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Aiming at the rational design and the identification of brilliant fluorescent reporters for targeted optical probes and fluorescence assays in biological matrices, we systematically assessed the correlation between dye–protein binding, dye aggregation, and dye hydrophilicity for bioanalytically relevant fluorescent labels. Here, we report on the influence of sulfonic acid groups on dye aggregation and dye–serum protein interactions exemplarily for a family of NIR-emissive cyanine dyes, the DY-67x fluorophores. For highly hydrophobic dyes like DY-675 and DY-676, which show a strong tendency for aggregation in phosphate buffer saline solution, the dye–protein binding constants determined spectroscopically using a 2-state binding model, which considers only protein-bound and unbound dye molecules, can be influenced by the dimerization of the unbound dyes. To consider and quantify this influence, we expanded this common photometric method to a 3-state model that accounts for the presence of dye aggregates in the binding studies. Our results can be exploited for the screening of fluorescent reporters, efficiently providing information on the size of dye–protein interactions and on maximally achievable fluorescence quantum yields in biological systems.
With rare exceptions, natural evolution is an extremely slow process. One particularly striking exception in the case of protein evolution is in the natural production of antibodies. Developing B cells activate and diversify their immunoglobulin (Ig) genes by recombination, gene conversion (GC) and somatic hypermutation (SHM). Iterative cycles of hypermutation and selection continue until antibodies of high antigen binding specificity emerge (affinity maturation). The avian B cell line DT40, a cell line which is highly amenable to genetic manipulation and exhibits a high rate of targeted integration, utilizes both GC and SHM. Targeting the DT40's diversification machinery onto transgenes of interest inserted into the Ig loci and coupling selective pressure based on the desired outcome mimics evolution. Here we further demonstrate the usefulness of this platform technology by selectively pressuring a large shift in the spectral properties of the fluorescent protein eqFP615 into the highly stable and advanced optical imaging expediting fluorescent protein Amrose. The method is advantageous as it is time and cost effective and no prior knowledge of the outcome protein's structure is necessary. Amrose was evolved to have high excitation at 633 nm and excitation/emission into the far-red, which is optimal for whole-body and deep tissue imaging as we demonstrate in the zebrafish and mouse model.