Diamond-lattice photonic crystals assembled from DNA origami.

Colloidal self-assembly allows rational design of structures on the micrometer and submicrometer scale. One architecture that can generate complete three-dimensional photonic bandgaps is the diamond cubic lattice, which has remained difficult to realize at length scales comparable with the wavelength of visible or ultraviolet light. In this work, we demonstrate three-dimensional photonic crystals self-assembled from DNA origami that act as precisely programmable patchy colloids. Our DNA-based nanoscale tetrapods crystallize into a rod-connected diamond cubic lattice with a periodicity of 170 nanometers. This structure serves as a scaffold for atomic-layer deposition of high-refractive index materials such as titanium dioxide, yielding a tunable photonic bandgap in the near-ultraviolet.

Site-directed placement of three-dimensional DNA origami.

The combination of lithographic methods with two-dimensional DNA origami self-assembly has led, among others, to the development of photonic crystal cavity arrays and the exploration of sensing nanoarrays where molecular devices are patterned on the sub-micrometre scale. Here we extend this concept to the third dimension by mounting three-dimensional DNA origami onto nanopatterned substrates, followed by silicification to provide hybrid DNA-silica structures exhibiting mechanical and chemical stability and achieving feature sizes in the sub-10-nm regime. Our versatile and scalable method relying on self-assembly at ambient temperatures offers the potential to three-dimensionally position any inorganic and organic components compatible with DNA origami nanoarchitecture, demonstrated here with gold nanoparticles. This way of nanotexturing could provide a route for the low-cost production of complex and three-dimensionally patterned surfaces and integrated devices designed on the molecular level and reaching macroscopic dimensions.

DNA Origami Fiducial for Accurate 3D Atomic Force Microscopy Imaging.

Atomic force microscopy (AFM) is a powerful technique for imaging molecules, macromolecular complexes, and nanoparticles with nanometer resolution. However, AFM images are distorted by the shape of the tip used. These distortions can be corrected if the tip shape can be determined by scanning a sample with features sharper than the tip and higher than the object of interest. Here we present a 3D DNA origami structure as fiducial for tip reconstruction and image correction. Our fiducial is stable under a broad range of conditions and has sharp steps at different heights that enable reliable tip reconstruction from as few as ten fiducials. The DNA origami is readily codeposited with biological and nonbiological samples, achieves higher precision for the tip apex than polycrystalline samples, and dramatically improves the accuracy of the lateral dimensions determined from the images. Our fiducial thus enables accurate and precise AFM imaging for a broad range of applications.

DNA Origami Curvature Sensors for Nanoparticle and Vesicle Size Determination with Single-Molecule FRET Readout.

Particle size is an important characteristic of materials with a direct effect on their physicochemical features. Besides nanoparticles, particle size and surface curvature are particularly important in the world of lipids and cellular membranes as the cell membrane undergoes conformational changes in many biological processes which leads to diverging local curvature values. On account of that, it is important to develop cost-effective, rapid and sufficiently precise systems that can measure the surface curvature on the nanoscale that can be translated to size for spherical particles. As an alternative approach for particle characterization, we present flexible DNA nanodevices that can adapt to the curvature of the structure they are bound to. The curvature sensors use Fluorescence Resonance Energy Transfer (FRET) as the transduction mechanism on the single-molecule level. The curvature sensors consist of segmented DNA origami structures connected via flexible DNA linkers incorporating a FRET pair. The activity of the sensors was first demonstrated with defined binding to different DNA origami geometries used as templates. Then the DNA origami curvature sensors were applied to measure spherical silica beads having different size, and subsequently on lipid vesicles. With the designed sensors, we could reliably distinguish different sized nanoparticles within a size range of 50-300 nm as well as the bending angle range of 50-180°. This study helps with the development of more advanced modular-curvature sensing devices that are capable of determining the sizes of nanoparticles and biological complexes.

Visible wavelength spectral tuning of absorption and circular dichroism of DNA-assembled Au/Ag core-shell nanorod assemblies.

Plasmonic nanoparticles have unique properties which can be harnessed to manipulate light at the nanoscale. With recent advances in synthesis protocols that increase their stability, gold-silver core-shell nanoparticles have become suitable building blocks for plasmonic nanostructures to expand the range of attainable optical properties. Here we tune the plasmonic response of gold-silver core-shell nanorods over the visible spectrum by varying the thickness of the silver shell. Through the chiral arrangement of the nanorods with the help of various DNA origami designs, the spectral tunability of the plasmon resonance frequencies is transferred into circular dichroism signals covering the spectrum from 400 nm to 700 nm. Our approach could aid in the construction of better sensors as well as metamaterials with a tunable optical response in the visible region.

DNA Origami Meets Bottom-Up Nanopatterning.

DNA origami has emerged as a powerful molecular breadboard with nanometer resolution that can integrate the world of bottom-up (bio)chemistry with large-scale, macroscopic devices created by top-down lithography. Substituting the top-down patterning with self-assembled colloidal nanoparticles now takes the manufacturing complexity of top-down lithography out of the equation. As a result, the deterministic positioning of single molecules or nanoscale objects on macroscopic arrays is benchtop ready and easily accessible.

DNA Origami-Enabled Plasmonic Sensing.

The reliable programmability of DNA origami makes it an extremely attractive tool for bottom-up self-assembly of complex nanostructures. Utilizing this property for the tuned arrangement of plasmonic nanoparticles holds great promise particularly in the field of biosensing. Plasmonic particles are beneficial for sensing in multiple ways, from enhancing fluorescence to enabling a visualization of the nanoscale dynamic actuation via chiral rearrangements. In this Perspective, we discuss the recent developments and possible future directions of DNA origami-enabled plasmonic sensing systems. We start by discussing recent advancements in the area of fluorescence-based plasmonic sensing using DNA origami. We then move on to surface-enhanced Raman spectroscopy sensors followed by chiral sensing, both utilizing DNA origami nanostructures. We conclude by providing our own views on the future prospects for plasmonic biosensors enabled using DNA origami.

DNA Origami Nano-Sheets and Nano-Rods Alter the Orientational Order in a Lyotropic Chromonic Liquid Crystal.

Rod-like and sheet-like nano-particles made of desoxyribonucleic acid (DNA) fabricated by the DNA origami method (base sequence-controlled self-organized folding of DNA) are dispersed in a lyotropic chromonic liquid crystal made of an aqueous solution of disodium cromoglycate. The respective liquid crystalline nanodispersions are doped with a dichroic fluorescent dye and their orientational order parameter is studied by means of polarized fluorescence spectroscopy. The presence of the nano-particles is found to slightly reduce the orientational order parameter of the nematic mesophase. Nano-rods with a large length/width ratio tend to preserve the orientational order, while more compact stiff nano-rods and especially nano-sheets reduce the order parameter to a larger extent. In spite of the difference between the sizes of the DNA nano-particles and the rod-like columnar aggregates forming the liquid crystal, a similarity between the shapes of the former and the latter seems to be better compatible with the orientational order of the liquid crystal.

Chiral Assembly of Gold-Silver Core-Shell Plasmonic Nanorods on DNA Origami with Strong Optical Activity.

The spatial organization of metal nanoparticles has become an important tool for manipulating light in nanophotonic applications. Silver nanoparticles, particularly silver nanorods, have excellent plasmonic properties but are prone to oxidation and are therefore inherently unstable in aqueous solutions and salt-containing buffers. Consequently, gold nanoparticles have often been favored, despite their inferior optical performance. Bimetallic, i.e., gold-silver core-shell nanoparticles, can resolve this issue. We present a method for synthesizing highly stable gold-silver core-shell NRs that are instantaneously functionalized with DNA, enabling chiral self-assembly on DNA origami. The silver shell gives rise to an enhancement of plasmonic properties, reflected here in strongly increased circular dichroism, as compared to pristine gold nanorods. Gold-silver nanorods are ideal candidates for plasmonic sensing with increased sensitivity as needed in pathogen RNA or antibody testing for nonlinear optics and light-funneling applications in surface enhanced Raman spectroscopy. Furthermore, the control of interparticle orientation enables the study of plasmonic phenomena, in particular, synergistic effects arising from plasmonic coupling of such bimetallic systems.