What are the limitations of fluorescent protein fluorophores in FRET?

As imaging progresses over time, fluorophores tend to degrade, resulting in a reduction of signal intensity. This decay in signal can distort the donor-to-acceptor ratios crucial for ratiometric FRET analysis. Another con is that fluorescent proteins are relatively large compared to small molecule dyes, which may affect the conformation and function of the fusion proteins they are attached to. Some may also oligomerize into tetramers.