Protein-induced fluorescence enhancement (PIFE) is a popular tool for characterizing protein-DNA interactions. PIFE has been explained by an increase in local viscosity due to the presence of the protein residues. This explanation, however, denies the opposite effect of fluorescence quenching. This work offers a perspective for understanding PIFE mechanism and reports the observation of a phenomenon that we name protein-induced fluorescence quenching (PIFQ), which exhibits an opposite effect to PIFE. A detailed characterization of these two fluorescence modulations reveals that the initial fluorescence state of the labeled mediator (DNA) determines whether this mediator-conjugated dye undergoes PIFE or PIFQ upon protein binding. This key role of the mediator DNA provides a protocol for the experimental design to obtain either PIFQ or PIFE, on-demand. This makes the arbitrary nature of the current experimental design obsolete, allowing for proper integration of both PIFE and PIFQ with existing bulk and single-molecule fluorescence techniques.
Bibliographical noteKAUST Repository Item: Exported on 2020-10-01
Acknowledged KAUST grant number(s): URF/1/3432-01-01
Acknowledgements: This work was supported by King Abdullah University of Science and Technology under Grant URF/1/3432-01-01 to S.M.H. We are grateful to Prof. Stefan T. Arold (KAUST) for providing access to time-resolved fluorescence spectrophotometer. We thank Daniela-Violeta Raducanu for her support in some experiments. We thank Yujing Ouyang for preparation of functionalized coverslips and Afnan Shirbini for some of the RPA used in this study. We also thank members of Samir M. Hamdan’s lab for helpful discussions.