Abstract
Here we describe a facile strategy of general applicability for controlling the immobilization of individual nanomoieties on nanopatterned surfaces with single-molecule control. We combine the ability of DNA nanostructures as programmable platforms, with a one-step Focused Ion Beam nanopatterning, to demonstrate the controlled immobilization of DNA origami functionalized with individual quantum dots (QDs) at predesigned positions on glass coverslips and silicon substrates. Remarkably, the platform developed is reusable after a simple cleaning process, and can be designed to display different geometrical arrangements.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Ishijima A, Yanagida T (2001) Single molecule nanobioscience. Trends Biochem Sci 26(7):438–444. https://doi.org/10.1016/S0968-0004(01)01860-6
Cordes T, Blum SA (2013) Opportunities and challenges in single-molecule and single-particle fluorescence microscopy for mechanistic studies of chemical reactions. Nat Chem 5(12):993–999. https://doi.org/10.1038/nchem.1800
Moth-Poulsen K, Bjørnholm T (2010) From nanofabrication to self-fabrication – tailored chemistry for control of single molecule electronic devices. CHIMIA Int J Chem 64(6):404–408. https://doi.org/10.2533/chimia.2010.404
Palma M, Abramson JJ, Gorodetsky AA, Penzo E, Gonzalez RL Jr, 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. https://doi.org/10.1021/ja201031g
Noh H, Hung AM, Choi C, Lee JH, Kim JY, Jin S, Cha JN (2009) 50 nm DNA nanoarrays generated from uniform oligonucleotide films. ACS Nano 3(8):2376–2382. https://doi.org/10.1021/nn900559m
Gerdon AE, Oh SS, Hsieh K, Ke Y, Yan H, Soh HT (2009) Controlled delivery of DNA origami on patterned surfaces. Small 5(17):1942–1946. https://doi.org/10.1002/smll.200900442
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. https://doi.org/10.1021/nl104378f
Kim JD, Ahn D-G, Oh J-W, Park W, Jung H (2008) Ribosome display and dip-pen nanolithography for the fabrication of protein Nanoarrays. Adv Mater 20(17):3349–3353. https://doi.org/10.1002/adma.200800027
Bulyk ML (2007) Protein binding microarrays for the characterization of DNA-protein interactions. Adv Biochem Eng Biotechnol 104:65–85. https://doi.org/10.1007/10_025
Demers LM, Ginger DS, Park SJ, Li Z, Chung SW, Mirkin CA (2002) Direct patterning of modified oligonucleotides on metals and insulators by dip-pen nanolithography. Science 296(5574):1836–1838
Lalander CH, Zheng Y, Dhuey S, Cabrini S, Bach U (2010) DNA-directed self-assembly of gold nanoparticles onto nanopatterned surfaces: controlled placement of individual nanoparticles into regular arrays. ACS Nano 4(10):6153–6161. https://doi.org/10.1021/nn101431k
Junkin M, Watson J, Geest J, Wong P (2009) Template-guided self-assembly of colloidal quantum dots using plasma lithography. Adv Mater 21(12):1247–1251. https://doi.org/10.1002/adma.200802122
Xie W, Gomes R, Aubert T, Bisschop S, Zhu Y, Hens Z, Brainis E, Van Thourhout D (2015) Nanoscale and single-dot patterning of colloidal quantum dots. Nano Lett 15(11):7481–7487. https://doi.org/10.1021/acs.nanolett.5b03068
Wang CJ, Huang L, Parviz BA, Lin LY (2006) Subdiffraction photon guidance by quantum-dot cascades. Nano Lett 6(11):2549–2553
Abramson J, Palma M, Wind SJ, Hone J (2012) Quantum dot Nanoarrays: self-assembly with single-particle control and resolution. Adv Mater 24(16):2207–2211
Scheible MB, Pardatscher G, Kuzyk A, Simmel FC (2014) Single molecule characterization of DNA binding and strand displacement reactions on lithographic DNA origami microarrays. Nano Lett 14(3):1627–1633. https://doi.org/10.1021/nl500092j
Koirala D, Shrestha P, Emura T, Hidaka K, Mandal S, Endo M, Sugiyama H, Mao H (2014) Single-molecule mechanochemical sensing using DNA origami nanostructures. Angew Chem Int Ed 53(31):8137–8141. https://doi.org/10.1002/anie.201404043
Voigt NV, Torring T, Rotaru A, Jacobsen MF, Ravnsbaek JB, Subramani R, Mamdouh W, Kjems J, Mokhir A, Besenbacher F, Gothelf KV (2010) Single-molecule chemical reactions on DNA origami. Nat Nanotechnol 5(3):200–203. https://doi.org/10.1038/nnano.2010.5
Sharma J, Chhabra R, Cheng A, Brownell J, Liu Y, Yan H (2009) Control of self-assembly of DNA tubules through integration of gold nanoparticles. Science 323(5910):112–116. https://doi.org/10.1126/science.1165831
Sharma J, Chhabra R, Liu Y, Ke Y, Yan H (2006) DNA-templated self-assembly of two-dimensional and periodical gold nanoparticle arrays. Angew Chem Int Ed Engl 45(5):730–735. https://doi.org/10.1002/anie.200503208
Sharma J, Ke Y, Lin C, Chhabra R, Wang Q, Nangreave J, Liu Y, Yan H (2008) DNA-tile-directed self-assembly of quantum dots into two-dimensional nanopatterns. Angew Chem Int Ed 47(28):5157–5159. https://doi.org/10.1002/anie.200801485
Schreiber R, Do J, Roller EM, Zhang T, Schuller VJ, Nickels PC, Feldmann J, Liedl T (2014) Hierarchical assembly of metal nanoparticles, quantum dots and organic dyes using DNA origami scaffolds. Nat Nanotechnol 9(1):74–78. https://doi.org/10.1038/nnano.2013.253
Ding B, Deng Z, Yan H, Cabrini S, Zuckermann RN, Bokor J (2010) Gold nanoparticle self-similar chain structure organized by DNA origami. J Am Chem Soc 132(10):3248–3249. https://doi.org/10.1021/ja9101198
Li Z, Chung SW, Nam JM, Ginger DS, Mirkin CA (2003) Living templates for the hierarchical assembly of gold nanoparticles. Angew Chem Int Ed Engl 42(20):2306–2309. https://doi.org/10.1002/anie.200351231
Macfarlane RJ, Lee B, Jones MR, Harris N, Schatz GC, Mirkin CA (2011) Nanoparticle superlattice engineering with DNA. Science 334(6053):204–208. https://doi.org/10.1126/science.1210493
Fu A, Micheel CM, Cha J, Chang H, Yang H, Alivisatos AP (2004) Discrete nanostructures of quantum dots/au with DNA. J Am Chem Soc 126(35):10832–10833. https://doi.org/10.1021/ja046747x
Huang D, Freeley M, Palma M (2017) DNA-mediated patterning of single quantum dot Nanoarrays: a reusable platform for single-molecule control. Sci Rep 7:45591. https://doi.org/10.1038/srep45591
Hung AM, Micheel CM, Bozano LD, Osterbur LW, Wallraff GM, Cha JN (2010) Large-area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. Nat Nanotechnol 5(2):121–126. https://doi.org/10.1038/Nnano.2009.450
Hung AM, Noh H, Cha JN (2010) Recent advances in DNA-based directed assembly on surfaces. Nanoscale 2(12):2530–2537. https://doi.org/10.1039/c0nr00430h
Zhang F, Nangreave J, Liu Y, Yan H (2014) Structural DNA nanotechnology: state of the art and future perspective. J Am Chem Soc 136(32):11198–11211. https://doi.org/10.1021/ja505101a
Samanta A, Banerjee S, Liu Y (2015) DNA nanotechnology for nanophotonic applications. Nanoscale 7(6):2210–2220. https://doi.org/10.1039/c4nr06283c
Kumar A, Hwang JH, Kumar S, Nam JM (2013) Tuning and assembling metal nanostructures with DNA. Chem Commun 49(26):2597–2609. https://doi.org/10.1039/c2cc37536b
Gopinath A, Rothemund PW (2014) Optimized assembly and covalent coupling of single-molecule DNA origami nanoarrays. ACS Nano 8(12):12030–12040. https://doi.org/10.1021/nn506014s
Acknowledgments
D.H. is financially supported by the Chinese Scholarship Council. We further gratefully acknowledge financial support from Queen Mary University of London.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2018 Springer Science+Business Media, LLC, part of Springer Nature
About this protocol
Cite this protocol
Huang, D., Freeley, M., Palma, M. (2018). Single-Molecule Patterning via DNA Nanostructure Assembly: A Reusable Platform. In: Zuccheri, G. (eds) DNA Nanotechnology. Methods in Molecular Biology, vol 1811. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-8582-1_16
Download citation
DOI: https://doi.org/10.1007/978-1-4939-8582-1_16
Published:
Publisher Name: Humana Press, New York, NY
Print ISBN: 978-1-4939-8581-4
Online ISBN: 978-1-4939-8582-1
eBook Packages: Springer Protocols