Fluorophore–quencher pair for monitoring protein motion

A fluorophore/quencher pair capable of detecting conformational changes of DNA-protein complexes is described. The system employs a fluorescent nucleoside analog 1,3-diaza-2-oxophenothiazine (tC) within duplex DNA and a non-fluorescent quencher (TEMPO) attached to an engineered cysteine residue of the protein. The straightforward labeling methodology allows for the placement of the fluorophore and quencher moieties at specific positions suited to studying the conformational change of interest. To illustrate the utility of the tC–TEMPO pair, we have monitored nucleotide-induced conformational changes of the Klenow fragment (KF) polymerase bound to duplex DNA. In this system, tC was incorporated in the primer strand of the duplex, adjacent to the 3′ end, while TEMPO was positioned at the end of the O-helix within the fingers domain of KF. Using steady-state fluorescence spectroscopy, we measured the quenching efficiency in a binary complex of tC-modified DNA and TEMPO-labeled KF and in ternary complexes containing cognate or non-cognate dNTP substrates. The quenching efficiency is significantly enhanced in the presence of a cognate dNTP, indicating that the O-helix has moved closer towards the DNA. In contrast, no significant tC quenching is observed in the presence of a non-cognate dNTP, indicating that the O-helix remains in a position that is beyond the distance reporting range of the tC–TEMPO pair. These results demonstrate that a cognate dNTP substrate induces a large conformational change of the O-helix, which can be sensitively detected using the tC–TEMPO pair. This fluorophore/quencher pair may be useful to study conformational changes associated with other DNA-enzyme complexes.