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The Role of DNA in Nanoarchitectonics

MIHRIMAH OZKAN

University of California, Riverside


CENGIZ S. OZKAN

University of California, Riverside


In the last several decades, the scaling of complementary metal oxide semiconductor (CMOS) technologies has fueled multiple industries, which have produced new industrial and defense products. However, the International Technology Roadmap for Semiconductors (ITRS) anticipates that scaling will necessarily end, perhaps by 2016, with a 22 nanometer (nm) pitch length (9 nm physical gate length). To address that eventuality, ITRS defines several potential avenues for research, such as bioinspired assembly, that could lead to new paradigms and alternative technologies. The ultimate goal is the development of highly controlled, high-throughput fabrication of nanoelectronics as stand-alone devices/systems or components/devices that could be integrated heterogeneously onto existing device platforms.

Deoxyribonucleic acid (DNA) and peptide nucleic acids (PNAs), which have base sequences that offer specificity, are attractive assembly linkers for bottom-up nanofabrication. Recent publications on bioassembly describe ex vivo-assembled discrete devices, such as DNA-single-walled carbon nanotubes (SWNTs) and virus-nanocrystal (NC) nanoarchitectures for electronics components (Tseng et al., 2006; Wang et al., 2006) and the programming of nucleic-acid sequences



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The Role of DNA in Nanoarchitectonics miHrimaH oZKan University of California, Riverside cengiZ S. oZKan University of California, Riverside In the last several decades, the scaling of complementary metal oxide semi- conductor (CMOS) technologies has fueled multiple industries, which have pro- duced new industrial and defense products. However, the International Technol- ogy Roadmap for Semiconductors (ITRS) anticipates that scaling will necessarily end, perhaps by 2016, with a 22 nanometer (nm) pitch length (9 nm physical gate length). To address that eventuality, ITRS defines several potential avenues for research, such as bioinspired assembly, that could lead to new paradigms and alter- native technologies. The ultimate goal is the development of highly controlled, high-throughput fabrication of nanoelectronics as stand-alone devices/systems or components/devices that could be integrated heterogeneously onto existing device platforms. Deoxyribonucleic acid (DNA) and peptide nucleic acids (PNAs), which have base sequences that offer specificity, are attractive assembly linkers for bottom-up nanofabrication. Recent publications on bioassembly describe ex vivo-assembled discrete devices, such as DNA-single-walled carbon nanotubes (SWNTs) and virus-nanocrystal (NC) nanoarchitectures for electronics components (Tseng et al., 2006; Wang et al., 2006) and the programming of nucleic-acid sequences 1

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2 FRONTIERS OF ENGINEERING for the large-scale assembly of nanostructures (Akin et al., 2007; Ruan et al., 2007). We believe that novel routes, which would be available with self-assembly processing and highly integrated materials, could circumvent current challenges of CMOS to achieve environmental friendliness, thermal balance, dielectric quality, and manageable capital costs of next-generation fabrication facilities—if we can develop massively parallel integration of SWNTs and semiconducting, defect- tolerant nanowires. Assembly based on biomolecular recognition is a promising approach for constructing complex architectures from molecular building blocks, such as SWNTs and NCs (Ravindran et al., 2003). In the Ozkans’ laboratories at the Uni- versity of California, Riverside (UCR), researchers are using a “tiered” approach to the nanomanufacturing of molecular electronics to address several issues: gain- ing an understanding of charge-carrier transport across bio-inorganic interfaces; ensuring error-free repeatability of the synthesis of hybrid building blocks; and directing the integration of nanoscale components (including assembled architec- tures, nanowires, and nanodevices) on silicon (Si) platforms. Figure 1 shows two a. TMV-Pt device Pt NPs-only device -4 10 1st scan Virus-Nanoparticle Memory 2nd -5 10 3rd Current (A) -6 10 -7 10 TMV-only device -8 10 A A -9 10 Nature [Ref. 96] TMV- Nanotechnology -10 10 (2006) -6 -4 -2 0 2 4 6 Bias (V) b. Current (A) SWNT-DNA-SWNT Resonant Tunneling Diode [Ref. 97] Small (2006) Voltage (V) FIGURE 1 (a) Tobacco Figure 1. Virus (TMV)Mosaic Virus (TMV) Mosaic (a) Tobacco for cross bar-memory applications. (b) templates for cross bar-memory applications. DNA-CNT nanoarchitectures for resonant tunneling diodes. (b) DNA-CNT nano architectures for resonant tunneling diodes.

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 ROLE OF DNA IN NANOARCHITECTONICS novel devices fabricated at UCR: (a) a virus-NC memory device with write-erase cycles, and (b) a resonant tunneling diode based on DNA-SWNT architectures. CARBON NANOTUBE-BASED FUNCTIONAL NANOSTRUCTURES The synthesis of hybrid nanoarchitectures based on SWNT-DNA or SWNT- PNA conjugates may offer unique possibilities for nanoelectronics and biotechnol- ogy (Figure 2). New structures would combine the electrical properties of SWNTs with the self-assembling properties of oligonucleotides or other biomaterials, such as proteins, enzymes, and viruses. For example, we recently demonstrated that SWNT-DNA-SWNT conjugates can be used to fabricate resonant tunneling diodes (Wang et al., 2006). Based on this result, we expect that novel devices and applications, such as bioelectronic devices, DNA sensors, mechanical actuators, templates for hierarchical assembly, and others, can be derived. Several studies have reported using SWNTs for imaging probes in scanning force microscopy (Bernholc et al., 2002; Wong et al., 1998), and electrochemical studies have shown that SWNTs can be used as enzyme-based sensors and DNA sensors (Britto et al., 1996; Davis et al., 1997; Melle-Franco et al., 2004; Wang et al., 2004c; zhao et al., 2002). Because SWNT electrodes have demonstrated RTD and FET Applications Gene and Drug Delivery DNA Sequencing Hierarchical Assembly FIGURE 2 SWNT-DNA sensors for hybrid nanoelectronics, biosensors, and bottom-up Figure 2. SWNT-DNA systems for hybrid nanofabrication. nanoelectronics, biosensors, and bottom- up nanofabrication.

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4 FRONTIERS OF ENGINEERING catalytic properties, they could also be used as electrodes in fuel cells and elec- trochemical detectors in medical and military settings (Que et al., 2004; Rubianes and Rivas, 2003; Sherigara et al., 2003; Wang et al., 2004a,b; Wohlstadter et al., 2003). Functionalized nanotubes have been used in fabricating FETs for use in nanoelectronics and biosensors (Bradley et al., 2004; Javey et al., 2003; Star et al., 2003); and several studies have shown that SWNTs and multiwalled nanotubes (MWNTs) can accommodate the encapsulation of nanoparticles, fullerenes, and metallized DNA fragments (Cui et al., 2004; Davis et al., 1998; Dennis and Briggs, 2004; Gao et al., 2003). Other studies have suggested that organic and inorganic molecules might be conjugated to the side walls of carbon nanotubes (CNTs) (Hirsch, 2002; Lin et al., 2003; Sarikaya et al., 2003; Shim et al., 2002). BOTTOM-UP FABRICATION: HYBRID NANOARCHITECTURES SWNTs are being used as active components in solid-state nanoelectron- ics (Tsukagoshi et al., 2002), and individual SWNTs have been used to realize molecular-scale electronic devices, such as single-electron (Postma et al., 2001) and field-effect transistors (Tans et al., 1998). Several SWNT-based devices have been successfully integrated into logic circuits (Bachtold et al., 2001) and transis- tor arrays (Javey et al., 2002). However, the difficulty of determining the precise location and interconnection of nanotubes has so far stymied progress toward the integration of larger scale circuits. The search for alternative routes based on molecular recognition between complementary strands of DNA has prompted an exploration of the electronic properties of DNA for use in molecular electronics and templated nanostructures (Arkin et al., 1996; Coffer et al., 1996; Heath and Ratner, 2003; Seeman, 1998, 1999, 2003). We have synthesized SWNT-DNA and SWNT-PNA conjugates, in which DNA or PNA sequences are covalently bonded to the ends of SWNTs to form a viable bio-inorganic interface (Figure 3). Research on the fabrication of oligonucleotide-based nanoarchitectures has been focused mostly on noncovalent interactions between DNA fragments and SWNTs (Dwyer et al., 2002; zheng et al., 2003). Because the intrinsically low conductivity of DNA limits its usefulness in electronic circuits, some investiga- tors have attempted to distribute metal particles on the backbone of DNA to lower its resistance (Spyro, 1980; Winfree et al., 1998). The synthesis of end-specific SWNT-DNA and SWNT-PNA complexes (Fig- ure 3) is a novel concept that was studied for the first time at UCR (Wang et al., 2006). In the preliminary experiments, we used ssDNA with a nine-base configu- ration of [5’(NH2)GCATCTACG] and ssPNA with a custom sequence of (NH2)- Glu-GTGCTCATGGTG-Glu-(NH2). In order to preserve the superior electrical characteristics of SWNTs, their side walls must be free of damage or defects. Therefore, functionalization of SWNTs only at the ends, before the assembly

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 ROLE OF DNA IN NANOARCHITECTONICS SWNT PNA SWNT Pt Islands FIGURE 3 (Top) Electron microscopy image of end-to-end assembly of two SWNTs via Figure 3. (Top) Electron microscopy image PNA. (Bottom) Electron microscopy image of Pt metallized PNA strand. Notice formation of Pt islands duringof end-to-end assembly of two SWNTs via the metallization process. PNA. (Bottom) Electron microscopy image of Pt metalized PNA strand. Notice formation of Pt islands during the process, is critical. Our work demonstrates the first successful end-to-end assem- metallization process. bly of SWNTs using nucleic acids. After placing physical metallic contacts on SWNTs, we investigated the electrical characteristics of this heterojunction. The results show negative resonance tunneling behavior that can be adopted to fabri- cate resonant tunneling diode circuits. METALLIZED NANOARCHITECTURES For an electrical circuit to have fast processing capability, the conductiv- ity of circuit elements can be important. Information must be delivered to the other parts of the circuit with no delay (or loss). To achieve this, we adjusted the conductivity of the assembled circuit elements. In functional assembly such as SWNT-PNA-SWNT, the PNA link may have to be engineered to make it more conductive. We used a metallization procedure to improve the conductivity of nucleic acid-based linkers. In one case, we developed a platinum (Pt) metallization process. The synthesis of Pt-decorated SWNT-ssDNA complexes requires a two-step chemical reduction and the deposition of metallic colloids (Mertig et al., 1998, 1999; Pompe et al., 1999; Richter et al., 2000). In the first step, SWNT-ssDNA conjugates were mixed with a salt solution (e.g., k2PtCl4 solution). After this activation step, the Pt (II)

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 FRONTIERS OF ENGINEERING was reduced to metallic platinum. In the reduction process, Pt dimers formed het- erogeneously on DNA molecules, and the initial heterogeneous Pt nuclei quickly developed into bigger particles, consuming the metal complex feedstock in the solution (Ciacchi, 2002) to create metallized linkers (Figure 2). Because oxidized SWNTs have higher adsorption capacities for heavy metal ions (Braun et al., 1998), the Pt ions would be absorbed on SWNTs if the metallization process was done after assembly. MODELING OF BAND STRUCTURES AND CARRIER TRANSPORT FOR BIO-INORGANIC INTERFACES An analysis of high-lying occupied molecular orbitals (HOMO) and low- lying unoccupied molecular orbitals (LUMO) reveals the structural and electrical properties of bio-inorganic interfaces, such as CNT/protein, quantum dot (QD)/ DNA, QD/protein, metal/DNA, and metal/protein systems. In a recent study, the electrical properties of the interfaces between SWNT-ssDNA and SWNT-ssPNA were deduced via density functional theory (DFT) calculations (Singh et al., 2006; Wang et al., 2006), in which two unit cells of zigzag (10,0) oxidized CNT were linked to a DNA sequence with amine to form an amide linkage. When the highest HOMO and lowest LUMO surface plots (shown in Figure 4) were generated, the HOMO-LUMO gap was found to be about 3.1 electron- volts (eV). For comparison, the HOMO-LUMO gap of SWNT alone is ~3.1 eV. LUMO (+3.09 eV) DNA backbone HOMO (0.00 eV) HOMO-1 (-0.04 eV) Guanine CNT Amide FIGURE 4 HOMO-LUMO calculation of SWNT. The gap is found to be 3.1eV. Similar Figure 4. HOMO-LUMO calculation of SWNT. modeling studies can reveal electrical characteristics of organic-inorganic interfaces. The gap is found to be 3.1eV. Similar modeling studies can reveal electrical characteristics of organic-inorganic interface.

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 ROLE OF DNA IN NANOARCHITECTONICS The large gap is the result of the shortness (just two unit cells) of the modeled SWNT. For an extended (10,0) CNT, the bandgap is ~0.98 eV. The HOMO orbital is confined on the SWNT, while the LUMO orbital extends across the amide link, suggesting a good possibility of electron transfer across the amide bridge for n- type SWNTs. Similar calculations for SWNT-ssPNA revealed that, although the HOMO orbital is confined to the glutamate link, the LUMO orbital extends over the SWNT, suggesting that SWNT-ssPNA conjugates might be used to build hole- conducting devices. Thus these preliminary studies suggest that bio-inorganic interfaces achieved by conjugating SWNTs with ssDNA and ssPNA might lead to the fabrication of n-type and p-type devices, which might someday provide an alternative or an enhancement to conventional CMOS technology. NANOPATTERNING vIA DIELECTROPHORESIS USING MICRO- AND NANOARRAYS Micro- and nanoarray platforms can be used to control the electrophoretic manipulation of (bio)molecules, particles, and micro-light emitting diodes (LEDs) as electronic elements. The platform shown in Figure 5 is used for electric-field- assisted manipulation and the assembly of nanoelements, such as metallic and semiconducting SWNTs, QDs, dendrimers, and/or conjugation molecules, such as DNA fragments. The nanochip platform (shown in Figure 5) enables rapid, paral- lel transport within seconds to a specific location on the chip array by providing independent current or voltage control on each electrode. Current commercialized applications of this platform include DNA hybridiza- tion and DNA analysis for molecular diagnostics via fluorescence detection using fluorophore-labeled reporters (Akin et al., 2007; Dubois and Nuzzo, 1992; Ruan et al., 2007; Salem et al., 2004). Commercial uses of DNA detection include highly multiplexed, fully validated assays and panels for identifying cystic fibrosis, respi- ratory viruses, hereditary hemochromatosis, and other medical conditions. So far, different types of arrays (with 10,000, 400, and 100 sites) have been developed using silicon micromachining with fully automated and robotized flu- idics. Figures 5c and 5d show the in situ assembly for the manipulation, direction, and assembly of nanoelements using electric-field assembly. The electrode array, with geometry configurable to the desired application, is energized to attract and combine different types of nanoelements (Figure 5b). When electric-field assembly is used, the process is significantly different from self-assembly in a static solution, because it enables site-specific assembly. In the future, the controlled parallel assembly of nanowires and nanotubes could be investigated by attaching one end of a nanowire to the target DNA immobilized on the nanoarray and the other end to a reporter-DNA sequence equipped with a fluorescent tag (Figure 5d). Upon hybridization, the presence of fluorescence could be used to assess and record in situ assembly.

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 FRONTIERS OF ENGINEERING A B C Universal reporter D GOLD Fluorophore Nanowire Green or Red functionalized with Key sequences Key sequence Tm dependent Lock Binding s equenc e region biotinylated Individual pads Specificity of different lock-key pairs E fluorescence detection S/N ratio: 28,000 F FIGURE 5 (A)–(C) Nanogen platform and microarray device for dielectrophoresis appli- cations. (D) Assembly of 5. (a)-(c) nanogen platform andnanowires onto Si arrays. Figure ssDNA sequences and functionalized microarray device for dielectrophoresis (E) Specificity of assembly of different lock and key ssDNA sequences. (F) High S/N ratio is obtained.applications. (d) Assembly of ssDNA sequences and functionalized nanowires onto Si arrays. (e) Specificity of assembly CONCLUSIONS of different lock and key ssDNA sequences. High S/N ratio is obtained. Clearly, chemical and biological assemblies are promising technologies. However, many new technologies must be developed and much science must be learned for that promise to be fully understood and realized. We anticipate that new engineering concepts will be discovered in the near future that will enable the massively parallel assembly of nanodevices. The future of assembly engineering

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