Maximizing the Accessibility in DNA Origami Nanoantenna Plasmonic Hotspots

Abstract

The LSPR effect is based on the interaction of electromagnetic radiation with conduction electrons of noble metal NPs and the resonance strongly depends on the correspondence of the excitation wavelength to size, shape, and material of the NP. [29,30] When placing a single fluorescent molecule in proximity, multiple effects simultaneously influence transitions between electronic states. The increased intensity of the local electric field, created by LSPR, and distance to NPs affect excitation rates, as well as radiative and non-radiative decay rates. [18,31,32] In consequence, the distance dependence results in a continuous transition from fluorescence quenching (FQ) in close proximity and fluorescence enhancement (FE) at an increased distance, reaching maximum FE values at a defined position (hotspot). [21,33,34] Besides their distance, the size of NPs influences the relation of quenching and enhancement. In first approximation, larger particles lead to higher FE. [35,36] Finally, electric field enhancement only occurs at the poles of particles or in between particles depending on the relative alignment of particles, emitters, and the excitation polarization.The first examples of so-called dimer nanoantennas (NAs) were achieved using electron-beam lithography, relying on dyes stochastically placed in the hotspot. [33] Controlled positioning of a fluorophore in the hotspot of two NPs was presented by Acuna et al., utilizing a pillar-shaped DNA origami that bears anchoring poly-adenine strands for the attachment of two gold (Au) NPs (functionalized via thiol chemistry with poly-thymine) at a fixed position, while placing a fluorophore in between (Figure 1a). [37,38] FE values up to 117-fold were achieved by positioning an ATTO647N molecule in the created 23 nm gap between two 100 nm Au NPs. [35,36] Although FE values of over 400-fold were reached in refined DNA origami structures, the mentioned NA designs suffered from the limitation that the hotspot region was blocked by the DNA origami itself, thereby prohibiting the placement of a detection assay in this region. [29,[39][40][41] To this end, the DNA origami NA proved to be applicable for the detection of Zika virus-specific oligonucleotides, both in buffer and heat-deactivated serum. [39] However, due to the steric hindrance in the hotspot, only the binding of one plasmonic NP was feasible, resulting in moderate FE values (approximately sevenfold) in the monomer NA arrangement.Only recently, a DNA origami dimer NanoAntenna with Cleared HOtSpot (NACHOS, Figure 1b) was realized that DNA nanotechnology has conquered the challenge of positioning quantum emitters in the hotspot of optical antenna structures for fluorescence enhancement. Therefore, DNA origami serves as the scaffold to arrange nanoparticles and emitters, such as fluorescent dyes. For the next challenge of optimizing the applicability of plasmonic hotspots for molecular assays, a Trident DNA origami structure that increases the accessibility of the hotspot is introduced, thereby improving the kinetics...

Single-Molecule FRET at 10 MHz Count Rates

“…Recent iterations of the DNA origami nanoantenna could accommodate even larger biomolecules and should further reduce the potential impact of the constricted environment on the experiments. 44 The development of new near-infrared fluorophores showing less blinking on the low microsecond time scale, 45 which potentially interferes with the maximumlikelihood analysis, should make it possible to further push the time resolution and possibly, in combination with more efficient sampling methods, bridge the gap toward the time scales of molecular dynamics simulations. 46…”

Pursuing excitonic energy transfer with programmable DNA-based optical breadboards

“…In this context, DNA scaffolding provides the ability to bring gold NPs, nanorods and other NPs into very close proximity with each other to permit formation of plasmonic hotspots. [19][20][21][22][23][24][25][26] It has been repeatedly confirmed in this context that DNA's prescriptiveness uniquely allows for nanoscale changes in material positioning across multiple parallel structures and this enables a direct comparison between theoretical prediction and experimental observation in a facile manner. An overview of these and similarly related applications are available in several excellent reviews and are not discussed further.…”

Lab-on-a-DNA origami: nanoengineered single-molecule platforms

“…In this case, an even larger open diffusion space is obtained without increasing the nanoparticles’ distance, resulting in a design with enhancements in the order of 76 fold. 86 At the same time, the larger area was used to detect DNA single strands with a length of 151 nucleotides. Such open space can further contribute to studies on biophysics since different active biomolecules, such as proteins, can be placed there to study dynamic processes.…”