Highly Localized SERS Measurements Using Single Silicon

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Highly Localized SERS Measurements Using Single Silicon Nanowires Decorated with DNA Origami-based SERS Probe ardeshir moeinian, Fatih Nadi Gür, Julio César González-Torres, Linsen Zhou, Vignesh Murugesan, Ashkan Djaberi Dashtestani, Hua Guo, Thorsten L Schmidt, and Steffen Strehle Nano Lett., Just Accepted Manuscript • DOI: 10.1021/acs.nanolett.8b04355 • Publication Date (Web): 08 Jan 2019 Downloaded from http://pubs.acs.org on January 9, 2019

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Highly Localized SERS Measurements Using Single Silicon Nanowires Decorated with DNA Origami-based SERS Probe Ardeshir Moeinian1, Fatih N. Gür2, Julio Gonzalez-Torres3, Linsen Zhou4, Vignesh D. Murugesan5, Ashkan Djaberi Dashtestani1, Hua Guo4, Thorsten L. Schmidt2,6 and Steffen Strehle1 1 Institute of Electron Devices and Circuits, Ulm University, 89081, Ulm, Germany. 2 Center for Advancing Electronics Dresden (cfaed), Technische Universität Dresden, 01062 Dresden, Germany 3 Área de Física Atómica Molecular Aplicada (FAMA), CBI, Universidad Autónoma Metropolitana-Azcapotzalco, Av. San Pablo 180, Col. Reynosa Tamaulipas, Mexico, DF, 02200, Mexico. 4 Department of Chemistry and Chemical Biology, University of New Mexico, Albuquerque, New Mexico, 87131, USA. 5 Institute of Functional Nanosystems, Ulm University, 89075, Ulm, Germany.

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6 B CUBE – Center for Molecular Bioengineering, Technische Universität Dresden, 01062 Dresden, Germany.

ABSTRACT

Surface enhanced Raman spectroscopy (SERS) measurements are conventionally performed using assemblies of metal nanostructures on a macro to micro sized substrate or by dispersing colloidal metal nanoparticles directly onto the sample of interest. Despite intense use, these methods allow neither the removal of the nanoparticles after a measurement nor a defined confinement of the SERS measurement position. So far, tip enhanced Raman spectroscopy is still the key technique in this regard but not adequate for various samples mainly due to diminished signal enhancement compared to other techniques, poor device fabrication reproducibility and cumbersome experimental setup requirements. Here, we demonstrate that a rational combination of only four gold nanoparticles (AuNPs) on a DNA origami template, and single silicon nanowires (SiNWs) yield functional optical amplifier nanoprobes for SERS. These nanoscale SERS devices offer a spatial resolution below the diffraction limit of light and still a high electric field intensity enhancement factor (EF) of about 105 despite of miniaturization.


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KEYWORDS: Surface Enhanced Raman Spectroscopy, DNA Origami, Gold Nanoparticles, Silicon Nanowire

Surface enhanced Raman spectroscopy (SERS) is a well-established analytical technique, in which high Raman signals originate in principle from electric field enhancement at the tight junctions or nanometer-sized gaps between individual plasmonic structures, called plasmonic hotspots.1,2 The actual sensing area is therefore, highly localized to only a few cubic nanometers between narrowly spaced metal nanostructures. This fact inheres in principle the possibility to scale-down SERS devices drastically to dimensions below the diffraction limit of visible light. However, the full scope of this advantageous potential must be still unleashed. Local confinement of Raman measurements is so far mainly achieved by scanning probe techniques, so-called tip-enhanced Raman spectroscopy (TERS).3 Nevertheless, TERS suffers for instance from diminished signal enhancement and limited reproducibility in comparison to SERS devices, which directly affects the performance and usability of TERS devices.4 SERS devices, on the other hand, usually consist of large-area assemblies of metal nanostructures on substrates of macro to micro dimensionality. They can be readily fabricated and provide a higher signal to noise ratio than TERS due to the ease of adjusting plasmonic nanostructure dimensions and gap sizes for instance by microfabrication techniques such as nanosphere lithography.5–7 Furthermore, structures with dimensions in the micro and nano regimes comprising arrangements of metallic nanowires, nanorods and colloids8,9, metal-nanoparticle decorated semiconductor nanowire arrays10–12 as well as DNA origami based nanostructures13–15 were previously studied as SERS platforms. However, nanoscale SERS devices based on only few plasmonic nanostructures situated on a single nanowire substrate have not yet been demonstrated and this can potentially open new doors for nanoscale sensing in diverse fields. Such SERS devices with subwavelength spatial sensing precision are required for minute sample


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volume analysis or for pathogen detection/metabolite analysis in cell cultures where molecular sensing with sub-cellular resolution is highly desirable. Biological SERS experiments with cells are conventionally performed by dispersing colloidal nanoparticles from a solution directly onto the cell culture.16,17 Notably, nanoparticles are taken up by the cells 18,19 and can significantly affect cell vitality as discussed by several studies.20–23 Therefore, the ability to retrieve all metal nanoparticles after a SERS measurement and to confine the overall nanoparticle exposure area are crucial for non-invasive measurements. The implementation of SiNWs as a nanoscale SERS substrate offers high spatial confinement of the sensing volume and, in principle, nanoscale position control if the SiNW is attached to an adequate scanning probe platform.24,25 Moreover, the entire probe and hence all metal nanoparticles can be thus completely retracted from the sample system after a measurement. Using silicon as a carrier substrate in general provides further benefits. Silicon is a well-established electronic material, which is also suitable for a short-term utilization in biological environments due to its chemical stability and non-toxicity. For these reasons, SiNWs assembled in field-effect-transistor (FET) configuration were already extensively explored within the last decade to resemble nanoscale transducers for label-free molecular sensing and even intracellular recordings.26 Although these charge-sensitive transducers reach down to the nanoscale, an analysis of complex samples with a single SiNW-FET is still not possible. Furthermore, SiNW-FET fabrication requires electrical integration by established but elaborate microtechnologies. SERS spectra, in contrast to these SiNW FETs, provide a significantly increased information content and the signal itself is read-out optically thus omitting any requirements for electrical wiring and related issues.


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Here, we demonstrate a single silicon nanowire (SiNW) based SERS device decorated with DNA origami-based SERS probe that allows measurements with high spatial resolution. In order to build an effective SiNW SERS device, plasmonic metal nanoparticles must be packed with nanometer spacing and with sufficient adhesion to the SiNW substrate. Metal nanoparticles can decorate in principle the entire nanowire surface, which should enhance the expected signal intensity and would confine the measurement already to the nanowire geometry. We show that the spatial resolution of SiNW based SERS probes can be set well below the nanowire dimension when only a specific nanowire area is covered with well-defined assemblies of a few closely spaced gold nanoparticles (AuNPs).

Figure 1. Schematic representation of a DNA origami-based SERS probe decorated single SiNW. (a) AuNP functionalization with thiol modified single-strand DNA oligonucleotides. (b) Assembly of the DNA origami-based SERS probe, four functionalized AuNPs are attached to 6-HB DNA origami nanotube. (c)A single silicon nanowire (SiNW) based SERS device decorated with DNA origami-based SERS probe.


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For this, the AuNPs were precisely arranged with the DNA origami method as described previously.27 DNA origami28,29 allows building fully addressable nanostructures with almost arbitrary shapes from synthetic oligonucleotides and a biological scaffold strand. A large variety of functional elements including biomolecules and inorganic nanoparticles at sub-nanometer resolution can be site-specifically attached to the DNA origami nanostructures.30 In this manner, four oligonucleotide-functionalized AuNPs were attached to the complementary single-stranded extensions (binding sites) on six helix bundle (6-HB) DNA origami nanotubes. The 6-HBs are six parallel, interconnected double DNA helices that have four binding sites with a spacing of 12 helical repeats, resulting in a distance of 42.2 nm between every two binding sites. In order to increase the plasmonic coupling between the nanoparticles, and to create strong hot spots 1,2,31–33, we used AuNPs with a diameter slightly larger than the distance between binding sites. The AuNPs were self-assembled onto the 6-HBs in a two-step process: the AuNPs were first functionalized with the thiolated poly-T single stranded oligonucleotides (ssDNA) as illustrated in Figure 1a, which were thereafter hybridized to their complementary single stranded extensions (binding sites) on the 6-HBs (Figure 1b). This complex is called “DNA origami-based SERS probe” hereafter. The accurate attachment of AuNPs to predefined binding sites on a 6-HB DNA origami enables the adjustment of the inter-particle distance and the number of attached plasmonic nanoparticles. The resulting DNA-origami-based SERS probe with an estimated inter-particle gap as small as 2 nm show a strong coupling of surface plasmon resonances and therefore highly increasing the signal enhancements in SERS measurements as shown in the following.30 Finally, the DNA-origami-based SERS probes were attached to single poly-(L-lysine) functionalized SiNWs. The negatively charged DNA origami and the oligonucleotide functionalized AuNPs adhere strongly to the positively charged poly-(l-lysine) functionalized


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SiNW surface, which ensures a successful decoration (Figure 1c). In order to ensure that each SiNW is decorated with a SERS probe, the ratio between the number of DNA-origami-based SERS probes and the number of SiNWs on the growth substrate was set to approximately 3. The

DNA-origami-based SERS probes are furthermore hardly prone to agglomeration, which is suppressed by the utilized 1XFB buffer. Crystalline SiNWs were synthesized using the wellestablished vapor-liquid-solid (VLS) method, where gold nanoparticles act as the catalyst for the bottom-up chemical vapor growth of nanowires.34,35 The synthesized SiNWs had a diameter of approximately 100 nm and a length of 25 µm (details of DNA origami SERS probe and SiNW synthesis can be found in Methods, in Supporting Information).


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Figure 2. (a) tSEM image of DNA origami-based SERS probe (b) SEM image of a single SiNW decorated with a DNA origami-based SERS probe. (c) Raman spectra of the positions indicated by arrows; spectrum 1 exhibiting no Raman peaks on the substrate where no SiNW is present; Spectrum 2 shows the c-Si peak at 521 cm-1 seen along the entire length of the nanowire; spectrum 3 shows both c-Si and (C-C) ring vibration of the MB molecule at around 521 and 1600 cm-1 respectively. (d) Raman intensity mapping of superposition of c-Si vibration (yellow color scale) and (C-C) aromatic ring vibration of methylene blue molecule (blue color scale) intensity profiles.

Figure 2a shows an example of a DNA origami-based SERS probe imaged by transmission mode scanning electron microscopy (tSEM). The DNA-origami, as shown in Figure 2a, was stained with a solution of 2% uranyl formate, which enabled the detection and visualization of the DNA backbone by tSEM. The ability to control the spatial arrangement of the plasmonic particles is a crucial factor, confining the SERS measurement only to a specific nanoscale region on the SiNW probe. The entire SERS device is depicted in Figure 2b showing a representative scanning electron microscopy (SEM) image of a single SiNW at a region decorated with a DNA origami-based SERS probe. In order to avoid any diminishing effects of the SERS measurements, the DNA-origami, as shown in Figure 2b, was not stained with 2% uranyl formate solution but an O2 plasma cleaning followed by a cleaning in acetone and isopropanol was performed to remove ideally all organic materials from the probe surface. That a SERS measurement can be consequently confined with SiNW-based SERS probes, is clearly shown in Figure 2c-d. The SERS spectra and intensity map shown in Figure 2c-d, are obtained from an area of a quartz substrate where an individual SiNW is also present. Notably, the


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substrate was entirely covered with methylene blue (MB) acting here as marker molecule. Generally, three principle kinds of Raman spectra were recorded during the experiments as shown Figure 2c. Firstly, the spectra that were recorded on the substrate, covered by MB where no SiNWs were present (labeled spectrum 1). These spectra do not exhibit any peaks arising from MB molecular vibrations. This proves that MB cannot be detected without a substantial signal enhancement in our Raman setup. Secondly, the spectra recorded along the single SiNWs show clearly and exclusively crystalline silicon (c-Si) peak at 521 cm-1. This peak corresponds to the first order transverse optical vibration mode of c-Si. Finally, the spectra recorded on the nanowire exhibit, in addition to the aforementioned exclusive c-Si peak at 520 cm-1, several other peaks such as the most prominent peak at 1620 cm-1 that corresponding to the C-C aromatic ring stretching mode of the MB blue molecule. A color-coded Raman intensity map was created by superimposing the local peak intensities which were measured at 520 cm-1 for silicon (yellow) and at 1620 cm-1 for MB (blue) (Figure 2d). As expected, the detection of the MB molecule is highly confined to a specific area at the SiNW. Considering the active sensing area, which is the area of the tight junctions created by AuNPs, the spatial resolution detection of the device is confined to a nanoscale region. However, one should take into account that Figure 2d cannot be directly used to extract the actual device resolution geometrically since the signal scattering limits the optical image resolution. The actual resolution for the local probing of analytes can be expected to be much better. However, local probing of analytes can only be realized if such SiNWs are attached to a 3D probe manipulator, which is a subject of future studies. Although the discussed results already demonstrate that nanoscale SERS devices can be realized, they allow so far only qualitative spectra evaluation. A quantitative study would require knowledge about the local electric field intensity enhancement factor (EF), offered by the DNA origami SERS


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probe, here based on the implemented MB molecule. In order to estimate EF, the area covered by each MB molecule needs to be estimated. Therefore, the molecule’s adsorption geometry and orientation, which effect the area covered by the molecule need to be determined. To this end, the adsorption geometry and the molecular vibrations of the MB molecule along with their direction dependent polarizability derivatives were investigated as shown in Figure 3.

Figure 3. (a) Optimized structure of the MB molecule. (b) Simulated Raman spectrum of the free form of the MB molecule. (c) Adsorption of MB molecule on Au (111) surface. To determine the MB molecular vibrations, density functional theory (DFT) was employed, within the generalized gradient approximation (GGA) with no geometry constraints. The hybrid Perdew−Burke−Ernzerhof functional (PBE0) 36 was selected to incorporate the exchange correlation energy, as well as the conductor-like polarizable continuum model to take into account the solvent effect on the molecule.37 Molecular vibrations of the MB molecule were determined using the ORCA 4.0.1 software 38 implementing quantum chemical theory.


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Figure 3a illustrates the optimized structure of the MB molecule, and a simulated Raman spectrum in its non-adsorbed (free) form is shown in Figure 3b. The blueshift of the MB molecule Raman vibrations in the simulated spectrum in comparison to the measured spectrum is due to neglecting molecule-molecule and molecule-surface interactions in the simulations. The adsorption geometry of the MB molecule on the Au (111) surface as a representation of the AuNPs was investigated as well through DFT calculations using the all electron/full potential electronic structure code FHI aims 39. Based on the assumption that for metal nanoparticles with face centered cubic structure the (111) facet has the lowest surface formation energy, gold nanoparticles should nucleate and grow into twinned and multiply twinned crystals exhibiting mostly a (111) surface facet termination.40–42 The Au (111) surface was modeled by (6×6) periodic unit cells with slabs consisting of 3 atomic layers separated by 3 nm of vacuum. A Monkhorst-Pack grid 43 of 2×2×1 points in the reciprocal space was used. The Tkatchenko−Scheffler PBE+vdWSurf approach 44 with screened van der Waals (vdW) interactions for adsorbates on surfaces and “tight” settings for standard numerical atom-centered orbitals basis sets were implemented in the calculations.45 The atomic zeroth-order regular approximation was applied for treating relativistic effects. The molecule adopts most likely in a planar geometry on the Au (111) surface, as illustrated in Figure 3c. There is negligible change in the geometry of the molecule upon adsorption. The planar adsorption geometry is due to the strong vdW interaction of the delocalized π electrons of the aromatic ring with the metal surface. The adsorption orientation can be further studied through SERS spectra characteristics. According to SERS spectroscopy selection rules, the vibrational modes with a higher perpendicular polarizability with respect to the surface of the SERS active structures undergo higher enhancements.46 This selection rule enables a more detailed analysis of the adsorption of the molecule and sheds light on adsorption orientation.


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According to the calculated polarizability derivatives of the molecule, the δ (C-N-C) and δ (C-S-C) (δ :skeletal deformation) vibrations that occur at 450 and 500 cm-1, have polarizability derivatives, which possess components parallel to the molecular plane (aromatic ring plane).47,48 Therefore, with a perpendicular adsorption orientation, the Raman peaks of the δ(C-N-C) and δ(C-S-C) vibrations would be highly enhanced and have therefore higher peak intensities relative to the C-C stretching vibration of the aromatic ring, as observed by reference 49. Perpendicular adsorption of the molecules is presumed at higher MB solution concentration. Although perpendicular adsorption of molecules can be expected at higher concentrations of the MB solution, adsorption orientations between horizontal and perpendicular states were so far experimentally not observed. In contrast, if the molecule is adsorbed parallel to the gold surface, the induced dipole moments would be parallel to the surface of the metal structure. Therefore, the δ(C-N-C) and δ(C-S-C) vibrations will have low Raman intensities relative to the C-C stretching vibration of the aromatic ring. The investigation of SERS spectrum and the calculated adsorption configuration both indicate that the MB molecule is adsorbed in our study with a horizontal configuration. Based on these findings, the SERS EF is here calculated by assuming the following equation:

𝐸𝐹 =

𝑁𝑅𝐸𝐹𝐼𝑆𝐸𝑅𝑆 𝑁𝑆𝐸𝑅𝑆𝐼𝑅𝐸𝐹

(1)

where 𝑁𝑅𝐸𝐹 and 𝑁𝑆𝐸𝑅𝑆 refer to the number of molecules in the reference sample and on the SERS structure respectively (details of the EF calculations are available in Supporting Information). 𝐼𝑆𝐸𝑅𝑆 is the Raman band intensity of a chosen enhanced vibration of the molecule on the SERS structure and 𝐼𝑅𝐸𝐹 is the Raman band intensity of the same vibration in the reference sample in the absence of SERS structures. Here, the Raman intensity of the C-C aromatic ring vibrations is chosen in the calculation of EF. 𝑁𝑅𝐸𝐹 is determined by calculating the number of molecules, which


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are present within the laser focus volume. The laser is operating in the fundamental transverse mode TEM00. Therefore, Gaussian optic approximations are used to calculate the laser focus width and volume. 𝑁𝑆𝐸𝑅𝑆 is estimated by assuming a full monolayer coverage of the AuNPs and horizontal MB molecule adsorption, at which each MB molecule consumes an area of 1.3 nm2. Based on the fact that the used assumption of a full MB molecule coverage of the AuNPs surface should represent an overestimation of the real number of molecules, the EF calculated here can be considered as a lower limit for SERS device performance.48 By adopting the aforementioned measurements, EF is calculated to be 1.1×105, which is within the broad range of EFs reported elsewhere.50,31 This result shows clearly that scaling down the active sensing region to nanoscale dimensions or three “hot spots” only, can be effectively performed while preserving a high and required signal enhancement. Furthermore, our results indicate that already two gold nanostructures should suffice to allow for a highly confined SERS measurement shrinking the current sensing area further down by a factor of two. In conclusion, SERS devices exhibiting an active sensing region of only few nanometers were demonstrated. For this, a 6-HB DNA origami nanotube was used to attach four AuNPs with interparticle spacing of about 2 nm. This DNA origami-based SERS probe was successively attached to single SiNWs to be used as an optical amplifier for SERS. This functional SERS device was successfully used to detect trace amounts of MB molecules. In order to quantify the electric field signal enhancement factor, the vibrations of MB along with their direction dependent polarizability derivatives were determined by DFT calculations and were compared to that of the measured SERS spectrum. Furthermore, the adsorption geometry of the molecule using the PBE + vdWSurf method allowed to estimate the number of molecules on the SERS active substrate, which in turn enables the calculation of the so-called SERS enhancement factor as a measure of


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the device performance. The obtained enhancement factor of 1.1×105 is within the broad range reported by similar studies and demonstrates that DNA origami-based SERS probe attached to a single SiNW represent an efficient optical amplifier for SERS measurements. The DNA Origamibased SERS probe enables SERS measurements with a spatial resolution beyond the diffraction limit of light by confining the decoration of plasmonic particles specifically to the position where the DNA origami-based SERS probe is present. Furthermore, attaching the DNA origami-based SERS probe to a SiNW can be exploited to gain control over the measurement position and the retraction of the AuNPs from the measurement area if utilized in a 3D probe-manipulator. ASSOCIATED CONTENT Supporting information contains further experimental and theoretical information regarding the fabrication of the DNA origami-based SERS probe, molecular vibrations, laser optics and enhancement factor calculation. AUTHOR INFORMATION Corresponding Authors Email: [email protected] ORCID Ardeshir Moeinian: 0000-0002-4517-6646 Fatih N. Gür: 0000-0003-3093-9329 Hua Guo: 0000-0001-9901-053X Gonzalez-Torres : 0000-0003-4193-4400


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Thorsten L. Schmidt: 0000-0002-6798-5241 Steffen Strehle: 0000-0002-1261-2894 Author Contributions: A. M. conceptualization, synthesis of SiNWs, decoration of SiNWs by ANP 6-HB DNA Origami, Raman Spectroscopy and Analysis; F. N. G. designed and synthesized DNA origami-based SERS probes; J. G. T. performed Orca simulations; L. Z and H. G. performed DFT analysis for MB adsorption geometry; A. D. D. Raman Spectroscopy; V. D. M. Laser Optics analysis and calculations; T. L. S. conceptualization, DNA origami-based SERS probes; S. S. conceptualization, project supervision. All authors wrote and revised the manuscript. Notes The authors have no competing financial interests. ACKNOWLEDGEMENTS The financial support by the German Federal Ministry of Education and Research (NanoMatFutur 13N12545) as well as the collaboration with the Research Training Group DFG/GRK 2203 is gratefully acknowledged. T.L.S is supported by the DFG through the Center for Advancing Electronics Dresden (cfaed) as well as Seed Grant 043_2615A6 by the DFG Center for Regenerative Therapies Dresden (CRTD). We also greatly thank S. Jenisch, M. Gonçalvez, O. Wittekindt, A.M. Steinbach, and P. Unger for their support. L.Z. and H.G. acknowledge the support of the Air Force Office of Scientific Research (Grant No. FA9550-15-1-0305). J.G.T thanks the supercomputing laboratory ABACUS (CINVESTAV) for the time assigned. REFERENCES


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Highly Localized SERS Measurements Using Single Silicon

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