title: Double-stranded RNA under force and torque: similarities to and striking differences from double-stranded DNA.
abstract: RNA plays myriad roles in the transmission and regulation of genetic information that are fundamentally constrained by its mechanical properties, including the elasticity and conformational transitions of the double-stranded (dsRNA) form. Although double-stranded DNA (dsDNA) mechanics have been dissected with exquisite precision, much less is known about dsRNA. Here we present a comprehensive characterization of dsRNA under external forces and torques using magnetic tweezers. We find that dsRNA has a force-torque phase diagram similar to that of dsDNA, including plectoneme formation, melting of the double helix induced by torque, a highly overwound state termed "P-RNA," and a highly underwound, left-handed state denoted "L-RNA." Beyond these similarities, our experiments reveal two unexpected behaviors of dsRNA: Unlike dsDNA, dsRNA shortens upon overwinding, and its characteristic transition rate at the plectonemic buckling transition is two orders of magnitude slower than for dsDNA. Our results challenge current models of nucleic acid mechanics, provide a baseline for modeling RNAs in biological contexts, and pave the way for new classes of magnetic tweezers experiments to dissect the role of twist and torque for RNA-protein interactions at the single-molecule level.
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands; Department of Physics, Nanosystems Initiative Munich, and Center for NanoScience, Ludwig Maximilians University Munich, 80799 Munich, Germany; and.
authors.forename: Jan
authors.initials: J
authors.lastname: Lipfert
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands;
authors.forename: Gary M
authors.initials: GM
authors.lastname: Skinner
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands;
authors.forename: Johannes M
authors.initials: JM
authors.lastname: Keegstra
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands;
authors.forename: Toivo
authors.initials: T
authors.lastname: Hensgens
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands;
authors.forename: Tessa
authors.initials: T
authors.lastname: Jager
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands;
authors.forename: David
authors.initials: D
authors.lastname: Dulin
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands;
authors.forename: Mariana
authors.initials: M
authors.lastname: Köber
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands;
authors.forename: Zhongbo
authors.initials: Z
authors.lastname: Yu
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands;
authors.forename: Serge P
authors.initials: SP
authors.lastname: Donkers
authors.affiliation: Departments of Biochemistry and.
authors.forename: Fang-Chieh
authors.initials: FC
authors.lastname: Chou
authors.affiliation: Departments of Biochemistry and Physics, Stanford University, Stanford, CA 94305.
authors.forename: Rhiju
authors.initials: R
authors.lastname: Das
authors.affiliation: Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands; n.h.dekker@tudelft.nl.
authors.forename: Nynke H
authors.initials: NH
authors.lastname: Dekker
mesh_terms: D004247:DNA / Q000737:chemistry*; D060328:Magnetic Phenomena; D009690:Nucleic Acid Conformation; D012330:RNA, Double-Stranded / Q000737:chemistry*; D013816:Thermodynamics; D019415:Torque
chemical_list: D012330:RNA, Double-Stranded; D004247:DNA
keywords: RNA; force; magnetic tweezers; nucleic acids; torque