Continuous-time random walk model for the diffusive motion of helicases

DNA helicases are molecular motors that use the energy from nucleotide hydrolysis to move along DNA, promoting the unwinding or rewinding of the double helix. Here, we use magnetic and optical tweezers to track the motion of three helicases, gp41, RecQ, and RecG, while they unwind or rewind a DNA hairpin. Their activity is characterized by measuring the helicase velocity and diffusivity under different force and ATP conditions. We use a continuous-time random walk framework that allows us to compute the mean helicase displacement and its fluctuations analytically. Fitting the model to the measured helicase velocity and diffusivity allows us to determine the main states and transitions in the helicase mechanochemical cycle. A general feature for all helicases is the need to incorporate an off-pathway pausing state to reproduce the data, raising the question of whether pauses play a regulatory role. Diffusivity measurements also lead to estimations of the thermodynamic uncertainty factor related to the motor efficiency. Assuming a tight mechano-chemical coupling, we find that the RecG helicase reaches a high efficiency when operating uphill, whereas the unwinding gp41 and RecQ helicases display much lower efficiencies. Incorporating the analysis of fluctuations allows for better characterization of the activity of molecular machines, which represents an advance in the field.