  Quantitative fluorescence analysis is often used to derive chemical
properties, including stoichiometries, of biomolecular complexes. One
fundamental underlying assumption in the analysis of fluorescence data --
whether it be the determination of protein complex stoichiometry by
super-resolution, or step-counting by photobleaching, or the determination of
RNA counts in diffraction-limited spots in RNA fluorescence {\it in situ}
hybridization (RNA-FISH) experiments -- is that fluorophores behave identically
and do not interact. However, recent experiments on fluorophore-labeled
DNA-origami structures such as fluorocubes have shed light on the nature of the
interactions between identical fluorophores as these are brought closer
together, thereby raising questions on the validity of the modeling assumption
that fluorophores do not interact. Here, we analyze photon arrival data under
pulsed illumination from fluorocubes where distances between dyes range from
2-10 nm. We discuss the implications of non-additivity of brightness on
quantitative fluorescence analysis.
