The molecular yo-yo method: Live jump detection improves throughput of single-molecule force spectroscopy for out-of-equilibrium transitions

• Published in: arXiv.org 2013-03
• Main Authors: Mack, A H, Schlingman, D J, Kamenetska, M, Collins, Robert, Regan, L, Mochrie, S G J
• Format: Article
• Language: English
• Subjects: Algorithms; Equilibrium; Error analysis; Error reduction; Free energy; Rewinding
• ISSN: 2331-8422
• DOI: 10.48550/arxiv.1303.3495

By monitoring multiple molecular transitions, force-clamp and trap-position-clamp methods have led to precise determinations of the free energies and free energy landscapes for molecular states populated in equilibrium at the same or similar forces. Here, we present a powerful new elaboration of the force-clamp and force-jump methods, applicable to transitions far from equilibrium. Specifically, we have implemented a live jump detection and force-clamp algorithm that intelligently adjusts and maintains the force on a single molecule in response to the measured state of that molecule. We are able to collect hundreds of individual molecular transitions at different forces, many times faster than previously, permitting us to accurately determine force-dependent lifetime distributions and reaction rates. Application of our method to unwinding and rewinding the nucleosome inner turn, using optical tweezers reveals experimental lifetime distributions that comprise a statistically-meaningful number of transitions, and that are accurately single exponential. These measurements significantly reduce the error in the previously measured rates, and demonstrate the existence of a single, dominant free energy barrier at each force studied. A key benefit of the molecular yoyo method for nucleosomes is that it reduces as far as possible the time spent in the tangentially-bound state, which minimizes the loss of nucleosomes by dissociation.