Environment-sensitive labels in multiplex fluorescence analyses of protein-DNA complexes

Fluorescein is widely used for protein labeling because of its high extinction coefficient and fluorescence emission quantum yield. However, its emission is readily quenched by various pathways, We exploit these properties of fluorescein to examine the self-association of a DNA binding protein and determine the amount of the protein in gel-shifted complexes with specific DNA. A construct (HSFDT385SH) of the heat shock transcription factor (HSF) was expressed that contains the DNA-binding and trimerization domains, residues 192-385 of HSF, with four additional COOH-terminal residues, GMLC, and then labeled at the COOH-terminal cysteine with fluorescein 5-maleimide to form HSFDT385-F1). The fluorescence increase accompanying the formation of heterotrimers on titration of HSFDT385-F1 with HSFDT385SH) led to an estimate of 3 x 10(-16) M(2) for the equilibrium constant for trimerization of HSFDT385SH. HSFDT385-F1 fluorescence also increased 1.7-fold on binding to specific DNA, but not to nonspecific DNA. The protein and DNA content of the several gel-shifted complexes of HSFDT385-F1 (lambda(max)(em) 532 nm) with specific DNA labeled noncovalently with the energy transfer heterodimer TOTAB (lambda(max)(em) 658 nm) were accurately determined by a two-color fluorescence emission assay with 488 nm excitation.