Dynamic probing of nucleic acid-protein interactions by biphotonic laser chemistry

In this study, we describe a new approach for a millisecond dynamic study with high spatial resolution of non-equilibrium protein-DNA interactions in solution. The approach is based on mapping the time-resolved UV laser-induced biphotonic DNA oxidative lesions during DNA recognition and binding of a specific protein. Our laser "photofootprinting" approach was applied for studying the interaction of the human necrosis factor NF-κB p50 homodimer bound to a 37 base pair DNA. Evidence is provided for the occurrence of a two-step process: rapid (30 ms) formation of the pre-equilibrium complex and slow (1 s) protein rearrangement and DNA conformation accommodation.