Interaction of fluorescence labeled single-stranded DNA with hexameric DNA-helicase RepA: A photon and fluorescence correlation spectroscopy study

Fluorescence correlation spectroscopy (FCS) was used to characterize the in teraction of fluorescence labeled single-stranded DMA (ssDNA) with hexameri c RepA DNA-helicase (hRepA) encoded by plasmid RSF1010. The apparent dissoc iation constants, K-d(app), for the equilibrium binding of 12mer, 30mer, an d 45mer ssDNA 5'-labeled with BFL to hRepA dimer in the presence of 0.5 mM ATP gammaS at pH 5.8 and 25 degreesC were determined to be 0.58 +/- 0.12, 0 .52 +/- 0.07, and 1.66 +/- 0.32 muM, respectively. Binding curves are compa tible with one binding site for ssDNA present on hRepA dimer, with no indic ation of cooperativity. At pH 7.6 in the presence of ATP gammaS and at pH 5 .8 in the absence of ATP gammaS, complex formation between ssDNA and hRepA was too weak for measuring complete binding curves by FCS. Under these cond itions, the dissociation constant, K-d(app), is in the range between 10 and 250 muM. The kinetics of complex formation at pH 5.8 are faster than the t ime resolution (approximately 10-20 s) of FCS experiments under pseudo-firs t-order conditions, with respect to BFL-ssDNA. Photon correlation spectrosc opy (PCS) experiments yielded, within the experimental error range, the sam e values for the apparent hydrodynamic radii, R-h, of hRepA dimer and its c omplex with ssDNA as determined by FCS (R-h = 6.6 +/- 1 nm). hRepA starts t o aggregate under acidic conditions (<pH 6.0) which are optimal for ssDNA b inding. CD spectra taken at pH 5.8 in the presence of ATP<gamma>S showed a structural change induced by ssDNA binding to hRepA which is not visible at pH 7.6 and with ADP as nucleotide cofactor.