Predicting fluorescence lifetimes and spectra of biopolymers

Use of fluorescence in biology and biochemistry for imaging and characterizing equilibrium and dynamic processes is growing exponentially. Much progress has been made in the last few years on the microscopic understanding of the underlying principles of what controls the wavelength and quenching of fluorescence in biopolymers, both of which are central to the utility of fluorescent probes. This chapter is concerned with the quantitative microscopic understanding and prediction of the fluorescence wavelength and/or intensity of a fluorescent probe molecule attached to a biopolymer as revealed by hybrid quantum and classical mechanical computation procedures. The aim is not only to provide a recipe, but also even more importantly, to communicate the qualitative basic concepts of interpretation of fluorescence. These are surprisingly simple, although not broadly appreciated at this time. In addition, an effort has been made to show how these techniques have led to an emerging understanding of the relation between time-dependent wavelengths shifts due to solvent relaxation and population decay of conformational sub-ensembles.