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Atomic force microscope-based single-molecule force spectroscopy of RNA unfolding
Authors:Hans A. Heus  Elias M. Puchner  Aafke J. van Vugt-Jonker  Julia L. Zimmermann  Hermann E. Gaub
Affiliation:aInstitute for Molecules and Materials, Radboud University Nijmegen, Heyendaalseweg 135, 6525 AJ Nijmegen, The Netherlands;bDepartment of Applied Physics and Centre for Nanoscience, University of Munich, Amalienstrasse 54, 80799 Munich, Germany
Abstract:Single-molecule force spectroscopy (SMFS) using the atomic force microscope (AFM) has emerged as an important tool for probing biomolecular interaction and exploring the forces, dynamics, and energy landscapes that underlie function and specificity of molecular interaction. These studies require attaching biomolecules on solid supports and AFM tips to measure unbinding forces between individual binding partners. Herein we describe efficient and robust protocols for probing RNA interaction by AFM and show their value on two well-known RNA regulators, the Rev-responsive element (RRE) from the HIV-1 genome and an adenine-sensing riboswitch. The results show the great potential of AFM–SMFS in the investigation of RNA molecular interactions, which will contribute to the development of bionanodevices sensing single RNA molecules.
Keywords:RNA   Atomic force microscopy   Single-molecule force spectroscopy   Rev-RRE   Riboswitch
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