Single Molecule Super-Resolution Microscopy Study on the Precision with Which DNA Nanostructures Can Orient Fluorescent Dyes

DNA nanotechnology enables the rapid, programmable self-assembly of novel structures and devices at the nanoscale. Utilizing the simplicity of Watson-Crick base pairing, DNA nanostructures are capable of assembling a variety of nanoparticles in arbitrary configurations with relative ease. Several emerging opto-electronic systems require a high degree of control of both the position and orientation of component fluorescent molecules, and while DNA nanostructures have demonstrated these capabilities, the precision with which DNA can orient fluorescent molecules is not well understood. Determining these bounds is critical in establishing the viability of DNA nanotechnology as a method of assembling fluorescent molecular networks. In this work, using a combination of single molecule emission dipole imaging and super-resolution microscopy techniques, we correlate the orientations of fluorescent dye molecules to the orientations of their DNA substrates along five degrees of freedom. Several species of dyes were embedded within a DNA sequence using either one or two covalent tethers. These strands were incorporated directly into DNA origami structures to investigate the dependence of the location and binding architecture of the dye on the orientational precision of DNA nanostructures. Dye functionalized strands were also folded into a simpler four-arm junction, which was then immobilized on an origami structure to study the influence of the DNA substrate on dye orientation. Correlated analysis of super-resolution images of origami structures and single molecule emission dipole images from the embedded fluorescent molecule within the same structure allowed us to directly measure the relative orientations of dye molecules within DNA nanostructures. The resulting measurements revealed a moderate degree of polar angle control but a large variation in azimuthal control for the majority of structures examined. These measurements establish a single-molecule method for measurement of correlated orientations and provide a powerful approach for future studies on increasing the precision in the orientational control of fluorescent dye molecule monomers by DNA nanostructures.