Nanolithography Based on Metalized DNA Templates for Graphene Patterning

Zhong Jin1, Wei Sun2, Peng Yin2, Michael S. Strano1

1 Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts, 2 Department of Systems Biology, Harvard Medical School, Boston, Massachusetts
Publication Name:  Current Protocols in Chemical Biology
Unit Number:   
DOI:  10.1002/9780470559277.ch130187
Online Posting Date:  June, 2014
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Abstract

DNA self‐assembly, such as DNA origami and single‐stranded tile (SST) assembly, can create complex nanostructures with prescribed two‐dimensional (2‐D) and three‐dimensional (3‐D) shapes. Distinct patterned DNA nanostructures can be used as templates or shadow masks for the lithographic patterning of 2‐D thin‐film materials for nanodevices. The protocols in this article describe a general procedure of metalized DNA nanolithography based upon DNA metalization and subsequent etching to transfer the shape information from DNA templates to graphene, such that the shape of complex graphene nanostructures can be rationally programmed. Spatial information within the predesigned DNA patterns, such as width, orientation, curvature, and angles, can be successfully transferred to the graphene nanostructures with sub–10 nm resolution. This method could be further generalized to enable patterning of nano‐sized modules of graphene and other 2‐D electronic materials with predesigned shapes for complex electronic and quantum circuits. Curr. Protoc. Chem. Biol. 6:53‐64 © 2014 by John Wiley & Sons, Inc.

Keywords: DNA self‐assembly; DNA metalization; templated nanolithography; masked etching; graphene nanostructure patterning

     
 
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Table of Contents

  • Introduction
  • Basic Protocol 1: Preparation of DNA Nanostructures with Predesigned Shapes
  • Basic Protocol 2: Preparation and Transfer of Large‐Area Monolayer Graphene
  • Basic Protocol 3: Metalization of DNA Nanostructures on Graphene
  • Basic Protocol 4: Metalized DNA Masked Etching of Graphene Nanopatterns
  • Reagents and Solutions
  • Commentary
  • Literature Cited
  • Figures
     
 
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Materials

Basic Protocol 1: Preparation of DNA Nanostructures with Predesigned Shapes

  Materials
  • M13 viral genome‐based scaffold strand (New England BioLabs)
  • Synthetic single‐strand DNA from IDT DNA and Bioneer (staple strands for DNA origami, and single‐stranded tile strands for DNA SST)
  • 10 mM Tris·Cl, pH 8.5
  • Folding buffer:
    • 0.05 M Tris·Cl, pH 7.9
    • 0.01 M EDTA
    • 0.0125 M MgCl 2
  • 2% native agarose gel (Voytas, 2000)
  • SYBR Safe gel stain (Invitrogen)
  • PCR tubes
  • Thermal cycler
  • Freeze 'N Squeeze DNA gel extraction spin columns (BioRad)
  • Pellet pestles purchased from Scientific America, agarose and 0.5× Tris‐Borate‐EDTA (TBE) purchased from Lonza)
  • Benchtop centrifuge (Thermo)
  • Additional reagents and equipment for agarose gel electrophoresis (Voytas, 2000)

Basic Protocol 2: Preparation and Transfer of Large‐Area Monolayer Graphene

  Materials
  • 0.1 M HCl
  • Acetone (electronic grade, Fisher Scientific)
  • Isopropanol (electronic grade, Fisher Scientific)
  • Polymethyl methacrylate (PMMA, 950 PMMA A4, MicroChem)
  • Mixed solution with final concentrations of 1 M CuCl 2 and 6 M HCl
  • Copper foils (Aldrich, purity 99.999%, 25 μm thick)
  • Nitrogen gun connected to a high‐purity N 2 gas cylinder
  • Low‐pressure CVD system consisting of a 1‐in. inner‐diameter Lindburg/Blue tube furnace and a fused quartz tube inside (AdValue Technology, cat. no. FQ‐T‐28‐25‐4); the upper stream of the quartz tube is connected with stop valves, mass flow controllers, and gas cylinders for high‐purity CH 4, H 2, and Ar; the downstream of the quartz tube is connected with a 275i series Vacuum Gauge (Lesker) and a RV3 Two Stage Rotary Vane Pump (Edwards RV3)
  • Spin‐coater (e.g., Laurell WS‐650Mz‐23NPP)
  • Hot plate
  • 2‐in. Petri dish
  • Plastic tweezers
  • Silicon wafers (with the size of ∼1.2 cm × 1.2 cm and 50‐ to 300‐nm‐thick thermally‐grown SiO 2 layer)

Basic Protocol 3: Metalization of DNA Nanostructures on Graphene

  Materials
  • Purified DNA nanostructures (as prepared in protocol 1)
  • 0.2% (v/v) glutaraldehyde in 0.5× TBE (see recipe for 1×)/10 mM MgCl 2 buffer (stored in −20°C freezer)
  • 0.5× TBE (see recipe for 1×)/10 mM MgCl 2 buffer
  • Monolayer graphene on SiO 2/Si substrates (as prepared in protocol 2)
  • 0.1 mg/ml 1‐pyrenemethylamine hydrochloride (Sigma‐Aldrich, cat. no. 401633) in methanol
  • 0.1 M solution of AgNO 3 in ammonia (∼ 0.3 M ammonia, pH 10.5, stored in the dark)
  • Gold Enhance EM Formulation (for the deposition of gold nanoparticles on DNA, containing four different doses: enhancer A, activator B, initiator C, and buffer D; http://www.nanoprobes.com)
  • MWCO 100 kDa centrifugal filters (Millipore)
  • Nitrogen gun connected to a high‐purity N 2 gas cylinder
  • PCR tubes

Basic Protocol 4: Metalized DNA Masked Etching of Graphene Nanopatterns

  Materials
  • Graphene sheets on SiO 2/Si substrate covered with metalized DNA masks ( protocol 3)
  • 0.1 M NaCN aqueous solution
  • 99.5% deionized formamide
  • Reactive plasma etching system (RIE, Nexx ECR plasma etch system; http://www.nexxsystems.com/)
  • Nitrogen gun connected to a high‐purity N 2 gas cylinder
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Figures

Videos

Literature Cited

Literature Cited
  Deng, Z. and Mao, C. 2003. DNA‐templated fabrication of 1D parallel and 2D crossed metallic nanowire arrays. Nano Lett. 3:1545‐1548.
  Dietz, H., Douglas, S.M., and Shih, W.M. 2009. Folding DNA into twisted and curved nanoscale shapes. Science 325:725‐730.
  Douglas, S.M., Dietz, H., Liedl, T., Hoegberg, B., Graf, F., and Shih, W.M. 2009. Self‐assembly of DNA into nanoscale three‐dimensional shapes. Nature 459:414‐418.
  Han, D., Pal, S., Nangreave, J., Deng, Z., Liu, Y., and Yan, H. 2011. DNA origami with complex curvatures in three‐dimensional space. Science 332:342‐346.
  He, Y., Ye, T., Su, M., Zhang, C., Ribbe, A.E., Jiang, W., and Mao, C. 2008. Hierarchical self‐assembly of DNA into symmetric supramolecular polyhedra. Nature 452:198‐201.
  Hung, A.M., Micheel, C.M., Bozano, L.D., Osterbur, L.W., Wallraff, G.M., and Cha, J.N. 2010. Large‐area spatially ordered arrays of gold nanoparticles directed by lithographically confined DNA origami. Nat. Nanotechnol. 5:121‐126.
  Jin, Z., Sun, W., Ke, Y., Shih, C.‐J., Paulus, G.L.C., Wang, Q.H., Mu, B., Yin, P., and Strano, M.S. 2013. Metallized DNA nanolithography for encoding and transferring spatial information for graphene patterning. Nat. Commun. 4:1663.
  Ke, Y., Ong, L.L., Shih, W.M., and Yin, P. 2012. Three‐dimensional structures self‐assembled from DNA bricks. Science 338:1177‐1183.
  Keren, K., Krueger, M., Gilad, R., Ben‐Yoseph, G., Sivan, U., and Braun, E. 2002. Sequence‐specific molecular lithography on single DNA molecules. Science 297:72‐75.
  Kuzyk, A., Schreiber, R., Fan, Z., Pardatscher, G., Roller, E.‐M., Hoegele, A., Simmel, F.C., Govorov, A.O., and Liedl, T. 2012. DNA‐based self‐assembly of chiral plasmonic nanostructures with tailored optical response. Nature 483:311‐314.
  Li, X., Cai, W., An, J., Kim, S., Nah, J., Yang, D., Piner, R., Velamakanni, A., Jung, I., Tutuc, E., Banerjee, S.K., Colombo, L., and Ruoff, R.S. 2009. Large‐area synthesis of high‐quality and uniform graphene films on copper foils. Science 324:1312‐1314.
  Lin, C., Liu, Y., Rinker, S., and Yan, H. 2006. DNA tile based self‐assembly: Building complex nanoarchitectures. Chemphyschem 7:1641‐1647.
  Liu, J., Geng, Y., Pound, E., Gyawali, S., Ashton, J.R., Hickey, J., Woolley, A.T., and Harb, J.N. 2011. Metallization of branched DNA origami for nanoelectronic circuit fabrication. ACS Nano 5:2240‐2247.
  Maune, H.T., Han, S.‐p., Barish, R.D., Bockrath, M., Goddard, W.A. III, Rothemund, P.W.K., and Winfree, E. 2010. Self‐assembly of carbon nanotubes into two‐dimensional geometries using DNA origami templates. Nat. Nanotechnol. 5:61‐66.
  Novoselov, K.S., Geim, A.K., Morozov, S.V., Jiang, D., Zhang, Y., Dubonos, S.V., Grigorieva, I.V., and Firsov, A.A. 2004. Electric field effect in atomically thin carbon films. Science 306:666‐669.
  Novoselov, K.S., Geim, A.K., Morozov, S.V., Jiang, D., Katsnelson, M.I., Grigorieva, I.V., Dubonos, S.V., and Firsov, A.A. 2005. Two‐dimensional gas of massless Dirac fermions in graphene. Nature 438:197‐200.
  Pal, S., Deng, Z., Wang, H., Zou, S., Liu, Y., and Yan, H. 2011. DNA Directed self‐assembly of anisotropic plasmonic nanostructures. J. Am. Chem. Soc. 133:17606‐17609.
  Pilo‐Pais, M., Goldberg, S., Samano, E., LaBean, T.H., and Finkelstein, G. 2011. Connecting the nanodots: Programmable nanofabrication of fused metal shapes on DNA templates. Nano Lett. 11:3489‐3492.
  Rothemund, P.W.K. 2006. Folding DNA to create nanoscale shapes and patterns. Nature 440:297‐302.
  Sacca, B., Meyer, R., Erkelenz, M., Kiko, K., Arndt, A., Schroeder, H., Rabe, K.S., and Niemeyer, C.M. 2010. Orthogonal protein decoration of DNA origami. Angew. Chem. Int. Ed. 49:9378‐9383.
  Sharma, J., Ke, Y., Lin, C., Chhabra, R., Wang, Q., Nangreave, J., Liu, Y., and Yan, H. 2008. DNA‐tile‐directed self‐assembly of quantum dots into two‐dimensional nanopatterns. Angew. Chem. Int. Ed. 47:5157‐5159.
  Voytas, D. 2001. Agarose gel electrophoresis. Curr. Protoc. Mol. Biol. 51:2.5A.1‐2.5A.9.
  Wei, B., Dai, M., and Yin, P. 2012. Complex shapes self‐assembled from single‐stranded DNA tiles. Nature 485:623‐626.
  Yan, H., Park, S.H., Finkelstein, G., Reif, J.H., and LaBean, T.H. 2003. DNA‐templated self‐assembly of protein arrays and highly conductive nanowires. Science 301:1882‐1884.
  Yin, P., Hariadi, R.F., Sahu, S., Choi, H.M.T., Park, S.H., LaBean, T.H., and Reif, J.H. 2008. Programming DNA tube circumferences. Science 321:824‐826.
  Zheng, J., Birktoft, J.J., Chen, Y., Wang, T., Sha, R., Constantinou, P.E., Ginell, S.L., Mao, C., and Seeman, N.C. 2009. From molecular to macroscopic via the rational design of a self‐assembled 3D DNA crystal. Nature 461:74‐77.
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