Three Dimensional Orientation of Anisotropic. Plasmonic Aggregates at Intracellular Nuclear. Indentation Sites by Integrated Light Sheet Super-

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1 Supporting Information Three Dimensional Orientation of Anisotropic Plasmonic Aggregates at Intracellular Nuclear Indentation Sites y Integrated Light Sheet Super- Resolution Microscopy Suresh Kumar Chakkarapani, Yucheng Sun, Seungah Lee, Ning Fang*,, Seong Ho Kang*,, Department of Chemistry, Graduate School, Kyung Hee University, Yongin-si, Gyeonggi-do 174, Repulic of Korea Department of Applied Chemistry and Institute of Natural Sciences, Kyung Hee University, Yongin-si, Gyeonggi-do 174, Repulic of Korea Department of Chemistry, Georgia State University, Atlanta, Georgia 3, United States *Corresponding authors: Ning Fang: Phone, ; , nfang@gsu.edu. Seong Ho Kang: Phone, ; , shkang@khu.ac.kr. S1

2 Contents Movie S1-S4 (AVI) S3 Figure S S4 Figure S S5 Figure S S6 Figure S S7 Figure S S8 Figure S S9 Figure S S Figure S S11 Figure S S12 Figure S S13 Figure S S14 Figure S S15 S2

3 Movie M1. Dual-view coupled astigmatism effect of AgNP and AuNR. Movie M2. Photo-switching of an isolated AuNR taken while turning the polarization with respect to the orientation of AuNR. Movie M3. Real time super-localization track of AuNR with respect to the orientation of the polarizer. Movie M4. 3D orientation of AuNRs in a live single HeLa cell, as numered in Figure 6. S3

4 a EMCCD DV CL IOL DOL L DM BE CL Slit M RP DP L M CAD HL z c i 2.9 cm DP holder Laser out of BE 9 CL Laser light sheet ii.4 cm 2.4 cm Laser out of BE 45 CL Laser light sheet iii 1.4 cm.4 cm Figure S1. (a) Photograph of 3D ilsrm setup on micro dove-type prism (red dashed ox). () Variation in laser light sheet thickness with respect to change in cylindrical lens (CL) angle. (c) Mirco dove-type prism and holder (i and ii) side view and (iii) top view. Areviations: EMCCD, electron-multiplying cooled charge-coupled device camera; DV, dual-view setup; RP, rotatory polarizer; CL, cylindrical lens; CAD, condenser aperture diaphragm; DOL, detecting ojective lens; IOL, illumination ojective lens; DP, micro dove-type prism; HL, halogen lamp; M, mirror; L, laser; BE, eam expander; DM, dichroic mirror. S4

5 RSI 2 (a.u) Intensity (a.u) a 1 µm Distance (µm) c d e 1 µm 1 µm Pixels d c Figure S2. Characterization of the laser light sheet. (a) Image of laser light and () intensity plot of the laser on the white dotted line in (a). (c) and (d) are the images of AuNR efore and after optimizing the width the Light sheet. (e) Relative scattering intensity plot of AuNR shown with dotted line in (c) and (d). S5

6 Asorance (a.u.) Longitudinal resonance e - e- e Transverse resonance e - e - e - e - e Wavelength (nm) Figure S3. Typical extinction spectra of 8 nm AuNR showing the two peaks corresponding to transverse and longitudinal resonance. S6

7 RSI (a.u.) a m Pixels 6 8 Pixels Pixels 6 8 Pixels 6 8 Pixels Figure S4. Numerical aperture analysis. (a) Scattering signals from single AuNR imaged with a ojectives lens y varying the numerical aperture (NA) from.6 to 1.3. () Relative scattering signal (RSI) was measured at the spot marked y a yellow ox in (a). S7

8 a No Filter 4/ nm 485/15 nm 5/ nm 575/ nm 68/ nm 5 m Figure S5. Wavelength-dependent scattering analysis of AuNRs. AuNRs were illuminated with (a) 671-nm wavelength laser source and () 473-nm wavelength source, and scattering signals were analyzed with different andpass filters: 4/ nm, 485/15 nm, 5/ nm, 575/ nm, and 68/ nm. S8

9 a AgNP CH 1 CH 2 AuNR nm c AuNR d AuNR e AgNP nm nm f AgNP nm nm 63 nm z x x y y nm nm z Figure S6. Wavelength-dependent 3D localization. (a) Scheme and () raw LSRM images of a 8 nm AgNP and a 8 nm AuNR located near each other. (c and e) 2D and 3D merged raw images of two channels (CHs) images. (d and f) 2D and 3D super-localized images of (c) and (e) using the 3D ilsrm system. S9

10 xy = 2.6 nm nm Figure S7. Wavelength-dependent scattering analysis of 8 nm AgNP. The PSF of the 8 nm AgNP was around nm with a xy localization precision of 2.6 nm. S

11 RSI (a.u) RSI (a.u) a z= nm z= z= + nm Distance (nm) Distance (nm) Distance (nm) Distance (nm) Distance (nm) Distance (nm) Figure S8. Relative scattering intensity (RSI) plot of (a) AgNP and () AuNR. 7 6 S11

12 RSI (a.u) a nm Frames Figure S9. Photo-switching of an isolated single AuNR. (a) Scattering images of AuNR with change in polarizer angle and () relative scattering intensity (RSI) with respect to the frames taken with continuous repetition of the turning polarizer. S12

13 a c nm nm nm Figure S. Super-localization AuNR. (a) LSM raw image of AuNR. LSRM super-localization images () efore and (c) after post processing. S13

14 RSI (a.u) RSI (a.u) RSI (a.u) RSI (a.u) a 45 c Wavelength (nm) Wavelength (nm) d Wavelength (nm) Wavelength (nm) Figure S11. FDTD simulation scattering spectra. (a-d) Relative scattering intensity profiles versus wavelength of two closely residing AuNR oriented at, 45, 9, and 18. The inset in each image is the TEM image of the aggregated AuNR where two NPs lie at the indicated angles to each other. S14

15 a c 5 m 5 m 5 m 5 m 5 m 5 m Figure S12. Super-resolution images of AuNR in live single HeLa cell. (a) DIC and () LSRM images of HeLa cell laeled with AuNRs. (c) Reconstructed ilsrm image of AuNR in a live HeLa cell. S15