Nanoaperture fabrication via colloidal lithography for single molecule fluorescence analysis
Autoři:
Ryan M. Jamiolkowski aff001; Kevin Y. Chen aff001; Shane A. Fiorenza aff002; Alyssa M. Tate aff001; Shawn H. Pfeil aff002; Yale E. Goldman aff001
Působiště autorů:
Pennsylvania Muscle Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
aff001; Department of Physics, West Chester University, West Chester, Pennsylvania, United States of America
aff002
Vyšlo v časopise:
PLoS ONE 14(10)
Kategorie:
Research Article
prolekare.web.journal.doi_sk:
https://doi.org/10.1371/journal.pone.0222964
Souhrn
In single molecule fluorescence studies, background emission from labeled substrates often restricts their concentrations to non-physiological nanomolar values. One approach to address this challenge is the use of zero-mode waveguides (ZMWs), nanoscale holes in a thin metal film that physically and optically confine the observation volume allowing much higher concentrations of fluorescent substrates. Standard fabrication of ZMWs utilizes slow and costly E-beam nano-lithography. Herein, ZMWs are made using a self-assembled mask of polystyrene microspheres, enabling fabrication of thousands of ZMWs in parallel without sophisticated equipment. Polystyrene 1 μm dia. microbeads self-assemble on a glass slide into a hexagonal array, forming a mask for the deposition of metallic posts in the inter-bead interstices. The width of those interstices (and subsequent posts) is adjusted within 100–300 nm by partially fusing the beads at the polystyrene glass transition temperature. The beads are dissolved in toluene, aluminum or gold cladding is deposited around the posts, and those are dissolved, leaving behind an array ZMWs. Parameter optimization and the performance of the ZMWs are presented. By using colloidal self-assembly, typical laboratories can make use of sub-wavelength ZMW technology avoiding the availability and expense of sophisticated clean-room environments and equipment.
Klíčová slova:
Light – Fluorescence microscopy – Ribosomes – Heat treatment – Fluorescence resonance energy transfer – Aluminum – Polystyrene – Glass science
Zdroje
1. Moerner WE, Fromm DP. Methods of single-molecule fluorescence spectroscopy and microscopy. Rev Sci Instrum. 2003;74(8):3597–619.
2. Yildiz A, Ha T, Goldman YE, Selvin PR. Myosin V Walks Hand-Over-Hand: Single Fluorophore Imaging with 1. 5-nm Localization. Science (80-). 2014;300(5628):2061–6.
3. McKinney SA, Déclais A-C, Lilley DMJ, Ha T. Structural dynamics of individual Holliday junctions. Nat Struct Biol. 2003;10(2):93–7. doi: 10.1038/nsb883 12496933
4. Forkey JN, Quinlan ME, Alexander Shaw M, Corrie JET, Goldman YE. Three-dimensional structural dynamics of myosin V by single-molecule fluorescence polarization. Nature. 2003;422(6930):399–404. doi: 10.1038/nature01529 12660775
5. Levene MJ, Korlach J, Turner SW, Foquet M, Craighead HG, Webb WW. Zero-Mode Waveguides for Single-Molecule Analysis at High Concentrations. Science (80-). 2003 Jan;299(5607):682–6. doi: 10.1126/science.1079700 12560545
6. Uemura S, Aitken CE, Korlach J, Flusberg BA, Turner SW, Puglisi JD. Real-time tRNA transit on single translating ribosomes at codon resolution. Nature. 2010 Apr;464(7291):1012–7. doi: 10.1038/nature08925 20393556
7. Moran-Mirabal JM, Craighead HG. Zero-mode waveguides: sub-wavelength nanostructures for single molecule studies at high concentrations. Methods. 2008 Sep;46(1):11–7. doi: 10.1016/j.ymeth.2008.05.010 18586103
8. Acuna G, Grohmann D, Tinnefeld P. Enhancing single-molecule fluorescence with nanophotonics. FEBS Lett. 2014;588:3547–52. doi: 10.1016/j.febslet.2014.06.016 24928436
9. Punj D, Ghenuche P, Moparthi SB, de Torres J, Grigoriev V, Rigneault H, et al. Plasmonic antennas and zero-mode waveguides to enhance single molecule fluorescence detection and fluorescence correlation spectroscopy toward physiological concentrations. Wiley Interdiscip Rev Nanomedicine Nanobiotechnology. 2014;6(3):268–82. doi: 10.1002/wnan.1261 24616447
10. Martin WE, Srijanto BR, Collier CP, Vosch T, Richards CI. A Comparison of Single-Molecule Emission in Aluminum and Gold Zero-Mode Waveguides. J Phys Chem A. 2016;120(34):6719–27. doi: 10.1021/acs.jpca.6b03309 27499174
11. Holzmeister P, Acuna GP, Grohmann D, Tinnefeld P. Breaking the concentration limit of optical single-molecule detection. Chem Soc Rev. 2014;43(4):1014–28. doi: 10.1039/c3cs60207a 24019005
12. Bethe HA. Theory of Diffraction by Small Holes. Phys Rev. 1944 Oct;66(7–8):163–82.
13. Genet C, Ebbesen TW. Light in tiny holes. Nature. 2007 Jan;445(7123):39–46. doi: 10.1038/nature05350 17203054
14. Rigneault H, Capoulade J, Dintinger J, Wenger J, Bonod N, Popov E, et al. Enhancement of Single-Molecule Fluorescence Detection in Subwavelength Apertures. Phys Rev Lett. 2005;95(11):117401. doi: 10.1103/PhysRevLett.95.117401 16197045
15. Fore S, Yuen Y, Hesselink L, Huser T. Pulsed-Interleaved Excitation FRET Measurements on Single Duplex DNA Molecules Inside C-Shaped Nanoapertures. Nano Lett. 2007;7(6):1749–56. doi: 10.1021/nl070822v 17503872
16. Samiee KT, Foquet M, Guo L, Cox EC, Craighead HG. λ-Repressor Oligomerization Kinetics at High Concentrations Using Fluorescence Correlation Spectroscopy in Zero-Mode Waveguides. Biophys J. 2005;88(3):2145–53. doi: 10.1529/biophysj.104.052795 15613638
17. Samiee KT, Moran-Mirabal JM, Cheung YK, Craighead HG. Zero mode waveguides for single-molecule spectroscopy on lipid membranes. Biophys J. 2006;90(9):3288–99. doi: 10.1529/biophysj.105.072819 16461393
18. Moran-Mirabal JM, Torres AJ, Samiee KT, Baird BA, Craighead HG. Cell investigation of nanostructures: zero-mode waveguides for plasma membrane studies with single molecule resolution. Nanotechnology. 2007;18(19):195101.
19. Leutenegger M, Gösch M, Perentes A, Hoffmann P, Martin OJF, Lasser T. Confining the sampling volume for Fluorescence Correlation Spectroscopy using a sub-wavelength sized aperture. Opt Express. 2006;14(2):956–69. doi: 10.1364/opex.14.000956 19503416
20. Perentes A, Utke I, Dwir B, Leutenegger M, Lasser T, Hoffmann P, et al. Fabrication of arrays of sub-wavelength nano-apertures in an optically thick gold layer on glass slides for optical studies. Nanotechnology. 2005 May;16(5):S273.
21. Foquet M, Samiee KT, Kong X, Chauduri BP, Lundquist PM, Turner SW, et al. Improved fabrication of zero-mode waveguides for single-molecule detection. J Appl Phys. 2008;103(3):34301.
22. Fischer UC, Zingsheim HP. Submicroscopic pattern replication with visible light. J Vac Sci Technol. 1981 Nov;19(4):881–5.
23. Deckman HW, Dunsmuir JH. Natural lithography. Appl Phys Lett. 1982 Aug;41(4):377–9.
24. Gang Z, Dayang W. Colloidal Lithography—The Art of Nanochemical Patterning. Chem–An Asian J. 2009;4(2):236–45.
25. Wang B, Zhao W, Chen A, Chua S-J. Formation of nanoimprinting mould through use of nanosphere lithography. Vol. 288, Journal of Crystal Growth—J CRYST GROWTH. 2006. 200–204 p.
26. Huang Z, Fang H, Zhu J. Fabrication of Silicon Nanowire Arrays with Controlled Diameter, Length, and Density. Adv Mater. 2007 Feb;19(5):744–8.
27. Tan BJY, Sow CH, Koh TS, Chin KC, Wee ATS, Ong CK. Fabrication of Size-Tunable Gold Nanoparticles Array with Nanosphere Lithography, Reactive Ion Etching, and Thermal Annealing. J Phys Chem B. 2005 Jun;109(22):11100–9. doi: 10.1021/jp045172n 16852354
28. Singh G, Gohri V, Pillai S, Arpanaei A, Foss M, Kingshott P. Large-Area Protein Patterns Generated by Ordered Binary Colloidal Assemblies as Templates. ACS Nano. 2011;5(5):3542–51. doi: 10.1021/nn102867z 21495685
29. Singh G, Pillai S, Arpanaei A, Kingshott P. Highly Ordered Mixed Protein Patterns Over Large Areas from Self-Assembly of Binary Colloids. Adv Mater. 2011;23(13):1519–23. doi: 10.1002/adma.201004657 21449054
30. Willets KA, Van Duyne RP. Localized Surface Plasmon Resonance Spectroscopy and Sensing. Annu Rev Phys Chem. 2007;58(1):267–97.
31. Hulteen JC, Van Duyne RP. Nanosphere lithography: A materials general fabrication process for periodic particle array surfaces. J Vac Sci Technol A. 1995 May;13(3):1553–8.
32. Haynes CL, McFarland AD, Smith MT, Hulteen JC, Van Duyne RP. Angle-Resolved Nanosphere Lithography: Manipulation of Nanoparticle Size, Shape, and Interparticle Spacing. J Phys Chem B. 2002 Feb;106(8):1898–902.
33. Iwasa T, Han Y-W, Hiramatsu R, Yokota H, Nakao K, Yokokawa R, et al. Synergistic effect of ATP for RuvA–RuvB–Holliday junction DNA complex formation. Sci Rep. 2015 Dec;5:18177. doi: 10.1038/srep18177 26658024
34. Kinz-Thompson CD, Palma M, Pulukkunat DK, Chenet D, Hone J, Wind SJ, et al. Robustly Passivated, Gold Nanoaperture Arrays for Single-Molecule Fluorescence Microscopy. ACS Nano. 2013 Sep;7(9):8158–66. doi: 10.1021/nn403447s 23987563
35. Denkov N, Velev O, Kralchevski P, Ivanov I, Yoshimura H, Nagayama K. Mechanism of formation of two-dimensional crystals from latex particles on substrates. Langmuir. 1992 Dec;8(12):3183–90.
36. Cheung CL, Nikolic RJ, Reinhardt CE, Wang TF. Fabrication of nanopillars by nanosphere lithography. Nanotechnology. 2006;17(5):1339–43.
37. Peng K, Zhang M, Lu A, Wong N-B, Zhang R, Lee S-T. Ordered silicon nanowire arrays via nanosphere lithography and metal-induced etching. Appl Phys Lett. 2007;90(16):163123.
38. Micheletto R, Fukuda H, Ohtsu M. A Simple Method for the Production of a Two-Dimensional, Ordered Array of Small Latex Particles. Langmuir. 1995 Sep;11(9):3333–6.
39. Vukusic P, Sambles JR. Photonic structures in biology. Nature. 2003 Aug;424(6950):852–5. doi: 10.1038/nature01941 12917700
40. Ball P. Nature’s Color Tricks. Sci Am. 2012;306(5):74–9. doi: 10.1038/scientificamerican0512-74 22550931
41. Rieger J. The glass transition temperature of polystyrene. J Therm Anal. 1996;46(3):965–72.
42. Kosiorek A, Kandulski A, Glaczynska H, Giersig M. Fabrication of Nanoscale Rings, Dots, and Rods by Combining Shadow Nanosphere Lithography and Annealed Polystyrene Nanosphere Masks. Small. 2005 Feb;1(4):439–44. doi: 10.1002/smll.200400099 17193469
43. Hanarp P, Käll M, Sutherland DS. Optical Properties of Short Range Ordered Arrays of Nanometer Gold Disks Prepared by Colloidal Lithography. J Phys Chem B. 2003 Jun;107(24):5768–72.
44. Degiron A, Lezec HJ, Yamamoto N, Ebbesen TW. Optical transmission properties of a single subwavelength aperture in a real metal. Opt Commun. 2004 Sep;239(1–3):61–6.
45. Shroder DY, Lippert LG, Goldman YE. Single molecule optical measurements of orientation and rotations of biological macromolecules. Methods Appl Fluoresc. 2016;4(4):042004. doi: 10.1088/2050-6120/4/4/042004 28192292
46. Roy R, Hohng S, Ha T. A practical guide to single-molecule FRET. Nat Methods. 2008;5(6):507–16. doi: 10.1038/nmeth.1208 18511918
47. Pollack G, Daniel S. Electromagnetism. 1st ed. Addison-Wesley; 2001.
48. McCann JJ, Choi UB, Zheng L, Weninger K, Bowen ME. Optimizing Methods to Recover Absolute FRET Efficiency from Immobilized Single Molecules. Biophys J. 2010 Aug;99(3):961–70. doi: 10.1016/j.bpj.2010.04.063 20682275
49. Chen C, Stevens B, Kaur J, Cabral D, Liu H, Wang Y, et al. Single-molecule fluorescence measurements of ribosomal translocation dynamics. Mol Cell. 2011 May;42(3):367–77. doi: 10.1016/j.molcel.2011.03.024 21549313
50. Jamiolkowski RM, Chen C, Cooperman BS, Goldman YE. tRNA Fluctuations Observed on Stalled Ribosomes Are Suppressed during Ongoing Protein Synthesis. Biophys J. 2017 Dec;113(11):2326–35. doi: 10.1016/j.bpj.2017.08.052 29211986
51. Nečas D, Klapetek P. Gwyddion: an open-source software for SPM data analysis. Cent Eur J Phys. 2012;10(1):181–8.
52. Schindelin J, Arganda-carreras I, Frise E, Kaynig V, Pietzsch T, Preibisch S, et al. Fiji—an Open Source platform for biological image analysis. Nat Methods. 2012;9(7):676–82. doi: 10.1038/nmeth.2019 22743772
53. Pan D, Qin H, Cooperman BS. Synthesis and functional activity of tRNAs labeled with fluorescent hydrazides in the D-loop. RNA. 2009 Feb;15(2):346–54. doi: 10.1261/rna.1257509 19118261
54. Kaur J, Raj M, Cooperman BS. Fluorescent labeling of tRNA dihydrouridine residues: Mechanism and distribution. RNA. 2011;7:1393–400.
Článok vyšiel v časopise
PLOS One
2019 Číslo 10
- Metamizol jako analgetikum první volby: kdy, pro koho, jak a proč?
- Parazitičtí červi v terapii Crohnovy choroby a dalších zánětlivých autoimunitních onemocnění
- Nejasný stín na plicích – kazuistika
- Masturbační chování žen v ČR − dotazníková studie
- Eliquis (apixaban) nově hrazen ze zdravotního pojištění
Najčítanejšie v tomto čísle
- Correction: Low dose naltrexone: Effects on medication in rheumatoid and seropositive arthritis. A nationwide register-based controlled quasi-experimental before-after study
- Combining CDK4/6 inhibitors ribociclib and palbociclib with cytotoxic agents does not enhance cytotoxicity
- Risk factors associated with IgA vasculitis with nephritis (Henoch–Schönlein purpura nephritis) progressing to unfavorable outcomes: A meta-analysis
- Prevalence of pectus excavatum (PE), pectus carinatum (PC), tracheal hypoplasia, thoracic spine deformities and lateral heart displacement in thoracic radiographs of screw-tailed brachycephalic dogs