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.

Dimensions and Global Twist of Single-Layer DNA Origami Measured by Small-Angle X-ray Scattering

“…They demonstrate that repeated geometrical features of DNA origami such as the interhelical spacing result in clearly discernible diffraction peaks which can be used to quantify their internal geometry. 26 They also show that SAXS can quantify the equilibrium distribution of conformational states providing useful thermodynamic information, 26,27 including the dependence of the folding of DNA origami structures and interhelical spacing, on temperature and the concentration of magnesium ions. 26 The opportunity to perform time-resolved SAXS experiments at high-flux synchrotron beamlines has also been utilized to perform kinetic measurements on conformational transitions and dimerization of DNA origami structures with millisecond temporal resolution.…”

Time-Resolved Small-Angle X-ray Scattering Reveals Millisecond Transitions of a DNA Origami Switch

“…where the coefficients f i and f f are fractional occupancies of the initial and final states. For stopped-flow experiments we used static reference profiles of switchD16 samples acquired at 4 To evaluate the goodness of the two-state fits, chi-squared values (χ 2 ) were calculated for each fit according to the following equation:…”

Untitled

“…DNA walking device is one of the most complex in both design and manufacture [7]. Normal walking activities are initiated by chain hybridization [8], enzy-matic reactions [9] and environmental stimuli [10]. The device has great application potential in sensors [11] and signal conversion media [12].…”