transitions (and all under close to physiological conditions), it is clear that NMR can make a strong contribution to molecular characterization. Here, we describe our current capabilities for studying protein–DNA interactions using NMR spectroscopy, identify the challenges and limitations in the presently available NMR methodology, and address several additional techniques that could be complimentary to the NMR results. We summarize recent examples from the literature in addition to some of our own studies on transcription and DNA repair. Possible problems related to sample production as well as biochemical and biophysical characterization are also addressed, as well as remedies to overcome major bottlenecks. Finally, future prospects are briefly outlined.