Nanotechnology Science and Computation Part 9 pot

Multicomponent Assemblies Including Long DNA and Nanoparticles 201 Fig. 1. Schematic illustration of the procedure for forming a chip-integrated nanowire: (a) DNA and microstructured chip as building blocks, (b) various stretch- ing methods, (c) DNA positioned in an electrode gap, (d) binding of metal ions or particles and subsequent enhancement lead to a metallized nanowire are used in our workgroup. The work on the optimization of the parameters, for example, DNA concentration, buffer conditions, and conditions for the sur- face modification steps, is very important but often tedious. Our experiments have shown that droplet sizes between 0.5 and 1 μl and DNA concentrations between0.6and6ngμl −1 are practicable. Also, surface modification with a simple PDMS (polydimethylsiloxane) vapor treatment in a petri dish offers a possibility to obtain suitable surfaces for the stretching and positioning of DNA strands. 2.1 Immobilization on Mica A simple method for stretching DNA on mica has been described by Li et al. [46] and Cherny et al. [15]. The DNA solution is incubated on one side of the piece of mica for some minutes and then blown off slowly at an angle of 45 ◦ . The functionalization of the surface is provided by cleavage of the mica. Subsequently applied magnesium ions are then able to bridge the net negatively charged surface and the negative backbone of the DNA. However, mica is not suitable for further technological applications because there is no easy possibility to contact the immobilized molecules and it is not very stable 202 A.Wolff,A.Csaki,W.Fritzsche Table 1. Overview of methods for stretching DNA Force Metho d Magnetic Magnetic tweezers Smith et al. [86] Optical Laser tweezers Perkins et al. [75, 76] Moving interface Drying droplet Bensimon et al. [7, 8], Jing et al. [39] Controlled meniscus motion Otobe and Ohtani [69] Moving meniscus Michalet et al. [60] Sliding of a coverslip edge Yokota et al. [107] Gas flow-driven droplet Li et al. [46] Spin stretching Yokota et al. [108] Bulk fluid flow Braun et al. [11] Dielectric Washizu et al. [97], Holzel et al. [36] for handling. For this reason, there is a need for methods using substrates such as glass or silicon, which are important technological materials. 2.2 Immobilization on Glass One of the most important impulses for stretching DNA molecules was the search for new methods for obtaining obtaining restriction maps of isolated chromatin and DNA molecules [35]. Optical methods for mapping individual DNA molecules have been described for yeast artificial chromosomes (YACs) [13, 14], restriction fragments and cosmid probes [72], and λ-DNA [98, 107], for example. The idea has been extended to human genomic DNA. One ap- plication was the mapping of microdeletions in the tuberous sclerosis 2 gene [60]. Fluorescence-stained stretched DNA can be determined optically with an accuracy of better than one micron. The literature describes many methods and variations for the immobilization of DNA in solution on planar substrates. There are many applications which use the interface between air and liquid. The DNA strands can be aligned on a surfaces either by the receding menis- cus of a drying droplet or by simply pulling the substrate out of the solution in a controlled way. In the first case, the molecules are positioned radially with a large concentration of DNA in the center of the drop and few ex- tended fibers/bundles in the peripheral region. The second approach leads to stretched strands in the direction in which the substrate is moved out of the solution. As mentioned above, all surfaces need a suitable functionalization for binding the DNA. Functionalizations usually provide a positive charge to attract and bind the DNA. The chemicals commonly used are APTES (3- aminopropyltriethoxysilane) [24], ODTS (octadecyltrichlorosilane) [92], and PMMA (polymethylmethacrylate) [30]. Multicomponent Assemblies Including Long DNA and Nanoparticles 203 2.3 Immobilization on Microstructured Chips The next step is the integration of DNA strands into technological environ- ments such as microstructured chips with electrodes or defined electrode gaps. Bridging such gaps with molecules followed by a metallization step leads to nanowires with ohmic behavior. Such a process has to be practicable, gener- ally applicable and reproducible. The binding of the DNA to the electrodes is typically done by interaction of complementary sequences [11] but can also be achieved by electrostatic interaction between negatively charged molecule ends and a positively charged surface on the electrode [52]. Ideally, one DNA molecule or bundle is immobilized in one gap. Thereby, bundles are made more stable for further imaging or metallization steps. In a highly parallel process, using the receding-meniscus method, precise positioning of DNA in several electrode gaps could be achieved [53]. Here the DNA follows the electrode structure, and also span the gaps. Fig.2.Left:atomic force microscope picture of an immobilized DNA strand in an electrode gap. Right: Electron-scanning microscope picture of a nanoparticle- labeled DNA strand, spanning an electrode gap. 3 Nanoparticle Binding on DNA Owing to their interesting and powerful properties, colloidal nanocrystals or nanoparticles find wide use in biology and adjacent fields, such as life sciences and nanotechnology. One main application is use as a label or a stain. To- gether with biological molecules [64, 61], they can work as building blocks, enabling the formation of complex patterns and assemblies. Molecular recog- nition leads, for example, to two-dimensional crystals and tubes [82, 83, 84]. Thereby, DNA can provide a nanoscale scaffold [65, 55], so that it is possi- ble to build up nanowires of metallized DNA [11, 80, 79], as we shall see in Section 4. Bioconjugation between DNA and nanoparticles can be performed 204 A.Wolff,A.Csaki,W.Fritzsche via simple adsorption [27] or with the well-known biotin–avidin system [85]. A very efficient and strong method is the use of thiol groups to attach DNA, as first described for thiolated oligonucleotides on planar gold surfaces and later applied to gold nanoparticles [2, 62, 23, 50, 17]. With these techniques, the nanoparticles were attached to a receptor (the oligonucleotide); now it is possible to bind these constructs to positions where a ligand (complemen- tary sequence) is present. This leads to programmable DNA patterns and opens the way to realizing nanocircuits, possibly using nanocrystals as single- electron transistors [43] or arranging them in a desired pattern on the surface [22]. A further simple but smart method is the electrostatic binding of ligand- stabilized nanoparticles to the DNA backbone. The result is an extended linear chain-like structure or ribbon-like structure composed of parallel nanoparticles [95]. Positively charged gold nanoparticles have been used to bind to a DNA strand spanning a microstructured gap [54]. The arrangement of nanoscale building blocks on biomolecular scaffolds demonstrated in this way is a viable approach to obtaining closely spaced assemblies and a step towards biomolec- ular nanolithography. 4 Metallization of DNA The last step process described above is the metallization of the aligned DNA strands. Conductivity is the main requirement for basic electronic building blocks such as wires, resistors, or p–n junctions. According to the predominant conventional wisdom, after a long period of dissent among different research groups, DNA is a poor conductor over longer distances. There are many theo- ries that describe how such electron transport can work. Fink and Schneberger [25] reported a direct measurement of electrical current across DNA molecules that were 600 nm long. They concluded that the inner p-electrons of the base indicated that the DNA had the properties of good semiconductor. On the other hand, photoinduced electron transfer experiments showed a poor macro- scopic electrical conductivity in DNA films [66, 12]. Removal of the water mantle around the double helix leads to reduced conductivity along lambda phage DNA and is strongly temperature-dependent around room tempera- ture [91]. Electronic-structure calculations and direct measurements through λ-DNA molecules adsorbed on mica exhibit values of 10 6 Ω cm −1 and also show a dramatic effect on the measured conductivity which rises to high values after low-energy electron bombardment [18]. The utility of electrostatic force microscopy for probing the conductance of DNA has been demonstrated and has revealed an insulating behavior, in contrast to conducting single-wall car- bon nanotubes [10]. Measurements between nanofabricated gold or platinum electrodes with different gap sizes (40500 nm) showed likewise that DNA is insulating over longer distances [88]. However, there is a consensus that charge transport takes place over the base pairs and their p-orbitals [28]. There are many advantages and disadvantages of these different methods but it seems Multicomponent Assemblies Including Long DNA and Nanoparticles 205 very probable that native DNA has to be discarded for electronic circuits, and replaced by additional materials to provide the desired properties. In ad- dition, the additional materials should have a geometry similar to that of the template DNA. 4.1 Metals and How to Obtain Wires from Them Table 2 shows the metals frequently used in approaches to making nanowire. Interestingly, all elements applied as nanowires are members of either the first or the eighth subgroup of the periodic system of elements. All of them exhibit a very good conductivity and are noble metals so that they can be easily reduced. The idea is to attach metallic clusters or metal particles to the DNA and to form so-called “pearl chains”. These can be used in the next step to form a continuous film on the biomolecule in order to achieve a conducting wire. The size of such mesoscopic clusters is in the range of the diameter of a DNA strand. This is important for homogeneous metal coverage after the enhancement step that will be discussed below. However, a chain of cationic gold colloids or Cd/S clusters [90] electrostatically bound to the anionic backbone of the DNA will not lead to a conducting wire, because the distance between the particles is too large. Therefore, growth of the clusters until they achieve spatial contact is needed. So, they are usually used as seeds in a two-step procedure. In this way, Cd/S clusters could be used to assemble an array of semiconductor nanoparticles matching the shape of the biopolymer, to form a nanowire [16]. Furthermore, selective localization of silver ions along the DNA through Ag + /Na + ion exchange can be used for the seed-binding step. The recognition capabilities of DNA was used to construct a metal wire 12 mm long and 100 nm wide, connecting two electrodes [11]. DNA metallization can also be accomplished by deposition of palladium. Palladium activates the template to form a continuous palladium film after a reducing step [79, 19]. The binding of palladium complexes is very similar to the process of binding of cis-platin, which is very well understood. The use of cis-platin is very important in cancer therapy. The binding of such complexes changes the tertiary structure of the DNA. Additionally, the B-structure of the DNA becomes changed dramatically in the binding region, and base pairs are broken [47, 67]. 4.2 The Final Step Towards Nanowires The surface of the DNA is now activated with metal complexes or nanopar- ticles which act as seeds and subsequently as catalysts in the subsequent re- ducing step, which leads to a homogeneous metal-covered wire where the gaps between the centers of the metal particles are closed. In the case of palladium, Richter et al. used a mix of sodium citrate, lactid acic, and dimethylamine borane [80, 79]. They achieved wires with a diameter of about 50 nm. Some 206 A.Wolff,A.Csaki,W.Fritzsche Table 2. Commonly used metals for nanowires Metal Subgroup Wire diameter (nm) Resistance (Ω) Gold I Keren et al. [41] 50–100 25 Silver I Braun et al. [11, 22] 100 7,000,000 Copper VIII Monson and Wooley [63] 3 Platinum VIII Mertig et al. [57] Palladium VIII Richter et al. [80, 79] 20 other reducing agents are hydroquinone or sodium borohydrate. Also well- known enhancement steps are the reduction of silver nitrate or silver acetate by hydroquinone [32] and the application of tetrachloroauric acid together with ammonium hydroxide [99, 100]. So, it is possible to deposit silver metal vectorially along a DNA molecule to obtain electrical functionality. The first step is the selective localization of silver ions along the DNA through sil- ver/sodium exchange. This is selective and is restricted to the DNA template only [11]. The subsequent “development” of these aggregates is done by the standard photographic procedure, with an acidic solution of hydroquinone and silver ions under low light conditions [9, 37]. Monson and coworkers [63] have shown that copper can also be used to form nanowirelike structures with a height of 3 nm. They deposited copper metal using aqueous copper nitrate so that the copper(II) was electrostatically associated with the DNA. It was then reduced by ascorbic acid to form a metallic copper sheath around the molecule. It was demonstrated that copper nanowires were valuable as inter- connects in nanoscale integrated circuitry. In ongoing experiments [29] cobalt nanoparticles have been assembled in situ on a template of double-stranded DNA to form magnetic nanowires. Palladium ions were bound to DNA and selectively reduced to zero-valence nanoclusters by deposition of Co(0) in a dimethylamine borane. The nanowires so formed were several microns long and 10 to 20 nm thick. 4.3 Sequence-Specific Molecular Lithography A very novel tool for assembling devices into functional circuits is sequence- specific molecular lithography on DNA as a substrate, described by Keren et al. [42]. Here RecA protein binds in a sequence-specific manner and protects the DNA against metallization. This means that the lithographic informa- tion for this accurate and stable pattern is encoded in the DNA itself. The molecular lithography works with high resolution over a broad range of length scales from nanometers to many micrometers. In another approach, based on recognition between molecular building blocks, a DNA scaffold is used to lo- calize semiconducting single-wall carbon nanotubes for the realization of a self-assembled carbon nanotube field-effect transistor operating at room tem- perature [41]. It has also been shown [40] that DNA can retain its biological Multicomponent Assemblies Including Long DNA and Nanoparticles 207 functionality during metallization by aldehyde derivatization. So, in this case the RecA protein protects the DNA molecules in a sequence-specific manner again and allows complex patterning of molecular-scale electronic circuits. 4.4 Sequence-Specific Molecular Lithography with Nanotubes As we have seen, carbon nanotubes also play an important role in the field of molecular nanotechnology. Single-walled carbon nanotubes (SWNTs) which have been covalently modified with DNA can hybridize selectively with com- plementary strands, with minimal nonspecific interactions with noncomple- mentary sequences [33]. These functionalized nanotubes can now act once again as molecular building blocks. Because of their interesting features and their behavior as either a metal or a semiconductor, they have emerged as im- portant materials for nanofabrication, in both electronic devices and sensors. Controlled and selective localization of SWNTs on aligned DNA molecules on surfaces was also shown by Wooley and coworkers and could represent a route to the manipulation and positioning of SWNTs on surfaces. There are approaches to generating masks for photolithographic processes using a small number of DNA sequences to build up a structure of any size. So, it has been possible to assemble carbon nanotube transistors into circuits by using DNA [20, 21]. This provides an important tool in bottom-up biotemplated nanofabrication. 5 Concluding Remarks Since we have been working on the integration of long DNA and nanoparti- cles, we have seen a great potential for these methods in new approaches to electronics. However, we have to point out that there remains a lot of work to be done. All the steps described here are well established as separate proce- dures. However, the combination of these steps into standard procedures has not yet been established. First of all, the problem of the parallelization of the integration of the molecules, which will be very important for commercial or forward-looking applications, has not been satisfactory solved. This is closely connected to the problem of suitable surfaces and both their modification and their functionalization. We have been working a lot on the development of simple, homogeneous surface modifications, especially on microstructured chips. But even the simple method of a drying droplet is not completely un- derstood today. 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