Super-Resolution Optical Lithography with DNA

Abstract

We developed an efficient, versatile, and accessible super-resolution microscopy method to construct a nanoparticle assembly at a spatial resolution below the optical diffraction limit. The method utilizes DNA and a photoactivated DNA cross-linker. Super-resolution optical techniques have been used only as a means to make measurements below the light diffraction limit. Furthermore, no optical technique is currently available to construct nanoparticle assemblies with a precisely designed shape and internal structure at a resolution of a few tens of nanometers (nm). Here we demonstrate that we can fulfill this deficiency by utilizing spontaneous structural dynamics of DNA hairpins combined with single-molecule fluorescence resonance energy transfer (smFRET) microscopy and a photoactivated DNA cross-linker. The stochastic fluorescence blinking due to the spontaneous folding and unfolding motions of DNA hairpins enables us to precisely localize a folded hairpin and solidify it only when it is within a predesigned target area whose size is below the diffraction limit. As the method is based on an optical microscope and an easily clickable DNA cross-linking reagent, it will provide an efficient means to create large nanoparticle assemblies with a shape and internal structure at an optical super-resolution, opening a wide window of opportunities toward investigating their photophysical and optoelectronic properties and developing novel devices.

Chemically modified nucleic acids and DNA intercalators as tools for nanoparticle assembly

“…plasmonic, fluorescent or magnetic) can be independently controlled within nanostructures and therefore the collective properties of nanostructures can be tuned by manipulation of the interparticle distances. The production of reconfigurable nanoparticle assemblies via DNA catenanes and rotaxanes with well-defined spatial orientation, represents a promising 94 Gold nanoparticle one-dimensional chain assemblies 95 Upconversion aggregate assemblies 96 Gold nanoparticle-biomolecules conjugate assemblies 97 Click chemistry DNA modifications (SPAAC) Gold nanoparticle dimer assemblies 99,100,102 Gold nanoparticle assemblies on graphene oxide nanosheets 101 Gold nanoparticle dimer, trimer, cross-shaped and chain assemblies on DNA origami frames 104 Vinyl DNA modifications Gold nanoparticle dimer, trimer, and tetramer assemblies 116 Gold and Silver nanoparticle three-dimensional superlattice assemblies 117 Gold nanoparticle two-dimensional assemblies 118 Polystyrene nanoparticle surface assemblies 120 Psoralen derivatives Gold nanoparticle wire assemblies on DNA template 129 Gold nanoparticle dimer, trimer, and tetramer assemblies 131,132 Gold nanoparticle three-dimensional superlattice assemblies 133 Iron oxide nanoparticle assemblies on DNA template 130 Azobenzene derivatives Gold nanoparticle dimer assemblies 152 Gold nanorod dimer assemblies on DNA reconfigurable templates 149 Gold nanoparticle trimer assemblies on DNA tetrahedra nanostructures 144 Gold nanoparticle assemblies on three-dimensional DNA nanotubes 153 Gold nanoparticle aggregate assemblies 145 Gold nanoparticle three-dimensional superlattice assemblies 154 Lipid unilamellar vesicles (LUVs) aggregate assemblies 150 Mechanically interlocked DNA nanostructures DNA rotaxanes Gold nanoparticles assembled on DNA ring and DNA axle 177 Gold nanoparticles assembled on DNA origami ring and DNA origami axle 172 DNA catenanes Gold nanoparticles assembled on three DNA interlocked rings (various configurations) 178,…”

“…Cyanovinyl carbazole has also been employed in two-dimensional (2D) lithography fabrication techniques. Kim et al 118 showed the efficacy of this modification by developing a super-resolution microscopy method to assemble nanoparticles employing a three-strand hairpin construct modified with a carbazole crosslinker. Selective UV crosslinking occurred only when the hairpins were found in their folded state, allowing the hairpin strand to remain in the folded state, even upon ‘warm’ washing (above the T m of the DNA hybridisation).…”

“…Reproduced with permission from Kim et al, Nano Lett. 2019, 19(9), 6035-6042, copyright r (2019) American Chemical Society 118.…”

Single Molecules Are Your Quanta: A Bottom-Up Approach toward Multidimensional Super-resolution Microscopy

“…125,126 In particular, utilizing the highly controllable interactions of DNA strands, new probes have enabled the SMLM imaging of cellular traction forces 127,128 and single-molecule-based superresolution labeling. 129,130 The rise of high-dimensional SMLM methods beyond the traditional multicolor and 3D efforts affords new challenges and opportunities. For polarization-resolved SMLM, one recurring finding is that the detected single-molecule polarization orientation, as well as its dynamics, depends strongly on both the molecular structure of the fluorescent probe and how it is tagged to the target.…”

“…Beyond the usual efforts to attain brighter probes, recent work has used novel interactions between biomolecules for encoding functional information into SMLM. , In particular, utilizing the highly controllable interactions of DNA strands, new probes have enabled the SMLM imaging of cellular traction forces , and single-molecule-based super-resolution labeling. , …”