Fabrication of DNA Nanowires by Orthogonal Self-Assembly and DNA

Langmuir 2008, 24, 13203-13211

13203

Fabrication of DNA Nanowires by Orthogonal Self-Assembly and DNA Intercalation on a Au Patterned Si/SiO2 Surface Katsuaki Kobayashi,*,† Naoya Tonegawa,† Sho Fujii,† Jiro Hikida,† Hisakazu Nozoye,‡ Ken Tsutsui,§ Yasuo Wada,§ Makoto Chikira,† and Masa-aki Haga*,† Department of Applied Chemistry, Faculty of Science and Engineering, Chuo UniVersity, 1-13-27 Kasuga, Bunkyo-ku, Tokyo 112-8551, Japan, ULVAC-PHI, INC., 370 Enzo, Chigasaki, Kanagawa 253-8522, Japan, and Graduate School of Interdisciplinary New Science, Toyo UniVersity, 2100 Kujirai, Kawagoe, Saitama 350-8585, Japan ReceiVed April 25, 2008. ReVised Manuscript ReceiVed September 8, 2008 A novel Ru complex bearing both an acridine group and anchoring phosphonate groups was immobilized on a surface in order to capture double-stranded DNAs (dsDNAs) from solution. At low surface coverage, the atomic force microscopy (AFM) image revealed the “molecular dot” morphology with the height of the Ru complex (∼2.5 nm) on a mica surface, indicating that four phosphonate anchor groups keep the Ru complex in an upright orientation on the surface. Using a dynamic molecular combing method, the DNA capture efficiency of the Ru complex on a mica surface was examined in terms of the effects of the number of molecular dots and surface hydrophobicity. The immobilized surface could capture DNAs; however, the optimal number of molecular dots on the surface as well as the optimal pull-up speed exist to obtain the extended dsDNAs on the surface. Applying this optimal condition to a Au-patterned Si/SiO2 (Au/SiO2) surface, the Au electrode was selectively covered with the Ru complex by orthogonal self-assembly of 4-mercaptbutylphosphonic acid (MBPA), followed by the formation of a Zr4+-phosphonate layer and the Ru complex. At the same time, the remaining SiO2 surface was covered with octylphosphonic acid (OPA) by self-assembly. The selective immobilization of the Ru complex only on the Au electrode was identified by timeof-flight secondary-ion mass spectrometry (TOF-SIMS) imaging on the chemically modified Au/SiO2 surface. The construction of DNA nanowires on the Au/SiO2 patterned surface was accomplished by the molecular combing method of the selective immobilized Ru complex on Au electrodes. These interconnected nanowires between Au electrodes were used as a scaffold for the modification of Pd nanoparticles on the DNA. Furthermore, Cu metallization was achieved by electroless plating of Cu metal on a priming of Pd nanoparticles on the Pd-covered DNA nanowires. The resulting Cu nanowires showed a metallic behavior with relatively high resistance.

Introduction The synthesis of nanowires and their self-assembly into functional architectures have received considerable attention from the scientific viewpoints of downsizing conventional siliconbased electronic devices into nanoscale ones.1 A variety of nanowires having a wide range of compositions with controlled length, diameter, charge, and functionality have been synthesized and used as functional materials.1,2 An interconnection of two gapped electrodes with nanowire building blocks and the positioning of nanowires into ordered arrays at selective locations are the real challenge in developing nanoscale electronics, optoelectronics, and photonic circuitry,1-3 and new innovative methods for fabrication and manipulation of nanowires are required. To tackle these problems, the use of biological templates is a promising avenue. Biological materials such as DNA and proteins generally exhibit high selectivity and recognition ability for the expression of biological functions and have been employed as a template for the fabrication of nanomaterials.4-6 Above all, DNA has potential * To whom correspondence should be addressed. E-mail: mhaga@ chem.chuo-u.ac.jp. Fax: +81-3-3817-1908. † Chuo University. ‡ ULVAC-PHI, INC. § Toyo University. (1) Ozin, G. A.; Arsenault, A. C. , NANOCHEMISTRY: A Chemical Approach to Nanomateirals; RSC Publishing: Cambrige, 2005, p 167. (2) Lu, W.; Lieber, C. M. J. Phys. D: Appl. Phys. 2006, 39, R387. (3) Belzig, W. Nat. Nanotechnol. 2006, 1, 167. (4) Katz, E.; Willner, I. Angew. Chem., Int. Ed. 2004, 43, 6042. (5) Gazit, E FEBS J. 2007, 274, 317. (6) Niemeyer, C. M. Angew. Chem., Int. Ed. 2001, 40, 4128.

as a template/ scaffold for nanowires. DNA itself has a characteristic duplex helical structure with a diameter of roughly 2.2 nm, in which the genetic information is stored through specific T-A and C-G nucleotide base pairing and base sequences in a DNA strand.7 The length of a dsDNA strand can be varied between several tens of nanometers and several micrometers by biochemical manipulation. Recently, DNA-based nanoarchitectures such as 1D nanowires8and nanosize 2D or 3D structures9-15 have been constructed through self-assembly to control the shapes with varied topology. Further, the polyanion character based on a DNA phosphodiester backbone allows a molecular association with cationic materials through coulombic interaction, which leads to the functionalization of DNA. Various metals and an alloy such as Ag,16-28 Pd,29-34 Ni,35,36 Cu,37-39 Pt,40,41 Au,42-56 (7) Long, E. C. In Bioorganic Chemistry: Nucleic Acids; Hecht, S. M., Ed.; Oxford University Press, Inc.: New York, 1996, p 3. (8) Taniguchi, M.; Kawai, T. Phys. E 2006, 33, 1. (9) Niemeyer, C. M.; Adler, M. Angew. Chem., Int. Ed. 2002, 41, 3779. (10) Seeman, N. C. Angew. Chem., Int. Ed. 1998, 37, 3220. (11) Rothemund, P. W. K. Nature 2006, 440, 297. (12) Aldaye, F. A.; Sleiman, H. F. J. Am. Chem. Soc. 2007, 129, 13376. (13) Erben, C. M.; Goodman, R. P.; Turberfield, A. J. J. Am. Chem. Soc. 2007, 129, 6992. (14) Chen, J.; Seeman, N. C. Nature 1991, 350, 631. (15) Goodman, R. P.; Schaap, I. A. T.; Tardin, C. F.; Erben, C. M.; Berry, R. M.; Schmidt, C. F.; Turberfield, A. J. Science 2005, 310, 1661. (16) Richer, J. Phys. E 2003, 16, 157. (17) Braun, E.; Eichen, Y.; Sivan, U.; Ben-Yoseph, G. Nature 1998, 391, 775. (18) Eichen, Y.; Braun, E.; Sivan, U.; Ben-Yoseph, G. Acta Polym. 1998, 49, 663. (19) Yan, H.; Park, S. H.; Finkelstein, G.; Reif, J. H.; LaBean, T. H. Science 2003, 301, 1882. (20) Ijiro, K.; Matsuo, Y. e-J. Surf. Sci. Nanotechnol. 2005, 3, 82. (21) Berti, L.; Alessandrini, A.; Facci, P. J. Am. Chem. Soc. 2005, 127, 11216.

10.1021/la801293e CCC: $40.75  2008 American Chemical Society Published on Web 10/22/2008

13204 Langmuir, Vol. 24, No. 22, 2008

and MoGe alloy57 have been studied for assembly into nanowires by DNA-templated metallization16 for the interconnection of two electrodes. In addition, electronic conductivity measurements on the microscale have been carried out using amphiphilic cation coated DNA modified by electrostatic interaction.58-60 Deposition of Co,61 Fe2O3,62 and CoFe2O4 particles63 on dsDNA has enhanced magnetic properties. Another chemical modification of dsDNA is the intercalation of many π-conjugated organic dye or metal complexes between two hydrophobic base pairs of DNA duplexes, which provides new photochemical or electrochemical functions in the modified DNA nanowires.64-66 (22) Wei, G.; Wang, L.; Zhou, H.; Liu, Z.; Song, Y.; Li, Z. Appl. Surf. Sci. 2005, 252, 1189. (23) Ijiro, K.; Matsuo, Y.; Hashimoto, Y. Mol. Cryst. Liq. Cryst. 2006, 445, 207. (24) Shemer, G.; Krichevski, O.; Markovich, G.; Molotsky, T.; Lubitz, I.; Kotlyar, A. B. J. Am. Chem. Soc. 2006, 128, 11006. (25) Park, S. H.; Prior, M. W.; LaBean, T. H.; Finkelstein, G. Appl. Phys. Lett. 2006, 89, 033901. (26) Sun, L.; Wei, G.; Song, Y.; Liu, Z.; Wang, L.; Li, Z. Appl. Surf. Sci. 2006, 252, 4969. (27) Berti, L.; Alessandrini, A.; Menozzi, C.; Facci, P. J. Nanosci. Nanotechnol. 2006, 6, 2382. (28) Cui, S.; Liu, Y.; Yang, Z.; Wei, X. Mater. Des. 2007, 28, 722. (29) Richer, J.; Seidel, R.; Kirsch, R.; Mertig, M.; Pompe, W.; Plaschke, J.; Schckert, H. K. AdV. Mater. 2000, 12, 507. (30) Richer, J.; Mertig, M.; Pompe, W.; Mönch, I.; Schackert, H. K Appl. Phys. Lett. 2001, 78, 536. (31) Richer, J.; Mertig, M.; Pompe, W.; Vinzelverg, H. Appl. Phys. A 2002, 74, 725. (32) Deng, Z.; Mao, C. Nano Lett. 2003, 3, 1545. (33) Hosogi, M.; Hashiguchi, G.; Haga, M.; Yonezawa, T.; Kakushima, K.; Fujita, H Jpn. J. Appl. Phys 2005, 44, L955. (34) Lund, J.; Dong, J.; Deng, Z.; Mao, C.; Parviz, B. A. Nanotechnology 2006, 17, 2752. (35) Becerril, H. A.; Ludtke, P.; Willardson, B. M.; Woolley, A. T. Langmuir 2006, 22, 10140. (36) Gu, Q.; Cheng, C.; Suryanarayanan, S.; Dai, K.; Haynie, D. T. Phys. E 2006, 33, 92. (37) Monson, C. F.; Woolley, A. T. Nano Lett. 2003, 3, 359. (38) Becerril, H. A.; Stoltenberg, R. M.; Wheeler, D. R.; Davis, R. C.; Harb, J. N.; Woolley, A. T. J. Am. Chem. Soc. 2005, 127, 2828. (39) Kudo, H.; Fujihira, M. IEEE Trans. Nanotechnol. 2006, 5, 90. (40) Ford, W. E.; Harnack, O.; Yasuda, A.; Wessels, J. M. AdV. Mater. 2001, 13, 1793. (41) Mertig, M.; Ciacchi, L. C.; Seidel, R.; Pompe, W. Nano Lett. 2002, 2, 841. (42) Karen, K.; Krueger, M.; Gilad, R.; Ben-Yoseph, G.; Sivan, U.; Braun, E. Science 2002, 297, 72. (43) Yonezawa, T.; Onoue, S.; Kimizuka, N. Chem. Lett. 2002, 1172. (44) Patolsky, F.; Weizmann, Y.; Lioubashevski, O.; Willner, I. Angew. Chem., Int. Ed. 2002, 41, 2323. (45) Nakao, H.; Shiigi, H.; Yamamoto, Y.; Tokonami, S.; Nagaoka, T.; Sugiyama, S.; Ohtani, T. Nano Lett. 2003, 3, 1391. (46) Yamada, F.; Sacho, Y.; Matsumoto, T.; Tanaka, H.; Kawai, T. e-J. Surf. Sci. Nanotechnol. 2004, 2, 222. (47) Ongaro, A.; Griffin, F.; Nagle, L.; Iacopino, D.; Eritja, R.; Fitzmaurice, D. AdV. Mater. 2004, 16, 1799. (48) Karen, K.; Braun, E. Chem. Eng. Technol. 2004, 27, 447. (49) Wang, G.; Murray, R. W. Nano Lett. 2004, 4, 95. (50) Weizmann, Y.; Patolsky, F.; Popov, I.; Willner, I. Nano Lett. 2004, 4, 787. (51) Nishinaka, T.; Takano, A.; Doi, Y.; Hashimoto, M.; Nakamura, A.; Matsushita, Y.; Kumaki, J.; Yashima, E. J. Am. Chem. Soc. 2005, 127, 8120. (52) Ongaro, A.; Griffin, F.; Beecher, P.; Nagle, L.; Iacopino, D.; Quinn, A.; Redmond, G.; Fitzmaurice, D. Chem. Mater. 2005, 17, 1959. (53) Kim, H. J.; Roh, Y.; Hong, B. J. Vac. Sci. Technol., A 2006, 24, 1327. (54) Fischer, M.; Simon, U.; Nir, H.; Eichen, Y.; Burley, G. A.; Gierlich, J.; Gramlich, P. M. E.; Carell, T. Small 2007, 3, 1049. (55) Satti, A.; Aherne, D.; Fitzmaurice, D. Chem. Mater. 2007, 19, 1543. (56) Kundu, S.; Maheshwari, V.; Saraf, R. F. Langmuir 2008, 24, 551. (57) Hopkins, D. S.; Pekker, D.; Goldbart, P. M.; Bezryadin, A. Science 2005, 308, 1762. (58) Ma, Y.; Zhang, J.; Zhang, G.; He, H. J. Am. Chem. Soc. 2004, 126, 7097. (59) Bardavid, Y.; Kotlyar, A. B.; Yitzchaik, S. Macromol. Symp. 2006, 240, 102. (60) Dong, L.; Hollis, T.; Fishwick, S.; Connolly, B. A.; Wright, N. G.; Horrocks, B. R.; Houlton, A. Chem.sEur. J. 2007, 13, 822. (61) Gu, Q.; Cheng, C.; Haynie, D. T. Nanotechnology 2005, 16, 1358. (62) Nyamjav, D.; Ivanisevic, A. Biomaterials 2005, 26, 2749. (63) Kinsella, J. M.; Ivanisevic, A. Langmuir 2007, 23, 3886. (64) Gu, J.; Tanaka, S.; Otsuka, Y.; Tabata, H.; Kawai, T. Appl. Phys. Lett. 2002, 80, 688.

Kobayashi et al.

The site-selective positioning, straightening, and alignment of DNA on the surface are of substantial importance to build a DNA-based functional nanodevice. Many approaches have been studied, many of which employed various physical methods using electrophoresis,33,67,68 optical tweezers,69-71 and the meniscus force at the air-water interface.32,72-78 Among these methods, the use of the meniscus force is a well-established method, which is known as a molecular combing method. The effect of surface treatment on the molecular combing method has been extensively studied from the standpoint of DNA extension, that is, Mg2+modified surface,32,34,36 silanized one,72,75,76 and polymer coated one.37,73,76 The molecular combing method has been extended to a Au patterned electrode surface; however, in almost of them, DNA nanowires were essentially trapped on the SiO2 surface and not on the Au surface. Recently, we reported point-to-point DNA nanowires on a mica surface, by using a Ru complex bearing naphthalene-1,4: 5,8-bis(dicarboximide) (ndi) as a dsDNA intercalating site.79,80 The Ru complex was fixed by two alkyl phosphonate anchoring groups on the mica surface. Double-stranded λ-DNA was captured by the Ru complex in a point-to-point extended manner. This result implied the possibility to define the location of DNA wiring by molecules. In this paper, we studied the interconnection of micrometer gap Au electrodes with DNA nanowires, using dsDNA intercalating molecules on the Au surface. For a dsDNA intercalating molecule, a novel Ru complex bearing both an acridine group as a DNA intercalator and anchoring phosphonate groups has been synthesized. In the Ru complex, four phosphonic acid groups act as multiple anchors, which ensure a self-sustained and upright orientation on the surface. Considering the molecular height of ∼ 2.2 nm for the present Ru complex, which is comparable to the reported DNA diameter (2.2 nm), the Ru complex with upright molecular orientation will become feasible to insert the dsDNA deeply like a wedge and to capture dsDNA through intercalation on a surface. Orthogonal self-assembly on a Au/SiO2 patterned Si substrate makes it possible to immobilize the Ru complex only on a Au surface. As a result, DNA nanowires were successfully interconnected with two Au electrodes using the molecular combing method. Furthermore, the modification of DNA nanowires by Pd or Cu nanoparticles was examined in order to improve electronic conduction by metallization.

Experimental Section Materials. 9-Acridinecarboxylic acid hydrate (Aldrich); 1,3,5tris(bromomethyl)-2,4,6-trimethylbenzene (Tokyo Chemical Industry (65) Gill, R.; Patolsky, F.; Katz, E.; Willner, I. Angew. Chem., Int. Ed. 2005, 44, 4554. (66) Boon, E. M.; Jackson, N. M.; Wightman, M. D.; Kelley, S. O.; Hill, M. G.; Barton, J. K J. Phys. B 2003, 107, 11805. (67) Oana, H.; Ueda, M.; Washizu, M. Biochem. Biophys. Res. Commun. 1999, 265, 140. (68) Ueda, M. J. Biochem. Biophys. Methods 1999, 41, 153. (69) Smith, S. B.; Cui, Y.; Bustamante, C. Science 1996, 271, 795. (70) Quake, S. R.; Babcock, H.; Chu, S. Nature 1997, 388, 151. (71) Moffitt, J. R.; Chemla, Y. R.; Izhaky, D.; Bustamante, C. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 9006. (72) Bensimon, A.; Simon, A.; Chiffaudel, A.; Croquette, V.; Heslot, F.; Bensimon, D. Science 1994, 265, 2096. (73) Nakao, H.; Hayashi, H.; Yoshino, T.; Sugiyama, S.; Otobe, K.; Ohtani, T. Nano Lett. 2002, 2, 475. (74) Nakao, H.; Gad, M.; Sugiyama, S.; Otobe, K.; Ohtani, T. J. Am. Chem. Soc. 2003, 125, 7162. (75) Yoda, S.; Han, S. P.; Kudo, H.; Kwak, K. J.; Fujihira, M Jpn. J. Appl. Phys 2004, 43, 6297. (76) Zhang, J.; Ma, Y.; Stachura, S.; He, H. Langmuir 2005, 21, 4180. (77) Bjo¨rk, P.; Holmstrom, S.; Ingana¨s, O. Small 2006, 2, 1068. (78) Kudo, H.; Suga, K.; Fujihira, M. Chem. Lett. 2007, 36, 298. (79) Haga, M.; Ohta, M.; Machida, H.; Chikira, M.; Tonegawa, N. Thin Solid Films 2006, 499, 201. (80) Haga, M.; Kobayashi, K.; Terada, K. Coord. Chem. ReV. 2007, 251, 2688.

DNA Nanowires on a Au Patterned SiO2/Si Surface (TCI), Ltd.); triethylphosphonate (TCI, Ltd.); 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide hydrochloride (WSCI) (TCI, Ltd.); and 4-dimethylaminopyridine (DIMAP) (TCI, Ltd.) were used as received. 2,6-Bis(benzimidazole-2-yl)-pyridine81 and 4′-(4-anilino)2,2′:6′,2′′-terpyridine82 were prepared according to methods cited in literature. Preparations. 4′-(9-Acridinecarboxy-4′-anilino)-2,2′:6′,2′′-terpyridine (acrdtpy). 9-Acridinecarboxylic acid hydrate (447 mg, 2.0 mmol) was dissolved in 35 mL of dimethylformamide (DMF), and subsequently 4′-(4-anilino)-2,2′:6′,2′′-terpyridine (714 mg, 2.2 mmol), WSCI (422 mg, 2.2 mmol), and DIMAP (5.3 mg, 2 mmol) were added to the solution. The mixture was stirred for 24 h at room temperature. Addition of ethyl acetate resulted in precipitation. A yellow powder was collected by centrifugation and filtration. Yield: 750 mg (71%). 1H NMR (300 MHz, DMSO-d6) δ ) 11.34 (s, 1H), 8.09 (m, 4H), 8.70 (d, 2H), 8.27 (d, 2H), 8.08 (m, 8H), 7.95 (t, 2H), 7.74 (t, 2H), 7.55 (t, 2H). FT-IR (KBr) ν (cm-1) ) 3057.67, 1676.18, 1599.86, 1518.40. 1-Bromomethyl-3,5-bis(diethylphosphonatomethyl)-2,4,6-methylbenzene. A 10 mL m-xylene solution of triethylphosphonate (8.4 g, 50.6 mmol) was dropped into 1,3,5-tris(bromomethyl)-2,4,6-trimethylbenzene (10 g, 25.1 mmol) in m-xylene (10 mL) for 5 h. The mixture was heated at 90 °C; this caused ethyl bromide gas to evolve. After 24 h, the solvent was removed by reduced pressure, and the resulting residue was purified by silica gel column chromatography using ethyl acetate as an eluent. The third eluted band was collected and evaporated in vacuo. A pale yellow oil was obtained. Yield: 5.19 g (43%). 1H NMR (500 MHz, CDCl3) δ ) 4.62 (s, 2H), 3.98 (m, 8H), 3.34 (d, 4H, J ) 21.8 Hz), 2.48 (s, 3H), 2.45 (s, 6H), 1.24 (t, 12H, J ) 7.0). 2,6-Bis(N-(2,4,6-methyl-3,5-dietylphosphonatometyl-benzyl)-benzimidazole-2-yl)-pyridine (XPOEt). NaH (oil dispersion 30%) (1.0 g, 25.0 mmol) was washed with dry n-pentane and then suspended in dried DMF (15 mL). To this suspension was added 2,6bis(benzimidazol-2-yl)pyridine (1.94 g, 6.27 mmol) under nitrogen atmosphere, and the mixture was heated at 80 °C for 12 h; during this period, the suspension slowly dissolved, and a yellow homogeneous solution was obtained. The resulting solution, transferred to a dropping funnel using cannula techniques, was added dropwise to 1-bromomethyl-3,5-methylbis(diethylphosphonyl)-2,4,6-trimethylbenzene (6.43 g, 12.5 mmol) in DMF (10 mL) at room temperature and heated at 70 °C for 24 h. After cooling to room temperature, a small amount of methanol (1 mL) was added and then the solvent was removed under reduced pressure. The resulting white residue was dissolved in dichloromethane and purified by column chromatography on silica gel with acetone as an eluent. The product was obtained as a yellow solid. Yield: 5.52 g (75%). 1H NMR (DMSOd6, 500 MHz) δ ) 8.40 (d, 2H, J ) 8.0 Hz), 8.24 (t, 1H, J ) 8.0 Hz), 7.68 (d, 2H, J ) 8.0 Hz), 7.13 (t, 2H, J ) 7.7 Hz), 6.91 (t, 2H, J ) 7.7 Hz), 6.76 (d, 2H, J ) 8.0 Hz), 6.26 (s, 4H), 3.83-3.65 (m, 16H), 3.20 (d, 8H, J ) 22.0 Hz), 2.35 (s, 6H), 2.30 (s, 12H), 1.01 (t, 24H, J ) 7.0). [Ru(XPOEt)Cl3]. XPOEt (1.22 g, 1.04 mmol) in ethanol (20 mL) was added to a solution of RuCl3 · 3H2O (0.26 g, 1.04 mmol) in ethanol (30 mL) at room temperature and heated under reflux for 12 h. After cooling to room temperature, the resulting solution was evaporated under reduced pressure to yield a brown powder as a crude product. The crude compound was purified by Sephadex LH20 column chromatography with methanol as an eluent. Yield: 1.20 g (83%). [Ru(acrdtpy)(XPOEt)](PF6)2 (1). [Ru(XPOEt)Cl3] (50 mg, 0.036 mmol) was added to an ethylene glycol solution (15 mL) of acrdtpy (23 mg, 0.043 mmol). The mixture was heated by microwave assisted heating at 650 W for 1 min. After cooling to room temperature, the addition of an excess amount of aqueous solution of NH4PF6 to the resulting mixture afforded a reddish brown precipitate. The precipitate was collected by suction filtration and dried under vacuum. (81) Xiaoming, X.; Haga, M.; Matsumura-Inoue, T.; Ru, Y.; Addison, A. W.; Kano, K. J. Chem. Soc., Dalton Trans. 1993, 2477. (82) Mutai, T.; Cheon, J.-D.; Arita, S.; Araki, K. J. Chem. Soc., Perkin Trans. 2001, 2, 1045.

Langmuir, Vol. 24, No. 22, 2008 13205 Purification was performed by Sephadex LH-20 column chromatography with MeOH/MeCN ) 3:1 as eluent. The desired complex, eluted as the third fraction band, was obtained as a reddish brown powder. Yield: 39.0 g (53%). 1H NMR (DMSO-d6, 500 MHz) δ ) 11.48 (s, 1H), 9.62 (s, 2H), 9.26 (br, 2H), 9.04 (d, 2H, J ) 7.4 Hz), 8,68 (d, 2H, J ) 7.4 Hz), 8.51 (t, 2H, J ) 7.4 Hz), 8.31 (d, 2H, J ) 8.0 Hz), 8.23 (d, 2H, J ) 6.9 Hz), 8.15 (d, 2H, J ) 8.0 Hz), 8.03 (t, 2H, J ) 6.8 Hz), 7.98 (d, 2H, J ) 6.9 Hz), 7.79 (t, 2H, J ) 6.8 Hz), 7.61 (br, 2H), 7.36 (br, 2H), 6.91 (m, 4H), 6.58 (d, 2H, J ) 6.3 Hz), 6.39 (s, 4H), 5.98 (d, 2H, J ) 6.9 Hz), 3.81 (br, 16H), 2.41 (s, 8H), 2.18 (s, 12H), 0.97 (br, 24H). MS (ESI-TOF) found, m/z ) 903.29; calcd for [M-2PF6]2+, 902.97; M ) C94H113N10O13F12P6Ru. [Ru(acrdtpy)(XPOH)](PF6)2 (2). To complex 1 (35 mg, 0.017 mmol) in DMF/acetonitrile (2 mL/30 mL v/v) was added Me3SiBr (250 µL, 0.031 mmol) dropwise. The mixture was heated under reflux for 16 h. After cooling to room temperature, excess MeOH was added to decompose the protected group, and the solvent was evaporated to one-third of the original volume in a rotary evaporator. Addition of MeCN to the resulting solution then yielded a brown precipitate of 2, which was collected and dried in vacuo. Yield: 33.0 mg (94%). 1H NMR (DMSO-d6, 400 MHz) δ ) 11.48 (s, 1H), 9.63 (s, 1H), 9.21 (br, 2H), 9.04 (br, 2H), 8.68 (br, 2H), 8.50 (br, 1H), 8.31 (br, 2H), 8.23 (br, 2H), 8.15 (br, 2H), 8.02 (br, 2H), 7.98 (br, 2H), 7.79 (br, 2H), 7.61 (br, 2H), 7.35 (br, 2H), 6.91 (br, 2H), 6.60 (br, 2H), 6.38 (s, 4H,), 8.23 (br, 2H), 5.97 (br, 2H), 3.56 (m), 2.41 (s, 8H), 2.18 (s, 6H), 2.08 (s, 12H). Fabrication of Au Patterned SiO2/Si Substrate by Photolithography. A 4 in. silicon wafer (thickness of SiO2 layer ) 200 nm) was wetted by hexamethyldisilazane (OAP, Tokyo Ohka Kogyo Co., Ltd.) to increase adhesiveness of the next resist layer. PMGI (MicroChem Corp.) was coated in a spin coater (MS-A200, Mikasa Co., Ltd.) and then annealed at 180 °C for 5 min. Subsequently, photoresist (TSMR, Tokyo Ohka Kogyo Co., Ltd.) was spread on the PMGI layer and annealed at 110 °C for 1.5 min. The thickness of each layer was adjusted to 0.15 µm for PMGI and 0.2 µm for TSMR, respectively. The resulting substrate was exposed to UV light of up to 40 mJ/cm2 (MA-6, Karl Suss) through a photomask. The substrate was then etched by NMD-3 (Tokyo Ohka Kogyo Co., Ltd.) for 1.5 min to develop. After post-baking (110 °C, 1.5 min) and H2SO4 (5%, 0.5 min) treatment, Ti and then Au were successively deposited by electron-beam evaporation (EBV-6DA, ULVAC, Inc.); the thickness was 10 nm for Ti and 20 nm for Au. After the resist layer was removed, TSMR was coated to protect the chips for substrate cutting. The substrate was then cut along the electrode patterns into pieces (1 cm × 1 cm size each) using a dicing cutter. The resulting Au patterned Si/SiO2 substrate was cleaned by washing with acetone, isopropyl alcohol, methanol, and water to remove the TSMR layer, and it was then treated with an ozone cleaner before use. Surface Modification. The freshly cleaved mica (1 cm × 2 cm size) was immersed in a 50 µM DMF solution of the Ru complex. By changing the immersion time, the surface density of the immobilized Ru complex on the surface could be controlled. After a certain period of time, the mica substrate was removed from the solution, rinsed with MeOH and water, and dried before the DNA wiring. Similarly, Au patterned Si/SiO2 surface modification was achieved by employing orthogonal self-assembly in a stepwise manner. First, a Au/SiO2 substrate was dipped into a 10 mL methanol solution of octylphosphonic acid (OPA) for 1 h. After rinsing with MeOH, the substrate was immersed into a 10 mM ethanol solution of 4-mercaptobutylphosphonic acid (MBPA) for 1 h. After removing excess MBPA by washing with ethanol, the immersion of the patterned substrate into a 20 mM ZrOCl2 aqueous solution led to Zr4+ binding onto the phosphonate group for 10 min. Finally, the resulting substrate was dipped into a DMF solution of the Ru complex mixed with OPA (1:100 v/v, Ru concentration ) 50 µm) for 30 min, rinsed with MeOH and water, and dried in N2 flow. DNA Wiring and Its Modification. The molecular combing method for DNA wiring was applied in the present study, according to a previously reported procedure.72 The Ru-modified substrate,

13206 Langmuir, Vol. 24, No. 22, 2008

Kobayashi et al.

Chart 1. Chemical Structure of [Ru(acrdtpy)(XPOH)]2+ for DNA Capture

Figure 1. Temporal evolution in the surface coverage of [Ru(acrdtpy)(XPOH)](PF6)2 on a mica surface: (a) plots of contact angle versus immersion time and (b) number of molecular dots versus immersion time.

which was suspended in a dip coater (DC4100, Aiden Co., Ltd.), was incubated in a 10 µM λ-DNA solution in 20 mM phosphate buffer containing 30 mM NaCl for 5 min under ambient conditions. The substrate was removed from the DNA solution at various constant speeds (10-100 µm/s) and then gently washed in ultrapure water and dried. For Pd metallization on the DNA nanowires, the DNA nanowires immobilized on the surface were exposed to 1 mM Pd(CH3COO)2 in a HEPES buffer at pH 6.5 for 1 h. Pd2+ ions attached on the DNA were reduced by reducing reagents containing a mixture of 10 mM sodium hypophosphite, 5 mM 85% lactic acid solution, and 12 mM ethylenediamine at pH ) 8.0 for 2 min. Further, electroless plating of the Pd nanowire by Cu nanoparticles was performed using Thru-Cup PSY (C. Uemura &Co. Ltd.). Atomic Force Microscopy (AFM) Measurements. AFM measurements were performed using a Shimadzu SPM-9500J3 SPM microscope in both dynamic and phase-sensitive modes. The height of the molecular dots from the DNA capture Ru complex on a mica surface was estimated from the height profile of each dot. Height data were collected with 220 dots on a 10 µm × 10 µm AFM image, of which the values were plotted as a histogram, which can be analyzed as a Gaussian distribution. The number of DNA was counted on a 25 µm × 25 µm mica surface and averaged from the values for AFM images of three different substrates. Physical Measurements. UV-visible absorption spectra were recorded on a Hitachi U-4000 spectrophotometer. Contact angle measurements were performed using a contact angle meter CA-X (Kyowa Interface Science Co, Ltd.). Time-of-flight secondary-ion mass spectrometry (TOF-SIMS) data were recorded on a ULVACPhi Inc. TOF-SIMS TRIFT IV instrument. A197 Au ions were irradiated to a surface as the primary ion source; the ions were accelerated at 30 kV, and the ion current was adjusted to 1 nA. Secondary ions were recorded using a TOF spectrometer and imaged. The I-V characteristics of the Cu nanowires were obtained, using a Keithley Model 4200 semiconductor parameter analyzer. All electrical measurements were made under ambient conditions.

Results and Discussion Molecular Design of DNA-Capturing Molecule and Its Immobilization on a Surface. A novel Ru complex bearing an acridine moiety for DNA intercalation was synthesized in order to capture dsDNAs from solution onto the solid surface, since the acridine moiety is known to intercalate into the dsDNA duplex.83 This molecule possesses four phosphonate anchoring groups (Chart 1), which can selectively bind mica and metal oxide substrates such as SiO2 and indium tin oxide (ITO).84-86 (83) Denny, W. A. In DNA and RNA Binders; Demeunynck, M., Bailly, C., Wilson, W. D., Eds.; Wiley-VCH: Weinheim, 2003; Vol. 2, p 482. (84) Gardner, T. J.; Frisbie, C. D.; Wrighton, M. S. J. Am. Chem. Soc. 1995, 117, 6927.

Furthermore, multiple anchor groups have been well documented to maintain the vertical orientation of the molecules on the surface.87,88 For the synthesis of the Ru complex, the reaction of [Ru(XPOEt)Cl3] with an equivalent molar ratio of acrdtpy ligand afforded the mixed-ligand complex, [Ru(acrdtpy)(XPOEt)](PF6)2. The protected groups in XPOEt were then removed by the reaction with Me3SiBr to yield the complex [Ru(acrdtpy)(XPOH)](PF6)2 having free phosphonic acid groups (Chart 1). The new Ru complex was characterized by 1H NMR, wherein the observed broad signals for the aromatic proton region were attributed to the slow proton exchange on phosphonic acids. The complex is soluble in methanol, and dimethyl sulfoxide (DMSO) but insoluble in CH2Cl2 and toluene. Its solubility in CH3CN/water or methanol/water (1:1 v/v) dramatically increased with the solution pH. Considering the UV-vis spectral change upon the addition of calf thymus DNA to an aqueous solution of the Ru complex [Ru(acrdtpy)(XPOH)]2+ (1) (Supporting Information, Figure S1), Ru complex 1 was intercalated into base pairs of dsDNA with a binding constant, Kb, of 4.5 × 105 M-1. Immobilization of the complex on the mica surface was carried out by the immersion of the substrate into the complex solution. After the solid substrate was been washed and dried, it was subjected to physical measurements and a DNA capture experiment. The time dependence of the immobilization process on the mica surface was monitored by both contact angle and AFM measurements. The contact angle increased with the immersion time, and simultaneously, the number of molecular dots, which were clearly observed in the AFM images shown in Figure 2A, increased. When temporal evolution in the surface coverage was analyzed by the kinetic Langmuir equation (eq 1), it was found that both curves could be fitted by a similar rate constant parameter, k, (Figure 1).

Γ(t) ) 1 - exp(kCt)

(1)

where Γ(t), k, C, and t are the surface coverage amounts, rate constant, concentration in the bulk solution, and time, respectively. Therefore, the adsorption of the Ru complex on the surface increased the surface hydrophobicity. Further, the number of molecular dots, which corresponds to the immobilized Ru complex, is controlled by the immersion time. Molecular Orientation and Surface Morphology on the Surface. Figure 2 shows the AFM image of the mica surface modified by the Ru complex, in which the scattered dot (85) Doudevski, I.; Schwartz, D. K. J. Am. Chem. Soc. 2001, 123, 6867. (86) Vercelli, B.; Zotti, G.; Schiavon, G.; Zecchin, S.; Berlin, A. Langmuir 2003, 19, 9351. (87) Li, G.; Fudickar, W.; Skupin, M.; Klyszcz, A.; Draeger, C.; Lauer, M.; Fuhrhop, J.-H. Angew. Chem., Int. Ed. 2002, 41, 1828. (88) Galoppini, E.; Gao, W.; Zhang, W.; Hoertz, P. G.; Qu, P.; Meyer, G. J. J. Am. Chem. Soc. 2002, 124, 7801.

DNA Nanowires on a Au Patterned SiO2/Si Surface

Langmuir, Vol. 24, No. 22, 2008 13207

Figure 2. (A) AFM image of DNA capture molecules immobilized on a mica surface (10 µm × 10 µm) and (B) molecular modeling of [Ru(acrdtpy)(XPOH)]2+. For the immersing condition, the concentration of the Ru complex and the immersion time were 5 × 10-5 M and 5 min, respectively.

Figure 3. Morphology of DNA nanowires fabricated by the immobilized Ru complex and molecular combing method on the surface with sparse molecular dots (A,C) and with dense molecular dots (B,D). The contact angle of each substrate was 22° for (A) and (C) and 41° for (B) and (D). The pull-up speed of the substrate upon molecular combing was 10 µm/s for (A) and (B) and 100 µm/s for (C) and (D).

morphology was seen. The height of the dots was estimated by the height profile of the AFM images. A histogram of dot heights is shown in Figure S2 in the Supporting Information. The observed heights were distributed around 2.47 nm with 0.83 nm halfwidth. The peak top at 2.47 nm is close to the predicted height for upright orientation from molecular modeling on Spartan02 (2.17 nm). Because of the larger cantilever curvature radius (