title: Dark states in monomeric red fluorescent proteins studied by fluorescence correlation and single molecule spectroscopy.
abstract: Monomeric red fluorescent proteins (mRFPs) have become indispensable tools for studying protein dynamics, interactions and functions in the cellular environment. Their emission spectrum can be well separated from other fluorescent proteins, and their monomeric structure preserves the natural function of fusion proteins. However, previous photophysical studies of some RFPs have shown the presence of light-induced dark states that can complicate the interpretation of cellular experiments. In this article, we extend these studies to mRFP1, mCherry, and mStrawberry by means of fluorescence correlation spectroscopy and prove that this light-driven intensity flickering also occurs in these proteins. Furthermore, we show that the flickering in these proteins is pH-dependent. Single molecule spectroscopy revealed reversible transitions from a bright to a dark state in several timescales, even up to seconds. Time-resolved fluorescence spectroscopy showed multiexponential decays, consistent with a "loose" conformation. We offer a structural basis for the fluorescence flickering using known crystal structures and point out that the environment of Glu-215 is critical for the pH dependence of the flickering in RFPs. We apply dual-color fluorescence correlation spectroscopy inside live cells to prove that this flickering can seriously hamper cellular measurements if the timescales of the flickering and diffusion are not well separated.
authors.affiliation: Laboratory of Biomolecular Dynamics, Department of Chemistry, Katholieke Universiteit Leuven, 3001 Heverlee, Belgium.
authors.forename: Jelle
authors.initials: J
authors.lastname: Hendrix
authors.forename: Cristina
authors.initials: C
authors.lastname: Flors
authors.forename: Peter
authors.initials: P
authors.lastname: Dedecker
authors.forename: Johan
authors.initials: J
authors.lastname: Hofkens
authors.forename: Yves
authors.initials: Y
authors.lastname: Engelborghs
mesh_terms: D016477:Artifacts; D003198:Computer Simulation; D008027:Light; D008164:Luminescent Proteins / Q000737:chemistry* / Q000528:radiation effects* / Q000648:ultrastructure; D036641:Microscopy, Fluorescence, Multiphoton / Q000379:methods*; D008956:Models, Chemical; D008958:Models, Molecular; D011487:Protein Conformation / Q000528:radiation effects; D013050:Spectrometry, Fluorescence / Q000379:methods*; D000097573:Red Fluorescent Protein
chemical_list: D008164:Luminescent Proteins; D000097573:Red Fluorescent Protein