Force unfolding kinetics of RNA using optical tweezers. I. Effects of experimental variables on measured results

Biophys J. 2007 May 1;92(9):2996-3009. doi: 10.1529/biophysj.106.094052. Epub 2007 Feb 9.

Abstract

Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped by dual-beam lasers and the other was held by a micropipette. Several experimental variables were changed while measuring the unfolding/refolding kinetics, including handle lengths, trap stiffness, and modes of force applied to the molecule. In constant-force mode where the tension applied to the RNA was maintained through feedback control, the measured rate coefficients varied within 40% when the handle lengths were changed by 10-fold (1.1-10.2 Kbp); they increased by two- to threefold when the trap stiffness was lowered to one-third (from 0.1 to 0.035 pN/nm). In the passive mode, without feedback control and where the force applied to the RNA varied in response to the end-to-end distance change of the tether, the RNA hopped between a high-force folded-state and a low-force unfolded-state. In this mode, the rates increased up to twofold with longer handles or softer traps. Overall, the measured rates remained with the same order-of-magnitude over the wide range of conditions studied. In the companion article on pages 3010-3021, we analyze how the measured kinetics parameters differ from the intrinsic molecular rates of the RNA, and thus how to obtain the molecular rates.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

  • Artifacts*
  • Computer Simulation
  • Elasticity
  • Kinetics
  • Micromanipulation / methods*
  • Models, Chemical*
  • Models, Molecular*
  • Nucleic Acid Conformation
  • Nucleic Acid Denaturation
  • Optical Tweezers*
  • RNA / chemistry*
  • RNA / ultrastructure*
  • Reproducibility of Results
  • Sensitivity and Specificity
  • Stress, Mechanical

Substances

  • RNA