Time-resolved emission spectroscopy as a tool to follow nucleic acid-protein interaction

Fluorescence spectroscopy is undoubtedly a useful tool to study the structural and functional aspects of nucleic acids-protein interactions as well as the catalytic functions of particular residues of multi-subunit enzyme complexes. The dynamic interaction of nucleic acids and proteins occurring at nanosecond time scale can now be monitored by making life-time measurements or by time-resolved emission spectroscopy. These measurements are made by exploiting the intrinsic fluorescent residues in proteins i.e. W or by the use of extrinsic fluorophores which are tagged on to particular residues and that are sensitive to the microenvironment changes. In this study we describe the use of time resolved emission spectroscopy to (a) analyse the transient binding between sigma 70 and DNA by monitoring the quenching of W residues and (b) monitor the various states which nucleosomes of active, inducible or inactive chromatin may adopt in vivo.