Active delivery of single DNA molecules into a plasmonic nanopore for. label-free optical sensing

Transcription

1 Supporting Information: Active delivery of single DNA molecules into a plasmonic nanopore for label-free optical sensing Xin Shi 1,2, Daniel V Verschueren 1, and Cees Dekker 1* 1. Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology; Van der Maasweg 9, 2629 HZ Delft, The Netherlands 2. Key Laboratory for Advanced Materials & School of Chemistry and Molecular Engineering, East China University of Science and Technology, Shanghai, , P. R. China. * c.dekker@tudelft.nl Supplementary Notes S1. Experimental setup S2. Backscattering mapping of dimer antenna array S3. Spatial field distribution of the electromagnetic hotspot in the plasmonic gaps Supplementary Figures and Tables Figure S1. Experimental setup for label-free single molecule plasmonic nanopore sensing Figure S2. More examples of plasmonic nanopore devices used in the experiments Figure S3. Additional Scattering and ionic current mappings over a large area Figure S4. Simulated electromagnetic field around the plasmonic antenna excited with transverse polarized light Figure S5. Simulated scattering cross section of plasmonic dimer antennas with different gap sizes Figure S6. The inhomogeneity of the electromagnetic field distribution in the gap of plasmonic antenna. Figure S7. IV curves of typical plasmonic nanopore with and without laser excitation Figure S8. Comparison of the signal durations of corresponding ionic current and backscattering events. S1

2 Supplementary Notes S1. Experimental setup The simultaneous scattering light intensity and current detection was performed using a custom-built setup. A schematic of the setup is shown in Fig. S1. The 785 nm polarized laser beam was expanded and passed through a non-polarizing beam splitter where 50% of the incident light was focused into the flow cell with a water-immersion objective (60x, 1.2NA, Nikon), while the other 50% of the laser was partly coupled into a fiber and sent to one of the input channels of a balanced photodetector. The backscattered light from the plasmonic nanopore structures was collected through the same objective and then sent to the complementary input channel of the photodetector. The difference between the photocurrents in the two photodiodes was amplified and sent into a DAQ board (USB-6251, National Instruments). A white-light LED is used to illuminate the sample during the sample alignment, and a camera was employed to acquire video images for sample alignment. The DC voltage was applied by a patch clamp amplifier (Axopatch 200B, Molecular Devices) via a pair of Ag/AgCl electrodes. The ionic current is acquired, amplified, send to the DAC board and read-out together with the amplified photocurrent using a synchronous call. The entire setup is operated with a customdesigned LabVIEW program and the digitized signals of both channels were recorded by a computer. S2

3 S2. Backscattering mapping of dimer antenna array Figure 2 (Main text) and Fig. S3 show backscattering maps of our plasmonic antenna arrays excited with a laser. Within the array, the dimer antennas have slightly different gap sizes between two particles, and accordingly show different backscattering intensities under longitudinal polarized excitation. Some of them even show lower light signal then the background (the reflection of the membrane). Here we briefly discuss the mechanism of such intensity variations. In our experiments, the backscattering light is collected by the same objective used for focusing the incident laser light. The detected light intensity reaching the photodiode I d can be written as follows 1 : I d = E r + E s 2 = E i 2 (r 2 + s 2 2r s cos θ), (S1) where E r, E s, and E i are the reference field (arising mainly from the reflection from the membrane surface), the scattering field (scattered field from the particle of interest), and the incident field, respectively, r is a real reference amplitude, s is a complex scattering amplitude, and θ is the phase difference between these two fields at a large distance. This phase difference contain contributions from the path length difference between the two fields, the Gouy shift, and phase shift due to the polarizability of the antennas. The first term on the right, E 2 i r 2, in our case, is chiefly the specularly reflected light from the SiN membrane, the second term, E 2 i s 2, is the pure scattering intensity from the nanoantenna, and the third term E 2 i 2r s cos θ is the interferometric scattering term that expresses the interference of the reflected and the scattered light. The scattering amplitude, s, is the quantity of interest and is strongly dependent on the material, size, and geometry of the nanoparticle. From our FDTD simulation results, shown in Fig S5, we learn that the magnitude of scattering cross section of dimer antennas under longitudinal excitation at our laser wavelength varies with gap size and changes drastically if the structure is merged or contains a gap. During the EBL fabrication, we fabricate an array of dimers with various gap sizes on each free-standing membrane, including some without gap (i.e. two merged particles). Therefore, the array contains a variety of nanostructures with strongly varying scattering cross-sections. The scattering maps can thus be interpreted as follows. The peaks in the maps correspond to excitation of plasmonic nanostructures with a gap. For these structures the backscattering cross-sections are large and the backscattered light intensities will be dominated by the pure scattering term (middle term equation S1). The exact intensities of these peaks vary somewhat because of the different gaps the nanostructures in the S3

4 array possess. The areas in between the nanostructures will just show a small background scattering intensity from the light reflected weakly at the membrane (first term equation S1). The dips can be explained by interferometric scattering (last term equation S1). When the scattering is weak, as is the case for antennas without gaps, the pure scattering term in equation S1 will negligible, but the interferometric term might not be. The scattered and reference beam, in our case, are in antiphase and thus we observe dips when the merged structures are illuminated. S4

5 S3. Spatial field distribution of the electromagnetic hotspot in the plasmonic gaps To illustrate inhomogeneity of the EM field in the plasmonic gap, we plot the simulated normalized EM field intensity distribution under 785 nm excitation in the XZ cross section of our plasmonic nanopore device, along the longitudinal axis of the dimer, in Fig. S6. As the simulation result shows, the squared electric field strength in the gap shows a distinct spatial inhomogeneity. The squared field strength near to the gold surface appears to be more than 4 times stronger than the squared field strength in the center of the gap. Since the plasmon shift produced by biomolecules in the hotspots is proportional to the local squared electric field intensity integrated over the molecule volume 2-3, molecules positioned at the surface of the sensor will produce stronger signals than molecules residing in the middle of the gap. As an advantage, such an extremely enhanced and confined EM field could in principle provide extraordinarily high spatial resolution 4 and could be used to determine substructure of biomolecules and biopolymers in future applications. For other applications where such confinement becomes limiting, it can be improved by changing the design of the plasmonic structures to create more homogeneous EM field. S5

6 Supplementary Figures Figure S1. Experimental setup for label-free single molecule plasmonic nanopore sensing. M: mirror; BS: non-polarizing beam splitter; PBS: polarizing beam splitter; ND: neutral density filter; BE: beam expander. S6

7 Figure S2. (a-c) Additional examples of plasmonic nanopore devices used in the experiments. Right panels are close-up TEM images of the corresponding structures in the left panels. S7

8 Figure S3. Additional example of scattering (a) and ionic current (b) mappings over a large area on the free-standing membrane containing an array of plasmonic nanoantennas. S8

9 Figure S4. Simulated electromagnetic field around the plasmonic antenna excited with transverse polarized light. Note the absence of any increased field intensity in the gap. S9

10 Figure S5. Simulated scattering cross section versus wavelength for plasmonic dimer antennas (disks of 90 by 70 nm) with various gap sizes under longitudinal excitation. For small variations in the gap size, the resonance peaks shift moderately, until the dimers merge when a dramatic shift occurs. At the wavelength of excitation (dashed line), the scattering will be almost minimal in that case. S10

11 Figure S6. The inhomogeneity of the optical field distribution in the gap of plasmonic antenna. The upper panel shows an XZ cross section of the squared electric field strength at the plasmonic antenna along the longitudinal axis. The squared field strength shows an extremely enhanced field around the lower corner of the antenna and decays very quickly away from the gold surface to the center of the gap. The lower panel shows a profile of the squared field at 1 nm above the upper surface of the SiN (dash line) demonstrating a 4 times difference in squared intensity E 2 / E 0 2 between the surface of the gold and the center of the gap. S11

12 Figure S7. Heating effect on plasmonic nanopores. Typical IV curve of a plasmonic nanopore device with (orange) and without (blue) laser illumination (785 nm, 100 μw, focused into a diffraction-limited spot). S12

13 Figure S8. Comparison of the signal durations of corresponding ionic current events (orange) and backscattering events (blue) under 300 mv bias. Two peaks of ionic current events can be observed, which can be attributed to translocation where post-translocation interaction is (peak at longer durations) or is not (peak at shorter durations) detected from the access region current blockade. On the contrary, the optical scattering data show a single broad peak that signals the prolonged presence of DNA molecules in the hotspots. S13

14 References (1) Jacobsen, V.; Stoller, P.; Brunner, C.; Vogel, V.; Sandoghdar, V., Interferometric Optical Detection and Tracking of Very Small Gold Nanoparticles at a Water-Glass Interface. Opt. Express 2006, 14, (2) Taylor, A. B.; Zijlstra, P., Single-Molecule Plasmon Sensing: Current Status and Future Prospects. ACS Sensors 2017, 2, (3) Yang, J.; Giessen, H.; Lalanne, P., Simple Analytical Expression for the Peak-Frequency Shifts of Plasmonic Resonances for Sensing. Nano Lett. 2015, 15, (4) Chikkaraddy, R.; Turek, V.; Kongsuwan, N.; Benz, F.; Carnegie, C.; Van De Goor, T.; de Nijs, B.; Demetriadou, A.; Hess, O.; Keyser, U. F., Mapping Nanoscale Hotspots with Single-Molecule Emitters Assembled into Plasmonic Nanocavities Using DNA Origami. Nano Lett. 2017, 18, S14