2004/05/05 by Maria Manosas, Maria Mañosas, Félix Ritort +1 · 2 citations
Biochemistry, Genetics and Molecular Biology · Engineering · Physics and Astronomy · #Force Microscopy Techniques and Applications #Mechanical and Optical Resonators #Molecular Junctions and Nanostructures #cond-mat.stat-mech #q-bio.BM
paper · pdf · doi:10.1529/biophysj.104.045344
36 pages, 37 figures. Submitted to Biophysical Journal
arxiv created 2004/05/05 · openalex publication_date 2005/03/11 · arxiv updated 2009/12/01 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/28
Recent single-molecule pulling experiments have shown how it is possible to manipulate RNA molecules using optical tweezers force microscopy. We investigate a minimal model for the experimental setup which includes a RNA molecule connected to two polymers (handles) and a bead, trapped in the optical potential, attached to one of the handles. Initially, we focus on small single-domain RNA molecules which unfold in a cooperative way. The model qualitatively reproduces the experimental results and allow us to investigate the influence of the bead and handles on the unfolding reaction. A main ingredient of our model is to consider the appropriate statistical ensemble and the corresponding thermodynamic potential describing thermal fluctuations in the system. We then investigate several questions relevant to extract thermodynamic information from the experimental data. Next, we study the kinetics using a dynamical model. Finally, we address the more general problem of a multidomain RNA molecule with Mg2+-tertiary contacts that unfolds in a sequential way and propose techniques to analyze the breakage force data in order to obtain the reliable kinetics parameters that characterize each domain.