Conformational Changes and Flexibility of DNA Devices Observed by Small-Angle X-ray Scattering. 2016

Linda K Bruetzel, and Thomas Gerling, and Steffen M Sedlak, and Philipp U Walker, and Wenjun Zheng, and Hendrik Dietz, and Jan Lipfert
Department of Physics, Nanosystems Initiative Munich, and Center for Nanoscience, LMU Munich , Amalienstrasse 54, 80799 Munich, Germany.

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.

UI MeSH Term Description Entries
D008958 Models, Molecular Models used experimentally or theoretically to study molecular shape, electronic properties, or interactions; includes analogous molecules, computer-generated graphics, and mechanical structures. Molecular Models,Model, Molecular,Molecular Model
D009690 Nucleic Acid Conformation The spatial arrangement of the atoms of a nucleic acid or polynucleotide that results in its characteristic 3-dimensional shape. DNA Conformation,RNA Conformation,Conformation, DNA,Conformation, Nucleic Acid,Conformation, RNA,Conformations, DNA,Conformations, Nucleic Acid,Conformations, RNA,DNA Conformations,Nucleic Acid Conformations,RNA Conformations
D004247 DNA A deoxyribonucleotide polymer that is the primary genetic material of all cells. Eukaryotic and prokaryotic organisms normally contain DNA in a double-stranded state, yet several important biological processes transiently involve single-stranded regions. DNA, which consists of a polysugar-phosphate backbone possessing projections of purines (adenine and guanine) and pyrimidines (thymine and cytosine), forms a double helix that is held together by hydrogen bonds between these purines and pyrimidines (adenine to thymine and guanine to cytosine). DNA, Double-Stranded,Deoxyribonucleic Acid,ds-DNA,DNA, Double Stranded,Double-Stranded DNA,ds DNA
D014961 X-Ray Diffraction The scattering of x-rays by matter, especially crystals, with accompanying variation in intensity due to interference effects. Analysis of the crystal structure of materials is performed by passing x-rays through them and registering the diffraction image of the rays (CRYSTALLOGRAPHY, X-RAY). (From McGraw-Hill Dictionary of Scientific and Technical Terms, 4th ed) Xray Diffraction,Diffraction, X-Ray,Diffraction, Xray,Diffractions, X-Ray,Diffractions, Xray,X Ray Diffraction,X-Ray Diffractions,Xray Diffractions
D053838 Scattering, Small Angle Scattering of a beam of electromagnetic or acoustic RADIATION, or particles, at small angles by particles or cavities whose dimensions are many times as large as the wavelength of the radiation or the de Broglie wavelength of the scattered particles. Also know as low angle scattering. (McGraw-Hill Dictionary of Scientific and Technical Terms, 6th ed) Small angle scattering (SAS) techniques, small angle neutron (SANS), X-ray (SAXS), and light (SALS, or just LS) scattering, are used to characterize objects on a nanoscale. Small Angle Scattering,Low Angle Scattering,Scattering, Low Angle,Angle Scattering, Low,Angle Scatterings, Low,Low Angle Scatterings,Scatterings, Low Angle

Related Publications

Linda K Bruetzel, and Thomas Gerling, and Steffen M Sedlak, and Philipp U Walker, and Wenjun Zheng, and Hendrik Dietz, and Jan Lipfert
February 2005, Structure (London, England : 1993),
Linda K Bruetzel, and Thomas Gerling, and Steffen M Sedlak, and Philipp U Walker, and Wenjun Zheng, and Hendrik Dietz, and Jan Lipfert
July 1988, Biochimica et biophysica acta,
Linda K Bruetzel, and Thomas Gerling, and Steffen M Sedlak, and Philipp U Walker, and Wenjun Zheng, and Hendrik Dietz, and Jan Lipfert
June 2023, Proceedings of the National Academy of Sciences of the United States of America,
Linda K Bruetzel, and Thomas Gerling, and Steffen M Sedlak, and Philipp U Walker, and Wenjun Zheng, and Hendrik Dietz, and Jan Lipfert
October 2012, European biophysics journal : EBJ,
Linda K Bruetzel, and Thomas Gerling, and Steffen M Sedlak, and Philipp U Walker, and Wenjun Zheng, and Hendrik Dietz, and Jan Lipfert
March 1996, Biochemistry,
Linda K Bruetzel, and Thomas Gerling, and Steffen M Sedlak, and Philipp U Walker, and Wenjun Zheng, and Hendrik Dietz, and Jan Lipfert
December 2011, Journal of molecular biology,
Linda K Bruetzel, and Thomas Gerling, and Steffen M Sedlak, and Philipp U Walker, and Wenjun Zheng, and Hendrik Dietz, and Jan Lipfert
June 2011, Journal of molecular biology,
Linda K Bruetzel, and Thomas Gerling, and Steffen M Sedlak, and Philipp U Walker, and Wenjun Zheng, and Hendrik Dietz, and Jan Lipfert
December 1952, Nature,
Linda K Bruetzel, and Thomas Gerling, and Steffen M Sedlak, and Philipp U Walker, and Wenjun Zheng, and Hendrik Dietz, and Jan Lipfert
January 1979, Methods in enzymology,
Linda K Bruetzel, and Thomas Gerling, and Steffen M Sedlak, and Philipp U Walker, and Wenjun Zheng, and Hendrik Dietz, and Jan Lipfert
January 1973, Methods in enzymology,
Copied contents to your clipboard!