title: Dimer formation of organic fluorophores reports on biomolecular dynamics under denaturing conditions.
abstract: Stacking interactions between organic fluorophores can cause formation of non-fluorescent H-dimers. Dimer formation and dissociation of two fluorophores site-specifically incorporated in a biomolecule result in fluorescence intermittency that can report on conformational dynamics. We characterize intramolecular dimerization of two oxazine fluorophores MR121 attached to an unstructured polypeptide. Formation of stable non-fluorescent complexes with nano- to microsecond lifetimes is a prerequisite for analysing the intermittent fluorescence emission by fluorescence correlation spectroscopy and extracting relaxation time constants on nano- to millisecond time scales. Destabilization of the generally very stable homodimers by chemical denaturation reduces the lifetime of H-dimers. We demonstrate that H-dimer formation of an oxazine fluorophore reports on end-to-end contact rates in unstructured glycine-serine polypeptides under denaturing conditions.
authors.affiliation: Department of Biotechnology and Biophysics, Julius-Maximilians University, 97074 Würzburg, Germany.
authors.forename: Stefan
authors.initials: S
authors.lastname: Bollmann
authors.forename: Marc
authors.initials: M
authors.lastname: Löllmann
authors.forename: Markus
authors.initials: M
authors.lastname: Sauer
authors.forename: Sören
authors.initials: S
authors.lastname: Doose
mesh_terms: D001704:Biopolymers / Q000737:chemistry*; D019281:Dimerization; D005456:Fluorescent Dyes / Q000737:chemistry*; D019791:Guanidine / Q000737:chemistry; D007700:Kinetics; D015394:Molecular Structure; D009038:Motion; D009691:Nucleic Acid Denaturation; D009842:Oligopeptides / Q000138:chemical synthesis / Q000737:chemistry; D010078:Oxazines / Q000737:chemistry; D011487:Protein Conformation; D011489:Protein Denaturation; D013050:Spectrometry, Fluorescence; D013053:Spectrophotometry; D013056:Spectrophotometry, Ultraviolet
chemical_list: D001704:Biopolymers; D005456:Fluorescent Dyes; C510593:MR121 oxazine fluorophore; D009842:Oligopeptides; D010078:Oxazines; D019791:Guanidine