Abstract
In this chapter, we present techniques, based on molecular-scale nanofabrication and selective self-assembly, for the presentation of biomolecules of interest (ligands, receptors, etc.) on a surface with precise spatial control and arbitrary geometry at the single-molecule level. Metallic nanodot arrays are created on glass coverslips and are then used as anchors for the immobilization of biological ligands via thiol linking chemistry. The nanodot size is controlled by both lithography and metallization. The reagent concentration in self-assembly can be adjusted to ensure single-molecule occupancy for a given dot size. The surrounding glass is backfilled by a protein-repellent layer to prevent nonspecific adsorption. Moreover, bifunctional surfaces are created, whereby a second ligand is presented on the background, which is frequently a requirement for simulating complex cellular functions involving more than one key ligand. This platform serves as a novel and powerful tool for molecular and cellular biology, e.g., to study the fundamental mechanisms of receptor-mediated signaling.
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References
Deniz AA, Mukhopadhyay S, Lemke EA (2008) Single-molecule biophysics: at the interface of biology, physics and chemistry. J R Soc Interface 5(18):15–45. doi:10.1098/rsif.2007.1021
Tinoco I, Gonzalez RL (2011) Biological mechanisms, one molecule at a time. Genes Dev 25(12):1205–1231. doi:10.1101/Gad.2050011
Peterson EM, Harris JM (2010) Quantitative detection of single molecules in fluorescence microscopy images. Anal Chem 82(1):189–196. doi:10.1021/ac901710t
Hanley DC, Harris JM (2001) Quantitative dosing of surfaces with fluorescent molecules: Characterization of fractional monolayer coverages by counting single molecules. Anal Chem 73(21):5030–5037. doi:10.1021/ac010572h
Lacy WB, Olson LG, Harris JM (1999) Quantitative SERS measurements on dielectric-overcoated silver-island films by solution deposition control of surface concentrations. Anal Chem 71(13):2564–2570. doi:10.1021/ac981024f
Ha T, Enderle T, Ogletree DF, Chemla DS, Selvin PR, Weiss S (1996) Probing the interaction between two single molecules: Fluorescence resonance energy transfer between a single donor and a single acceptor. Proc Natl Acad Sci U S A 93(13):6264–6268. doi:10.1073/pnas.93.13.6264
Boukobza E, Sonnenfeld A, Haran G (2001) Immobilization in surface-tethered lipid vesicles as a new tool for single biomolecule spectroscopy. J Phys Chem B 105(48):12165–12170. doi:10.1021/jp012016x
Rhoades E, Gussakovsky E, Haran G (2003) Watching proteins fold one molecule at a time. Proc Natl Acad Sci U S A 100(6):3197–3202. doi:10.1073/pnas.2628068100
Heider EC, Peterson EM, Barhoum M, Gericke KH, Harris JM (2011) Quantitative Fluorescence Microscopy To Determine Molecular Occupancy of Phospholipid Vesicles. Anal Chem 83(13):5128–5136. doi:10.1021/ac200129n
Roy R, Hohng S, Ha T (2008) A practical guide to single-molecule FRET. Nat Methods 5(6):507–516. doi:10.1038/Nmeth.1208
Ha T, Zhuang XW, Kim HD, Orr JW, Williamson JR, Chu S (1999) Ligand-induced conformational changes observed in single RNA molecules. Proc Natl Acad Sci U S A 96(16):9077–9082. doi:10.1073/pnas.96.16.9077
Hua BY, Han KY, Zhou RB, Kim HJ, Shi XH, Abeysirigunawardena SC, Jain A, Singh D, Aggarwal V, Woodson SA, Ha T (2014) An improved surface passivation method for single-molecule studies. Nat Methods 11(12):1233. doi:10.1038/Nmeth.3143
Kuzmenkina EV, Heyes CD, Nienhaus GU (2005) Single-molecule Forster resonance energy transfer study of protein dynamics under denaturing conditions. Proc Natl Acad Sci U S A 102(43):15471–15476. doi:10.1073/pnas.0507728102
Morimatsu M, Mekhdjian AH, Adhikari AS, Dunn AR (2013) Molecular tension sensors report forces generated by single integrin molecules in living cells. Nano Lett 13(9):3985–3989. doi:10.1021/nl4005145
Whitesides GM (2003) The ‘right’ size in nanobiotechnology. Nat Biotechnol 21(10):1161–1165. doi:10.1038/nbt872
Torres AJ, Wu M, Holowka D, Baird B (2008) Nanobiotechnology and cell biology: micro- and nanofabricated surfaces to investigate receptor-mediated signaling. Annu Rev Biophys 37:265–288. doi:10.1146/annurev.biophys.36.040306.132651
Manz BN, Jackson BL, Petit RS, Dustin ML, Groves J (2011) T-cell triggering thresholds are modulated by the number of antigen within individual T-cell receptor clusters. Proc Natl Acad Sci U S A 108(22):9088–9094. doi:10.1073/pnas.1018771108/-/DCSupplemental
Kinz-Thompson CD, Palma M, Pulukkunat DK, Chenet D, Hone J, Wind SJ, Gonzalez RL (2013) Robustly passivated, gold nanoaperture arrays for single-molecule fluorescence microscopy. ACS Nano 7(9):8158–8166. doi:10.1021/Nn403447s
Eid J, Fehr A, Gray J, Luong K, Lyle J, Otto G, Peluso P, Rank D, Baybayan P, Bettman B, Bibillo A, Bjornson K, Chaudhuri B, Christians F, Cicero R, Clark S, Dalal R, Dewinter A, Dixon J, Foquet M, Gaertner A, Hardenbol P, Heiner C, Hester K, Holden D, Kearns G, Kong XX, Kuse R, Lacroix Y, Lin S, Lundquist P, Ma CC, Marks P, Maxham M, Murphy D, Park I, Pham T, Phillips M, Roy J, Sebra R, Shen G, Sorenson J, Tomaney A, Travers K, Trulson M, Vieceli J, Wegener J, Wu D, Yang A, Zaccarin D, Zhao P, Zhong F, Korlach J, Turner S (2009) Real-time DNA sequencing from single polymerase molecules. Science 323(5910):133–138. doi:10.1126/science.1162986
Fazio T, Visnapuu ML, Wind S, Greene EC (2008) DNA curtains and nanoscale curtain rods: high-throughput tools for single molecule imaging. Langmuir 24(18):10524–10531. doi:10.1021/la801762h
Aydin D, Schwieder M, Louban I, Knoppe S, Ulmer J, Haas TL, Walczak H, Spatz JP (2009) Micro-nanostructured protein arrays: a tool for geometrically controlled ligand presentation. Small 5(9):1014–1018. doi:10.1002/smll.200801219
Groll J, Albrecht K, Gasteier P, Riethmueller S, Ziener U, Moeller M (2005) Nanostructured ordering of fluorescent markers and single proteins on substrates. Chembiochem 6(10):1782–1787. doi:10.1002/cbic.200500041
Cherniavskaya O, Chen CJ, Heller E, Sun E, Provezano J, Kam L, Hone J, Sheetz MP, Wind SJ (2005) Fabrication and surface chemistry of nanoscale bioarrays designed for the study of cytoskeletal protein binding interactions and their effect on cell motility. J Vac Sci Technol B 23(6):2972. doi:10.1116/1.2132332
Wolfram T, Belz F, Schoen T, Spatz JP (2007) Site-specific presentation of single recombinant proteins in defined nanoarrays. Biointerphases 2(1):44–48. doi:10.1116/1.2713991
Chai JA, Wong LS, Giam L, Mirkin CA (2011) Single-molecule protein arrays enabled by scanning probe block copolymer lithography. Proc Natl Acad Sci U S A 108(49):19521–19525. doi:10.1073/pnas.1116099108
Cai H, Wolfenson H, Depoil D, Dustin ML, Sheetz MP, Wind SJ (2016) Molecular occupancy of nanodot arrays. ACS Nano 10(4):4173–4183. doi:10.1021/acsnano.5b07425
Rosi NL, Mirkin CA (2005) Nanostructures in biodiagnostics. Chem Rev 105(4):1547–1562. doi:10.1021/Cr030067f
Wingren C, Borrebaeck CAK (2007) Progress in miniaturization of protein arrays - a step closer to high-density nanoarrays. Drug Discov Today 12(19–20):813–819. doi:10.1016/j.drudis.2007.08.003
Palma M, Abramson JJ, Gorodetsky AA, Penzo E, Gonzalez RL, Sheetz MP, Nuckolls C, Hone J, Wind SJ (2011) Selective biomolecular nanoarrays for parallel single-molecule investigations. J Am Chem Soc 133(20):7656–7659. doi:10.1021/Ja201031g
Schvartzman M, Nguyen K, Palma M, Abramson J, Sable J, Hone J, Sheetz MP, Wind SJ (2009) Fabrication of nanoscale bioarrays for the study of cytoskeletal protein binding interactions using nanoimprint lithography. J Vac Sci Technol B 27(1):61–65. doi:10.1116/1.3043472
Schvartzman M, Palma M, Sable J, Abramson J, Hu X, Sheetz MP, Wind SJ (2011) Nanolithographic control of the spatial organization of cellular adhesion receptors at the single-molecule level. Nano Lett 11(3):1306–1312. doi:10.1021/nl104378f
Arnold M, Cavalcanti-Adam EA, Glass R, Blummel J, Eck W, Kantlehner M, Kessler H, Spatz JP (2004) Activation of integrin function by nanopatterned adhesive interfaces. Chemphyschem 5(3):383–388. doi:10.1002/cphc.200301014
Cavalcanti-Adam EA, Volberg T, Micoulet A, Kessler H, Geiger B, Spatz JP (2007) Cell spreading and focal adhesion dynamics are regulated by spacing of integrin ligands. Biophys J 92(8):2964–2974. doi:10.1529/biophysj.106.089730
Huang JH, Grater SV, Corbellinl F, Rinck S, Bock E, Kemkemer R, Kessler H, Ding JD, Spatz JP (2009) Impact of order and disorder in RGD nanopatterns on cell adhesion. Nano Lett 9(3):1111–1116. doi:10.1021/Nl803548b
Jaehrling S, Thelen K, Wolfram T, Pollerberg GE (2009) Nanopatterns biofunctionalized with cell adhesion molecule DM-GRASP offered as cell substrate: spacing determines attachment and differentiation of neurons. Nano Lett 9(12):4115–4121. doi:10.1021/nl9023325
Ranzinger J, Krippner-Heidenreich A, Haraszti T, Bock E, Tepperink J, Spatz JP, Scheurich P (2009) Nanoscale arrangement of apoptotic ligands reveals a demand for a minimal lateral distance for efficient death receptor activation. Nano Lett 9(12):4240–4245. doi:10.1021/nl902429b
Lohmuller T, Triffo S, O’Donoghue GP, Xu Q, Coyle MP, Groves JT (2011) Supported membranes embedded with fixed arrays of gold nanoparticles. Nano Lett 11(11):4912–4918. doi:10.1021/nl202847t
Lohmuller T, Xu Q, Groves JT (2013) Nanoscale obstacle arrays frustrate transport of EphA2-ephrin-A1 clusters in cancer cell lines. Nano Lett 13(7):3059–3064. doi:10.1021/nl400874v
Liu Y, Medda R, Liu Z, Galior K, Yehl K, Spatz JP, Cavalcanti-Adam EA, Salaita K (2014) Nanoparticle tension probes patterned at the nanoscale: impact of integrin clustering on force transmission. Nano Lett 14(10):5539–5546. doi:10.1021/nl501912g
Vogel V, Sheetz M (2006) Local force and geometry sensing regulate cell functions. Nat Rev Mol Cell Biol 7(4):265–275. doi:10.1038/Nrm1890
Geiger B, Spatz JP, Bershadsky AD (2009) Environmental sensing through focal adhesions. Nat Rev Mol Cell Biol 10(1):21–33. doi:10.1038/nrm2593
Moghimi SM, Hunter AC, Murray JC (2005) Nanomedicine: current status and future prospects. FASEB J 19(3):311–330. doi:10.1096/fj.04-2747rev
Deeg J, Axmann M, Matic J, Liapis A, Depoil D, Afrose J, Curado S, Dustin ML, Spatz JP (2013) T cell activation is determined by the number of presented antigens. Nano Lett 13(11):5619–5626. doi:10.1021/nl403266t
Matic J, Deeg J, Scheffold A, Goldstein I, Spatz JP (2013) Fine tuning and efficient T cell activation with stimulatory aCD3 nanoarrays. Nano Lett 13(11):5090–5097. doi:10.1021/Nl4022623
Delcassian D, Depoil D, Rudnicka D, Liu ML, Davis DM, Dustin ML, Dunlop IE (2013) Nanoscale ligand spacing influences receptor triggering in T cells and NK cells. Nano Lett 13(11):5608–5614. doi:10.1021/Nl403252x
Cai H, Depoil D, Palma M, Sheetz MP, Dustin ML, Wind SJ (2013) Bifunctional nanoarrays for probing the immune response at the single-molecule level. J Vac Sci Technol B Nanotechnol Microelectron 31(6):6F902. doi:10.1116/1.4823764
Kalos M, Levine BL, Porter DL, Katz S, Grupp SA, Bagg A, June CH (2011) T cells with chimeric antigen receptors have potent antitumor effects and can establish memory in patients with advanced leukemia. Sci Transl Med 3(95). doi:10.1126/scitranslmed.3002842 ARTN 95ra73
Love JC, Estroff LA, Kriebel JK, Nuzzo RG, Whitesides GM (2005) Self-assembled monolayers of thiolates on metals as a form of nanotechnology. Chem Rev 105(4):1103–1169. doi:10.1021/Cr0300789
Schenk FC, Boehm H, Spatz JP, Wegner SV (2014) Dual-functionalized nanostructured biointerfaces by click chemistry. Langmuir 30(23):6897–6905. doi:10.1021/La500766t
Falconnet D, Koenig A, Assi T, Textor M (2004) A combined photolithographic and molecular-assembly approach to produce functional micropatterns for applications in the biosciences. Adv Funct Mater 14(8):749–756. doi:10.1002/adfm.200305182
Zhen G, Falconnet D, Kuennemann E, Vörös J, Spencer ND, Textor M, Zürcher S (2006) Nitrilotriacetic acid functionalized graft copolymers: a polymeric interface for selective and reversible binding of histidine-tagged proteins. Adv Funct Mater 16(2):243–251. doi:10.1002/adfm.200500232
Sweetman MJ, Shearer CJ, Shapter JG, Voelcker NH (2011) Dual silane surface functionalization for the selective attachment of human neuronal cells to porous silicon. Langmuir 27(15):9497–9503. doi:10.1021/la201760w
Dustin ML, Starr T, Varma R, Thomas VK (2007) Supported planar bilayers for study of the immunological synapse. In: Current protocols in immunology. JohnWiley & Sons, New York, pp 18.13.11–18.13.35
Haynes CL, Van Duyne RP (2001) Nanosphere lithography: a versatile nanofabrication tool for studies of size-dependent nanoparticle optics. J Phys Chem B 105(24):5599–5611. doi:10.1021/jp010657m
Sun SQ, Mendes P, Critchley K, Diegoli S, Hanwell M, Evans SD, Leggett GJ, Preece JA, Richardson TH (2006) Fabrication of gold micro- and nanostructures by photolithographic exposure of thiol-stabilized gold nanoparticles. Nano Lett 6(3):345–350. doi:10.1021/Nl052130h
Schvartzman M, Wind SJ (2009) Robust pattern transfer of nanoimprinted features for sub-5-nm fabrication. Nano Lett 9(10):3629–3634. doi:10.1021/nl9018512
Hu WC, Sarveswaran K, Lieberman M, Bernstein GH (2004) Sub-10 nm electron beam lithography using cold development of poly(methylmethacrylate). J Vac Sci Technol B 22(4):1711–1716. doi:10.1116/1.1763897
Chen W, Ahmed H (1993) Fabrication of 5–7 Nm wide etched lines in silicon using 100 kev electron-beam lithography and polymethylmethacrylate resist. Appl Phys Lett 62(13):1499–1501. doi:10.1063/1.109609
Chou SY, Krauss PR, Zhang W, Guo L, Zhuang L (1997) Sub-10 nm imprint lithography and applications. J Vac Sci Technol B 15(6):2897–2904
Blummel J, Perschmann N, Aydin D, Drinjakovic J, Surrey T, Lopez-Garcia M, Kessler H, Spatz JP (2007) Protein repellent properties of covalently attached PEG coatings on nanostructured SiO2-based interfaces. Biomaterials 28(32):4739–4747. doi:10.1016/j.biomaterials.2007.07.038
Zhu B, Eurell T, Gunawan R, Leckband D (2001) Chain-length dependence of the protein and cell resistance of oligo(ethylene glycol)-terminated self-assembled monolayers on gold. J Biomed Mater Res 56(3):406–416. doi:10.1002/1097–4636(20010905)56:3<406::Aid-Jbm1110>3.0.Co;2-R
Irvine DJ, Purbhoo MA, Krogsgaard M, Davis MM (2002) Direct observation of ligand recognition by T cells. Nature 419(6909):845–849
Crites TJ, Maddox M, Padhan K, Muller J, Eigsti C, Varma R (2015) Supported lipid bilayer technology for the study of cellular interfaces. Curr Protoc Cell Biol 68:24 5.1–24 531. doi:10.1002/0471143030.cb2405s68
Liou HC, Pretzer J (1998) Effect of curing temperature on the mechanical properties of hydrogen silsesquioxane thin films. Thin Solid Films 335(1–2):186–191. doi:10.1016/S0040–6090(98)00881–5
Love JC, Wolfe DB, Haasch R, Chabinyc ML, Paul KE, Whitesides GM, Nuzzo RG (2003) Formation and structure of self-assembled monolayers of alkanethiolates on palladium. J Am Chem Soc 125(9):2597–2609. doi:10.1021/Ja028692
Palma M, Abramson JJ, Gorodetsky AA, Nuckolls C, Sheetz MP, Wind SJ, Hone J (2011) Controlled confinement of DNA at the nanoscale: nanofabrication and surface bio-functionalization. In: Zuccheri G, Samorì B (eds) DNA nanotechnology: methods and protocols. Humana Press, Totowa, NJ, pp 169–185. doi:10.1007/978-1-61779-142-0_12
White LD, Tripp CP (2000) Reaction of (3-aminopropyl)dimethylethoxysilane with amine catalysts on silica surfaces. J Colloid Interface Sci 232(2):400–407. doi:10.1006/jcis.2000.7224
Roiter Y, Ornatska M, Rammohan AR, Balakrishnan J, Heine DR, Minko S (2008) Interaction of nanoparticles with lipid membrane. Nano Lett 8(3):941–944
Roiter Y, Ornatska M, Rammohan AR, Balakrishnan J, Heine DR, Minko S (2009) Interaction of lipid membrane with nanostructured surfaces. Langmuir 25(11):6287–6299. doi:10.1021/la900119a
Acknowledgments
The authors thank Dr. M. Palma for guidance on nanoarray functionalization and Dr. Silvia Curado for coordinating our collaboration. This work was supported primarily by the National Science Foundation (NSF) under award no. CMMI-1300590 and by the National Institutes of Health (NIH) Common Fund Nanomedicine program grant PN2 EY016586. The authors are grateful to the Columbia Nano Initiative for providing cleanroom and other facilities used in this work.
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Cai, H., Depoil, D., Muller, J., Sheetz, M.P., Dustin, M.L., Wind, S.J. (2017). Spatial Control of Biological Ligands on Surfaces Applied to T Cell Activation. In: Baldari, C., Dustin, M. (eds) The Immune Synapse. Methods in Molecular Biology, vol 1584. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-6881-7_18
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