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.


Please do not adjust margins
Please do not adjust margins AuNRs 32uL of thiol-T19 and 288uL of thiol-T8 were mixed together and added to 480uL of AuNRs dispersed in 0.1% SDS. The mixture was vortexed for 5s, and kept at -80 o C for 30min. The 800uL mixture was then thawed and centrifuged to concentrate it down to ~100uL. Agarose gel electrophoresis was used to separate the functionalised AuNRs from excess thiol-DNA. A 1% gel was cast and the run parameters were 100V, 250mA, 1hour. The relevant gel bands were excised and squeezed between a glass slide and parafilm to extract the liquid sample.

AuAgNRs
In a typical experiment, after washing, the rods were centrifuged and resuspended in 0.1% SDS to a final volume of 480uL. 32uL of thiol-T19 and 288uL of thiol-T8 were mixed together and added to the rod dispersion. The mixture was vortexed for 5s, and kept at -80 o C for 30min. The 800uL mixture was then thawed and centrifuged to concentrate it down to ~100uL. Agarose gel electrophoresis was used to separate the functionalised AuNRs from excess thiol-DNA.
A 1% gel was casted and the run parameters were 100V, 250mA, 1 hour in 'Gel-buffer' (40mM Tris, 20mM Acetic acid, 1mM EDTA and 11mM Mg 2+ ). The relevant gel bands were excised and squeezed between a glass slide and parafilm to extract the liquid sample.

DNA Origami
Staple strands and the scaffold strand (modified 8064 nt long M13mp18 ssDNA) were mixed together to a target concentration of 200nM and 25nM respectively in 16mm MgCl 2 , 10mM Tris and 1mM EDTA. The mixture was divided into 100uL aliquots in PCR tubes and annealed from 65 o C to 20 o C over ~ 16 hours (detailed program below). 4. Discard the filtrate. Add 420 µL TE-12.5 buffer and spin at 6000 rcf for 6 min.
6. Invert the filter into a clean tube and spin at 6000 rcf for 2 min to collect the purified origami.
All experiments in this manuscript were performed using a single batch of 800uL origami (for both the X-shape and L-shape structures) which was folded and purified using this method above. After amicon purification, the origami were diluted to a concentration of 30nM.
Please do not adjust margins Please do not adjust margins TEM sample preparation TEM grids were exposed to Argon plasma for 30s before sample deposition. The deposition duration for DNA origami (~ 5nM) was 30s, and for the NR-origami structures was 15min. The grid was then dipped on a 5uL droplet of 2% Uranyl formate (UFo) solution (containing 25mM NaOH) which was then wicked off immediately. The grid was then dipped in another UFo droplet, incubated for 10s and then wicked off. It was allowed to dry before imaging.

TEM images -Nanorods
Figure S1. Agarose gel electrophoresis of a) AuAgNRs of varying Ag shell thickness and b) the X-shape chiral metamolecules constructed from the AuAgNRs. The Ag + concentration used for synthesising the Ag shells is mentioned above the respective lane.

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Please do not adjust margins TEM images -Chiral metamolecules (L-shape)

Supplementary note S2 -Numerical Section Numerical Simulations
Numerical simulations were performed using the finite-element method (FEM), implemented in the solver JCMsuite. (4) Within all simulations, a polynomial degree of the FEM ansatz function p=2 was used. The discretisation was realised by a tetrahedral mesh with edge sizes smaller than 16 nm for the background, 4nm for the Ag shell, and 3.5 nm for the Au NPs. Transparent boundary conditions were realised using perfectly matched layers (PML).
Each side of the computational domain was illuminated by one left and one right-handed circularly polarised plane wave (LCP and RCP). The absorbed electromagnetic field energy and the electromagnetic field energy scattered outwards were recorded for each source. The total extinction was given by the sum of absorption and scattering for LCP and RCP, and all six directions of incidence. All graphs of the total extinction were normalised to their maximum value. The CD spectrum was given as the difference of extinction of LCP and of RCP. The graphs of the CD were normalised to their maximum to dip value, corresponding to the curves of the experimental data.
The simulation results, shown in Fig. 1 and Fig. 4 were computed using a scripting language (Matlab), to auto-generate the input files and to distribute the FEM computations to various threads on a workstation for parallel computation of the wavelength and parameter scans.

Geometry
The basic geometry for a single coated rods is depicted in Fig. S5a. It consists of an inner rod made of gold with diameter nm and height of = 15 nm and an outer shell with diameter and height , that represents the silver coating. The thickness of the silver coating is given as at the ℎ = 61 ℎ side of the rods and at the top, in the case of homogeneous coating the thickness is given as . The cap rounding radii of rod and shell are _ℎ ℎ = = ℎ , resp. . Three different arrangements were analyzed, a single NR and NR-NR arrangements in X-and L-shape. The thickness of the silver coating /2 /2 was varied within the different cases for each arrangement. The sizes for the outer rod are given in Table S1 for the graphs of the numerical simulation in. 1 and Fig. 4, and in Table S2 for the graphs in Fig. S6 and Fig. S7 in this supplementary section. The NR-NR arrangement in X-shape, see Fig. S5b consists of two rods, with the rear one rotated 45° counterclockwise. The NR-NR arrangement in L-shape, shown in Fig. S5c consists of two rods, with the lower one rotated 90° counterclockwise. The offset between the rods is 11 nm from surface to surface, for both arrangements, X-and L-shape.  Table S1. Measured sizes of the outer rod for all three arrangements, corresponding to the simulations for Fig. 1 and Fig. 4 Table S2. Homogenous silver coating with starting from 5 nm in 2 nm steps up to 33 nm, corresponding to the simulations of ℎ = = ℎ Fig. S6 and Fig. S7

Supplementary note S5 -Thin shells
The realization of very thin Ag coatings, smaller than 5nm are technically not trivial. The experiments have shown that these arrangements do not remain sufficiently stable to be able to carry out measurements. Therefore, coating thicknesses from 1nm to 5nm are investigated numerically. For a single coated rod, the model and the numerical simulation procedure from Section S2-Numerical Section is used. The Ag coating is varied from 1nm to 5nm. The dimensions are given in Table S3. The results for the normalised total extinction is shown in Figure S11, where corresponds to a pure gold rod without silver ℎ = 0 coating. For thicker coatings the resonance in the higher wavelength regime is blue shifted and a second resonance around 350nm is occuring. The curves lie within the range between the pure Au NR and the smallest AuAg NR with smallest coating in Fig. 1.
For the X-shape and L-shape arrangements, the models and the numerical simulation procedure from Section S2-Numericlal Section are used. The Ag coating thickness is varied homogeneously from 1nm to 5nm, for dimensions see Table S3. The results of the normalised Circular Dicroism (CD) for X-and L-shape with different shell thickness are depicted in figure S 12. A layer thickness of 0 nm corresponds to pure gold rods. The CD has two peaks, the transverse ℎ = mode in the range of 650nm -850nm and the longitudinal mode in the range of 700nm -900nm. For thicker Ag films, both peaks are blue shifted. The thicker the Ag layer, the more blue shifted is the CD. In addition, the distances between the CDs becomes smaller. The CD of the thinnest silver coating is very close to the result of the CD for pure Au rods (t_sh = 0nm). For both arrangements the curves lie within the range between the pure Au NR and the smallest AuAg NR with smallest coating in Fig. 4. Table S3 Homogenous silver coating with starting from 1 nm in 1 nm steps up to 5 nm, corresponding to the simulations of ℎ = = ℎ Fig. S11, Fig. S12 Figure S12. Numerically obtained total extinction as function of illumination wavelength for a single coated rod with different, homogeneous silver shell thicknesses, varied from 1 nm up to 5 nm in 1 nm steps and normalized total extinction for pure gold rods ( ℎ nm). a) NR-NR arrangement in X-shape, b) NR-NR arrangement in L-shape.

Supplementary note S5 -Thick shells
The evolution of the aspect ratio of the AuAgNRs with increasing Ag + concentration is tied to the aspect ratio of the underlying core AuNRs. For the AuNRs used in this paper (with dimensions ~ 61 nm x 15 nm), using 12mM Ag + in the growth solution led to Au/AgNRs that were almost isotropic (Fig. S11a,b), which makes it difficult to define the length vs width and thus, makes the calculation of the aspect ratio unreliable.
This isotropic nature of the Au/AgNRs is also mirrored in their extinction spectra, which no longer exhibits separate longitudinal and transverse modes but rather shows an almost total overlap between the two (Fig. S11c). Figure S14. Growing thick Ag shells. a) TEM image of AuAgNRs grown using 12mM Ag + . b) A close-up of the AuAgNRs. c) Normalized total extinction of the Au/AgNRs. Scale bars : 50 nm.