NANO LETTERS
Construction and Characterization of a Gold Nanoparticle Wire Assembled Using Mg2+-Dependent RNA−RNA Interactions
2006 Vol. 6, No. 3 445-448
Andrew D. Bates,† Benjamin P. Callen,†,⊥ Jonathan M. Cooper,‡ Rick Cosstick,§ Cody Geary,| Andrew Glidle,‡ Luc Jaeger,| John L. Pearson,‡,⊥ Marı´a Proupı´n-Pe´rez,§,⊥ Cigang Xu,‡,⊥ and David R. S. Cumming*,‡ School of Biological Sciences, UniVersity of LiVerpool, The Biosciences Building, Crown Street, LiVerpool L69 7ZB, U.K., Department of Electronics and Electrical Engineering, UniVersity of Glasgow, Glasgow G12 8LT, U.K., Department of Chemistry, UniVersity of LiVerpool, Crown Street, LiVerpool, L69 7ZD, U.K., and Department of Chemistry and Biochemistry, Biomolecular Science and Engineering Program, UniVersity of California, Santa Barbara, California 93106-9510 Received November 23, 2005; Revised Manuscript Received January 6, 2006
ABSTRACT Magnesium-ion-mediated RNA−RNA loop−receptor interactions, in conjunction with gold nanoparticles derivatized with DNA, have been used to make self-assembled nanowires. A wire located between lithographically fabricated nanoelectrodes is demonstrated that exhibits activated conduction by electron hopping at temperatures in the 150−300 K range. These techniques have the ability to link particles between devices and in the future may be used to assemble practical circuits.
There is intense interest in new ways of fabricating electronic devices and wiring with dimensions considerably below 100 nm. Conventional lithographic techniques are costly and are progressing toward their limits of resolution.1,2 Integrated circuit transistors are currently of 65-nm gate length with plans to achieve smaller dimensions.1 However, transistors with gate lengths as small as 8 nm have been demonstrated,3 and alternative technologies such as carbon nanotubes4 and single molecule gating5,6 are emerging. In addition, it is clear that a limiting factor for microelectronic technologies is not only the performance of the device but also the interconnecting wires.7 A further challenge is the need to overcome the nanolithographic limitations of optical techniques at reasonable cost.2 One promising solution is molecular selfassembly.8 In particular, DNA has been demonstrated as a self-assembling tool that has the potential to direct gold nanoparticles into fixed locations.9 In an alternative approach, dielectrophoresis has been used to manipulate a single chain of gold nanoparticles10 in microelectrode gaps. A candidate * Corresponding author. E-mail:
[email protected]. † School of Biological Sciences, University of Liverpool. ‡ University of Glasgow. § Department of Chemistry, University of Liverpool. | University of California. ⊥ These authors contributed equally to this work. 10.1021/nl052316g CCC: $33.50 Published on Web 01/31/2006
© 2006 American Chemical Society
self-assembly technology should provide coverage over many micrometers in order to build systems, contain nanometerscale features comparable to the device dimensions, allow controllable functionalization, and be capable of precise location of different materials on to a substrate. Selfassembled RNA that relies on the specific interaction between RNA motifs has been shown previously to have the first two of these properties.11-13 We have developed RNA molecules designed to exhibit Mg2+-dependent interactions between specific tertiary structural motifs. Using such RNAs tethered to gold nanoparticles, we show that we can make a nano-interconnection on a silicon chip with a process that differentiates between particle types. We designed a pair of RNA stem-loop molecules, E1 and G2 (Figure 1), based on the molecules described by Jaeger and co-workers.11,12 The RNA molecules associate, forming heterodimers by two distinct Mg2+-dependent tetraloopreceptor interactions, one (L1-R1) derived from a natural group I ribozyme structure14 and the other (L2-R2) the product of in vitro selection.15 As illustrated in Figure 1, the RNA molecules have extensions designed to allow attachment to nanoelectrodes, or to two sizes or types of gold nanoparticles, by hybridization to DNA oligonucleotides (oligodeoxynucleotides, ODNs). A control RNA, GX, a
Figure 1. Experimental design. (A) Schematic of the sequences, structures, and interactions of the nucleic acids used. RNA hairpin molecules E1 and G2 interact through two distinct Mg2+-dependent loop-receptor interactions: L1-R1 (red) and L2-R2 (green). The sequence modification introduced to form the noninteracting derivative GX is shown in yellow. The thiol-derivatized ODNs for attachment to gold nanoparticles or electrodes are shown in blue. The ODN for attachment of E1 to the gold electrode does not contain a 5′-A10 extension. (B) Schematic showing the sequential addition of 30- and 15-nm gold nanoparticles (decorated with an illustrative number of RNA motifs; see the text) to nanopatterned electrodes through RNA-RNA interactions, shown with the same color-coding used in A. The figure is approximately to scale, although the nucleic acids have some flexibility, and thus the distance between particles may be an overestimate.
derivative of G2 with an altered tetraloop sequence, was also designed to exhibit no interaction with E1.16 The RNA molecules were synthesized by in vitro transcription of PCR-generated templates12 and tested for their ability to form complexes by a mobility shift assay on a polyacrylamide gel in the presence of magnesium ions. Increasing concentrations of E1 were incubated with radiolabeled G2, and the resulting complexes were subjected to electrophoresis (Figure 2). E1 and G2 form a tight association in the presence of 15 mM Mg2+ with a Kd of 50 nM (Figure 2D) that is probably due to adventitious hybridization between the single-stranded tails, and which was abolished in the presence of the complementary DNA strand (Figure 2E). As expected, RNA GX showed no detectable association with E1 (data not shown). In preparation for RNA functionalization, small (15 nm) or large (30 nm) citrate-stabilized gold nanoparticles were coated with either 5′ or 3′ thiol-derivatized single-stranded ODNs,17 which were designed to hybridize with the extension 446
Figure 2. RNA-RNA interactions analyzed by mobility shift assays on polyacrylamide gels. Low concentrations of radiolabeled G2 (1 nM) or E1 (0.5 nM) were incubated with the indicated concentrations in nM of unlabeled RNAs, in the presence or absence of the corresponding complementary ODNs, and the complexes separated on an 8% native polyacrylamide gel. The complexes containing radiolabel were visualized using a phosphorimager. An asterisk (e.g., G2*) indicates the radiolabeled species, and the pictograms illustrate the components of the reactions using the same color coding as that in Figure 1. The blue star indicates the location of the radiolabel. (A) G2-E1 dimerization. (B) G2-E1 dimerization in the presence of complementary ODNs. (C) Self-association of G2. (D) Self-association of E1. (E) Self-association of E1 in the presence of complementary ODN.
sequences present on RNAs E1 and G2 (see Figure 1). Using fluorescently labeled ODNs, the small particles were shown to have an average of approximately 150 ODN ligands per particle of which 50% were accessible for hybridization to complementary RNA (data not shown). Initially, to establish the feasibility of nanoparticle association through the magnesium-dependent RNA loop-receptor interactions, samples of small and large gold particles were functionalized with E1 and G2, respectively. Analysis of a mixture of the two sets of particles by transmission electron microscopy (TEM) showed that the particles were dispersed in the absence of Mg2+, but in the presence of 20 mM Mg2+ they formed aggregates with specific small-particle-large-particle interactions (Figure 3A). Importantly, the aggregation was reversed by the addition of the Mg2+ chelator, EDTA (Figure 3B). The specificity of the association was demonstrated in control experiments using large particles functionalized with GX in place of G2; no aggregation was observed in the presence of Mg2+. Using simple geometrical arguments and the RNA/ODN surface coverage above, if these are uniformly dispersed over the surface then there may be of the order of Nano Lett., Vol. 6, No. 3, 2006
Figure 3. Electron micrographs showing association of RNAderivatized gold particles. Samples for transmission electron microscope inspection (A-C) were prepared and examined as described previously (ref 17). (A) A mixture of large particles (0.3 nM) derivatized with G2 and small particles (3.0 nM) derivatized with E1 in phosphate buffer (10 mM, pH 7.0) containing NaCl (0.3 M) in the presence of Mg2+ (30 mM). (B) Same as A with the addition of EDTA (100 mM). (C) Same as A but using small and large particles with a reduced number of E1 ligands. (D) shows a scanning electron micrograph of a pair of nanoelectrodes with gold nanoparticles immobilized into the gap using the same materials as those in C.
five RNA/RNA interactions between two particles. Although at this low density of coverage only one or two of the five possible pairings may hold any two particles together, the density is sufficient to allow the formation of branched structures. An illustration of this may be seen by comparing the TEM images of Figure 3A and 3C where, by reducing the number of RNA molecules per particle (through the addition of ODNs that compete with the RNA hybridization sites), the size and complexity of the nanoparticle ensembles formed can be limited. Guided by the nanoparticle association observed in the above TEM images, the preparative method was further optimized in order to immobilize a chain of nanoparticles between two lithographically fabricated nanoelectrodes (see Figures 1 and 3D). The gold nanoelectrodes were fabricated using electron beam lithography on a silicon wafer with a 300-nm thermally grown oxide surface layer. The electrodes had a triangular taper and were separated by 50 nm at their closest point. The nanoparticle-decorated structure of Figure 3D was prepared by first using thiol-terminated ODNs with a sequence complementary to the ODN extension on RNA E1 to form self-assembled monolayers on each of the gold nanoelectrodes. The derivatized substrates were then immersed in a solution containing RNA E1. After hybridization, the substrate was washed thoroughly with buffer [phosphate (10 mM, pH 7.0) containing NaCl (0.3M)] and then Nano Lett., Vol. 6, No. 3, 2006
immersed in a solution similar to that used for the TEM preparations above, containing Mg2+ and 30-nm gold nanoparticles that had been functionalized previously with RNA G2. After allowing Mg2+-mediated E1-G2 association to occur, the electrodes were rinsed with 10 mM phosphate buffer solution and then immersed in a solution containing Mg2+ and 15-nm gold nanoparticles functionalized with RNA E1. Finally, the substrate was reimmersed in the Mg2+/30 nm RNA G2 functionalized gold nanoparticle solution and the electrodes were inspected in a scanning electron microscope (SEM) after a reaction period of ∼1 h followed by thorough washing (Figure 3D). As Figure 3D shows clearly, this protocol leads to the formation of a wire composed of gold nanoparticles between the two 50-nm-separated lithographically fabricated electrodes. Examination of substrates from a variety of control experiments, which included the use of nanoparticle solutions free of Mg2+ electrolyte and electrode substrates that were not modified with suitable thiol-terminated ODNs, indicated that gold nanoparticle immobilization or nanoparticlenanoparticle association did not occur. Thus, we have shown that the formation of the nanoparticle wire is due to Mg2+mediated interactions between appropriate folded RNA motifs that have been tethered to variously sized gold nanoparticles. We also found, using different nanoparticle concentrations and reaction times, that it was possible to either form larger clusters of nanoparticles bridging the electrode gap or immobilize a smaller number of particles that did not bridge the gap. The conduction properties of devices containing large clusters of nanoparticles in the electrode gap showed low resistance and linear current-voltage (IV) behavior at room temperature. However, when the nanoparticles formed a single chain, or wire as shown in Figure 3D, the roomtemperature conduction was nonlinear. Consequently, these devices were characterized as a function of temperature (T) in a vacuum cryogenic measurement system. The resistance at 293 K was found to be approximately 7 MΩ. Using low bias voltages in the -0.2 to 0.2 V range, IV plots were obtained for temperatures down to 100 K. Representative data for a particular device is shown in Figure 4A. The IV characteristics are Ohmic in nature, although characteristics compatible with single electron phenomena, such as those proposed for metallic nanoparticle motion,18 are observed at 100 and 130 K (Figure 4A (inset)). The conductivity (σ) at low bias (as V f 0) decreases rapidly with decreasing temperature above 160 K and is typical of activated transport. Below this temperature, the rate of change of conductivity with temperature is much reduced. Conduction properties of this nature have been studied rigorously for metal and semiconductor systems.19 In the high-temperature regime our data is modeled as σ ) σ0 exp(-W/kT) where σ0 is the maximum conductivity, W is the activation energy, and k is the Boltzman constant. We find W ) 0.29 eV and σ0 ) 10 mS (see Figure 4B). In our device, we expect that the oligomers will remain between the gold particles, but we do not attribute the observed conductivity to this material because there is some evidence 447
iteration of the technology may involve the incorporation of additional directionality into the RNA-RNA assembly so as to “program” the branching patterns of nanoparticle structures such as those of Figure 3A. This would have the potential of leading to the deposition of highly structured assemblies, possibly containing ordered arrangements of metallic and nonmetallic nanoparticles, onto addressable substrates. Applications include the fabrication of microelectronic architectures, hybrid electronic devices, and sensing. Acknowledgment. This work was supported by EU project IST-2001-32152 (MINT) and NSF grant CHE0317154. We thank Andrew Long for use of vacuum cryogenic facilities and Don Bethell and John Davies for valuable discussions. Note Added after ASAP Publication. Changes were required in the author byline, in Figures 2 and 3 and their captions, and in the surrounding text where Figures 2 and 3 are discussed in the version published ASAP on January 31, 2006; the corrected version was published ASAP February 3, 2006. References
Figure 4. (A) Current-voltage (IV) characteristics at low bias of a self-assembled wire for temperatures in the 100-293 K range. The inset shows a detailed IV characteristic at 130 K with a larger bias voltage. (B) An Arrhenius plot of the conductivity at low bias. The data fits to a straight line for T > 150 K, but dσ/dT f 0 at lower temperatures.
from work on DNA that the material will be highly resistive or even insulating.20 We also do not attribute the conductivity to the presence of water at such low temperatures. We therefore conclude that the transport is due to the gold particles and thermally activated electron hopping between the particles, as has been observed in 2D Au nanoparticle films. At low temperatures in 1D and 2D systems, the conductivity has previously been attributed to variable range hopping.21 However, in the present device we observe that dσ(T)/dT f 0 at low temperature; hence, it is our conjecture that the conductivity is dominated by a single tunnel barrier in the wire. In conclusion, we describe a method based on the Mg2+dependent interaction between RNA motifs to assemble an Au nanoparticle wire that exhibits activiated charge transport. The techniques demonstrated have the ability to combine and link two or more particles or devices to form complex functional structures and in the future may be used to assemble practical circuits. The more sophisticated 2D structures shown by Chworos et al.13 indicate that a future
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(1) Semiconductor Industry Association, International Technology Road Map for Semiconductors; SEMATECH: Austin, TX, 2002. (2) Marrian, C. R. K.; Tennant, D. M. J. Vac. Sci. Technol., A 2003, 21, S207-S215. (3) Wakabayashi, H.; Yamagami, S.; Ikezawa, T.; Ogura, A.; Narihiro, M.; Arai, T. 2003 IEEE International Electron Devices Meeting, Tech. Dig. 2003, 989-991. (4) Tans, S. J.; Verschueren, A. R. M.; Dekker, C. Nature 1998, 393, 49-52. (5) Gittins, D. I.; Bethell, D.; Schiffrin, D. J.; Nichols, R. J. Nature 2000, 408, 67-69. (6) Piva, P. G.; DiLabio, G. A.; Pitters, J. L.; Zikovsky, J.; Rezeq, M.; Dogel, S.; Hofer, W. A.; Wolkow, R. A. Nature 2005, 435, 658661. (7) Keyes, R. W. Proc. IEEE 2001, 89, 227-239. (8) Yan, H.; Park, S. H.; Finkelstein, G.; Reif, J. H.; LaBean, T. H. Science 2003, 301, 1882-1884. (9) Chung, S.-W.; Ginger, D. S.; Morales, M. W.; Zhang, Z.; Chandrasekhar, V.; Ratner, M. A.; Mirkin, C. A. Small 2005, 1, 64-69. (10) Kretschmer, R.; Fritzsche, W. Langmuir 2004, 20, 11797-11801. (11) Jaeger, L.; Leontis, N. B. Angew. Chem., Int. Ed. 2000, 39, 25212524. (12) Jaeger, L.; Westhof, E.; Leontis, N. B. Nucleic Acids Res. 2001, 29, 455-463. (13) Chworos, A.; Severcan, I.; Koyfman, A. Y.; Weinkam, P.; Oroudjev, E.; Hansma, H. G.; Jaeger, L. Science 2004, 306, 2068-2072. (14) Cate, J. H.; Gooding, A. R.; Podell, E.; Zhou, K.; Golden, B. L.; Kundrot, C. E.; Cech, T. R.; Doudna, J. A. Science 1996, 273, 16781685. (15) Geary, C.; Baudrey, S.; Leontis, N.; Jaeger, L., unpublished work. (16) Liu, B.; Baudrey, S.; Jaeger, L.; Bazan, G. C. J. Am. Chem. Soc. 2004, 126, 4076-4077. (17) Kanaras, A. G.; Wang, Z.; Bates, A. D.; Cosstick, R.; Brust, M. Angew. Chem., Int. Ed. 2003, 42, 191-194. (18) Nishiguchi, N. Phys. ReV. Lett. 2002, 89, 066802. (19) Ando, T.; Fowler, A. B.; Stern, F. ReV. Mod. Phys. 1982, 54, 437672. (20) Storm, A. J.; van Noort, J.; de Vries, S.; Dekker, C. Appl. Phys. Lett. 2001, 79, 3881-3883. (21) Schmid, G.; Simon, U. Chem. Commun. 2005, 697-710.
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Nano Lett., Vol. 6, No. 3, 2006
