# Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments Source: [Force unfolding kinetics of RNA using optical tweezers. II. Modeling experiments]() Collection index: [llms.txt]() Data updated: 2025-10-28T13:53:14.173Z Authors: M. Manosas, J.-D. Wen, P. T. X. Li, S. B. Smith, C. Bustamante, I. Tinoco, Jr., F. Ritort Published: 2007-07-04T15:40:05.000Z ## Abstract By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a mesoscopic model to analyze the hopping kinetics of RNA hairpins in an optical tweezers setup. The model includes different elements of the experimental setup (beads, handles and RNA sequence) and limitations of the instrument (time lag of the force-feedback mechanism and finite bandwidth of data acquisition). We investigated the influence of the instrument on the measured hopping rates. Results from the model are in good agreement with the experiments reported in the companion article (1). The comparison between theory and experiments allowed us to infer the values of the intrinsic molecular rates of the RNA hairpin alone and to search for the optimal experimental conditions to do the measurements. We conclude that long handles and soft laser traps represent the best conditions to extract rate estimates that are closest to the intrinsic molecular rates. The methodology and rationale presented here can be applied to other experimental setups and other molecules. ## Recorded benchmark results A research result applies to its stated dataset, split, metric and evaluation configuration. Compare like-for-like settings, preserve the metric's unit and direction, and distinguish paper-reported results from independent reproduction. The best result recorded here is not a claim of exhaustive, current global coverage. ## Original sources and implementation [Original paper]() [PDF]()