Download Origami Editor 3D for free. Virtual paper folding program. Origami Editor 3D is an advanced paper folding simulator. It uses a what-you-see-is-what-you-get interface and operates with a geometric abstraction of the Yoshizawa-Randlett system. Project Rubric: Origami Paper Crane Criteria: Completed All Steps 3 Crane is completely constructed. 2 Much effort was made; Crane is mostly constructed. Folds are mostly neat and even. Neatness of Folds Folds are neatly creased and even. Cooperation and behavior Student.
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Plasmonic sensors are extremely promising candidates for label-free single-molecule analysis but require exquisite control over the physical arrangement of metallic nanostructures. Here we employ self-assembly based on the DNA origami technique for accurate positioning of individual gold nanoparticles.
Our innovative design leads to strong plasmonic coupling between two 40 nm gold nanoparticles reproducibly held with gaps of 3.3±1 nm. This is confirmed through far field scattering measurements on individual dimers which reveal a significant red shift in the plasmonic resonance peaks, consistent with the high dielectric environment due to the surrounding DNA. We use surface-enhanced Raman scattering (SERS) to demonstrate local field enhancements of several orders of magnitude through detection of a small number of dye molecules as well as short single-stranded DNA oligonucleotides. This demonstrates that DNA origami is a powerful tool for the high-yield creation of SERS-active nanoparticle assemblies with reliable sub-5 nm gap sizes. ( a) A schematic (not to scale) of the NP dimers assembled on the DNA origami platform. The NPs are coated with a ssDNA brush to prevent aggregation as well as facilitate attachment to the origami platform. ( b) Correctly formed dimer structures are separated from free NPs and aggregates by gel electrophoresis on a 0.7% agarose gel and imaged using a TEM (scale bar, 50 nm).
The yield of these structures is around 61±5% (mean±s.d.) as measured by the intensity of the dimer and aggregate bands. ( c) A schematic of the custom built setup for measuring the scattering spectra of single dimer nanostructures. KG: heat absorbing filter; ND: neutral density filter; LP: linear polarizer; BB: beam block; and BS: beam splitter. Assembly of NP dimers with a sub-5 nm gapAn overview of the experimental scheme is depicted in. A multi-layer 40 × 45 nm 2 DNA origami platform is assembled as described in Methods section. By varying the number of layers along the origami structure, two grooves are created to facilitate the correct positioning of two 40 nm Au NPs.
These grooves are separated and isolated from each other by a ridge of double helices. At its highest the ridge is six helices (15 nm) high. Crucially, in the gap directly between the NPs, the ridge is only two helices (5 nm) thick, which leaves the gap free for utilization of single-molecule spectroscopic techniques. Gold NPs are attached to correctly folded origami structures using a protocol given in Kuzyk et al.
Agarose gel electrophoresis is used to isolate the dimers from aggregates and incorrectly assembled structures as well as the large excess of free NPs. Based on an intensity analysis of the dimer and aggregate bands in, the yield is 61±5%.
While a small number of structures with only one NP attached are present within the dimer band, these are easily identifiable from the dimers due to their dramatically different spectral response. From transmission electron microscope (TEM) images of correctly assembled structures , we measure an average NP separation of 3.3±1.0 nm which is one of the shortest controllable gaps yet achieved with DNA origami assembly.
Characterization of plasmonic propertiesWe examined carefully the contributions of individual components of the assembled nanostructures to the plasmonic resonance of the NPs. A supercontinuum laser was employed in a reflective dark-field geometry to collect far-field scattering spectra of individual structures. We obtained spectra from both individual ssDNA-coated NPs as well as single ssDNA-coated NPs attached to a flat DNA origami sheet and immobilized on a poly-( L)-lysine-coated glass slide. Heat absorbing and neutral density filters were used to ensure radiant flux densities are below the damage threshold of the DNA origami structures. In all cases, the presence of the DNA changes the dielectric properties of the environment around the NPs, allowing an effective refractive index for both layers to be calculated.Three representative spectra for single ssDNA-coated NPs are shown in, their similar intensities are further verification of consistent single NP measurements.
The peak intensity of these NPs already displays an average red shift of 6±1 nm (mean ± s.e.) from bare NPs on glass (scattering peak at 530±1 nm, data shown in ). From TEM images, the thickness of the ssDNA coating was found to be 2.5±0.5 nm. This value was used in numerical simulations to estimate the effective refractive index n ssDNA of the ssDNA layer.
A value of n ssDNA=1.7±0.1 was found to best fit the measured spectra (, ). Simulations for the scattering cross-section are presented in ( b, e), the other panels are experimental data. Errors quoted are s.e. A single peak is obtained for ssDNA-coated NPs ( a) with an average red shift of 6±1 nm from the bare NP peak ( c). This corresponds to an effective refractive index of n ssDNA=1.7 ( b).
A single peak ( d) with a further red shift of 20±1 nm is obtained for single nssDNA-coated NPs attached to flat origami sheets ( f). Using n ssDNA=1.7 from ( b), the best fit is obtained for n origami=2.1 ( e).
The two peaks for the NP dimer structures ( g) correspond to the transverse and longitudinal modes. The overlaid scattering cross-section obtained from simulations (red dashed line, no free parameters) has peaks at 554 and 646 nm, in good agreement with the experimental data ( g, h). The controlled attachment of single ssDNA-coated NPs to flat DNA origami sheets allowed for the characterization of any red shift caused by the DNA origami sheet and subsequent extraction of the effective refractive index of DNA origami. Binding of single NPs was achieved by designing an origami sheet with sufficient DNA docking sites for only a single NP.
A lower NP: origami ratio was used and the monomers were carefully isolated using gel electrophoresis. Once again, the scattering intensities are similar for each nanostructure.
The scattering peaks also display a more pronounced red shift of 20±1 nm and 26±1 nm as compared with the peaks for ssDNA-coated and bare NPs , respectively. This increased red shift is clearly attributable to the underlying origami structure. To simplify the simulations, the underlying origami sheet was modelled as an infinite lateral sheet of 5 nm thickness, with the ssDNA coating described by n ssDNA=1.7. The best fit to the experimental data was obtained for n origami=2.1 (, ). Given the density of the DNA in the sheet compared with the ssDNA on the particles, this increased effective n origami=2.1±0.05 is not surprising.Finally, individual dimer structures were characterized.
Correctly assembled dimers were easily identifiable due to their characteristic polarization-dependent response and enhanced scattering ( and ). Typically, the longitudinal mode (excited by light polarized along the dimer axis) is expected to be strongly red-shifted due to the plasmonic coupling between the NPs, whereas the transverse mode (light polarized perpendicular to the dimer axis) should remain nearly unchanged from the single NP resonance. Indeed as clearly evident, the transverse mode peak for NP dimer structures coincides almost exactly with the scattering peak for single ssDNA-coated NPs on origami sheets. The two parameter values n ssDNA=1.7 and n origami=2.1 were used to simulate the scattering cross-section of the dimer structures. The dimers were modelled as a pair of NPs covered with a 2.5 nm thick ssDNA layer separated by 3.3 nm on an infinite origami sheet of 5 nm thickness.
The simulations are shown by the red-dashed line in and are in very good agreement with the experimental data. Our values of n origami=2.1 and n ssDNA=1.7 are very similar to those reported for 54 bp ( n=2.1) and 24 bp ( n=1.75) long dsDNA coating around 20 nm gold NPs, also measured using plasmon resonances.We also repeated all scattering measurements with the structures surrounded by buffer instead of air.
The resonance peak for ssDNA-coated NPs is red-shifted by 5±1 nm, as expected given the higher refractive index of water compared with air. However, for single ssDNA-coated NPs on flat DNA origami sheets, no shift in the resonance peak is observed, whereas for the dimer structures, the longitudinal mode is blue-shifted by 10±2 nm. This blue shift, despite the increased refractive index of water as surrounding medium could be caused by an increase in spacing between the NPs as the ssDNA coating gets hydrated.
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These measurements are further proof of the strong plasmonic coupling in our dimer structures, and that the architecture can be controlled by flexing of the DNA origami under appropriate stimulation. SERS measurements of external analytesAfter the careful characterization of our dimer structures, we investigated their potential for SERS measurements of external analytes. Individual dimer structures are immobilized on a gold-coated silicon wafer as described in Methods. The gold coating reduces background Raman emissions from the silicon wafer.
The immobilized dimer structures are incubated briefly in a 100 μM solution of Rhodamine 6G to form a monolayer on the dimer structures before the solution is removed. Rhodamine 6G is a model Raman analyte with many characteristic peaks.
SERS measurements were carried out with a Renishaw inVia Raman microscope using a 100 × objective with NA=0.85. Laser-induced damage to the dimers was prevented by illuminating with low intensities (see ). The spectra were taken on individual dimers which can be identified on the gold surface.
A collection of spectra, each obtained from a different dimer structure are shown in. Typical Rhodamine 6G modes common to all spectra are highlighted by red-dashed lines.
We employed a laser excitation line at 632.8 nm, which is in close proximity to the longitudinal dimer mode. Hence, the observed enhancement is highly sensitive to the polarization of the laser with respect to the dimer axis. Assuming a monolayer coverage.
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