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Enhancement of gold nanoparticle coupling with a 2D plasmonic crystal at high incidence angles Mengdi Lu, Long Hong, Yuzhang Liang, Benjamin Charron, Hu Zhu, Wei Peng, and Jean-François Masson Anal. Chem., Just Accepted Manuscript • DOI: 10.1021/acs.analchem.8b00496 • Publication Date (Web): 08 May 2018 Downloaded from http://pubs.acs.org on May 9, 2018

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Analytical Chemistry

Enhancement of gold nanoparticle coupling with a 2D plasmonic crystal at high incidence angles

Mengdi Lu1,2, Long Hong3, Yuzhang Liang4, Benjamin Charron2, Hu Zhu2, Wei Peng1*, Jean-Francois Masson2*

1

College of Physics and Optoelectronics Engineering, Dalian University of

Technology, Dalian 116024, China 2

Département de chimie and Centre Québécois sur les Matériaux Fonctionnels

(CQMF), Université de Montréal, CP. 6128 Succ. Centre-Ville, Montreal, QC H3C 3J7, Canada 3

School of Life Sciences, Peking University, Beijing 100871, China

4

National Laboratory of Solid State Microstructures, Nanjing University,

Nanjing 210093, China

Contact information: * Jean-Francois Masson: [email protected], +1-514-343-7342 * Wei Peng: [email protected]; 1

ACS Paragon Plus Environment

Analytical Chemistry 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60

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ABSTRACT

2D nanoplasmonic substrates excited in transmission spectroscopy are ideal for several biosensing, metamaterials, and optical applications. We show that their excellent properties can be further improved with plasmonic coupling of Au nanoparticles (Au NPs) on gold-coated nanodisk arrays excited at large incidence angles of up to 50o. The Bragg modes (BM) thereby strongly couple to Au NP immobilized on the plasmonic substrate due to shorter decay length of the plasmon at higher incidence angles, leading to a further enhanced field between the Au NP and the plasmonic substrate. The field was highest and two hotspots were created at orthogonal positions for Au NP located close to the corner of the Au film and Au nanodisk, which was also observed for Au NP dimers. Hybridization between single-stranded DNA (ssDNA) immobilized on the surface of the AuNPs and the capture ssDNA on the gold-coated nanodisk arrays led to at least a 5-fold signal improvement and a 7-fold lower limit of detection at 7 pM for ssDNA-functionalized Au NPs at large incident angles. Thus, we demonstrate that higher field strength can be accessed and the significant advantages of working with high incidence angles with Au NP on a 2D plasmonic crystal in plasmonic sensing.

KEYWORDS Gold-coated nanodisk arrays, plasmonic sensing, nanoparticles, Nanoparticle coupling mechanism, DNA

2


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INTRODUCTION

The optical properties near a metallic interface due to surface plasmons have been widely employed in various fields 1 and is drawing particular attention biochemistry 2, nanophotonics 3, and optoelectronics 4, among others. Amidst the different plasmonic nanostructures, the enhanced transmission through metallic structures with subwavelength and periodic features is particularly interesting to fabricate large arrays of ordered nanostructures for high throughput biosensing applications 5-7. Efforts have thus been deployed for optimizing 2D plasmonic nanostructures for biosensing

8-9

.

Several physical factors have been identified as critical for achieving maximum plasmonic enhancement. Periodic nanostructures such as gold nanodisk arrays typically provide sharper plasmonic absorption and thus higher refractive index (RI) resolution than randomly distributed nanostructures 10. Fabrication parameters of the nanostructure arrays including the size and periodicity of nanodisk and the thickness of gold can be tuned to optimize the RI sensitivity and figure of merit (FOM) 11. Thus, proper design of 2D plasmonic crystals such as gold nanodisk arrays is crucial for obtaining maximum sensing properties.

While it has been recognized early on that angled illumination could control the plasmon resonance wavelength12-14, this effect has rarely been exploited in sensing and for other plasmonic applications. One of the main advantages of angled illumination concerns the higher surface sensitivity, a main quantitative parameter in biosensing

15

. The sensitivity of 2D plasmonic crystals to adsorbed molecular layers 3



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of varying thickness was reported to increase with illumination angle 16, due to the shorter penetration depth in these conditions 17. Lower detection limits can therefore be reached and is highly beneficial for sensing purposes. Thereby, the introduction of angle-tuned plasmonics nanostructures with high surface sensitivity provides new opportunities in optical biosensing.

For many analytes, secondary detection using gold nanoparticles (Au NP) is used to enhance the response through plasmonic coupling between a gold substrate and the Au NP 18-19. While the interaction of a Au NP on a mirror is well understood 20-24, our general understanding about the properties of nanoparticle-nanostructure interaction is more limited. For example, it has been reported that biomolecules binding to the edges of nanostructures leads to larger plasmonic response 25, which was also demonstrated for nanoparticles 26. The coupling of Au NP to metallic nanostructure is especially interesting27-31, as it is a concept commonly applied for biosensing. However, the influence of the coupling conditions between a Au NP and a 2D plasmonic crystal is not well characterized, despite being of utmost importance in the context of designing new generations of highly sensitive sensors.

Noble metals colloidal nanoparticles has been recognized as effective amplification stage for DNA detection

32-33

and for many biomedical applications 19.

Refractometric biosensing using plasmon resonances is often used for monitoring hybridization reaction between DNA-modified nanoparticles and capture DNA on the surface of the sensor, which has been applied in the field of genetic disease 4


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diagnostics among others

34-35

. In this field, tuberculosis (TB) still receives sustained

attention for global public health due to its high infectivity, recent resurgence and high mortality. TB is still the second leading cause of death after HIV 36. Treatment of TB infection relies primarily on the use of isoniazid and rifampicin 37. However, the threat posed by TB is increasing with the emergence of drug-resistant TB 38, which was associated with mutations in several genes. Rifampicin resistance was mostly related to mutations in ropB gene 39, while Isoniazid resistance is commonly associated to katG 40. Thus, DNA detection associated to TB mutation is of utmost importance and also provides an excellent model to study the coupling of Au NP with a periodic nanostructure (gold-coated nanodisk arrays) at different incident angles.

METHODS

Materials.

All chemicals were purchased from Sigma-Aldrich and ssDNA strands were acquired from Integrated DNA Technologies (Coralville, IA, USA). Ultrapure water (18.2 MΩ cm) was used for all experiments. All glassware was washed with aqua regia and rinsed with ultrapure water before use. The 96-well plate reader was used as previously described 41.

Layer-by-layer (LBL) polyelectrolyte deposition.

Poly (allylamine) hydrochloride (PAH, 20 wt% in water, 65 kDa) as the cationic 5



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polyelectrolyte and poly (4-styrene sulfonate) (PSS, 18 wt% in water, 75 kDa) as the anionic polyelectrolyte were employed in our study. The PAH solution (1 mg/mL, 0.1 M NaCl, pH 5.0) was first injected in the fluidic cell for 1 minute, and a PSS solution (1 mg/mL, 0.1 M NaCl, pH 4.0) was then exposed to the surface for also 1 minute. A washing step was performed with ultrapure water after the deposition of each layer. The first PAH layer was formed directly on the nanodisk surface due to the negative charge of the gold film.

AuNPs-enhanced plasmonic biosensing of DNA hybridization. Firstly, the gold-coated nanodisk arrays were prepared as described elsewhere 42. A self-assembled monolayer was formed on the gold-coated nanodisk arrays with an overnight immersion in a 10 mM 11-mercaptoundecanoic acid (MUA) solution in ethanol. Then, 3 µΜ amine-labeled 22-mer capture ssDNA (5'-AGG GGC CCA ACA TCG GTC TGA T/3AmMO/-3'), with a sequence complementary to the probe ssDNA, was coupled to the carboxylate groups on the surface via EDC/NHS (0.5 M/0.5 M) cross-linking.

A thiol-labeled 28-mer ssDNA (probe ropB 5'-ATC AGA CCG ATG TTG GGC CCC TAA AAA A/3ThioMC3-D/-3') was selected as probe ssDNA. For the control experiment, probe katG (5'-TTG ACC TCC CAC CCG ACT TGT GAA AAA A/3ThioMC3-D/-3') was used as a non-complementary DNA strand, of relevance to TB analysis. This reference strand was not expected to bind to the capture ssDNA. Au NPs were prepared using a standard citrate reduction method. 20 mg of 6


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HAuCl4∙ 3H2O were dissolved in 200 mL of water at room temperature and heated until boiling. 40 mg of sodium citrate in 4 mL water was added and the solution was boiled for another 15 minutes before cooling to room temperature. Constant stirring was maintained throughout the synthesis. Finally, 1 mL of AuNPs solution and 1.25 µL probe ssDNA were mixed, in a NaOH treated glass vial to obtain a final DNA: Au NPs ratio of 200:1 (100:1, 50:1 were also tried). The solution was then gently mixed and left to react for 30 min at room temperature. A 2% poly (ethylene glycol) (PEG) solution was added to reach a final solution volume of 1.25 mL for another 30 min. The solution was salt-aged using a stepwise increase of the NaCl concentration up to 0.1 M, which was followed by an overnight incubation at room temperature under gentle shaking. The DNA/Au NP solution was then washed twice by sequential centrifugation (10,000 rpm, 30 min) to remove excess ssDNA. The wash buffer was 10 mM sodium citrate and 2% PEG at pH 5.7. Then, the nanoparticles were resuspended in 0.3 M NaCl, 2% PEG and 10 mM phosphate buffer (hybridization buffer), pH 7.0 and stored at 4oC until use.

Calibration curve for free ropB DNA.

On a MUA-functionalized gold-coated nanodisk array, 3 µΜ amine-labeled 11-mer capture ssDNA (capture: 5’-/5AmMC6/AG GGG CCC AAC-3’), consisting to half of the complementary sequence to ropB ssDNA (target: 5’-ATC AGA CCG ATG TTG GGC CCC T-3’), was coupled to the carboxylate groups on the surface via EDC/NHS (0.5 M/0.5 M) coupling for 30 min. A thiol-labeled 17-mer ssDNA (probe:

7



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5’-ATC GGT CTG ATA AAA AA/3ThioMC3-D/-3’), consisting to the other half of the sequence complementary to ropB ssDNA, was selected as probe ssDNA on the Au NPs. The probe ssDNA/Au NP solution was prepared as mentioned above, the diameter of Au NPs was 24 nm, the ratio of DNA/Au NP was 200:1 and the concentration of the DNA- functionalized Au NPs was 200 pM. Different concentrations of target ssDNA (from 0 to 40 nM) were hybridized with capture ssDNA on the nanodisk surface for 1 h, and then washed with hybridization buffer. After that, the probe DNA- functionalized Au NPs solution was injected for 3 h to amplify the hybridization signal. We collected the spectra before and after the amplification process in hybridization buffer when the incident angle was 50°. The same concentration of target ropB DNA in the sandwich configuration (capture DNA – target DNA – Au NP/DNA) for comparison.

Surface-enhanced Raman scattering (SERS)

SERS experiments were performed with 4-nitrobenzenethiol deposited on AuNP immobilized on the gold nanodisk arrays with 1,6-hexanedithiol (HDT). Control experiments were also performed on a gold film with Au NP deposited with HDT and directly on the gold coated nanodisk arrays. All measurements were acquired at 633 nm with a laser power of 3.85 mW on a Renishaw InVia Raman microscope, using a 10 s acquisition time and a 20X microscope objective. All intensities are reported after background subtraction.

RESULTS AND DISCUSSION 8


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Optical characterization of the gold-coated nanodisk arrays at high incidence angles

The fabrication process and the instrumentation for analyzing the gold-coated nanodisk arrays were based on previous reports 42-43 (Fig. 1). The nanodisk arrays were made of a 75 nm gold film and 75 nm gold disk (the diameter of the disk was 720 nm) with 1200 nm periodicity on top of the gold film, which was shown to excite different modes of propagating surface plasmon (PSP) 44 and led to a series of BMs owing to the change of the in-plane wavevector of the PSP 45. By simply tuning the incident angle, the various plasmonic bands due to BMs of the nanodisk array were excited at different wavelengths (Fig. 1b), but we will focus exclusively on the (1,0) mode in this article as this is the most sensitive and intense. BMs of higher order were observed since the period of the arrays was larger than the wavelengths of our measured spectral range (visible-NIR). We also identified the major modes from equation S4 (white lines) for the metal-dielectric interface (Fig. 2). Bulk RI sensitivity and resolution are conventional analytical parameters for different plasmonic sensors. The RI sensitivity was then assessed at a series of angles between 21° and 50°. We observed that the sensitivity was at nearly 1000 nm/RIU for incident angles below 34° and lower for angles greater than 34° at nearly 700 nm/RIU (Fig. 2(c) and Table 1). The deviation between experimental and FDTD results might be caused by the coexcitation of higher order BMs with the blue-shifted (1, 0) mode as the incident angle increased. The (1,0) mode was solely excited at angles below 34o with the sensitivity in good agreement with the FDTD. However, a series of lower sensitivity higher order modes are co-excited at higher angles, decreasing the measured sensitivity. FDTD calculations do not take into account these modes and 9



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thus overestimated the sensitivity. We also report that the different incident angle did not significantly affect RI resolution with a value that was approximately 3.4 x 10-5 RIU for angles between 29° and 50°. This value was better than the classical spherical nanoparticle arrays (10-4 RIU)

46

and identical to nanohole arrays 47 and suspended

nanodisk arrays (10-5 RIU) 48. The plasmonic signal of the (1,0) mode at water-metal interface was very sharp with a full width at half maximum (FWHM), which decreased by 33% from 27 to 18 nm at higher angles (Table 1). The sharper plasmon resonance at higher angles can be explained by the change in the optical constant of Au from 29° (λplasmon about 925 nm) to 50° (λplasmon about 700 nm), where k drops from about 6 to 4 approximately

a

33%

decrease).

Hence,

the

figure

of

merit

49

(also

(FOM

=

Sensitivity/FWHM) increased from 36 to 43 at higher angles, which was comparable to the best plasmonic nanostructures recently reported 42. In summary, the gold-coated nanodisk in (1,0) mode at large incident angles has shown excellent refractometric sensing performance including the high sensitivity, RI resolution and FOM.

Plasmonic sensing also relies significantly on the change in RI caused by binding events on the surface. The surface sensitivity of the nanodisk is a function of the penetration depth of the surface plasmon in nanodisk arrays. Shorter penetration depth is ideal and lead to more a sensitive detection of molecular adsorption events. A simple layer-by-layer (LBL) polyelectrolyte deposition method was used for systematically increasing coating thickness, which served for the determination of the decay length (penetration depth) of the gold-coated nanodisk arrays substrate (Fig. S1). The average penetration depth was estimated at 654, 386 and 217 nm 10


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respectively, for the incident angles of 29o, 34o and 50o. The experimental estimation of the penetration depth was in good agreement with the FDTD simulation of the electric field intensity of the X-Z plane at their plasmon resonance wavelength for (1,0) mode (Fig. S1 and S2). This result is in agreement with previous observations of reduced penetration depth on nanohole arrays, demonstrating that tuning penetration depth is ubiquitous with higher incident angles. Hence, adjusting the incident angle of light on gold-coated nanodisk arrays lead to good RI resolution, better FOM, shorter penetration depth, all improvement in analytical parameters that should lead to enhanced surface sensitivity in biosensing.

Investigation of Au NP coupling with a 2D plasmonic crystal

We then studied the influence of the penetration depth and of the incidence angle on plasmonic nanoparticle coupling with the gold-coated nanodisk arrays. This phenomenon has not been studied in the past to the best of our knowledge, but has tremendous impact on the design of biosensors and other applications. To demonstrate the capability of the nanodisk-based transmission platform as a biosensor and to establish its surface sensitivity and specificity with different incident angles in (1,0) mode, the gold nanodisk layer was functionalized with a capture ssDNA. The sensor was then hybridized with Au NPs modified with the complementary ssDNA strands (Fig. 3(a)). Typically, probe ssDNA sequences are designed with an A6 spacer region between the alkanethiol and the recognition sequence. This spacer serves the purpose 11



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of moving the recognition sequence away from the nanoparticle surface, thereby reducing stearic crowding of the region during hybridization steps 50. As shown in Fig. 2, the probe ssDNA attached to Au NPs was functionalized based on previous reports 51-52

and as described in the method section. Specifically, the presence of PEG

molecules during the synthesis of the DNA-modified Au NP improved reproducibility, increased the probe ssDNA loading speed and concentration on the nanoparticle since these molecules reduce inter-nanoparticle interactions or to surfaces

50

and is

beneficial for sensing nucleotides {Hong, 2018 #18}.

Au NPs have been used for the preparation of probe DNA/Au NPs conjugates. Au NPs were synthesized and functionalized with probe ssDNA as previous reports 35, 53-55

with minor modification as mentioned in the method section. The size of the

AuNPs and its concentration were calculated from the UV-vis spectra, according to the method reported by Haiss et al. 56. As shown in Fig. 3b, size and concentration of the particles were calculated to be 24 nm and 0.36 nM (for the 15 nm and 30 nm AuNPs, see Fig. S3). Au nanoparticles with uniform sizes have been observed from the TEM image (Fig. 3b) and were functionalized with probe SH-ssDNA. Highly uniform particle size is necessary to control the density of ssDNA on each particle and to understand the influence of nanoparticle size on plasmonic coupling at different incidence angles.

The nanodisk arrays functionalized with capture ssDNA on MUA was used for DNA/Au NP detection. A 96-multiwell plate reader was used to achieve a broadly

12


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multiplexed platform 41. The plasmonic wavelength of the hybridization buffer was measured before and after the hybridization process to obtain the resonance shift caused by DNA/Au NP binding. Different nanoparticle size (15, 24, and 30 nm), DNA/Au NPs concentration (from 20 to 200 pM) and the density of ssDNA on the particle (reaction ratio of 200:1, 100:1, 50:1 for DNA/Au NP) for both hybridization and the control experiment were measured for comparison. Nanoparticle binding was clearly observed from the SEM images after 3 hours hybridization with 24 nm/200 pM DNA/Au NP solution (Fig. 3c). The DNA/Au NPs covered the whole scanned area uniformly.

24 nm Au NPs were employed to demonstrate the effects on hybridization ratio of ssDNA concentration and the density on the particle effect. The plasmonic response from the hybridization and the number of Au NPs on the surface increased with the concentration of DNA/Au NP solution (Fig. S4) and the density of probe ssDNA on the particle (Fig. S5). As expected, the nanoparticles coverage for the specific detection of ropB-modified nanoparticles reduced with DNA/Au NPs concentration decreasing from 200 to 20 pM, while little nonspecific adsorption was observed from katG-modified nanoparticles for every concentration tested. These SEM images clearly showed that the ropB-modified nanoparticles were randomly distributed on the surface, and the nonspecific adsorption of the nanoparticles with katG was negligible.

The density of probe ssDNA on the particle was another important factor to optimize the surface coverage of the Au NP on the plasmonic substrate. We therefore

13



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compared the nanoparticles coverage for three different density of probe ssDNA on the particle including 200:1, 100:1 and 50:1, while the concentration of DNA/Au NPs solution was 200 pM. We found that the ropB-modified nanoparticles coverage reduced as the ratio of ropB on the particle was reduced and uniformity of the coverage was better at larger ratio. Moreover, the nonspecific adsorption of the nanoparticles with katG was higher at lower ssDNA coverage (Fig. S5). Hence, we selected a DNA: Au NP ratio of 200:1 for the following experiments.

The presence of uniform coverage of nanoparticles prompted us to study the impact of the location of the Au NP binding on the gold-coated nanodisk arrays on the plasmonic properties. It is important to note that the hydridization of the Au NP did not lead to the appearance of other plasmonic bands, but only shifted the plasmon resonance by approximately 5 to 20 nm (Fig. S6). The FDTD simulations show the field distribution for the plasmonic coupling between DNA/Au NPs and different locations of the nanodisk arrays excited at the incident angle of 50o (Fig. 4b). Every simulation was carried at the plasmon wavelength for (1,0) mode. We found that the nanoparticles indeed increased the localized field intensity, but at different magnitude depending on the location of the Au NP on the gold-coated nanodisk arrays. The strongest localized enhancement occurred at the corner of the disk and the film while the weakest was for Au NP located on the planar gold film. Interestingly, we found the presence of two hotspots at orthogonal locations for the nanoparticles located near the corner of the nanodisks. These orthogonal hotspots are due to the in-plane and out-of-plane wavevectors of the incident light beam at angled incidence. This suggests 14


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that higher sensitivity could be achieved for nanoparticles binding at this location in plasmonic sensing, but also in surface enhanced spectroscopy as shown for surface-enhanced Raman scattering (SERS) of 4-nitrobenzenethiol (4-NBT) on the gold-coated nanodisk arrays modified with Au NPs (Fig. S7). The response for the gold-coated nanodisk arrays was three time better than the one of the Au film with Au NPs or the gold-coated nanodisk arrays. Higher fields were observed for simulations with 15 and 30 nm Au NP (Fig. S8), indicating that this conclusion was generally applicable to different particle sizes.

The effect of the incident angle on the field intensity between DNA/Au NPs and nanodisk arrays was then investigated. Fig. 4 (a)-(a’’) demonstrate that increasing the incident angle from 29o to 50o led to an increase in the calculated field intensity from X to Z. The increasing nanoparticle size (15, 24 and 30 nm) also enhanced the calculated field intensity in the X-Z plane (Fig. 4 (b)-(b’’)). Thus, working with larger Au NP and at a high incidence angle is advantageous for strong plasmonic coupling.

The inter-Au NP coupling was also modeled to understand the influence of the incidence angle on the field intensity (Fig. 4 (c)-(c’’)). The distance between two Au NPs was varied from 0 to 10 nm at a constant height of 5.2 nm from the top of the nanodisk (see details in Supporting Information), an incident angle of 50o and with Au NPs of 24 nm diameter. As expected, the shorter distance between nanoparticles led to stronger interparticle coupling as clearly seen from the higher field. A Au film-Au NP plasmonic mode has previously been reported in nanoparticle dimers 22, but we also

15



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observed that the field intensity was greater between the Au NP and the nanodisk arrays with shorter interparticle distance at higher incidence angle. This result indicated that the interparticle and Au NP-nanodisk modes are coupled, an important finding for surface-enhanced spectroscopy.

Sensing performance at different incidence angle for a Au NP enhanced assay

To further characterize the performance of the (1,0) mode for plasmonic biosensing at different incident angles, we analyzed the resonance wavelength shift with various Au NP sizes, ssDNA density, DNA/Au NPs concentration and incident angles (Fig. 5). Due to the spectrometer detection range set from 550 to 1100 nm and the maximum angle of 52o that can be reached by the instrumental setup, we selected angles of 29o , 34o and 50o for demonstrating the impact of incidence angle on the plasmonic sensing properties. The plasmonic response clearly showed the selective detection of ropB at a concentration of DNA/Au NPs of 200 pM, an incident angle of 50 o and AuNPs of 24 nm. Significantly lower signal was observed for the reference probe katG (Fig. 5a). The response was also selective at significantly lower ssDNA density. Interestingly, we also noticed that the specific shift decreased for ropB at lower DNA: Au NP ratio while the nonspecific response increased for katG. The plasmonic responses were in good agreement with the SEM images (Fig. S5). Similar results were also obtained with Au NPs of 15 and 30 nm (Fig. S9). Thus, a ratio of 200:1 was optimal. 16


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The effect of Au NP diameter was then investigated. It was apparent that the plasmonic response was larger and the sensitivity was greater with increasing diameters of DNA/Au NPs (Fig. 5b). This result was in agreement with the FDTD data showing that the plasmonic coupling was stronger for the largest AuNPs and can be explained by the particle on a mirror theory 23. However, we noticed that the signal from katG was also increased when using larger Au NPs (Fig. 5a, Fig. S9 (a) and (a’)). The 24 nm Au NPs were regarded as the optimal size, thereby both high ropB signal and low nonspecific katG signal could be achieved. The plasmonic shift was improved by increasing the incident angle from 29o to 50o (Fig. 5c). While sensing with (1,0) mode barely provided the sensitivity to detect DNA/Au NP hybridization below 50 pM (∆λ = 1.26 nm) at 29o incidence angle, the plasmonic response significantly improved with a larger angle and for example, had a 6.4 nm shift for 50o in otherwise the same experimental conditions, leading to a large improvement of the detection limit. From these data, we estimated the surface density at the limit of detection to be nearly 2 pM mm-2, 1 pM mm-2, and 0.4 pM mm-2 for the incidence angles of 29 o , 34o, and 50o respectively. It was determined that the higher surface sensitivity was obtained at larger incident angle. These results corresponded to the reduction of the penetration depth, and the strong coupling between Au NPs and nanodisk arrays, which we predicted from the FDTD simulation above.

As a negative control, probe katG was analyzed in the same conditions to confirm that the positive response from ropB was specific and allowed to evaluate nonspecific

17



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adsorption of DNA/Au NP on the nanodisk arrays. The effective plasmonic shift (calculated as the difference in shifts between ropB and katG) showed linearity with increasing concentration of DNA/Au NPs solution at the incident angle of 50o for (1,0) mode. A good linear relationship between the effective shift and DNA/Au NPs concentration was achieved in range of 20–200 pM with a coefficient of determination (R2) of 0.985 and the effective limit of detection was calculated to be nearly 7 pM at 50o, while the limits of detection were higher at 22 pM and 47 pM for 34o and 29o respectively (Fig. 5d). In addition, we tested a double mismatch DNA strand 5’-ATC AGA CCG AAG TTG GGC CGC TAA AAA A/3ThioMC3-D/-3’ on the Au NPs and analyzed at an angle of 50o. The response from the double mismatch ropB DNA strand was smaller than the positive response, but higher than for the noncomplementary katG DNA strand (Fig. S10). The reproducibility of the sensor was investigated by measuring five replicates. We found that the (1,0) mode at large incident angle 50o displayed high surface sensitivity and good reproducibility of 7% for a concentration of 200 pM. Hence, this method could be applied to quantification of ropB at low concentrations. In short, the (1,0) mode of gold-coated nanodisk arrays had significantly better biosensing performance for Au NP-modified DNA detection analyzed at large incident angle 50o owing to the low penetration depth and strong coupling between Au NPs and the gold-coated nanodisk arrays.

A direct detection assay was then established to provide realistic conditions for analyzing ropB DNA. A capture strand consisting of half the complementary sequence to ropB DNA was immobilized on the gold-coated nanodisk array and the 18


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other half of the complementary sequence was immobilized on the Au NPs. Compared with the wavelength shift of the full ropB DNA sequence in (Fig. 5(a)), the wavelength shift for the sandwich configuration was lower than the direct configuration when we used the same ropB concentration (Fig. 6). For example, the wavelength shift was about 28 nm for the full sequence, while the response was about 18 nm, which approached the saturation response of the assay. The lower shift might with the sandwich assay may be caused by the lower hybridization rate and stability of the hybridization with the shorter DNA strands. Nonetheless, a large response was obtained for the ropB for low nanomolar concentrations.

CONCLUSION

In summary, the gold-coated nanodisk arrays exhibited multiple BMs plasmonic bands when excited at different incident angle. By tuning the incident light to large angles, the plasmonic wavelength of the (1,0) mode blue-shifted by hundreds of nanometers and was thus excited in the NIR range. In addition, the increasing incidence angle significantly reduced the electric field penetration depth, which was determined by LBL polyelectrolyte deposition method and confirmed by FDTD simulation. Lower penetration depth at large incidence angles for (1,0) mode was essential to improving the surface-enhanced spectroscopy and biosensing applications of the nanodisk arrays with a significantly stronger coupling between the Au NP and the gold-coated nanodisk arrays. It was observed that the field was strongest for 19



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coupling at high incidence angle, for Au NP located at the corner of the flat film and nanodisks, for larger Au NP and for Au NP dimers with shorter interparticle spacing. The larger incident angle also led to multiple plasmon modes that are coupled, as shown with the Au NP dimers.

Finally, improved sensing was clearly demonstrated with DNA-functionalized Au NPs. This system experimentally demonstrated the potential of Au NP coupling with nanodisk arrays for biosensing and showed the larger surface enhancement due to the coupling between Au NPs and nanodisk arrays at higher incident angles and Au NP sizes. The detection limit for DNA hybridization of gold-coated nanodisk arrays was significantly better at higher incident angles and thus, very promising for developing a high performance biomedical and broadly multiplexed platform sensing.

ASSOCIATED CONTENT

Supporting Information

Simulation methods of the plasmonic wavelength, parameters of FDTD simulation modes, simulated Z-electric field intensity, UV-vis spectra of AuNPs, SEM images after DNA hybridization, FDTD simulation of AuNPs coupling with nanodisk arrays, corresponding comparison experiments.

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ACKNOWLEDGEMENTS

We acknowledge funding from the Natural Science and Engineering Research Council (NSERC) of Canada (Grant RGPIN-2016-03864), the Fonds de Recherche du Québec—Nature et Technologies (FRQ-NT) (Grant 205260), the National Nature Science Foundation of China (NSFC) (Grant Nos. 61727816, 61520106013, and 11474043) and the support from China Scholarship Council (CSC).

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Table 1. Plasmonic sensing properties of the gold-coated nanodisk arrays for (1,0) mode. Incident angle Sensitivity [nm/RIU] FWHM [nm] FOM [RIU-1] RI resolution [RIU]

29° 982 27 36 3.4 × 10ିହ

34° 932 24 39 3.8 × 10ିହ

50° 775 18 43 3.2 × 10ିହ

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Figure 1. (a) Schematic diagram of the incident angle configuration for enhanced optical transmission measurements. The nanodisk substrate was analyzed in a PDMS fluidic cell working in transmission mode and illuminated with collimated broadband light impinging via the liquid medium side. (b) Plasmonic response of nanodisk arrays excited in water for an incident angle of 0° and 50°. SEM image of the nanodisk arrays was shown as the inset. (c) Schematic representation of the gold-coated nanodisk arrays with a periodicity of 1200 nm and a disk diameter of 720 nm.

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Figure 2. (a) Plasmonic dispersion curves for different orders of BM for the gold-coated nanodisk arrays. The calculated modes (white lines) were for the metal/water interface. The color map represents the relative transmission intensity with different incident angles. Experimental and simulated (b) plasmon resonance wavelength and (c) bulk refractive index sensitivity of the (1,0) mode in water for different incident angles.

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Figure 3. (a) Schematic diagram of AuNPs-enhanced plasmonic biosensing of DNA hybridization representing the preparation of DNA-functionalized AuNPs. (b) UV-vis spectra of the AuNPs before and after DNA functionalization. Inset: TEM image of the AuNPs confirms the average size of 24 nm. Photograph of the color change from red to pinkish after DNA functionalization. (c) Left) SEM image after DNA hybridization (the size of AuNPs was 24 nm and the concentration was 200 pM) showing a high density of AuNP on the gold-coated nanodisk arrays. Right) FDTD simulations of the field distribution in the X-Z plane (cross-section of the nanodisk arrays) for the coupling between AuNPs and different locations of nanodisk arrays (top of nanodisk, corner of nanodisk, single gold film) at the incident angle of 50o. 28


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Figure 4. FDTD simulations of the field distribution in the X-Z plane (cross-section of the nanodisk arrays) for the coupling between AuNPs and nanodisk arrays. The coupling was calculated on the top of the nanodisk with 24 nm AuNPs at the incident angle of (a) 29o; (a’) 34o and (a’’) 50o. The coupling was then simulated on the top of the nanodisk with (b) 15 nm; (b’) 24 nm and (b’’) 30 nm AuNPs at the incident angle of 50o. The coupling between particles was finally simulated with different interparticle distances of (c) 10 nm; (c’) 5 nm and (c’’) 0 nm with 24 nm AuNPs

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dimers. The incidence angle was 50o and the simulation was also performed on the top of the nanodisk.

Figure 5. The plasmonic wavelength shift after DNA hybridization on nanodisk arrays for (1,0) mode; (a) with various DNA density of ropB and katG for 24 nm/200 pM DNA/AuNP solution at the incident angle of 50o. (b) with various DNA/AuNPs concentration and particle size at the incident angle of 50o. (c) with various DNA/AuNPs (24 nm) concentration at different incident angles. (d) with various DNA/AuNPs (24 nm) concentration of ropB and katG at the incident angle of 50o.

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Figure 6. Calibration curve for a sandwich assay for ropB DNA on nanodisk arrays. The assay was performed with 24 nm Au NPs with (1,0) mode at the incident angle of 50o.

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