you may want to check out LOV photoreceptor domains that are smaller and have been customized for this purpose. see for example Chapman, S., Faulkner, C., Kaiserli, E., Garcia-Mata, C., Savenkov, E. I., Roberts, A. G., Oparka, K. J., and Christie, J. M. (2008) The photoreversible fluorescent protein iLOV outperforms GFP as a reporter of plant virus infection. Proc Natl Acad Sci U S A 105, 20038–43

you can try SNAP tags, these tags allow the covalanet binding of various flourescent dyes.