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Using Monte-Carlo simulations, we deconvolved the sliding and hoppingkinetics of GFP-LacI proteins on elongated DNA from their experimentallyobserved seconds-long diffusion trajectories. Our simulations suggest thefollowing results: (1) in each diffusion trajectory, a protein makes on averagehundreds of alternating slides and hops with a mean sliding time of severaltens of ms; (2) sliding dominates the root mean square displacement of fastdiffusion trajectories, whereas hopping dominates slow ones; (3) flow andvariations in salt concentration have limited effects on hopping kinetics,while in vivo DNA configuration is not expected to influence sliding kinetics;furthermore, (4) the rate of occurrence for hops longer than 200 nm agrees withexperimental data for EcoRV proteins.

Protein sliding and hopping kinetics on DNA