Modulation of Fluorescence Signals from Biomolecules along

Letter pubs.acs.org/NanoLett

Modulation of Fluorescence Signals from Biomolecules along Nanowires Due to Interaction of Light with Oriented Nanostructures Rune S. Frederiksen,† Esther Alarcon-Llado,‡ Morten H. Madsen,§ Katrine R. Rostgaard,† Peter Krogstrup,∥ Tom Vosch,⊥ Jesper Nygård,∥ Anna Fontcuberta i Morral,‡ and Karen L. Martinez*,† †

Bio-Nanotechnology and Nanomedicine Laboratory, Department of Chemistry & Nano-Science Center, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark ‡ Laboratory of Semiconductor Materials, Institute of Materials, School of Engineering, EPFL, 1015 Lausanne, Switzerland § Danish Fundamental Metrology A/S, Matematiktorvet 307, 2800 Kgs. Lyngby, Denmark ∥ Nano-Science Center & Center for Quantum Devices, Niels Bohr Institute, University of Copenhagen, Universitetsparken 5, DK-2100 Copenhagen, Denmark ⊥ Nano-Science Center/Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100 Copenhagen, Denmark S Supporting Information *

ABSTRACT: High aspect ratio nanostructures have gained increasing interest as highly sensitive platforms for biosensing. Here, well-defined biofunctionalized vertical indium arsenide nanowires are used to map the interaction of light with nanowires depending on their orientation and the excitation wavelength. We show how nanowires act as antennas modifying the light distribution and the emitted fluorescence. This work highlights an important optical phenomenon in quantitative fluorescence studies and constitutes an important step for future studies using such nanostructures. KEYWORDS: InAs, nanowire, protein, optical properties, biosensing, Meep simulation cules, the fluorescence properties of the fluorophores, and the light fluxes interacting with the biofunctionalized NSs. However, a detailed study to understand how the interaction between NW and light influences the fluorescence properties of surface-bound fluorescently labeled biomolecules has not yet been addressed. Various types of biomolecules, notably several types of proteins used for diagnostics, have been interfaced with NSs.12,20−24 The NS shape has been suggested to affect the immobilization of the proteins, for example, with a preferred immobilization of biomolecules at the end of NSs due to steric constraints,25,26 resulting in a variation of protein concentration along the NSs and in heterogeneous fluorescence signal along the NSs.27,28 Moreover, the fluorescence properties of fluorescently labeled biomolecules have been reported to be altered by the proximity to the NSs.29−31 In addition, several studies have reported on a complex interaction of light with NSs due to their intrinsic optical properties. For example, it has been reported that NSs, such as NWs, can absorb,32 scatter,33 guide,34,35 emit,36,37 and collect/

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he number of applications interfacing high aspect ratio nanostructures (NSs) and biology has increased rapidly in the past years, creating a range of new powerful tools for biosensing within basic research, green technology, drug screening, and diagnostics.1−3 Platforms of vertical NSs such as nanowires4 (NW), nanopillars,5−8 and carbon nanotubes/ rods have demonstrated promising potential for fluorescencebased applications,9 such as DNA screening,10,11 protein bioanalytics,12,13 and single cell studies.14−16 Indeed, the high aspect ratio of vertical NSs provides increased biosensing sensitivity due to protein up-concentration in a small volume, in addition to the possibilities of reduced material consumption and multiplexed detection for the analysis of purified sampled or crude cell lysates.6,12 Furthermore, the recent use of vertical NSs for live-cell applications opens numerous perspectives in drug discovery and diagnostics, based on fluorescence microscopy.3,17,18 To evaluate the full potential of the NS fluorescence-based applications, such as for the detection of light biosensing suggested by Siethoff et al.,19 it is critical to assess the fluorescence signal on the NSs in order to avoid any possible misleading and false interpretation of fluorescent signals. Indeed, on the basis of fluorescence studies, NSs have been suggested to influence the quantity of immobilized biomole© XXXX American Chemical Society

Received: August 31, 2014 Revised: November 7, 2014

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concentrate light.38 Moreover, these unique optical properties of NSs are dependent on the material, orientation, diameter, length, and internal spacing of the NSs,39 as well as on the wavelength and incident angle of the light.38,40 In this study we explore the impact of NSs on the fluorescence of fluorescently labeled biomolecules attached to InAs NWs. We recently demonstrated several proof-ofconcepts for biosensing of isolated proteins and of living cells, using InAs NWs.12,14,41,42 We have also reported on the fabrication of InAs NW arrays with well-defined dimensions and a high degree of reproducibility,43 which minimizes effects from sample-to-sample variations. This previous work has enabled us to study in the present communication the optical properties of InAs NWs using a biological model system consisting of biotinylated bovine serum albumin (BSA−biotin) and fluorescently labeled streptavidin. In this work we demonstrate the influence of the NW geometry and orientation on fluorescence signals. Fluorescence Intensity along Vertical InAs NWs. To study the influence of the NW morphology on the fluorescence signals of fluorescently labeled biomolecules, regular arrays of uniform, single crystal InAs NW were grown via the vapor− liquid−solid mechanism on a InAs (111)B substrate with a lithography defined gold nanoparticle mask.43 NW diameter and height had a distribution of, respectively, 92 ± 9 nm and 4.4 ± 0.3 μm (over one growth containing up to 100 samples). The well-controlled reproducible NW arrays enabled investigations of the impact of NWs dimensions on the fluorescence signal. For a fast, efficient, and reproducible biofunctionalization of the NWs, they were modified with a biological model system consisting of BSA−biotin suitable for the recognition of streptavidin fluorescently labeled with Alexa 488 (SA-488) as described earlier12 and schematically illustrated in Figure 1a.

stack were combined to create a tridimensional image of the fluorescence intensity (see Figure 1b). Here, a fluorescence enhancement at the NW tip was observed. No fluorescence signal was detected using nonfluorescence labeled biomolecules; data not shown. A similar tip phenomenon has been observed in the case of living cells interfaced with NWs (Figure 1d,e), where the fluorescently labeled cell membrane in close contact with the NWs appeared nonuniform.41 The origin of this nonuniform fluorescence signal along the NW was examined through investigations of the influence of the NW on interactions with biomolecule and light. Distribution of Biomolecules along the NWs. A fluorescence enhancement at the NW tip due to increased protein coverage compared to the rest of the NS has previously been reported.25 To evaluate the protein density along the NW, we functionalized NWs with BSA−biotin and labeled randomly a fraction of the immobilized protein with a solution of 20 nm streptavidin coated gold nanoparticles (SA-NP). The distribution of SA-NP along the NWs was then evaluated by scanning electronic microscopy (SEM) on a representative sample of NWs. Figure 2a is a representative example of a single NW modified with a low (nonsaturating) concentration of SA-NP (see zoom in Figure 2b). Each NW in the sample was divided into 8 segments, and the density of SA-NP evaluated on each NW segment was homogeneous (Figure 2c). To exclude that the observed fluorescence profiles were caused by an increased surface area available for biofunctionalization at the NW tip, a calculation was performed assuming a homogeneous protein distribution along the NW, including the tip. A two-component Gaussian point-spread function was used to describe the CLSM confocal volume (explained in the Supporting Information (SI)).44 As shown in the simulation of Figure 2d, no significant signal increase is expected at the NW tip due to surface increase at the tip. These results thus suggest that the increased fluorescence intensity observed at the tip of the NW is not due to a heterogeneous biomolecule distribution but could be due to an optical effect related to the NWs. NW Fluorescence Profile Dependence on NW Orientation and Composition. To evaluate whether the NW orientation influences its interaction with light, as reported earlier by Krogstrup et al.,45 fluorescence profiles along vertical (i.e., standing on InAs substrate) and horizontal (i.e., lying down on glass) NWs were evaluated after biofunctionalization using a confocal fluorescence microscope with identical imaging conditions. The NW arrays were functionalized with BSA− biotin and SA-488 as described earlier. The fluorescence profiles of several hundred individual vertical NWs were measured while functionalized NWs were deposited on a glass coverslip for the imaging of horizontal NW fluorescence. Figure 2e shows representative fluorescence profiles of both cases. An increase of detected emission at the tip is only observed in the case of vertical NW arrays, suggesting that the effect is due to the vertical orientation of the NW. These results are confirmed by simulations of the two configurations, as described later in the letter. NWs exhibit a small gold head at their tip used as catalyst during the NW growth. Because gold NPs are known to amplify fluorescence signals,46 the influence of the NW gold head on the fluorescence signal was evaluated, using selfcatalyzed NWs, grown without gold-NP tip. As seen in Figure S1, SI, similar Z-profiles are observed, suggesting that the goldNP is not the main reason for the modification of the

Figure 1. Fluorescence confocal imaging of biologically functionalized InAs NW arrays. (a) Illustration of a single NW modified with BSA− biotin and SA-488.12 (b) xy confocal image of a NW array with 3 μm spacing functionalized with SA-488, representing a top view of the sample. (c) xz cross section of a stack of confocal fluorescence images, representing a side view of the dotted line in panel b. (d) xy confocal image, representing a top view of a living cell expressing a fluorescently labeled membrane protein interfaced with a NW array with 4 μm spacing.41 (e) xz cross section of a stack of confocal fluorescence images, representing a side view of the dotted line in panel d.

The fluorescence signal along the NW was evaluated by recording fluorescence images of the labeled NW array at different heights. A confocal laser-scanning microscope (CLSM) was used to create two-dimensional images through raster-scanning in the xy-plane with an internal plane distance of 0.17 μm in a Z-stack (along the NW). The images in the ZB

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Figure 2. (a) SEM image of single InAs NW modified with SA-NP. (b) Zoom-in of three sections along the NW, the NPs are identified with arrows. (c) Z-profile of the average protein density, estimated from SA-NP density along each of the 8 NWs. (d) Calculation of the detected fluorescence Zprofile from proteins immobilized on a NW, by convoluting a homogeneous fluorescently labeled protein distribution on the NW with a 3D Gaussian profile of fwhm (ωz = 840 nm and ωxy = 240 nm) and considering an increased surface area at the tip. (e) Fluorescence profiles from horizontal and vertical NW modifed with BSA−biotin and SA-488.

Figure 3. (a) Normalized fluorescence decay curves of the SA-488 in solution and bound to InAs and the instrument response function (IRF). (b) The influence of the excitation wavelength on the normalized fluorescence Z-profile of three different fluorophores (SA-488, SA-555, and SA-633).

whereas at higher wavelengths (633 nm) the fluorescence signal was broadened along the NW. This suggests that the light flux is modified along the NW surface. This phenomenon was investigated further using theoretical simulations. Interaction of Light with Vertically Oriented InAs NW: Theoretical Simulations. In order to shed light onto the NW influence on the fluorescence signal and further elucidate the phenomena observed, we carried out theoretical simulations by evolving Maxwell’s equations over finite time steps. In this way, the light interaction with InAs NWs is assessed. Simulations were performed on a single NW, vertically standing on an InAs substrate as in the experiments. Further simulation details can be found in the SI. We start by considering the effects of NW−light interaction on the fluorophore excitation process. For this, a plane wave incident in the vertical direction along the NW axis was considered. The results are shown in Figure 4. To elucidate the physical origin of the spatial dependence of the fluorophore excitation along the NW axis, we show the normalized 2D electric field energy map (|E|2), for a section of the simulation cell for the smallest and largest wavelengths (488 and 633 nm, respectively). In the cross section, the electric field energy is clearly periodic along the vertical direction, due to interference effects with the reflected light by the substrate. More interestingly, it can be seen that, at the NW surface, the electric field energy is more intense at the tip for the blue (488 nm) wavelength. However, the opposite happens for red-light excitation (633 nm). The maximum of the field energy moves toward the NW bottom by increasing the excitation wave-

fluorescence signal and that the effect is specifically related to the orientation of the NW. Influence of Vertical NWs on Optical Properties of Biomolecules. The emission spectra of the fluorophore at different positions along the NW are similar (Figure S3, SI). It has been previously reported that NSs can modify the fluorescence quantum yield of fluorophores.29 A change of quantum yield or quenching degree of the fluorophore along the NWs is expected to affect its fluorescence decay time. As shown in Figure 3a, the fluorescence decay time was affected by the immobilization of the fluorophore on InAs. However, this phenomenon was identical on the planar InAs surface and along InAs NWs and is thus independent of its location on the NW. These findings (Figure S3, SI) support the idea that the observed tip effect is not due to the alteration of the excited state decay time or the emission spectra along the NW. To evaluate whether the tip effect is a photonic effect intrinsic to the NW geometry, we studied the fluorescent Zprofile as a function of the wavelength, as the NW−light interaction is wavelength dependent.32 Here, we exploited the versatility of the model protein chosen (streptavidin) by using proteins labeled with fluorophores of distinct optical properties (Alexa 488, Alexa 555, and Alexa 633 for SA-488, SA-555, and SA-633, respectively) and took advantage of the established uniform distribution along the NW (Figure 2b). It was observed that tuning the wavelength altered the fluorescence Z-profile, with a significant shift in the confinement of the fluorescence (Figure 3b). At lower wavelengths (488 and 555 nm) the fluorescence was mainly detected at the NW tip, C

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but around 2 μm deeper down. These results are supported by the photobleaching experiments shown in Figure S2, SI. We also noted that the effect is dependent on the NW diameter (see Figure S7, SI). Although these results are in accordance with the trend observed experimentally, they do not fully explain the results, where the maximum signal is always observed close to the tip. Thus, we also evaluate the light−NW interaction for a single dipole emitting at the NW surface (see SI and Figure S4 for further details). In Figure 4b we represent the electric field energy cross section for a dipole emitting at 5 nm away from the InAs NW surface and at a distance d = 50, 500, and 2000 nm from the tip. Here, only a vertical range of ±600 nm from the dipole is represented. We find that for dipoles emitting close to the NW tip, some of the light guided along the NW surface can be released through the tip, which would result in a slightly stronger signal being detected for fluorophores emitting around the first micron from the tip. Similar results were found without the gold particle, indicating that the phenomenon is not due to the gold particle. In any case, the NW edge acts like an antenna and re-emits the light that coupled to the NW. In order to quantify such an effect, we assessed the outgoing flux for a solid angle of 1.47 sr (corresponding to an angular aperture of 40°). For more details about the flux calculations, please refer to Figure S5, SI. The normalized flux profile is then represented in Figure 4c as filled circles. Because of computational restrictions, the deepest position that could be simulated with such an angular aperture and resolution was 2.5 μm below the NW tip. Simulations were also performed for shorter nanowires without significant difference in the outcome (Figure S7, SI). The dotted lines correspond to an extrapolation of the simulated data. As expected from the 2D field energy map, the light flux is much stronger for dipoles emitting at the tip. Similar to what was found for the excitation profiles, longer wavelengths are able to further propagate along the NW. Thus, light coming from dipoles emitting at longer wavelengths and further down on the NW can still be reemitted at the tip. Contrary to the excitation profiles though, the maximum signal strength is located close to the NW tip for all wavelengths. A combination of both effects (excitation and emission along NWs) was explored through the product of both strength quantities. Afterward, the data was convoluted with a Gaussian signal (as explained earlier in this letter) to take into account the confocal microscope resolution. The result is plotted in Figure 5 along with the experimental data. The simulation is in good agreement with the experiment. These distributions are characteristic only for vertically standing NWs, proving that NS interaction with the incident and outgoing light has a strong influence on the overall detected signal from the fluorophores and thereby highlighting the necessary understanding of these phenomena before performing any quantitative studies along high aspect NSs. Conclusions. In summary, it has been shown earlier by us and others, that NWs are an extremely promising platform for protein arrays and fluorescence investigations of individual living cells. We have demonstrated in this study that light interaction between the NW and the environment plays an extremely important role in the 3D detection scheme and that NW−light interaction as well as NW orientation need to be considered both in the absorption and emission processes. Using a simple and straightforward experimental procedure and MEEP simulations, we observed how, by tuning the

Figure 4. (a) Normalized time-averaged electric field energy density (| E|2) in a cross section through the center of a vertical InAs NW on an InAs substrate for an incident plane wave propagating along the vertical axis, z, and for a wavelength of 488 and 633 nm. (b) Vertical cross section of the normalized time-averaged electric field energy density for an emitting dipole on top of the NW surface at a distance d from the tip. The dipole emission wavelength is 507 nm and the represented area corresponds to ±0.6 μm from the dipole position in the vertical direction to elucidate the light “escaping” from the NW for dipoles close to the tip. (c) Quantitative representation of the simulated local excitation and emission strengths as a function of fluorophore position. The excitation is represented by the electric field energy density at 5 nm distance from the NW surface. The data was averaged with nearest neighbors in order to eliminate light interferences created by the substrate (see Figure S6, SI for further details). The emission was assessed through the energy flux at a certain distance from the NW tip (see SI).

length. Such an effect can be better discerned in Figure 4c, where the normalized field energy at 5 nm distance from the NW surface (considering the protein size) is represented in triangles as a function of position along the vertical axis. In order to eliminate light interferences, an average between neighboring points was performed. The averaged data is consistent with the profiles obtained for simulations performed with and without considering a substrate (see Figure S6, SI). At short wavelengths, the field strength is maximal at the NW tip. After the first 500 nm away from the tip, the energy strength is reduced to about 40%. A similar trend is found for the case of an excitation at 546 nm, although the energy strength decay from the NW tip is less sharp. In contrast, for a wavelength of 633 nm, the maximum strength is no longer found at the tip, D

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by the Danish Ministry for Science, Technology and Innovation), the Danish Advanced Technology Foundation, the ERC Stg ‘UpCon’, the ITN network ‘Nanoembrace’, and the Lundbeck Center for Biomembrane and Nanomedicine.

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Figure 5. Experimental and simulated signal profile for fluorophorecovered InAs vertical NWs for the excitation−emission wavelengths of 488−507 nm (blue), 546−560 nm (green), and 633−650 nm (red). The simulation is given by the product of excitation and emission profiles from Figure 4c and convoluted for a Gaussian detection profile.

wavelength, the electric field energy distribution is modulated along the NW and affects the fluorescence signal detected. The electric field resonances are focused at the NW tip for shorter wavelengths, while resonances are spread out along the NW for longer wavelengths, which in both cases results in a brighter fluorescence signal at the tip of NW. These results are essential for quantitative studies of biological phenomena along NWs as they prevent misinterpretation of modulated fluorescence intensities along NWs. Indeed, we show that a brighter signal at the tip of NWs in the case of protein arrays or studies in living cells (shown in Figure 1) does not indicate a higher concentration of fluorescent molecules at the tip of the NWs. The phenomenon described here in the case of InAs NWs is expected to be present in various types of NSs but will vary depending on the NS material and geometry. It is thus essential to take such phenomenon into account in the quantitative analysis of fluorescence studies performed on NWs in the future, and some recent results might require further analysis to prevent any overinterpretation of fluorescence data. The present letter has thus established an important understanding of 3D nanoscale detection schemes for biological systems. Achieving highly sensitive and quantitative biosensing with NWs is an essential step in the emerging field dedicated to the use of NSs arrays for biological applications.3,47

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ASSOCIATED CONTENT

S Supporting Information *

Detailed experimental protocols, data on self-catalyzed NWs, and detailed information on the influence of InAs NWs on fluorescence properties of the fluorophores. This material is available free of charge via the Internet at http://pubs.acs.org.

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REFERENCES

AUTHOR INFORMATION

Corresponding Author

*E-mail: [email protected]. Notes

The authors declare no competing financial interest.

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ACKNOWLEDGMENTS For financial support, we thank the Danish Agency for Science Technology and Innovation (The Danish Council for Strategic Research−ANaCell project), UNIK Synthetic Biology (funded E

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