title: Conformational Changes and Flexibility of DNA Devices Observed by Small-Angle X-ray Scattering.
abstract: Self-assembled DNA origami nanostructures enable the creation of precisely defined shapes at the molecular scale. Dynamic DNA devices that are capable of switching between defined conformations could afford completely novel functionalities for diagnostic, therapeutic, or engineering applications. Developing such objects benefits strongly from experimental feedback about conformational changes and 3D structures, ideally in solution, free of potential biases from surface attachment or labeling. Here, we demonstrate that small-angle X-ray scattering (SAXS) can quantitatively resolve the conformational changes of a DNA origami two-state switch device as a function of the ionic strength of the solution. In addition, we show how SAXS data allow for refinement of the predicted idealized three-dimensional structure of the DNA object using a normal mode approach based on an elastic network model. The results reveal deviations from the idealized design geometries that are otherwise difficult to resolve. Our results establish SAXS as a powerful tool to investigate conformational changes and solution structures of DNA origami and we anticipate our methodology to be broadly applicable to increasingly complex DNA and RNA devices.
authors.affiliation: Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany.
authors.forename: Linda K
authors.initials: LK
authors.lastname: Bruetzel
authors.affiliation: Physik Department, Walter Schottky Institute, Technische Universität München , Am Coulombwall 4a, 85748 Garching near Munich, Germany.
authors.forename: Thomas
authors.initials: T
authors.lastname: Gerling
authors.affiliation: Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany.
authors.forename: Steffen M
authors.initials: SM
authors.lastname: Sedlak
authors.affiliation: Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany.
authors.forename: Philipp U
authors.initials: PU
authors.lastname: Walker
authors.affiliation: Physics Department, State University of New York at Buffalo , Buffalo, New York 14260, United States.
authors.forename: Wenjun
authors.initials: W
authors.lastname: Zheng
authors.affiliation: Physik Department, Walter Schottky Institute, Technische Universität München , Am Coulombwall 4a, 85748 Garching near Munich, Germany.
authors.forename: Hendrik
authors.initials: H
authors.lastname: Dietz
authors.affiliation: Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany.
authors.forename: Jan
authors.initials: J
authors.lastname: Lipfert
mesh_terms: D004247:DNA / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D053838:Scattering, Small Angle; D014961:X-Ray Diffraction
chemical_list: D004247:DNA
keywords: DNA origami; SAXS; conformational changes; normal modes; small-angle X-ray scattering