DNA-Templated Pd Conductive Metallic Nanowires

  • Khoa Nguyen
  • Stephane Campidelli
  • Arianna Filoramo
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 749)

Abstract

We here present a protocol for the metallization of DNA scaffolds by palladium. The method is based on the initial slow precipitation of palladium oxide onto DNA strands. A reduction step follows to create conductive metallic nanowires. The slow oxide precipitation approach enables the formation of thin and continuous coatings on the DNA strands with negligible parasitic metallization of the remaining substrate surface.

Key words

DNA metallization Metal nanowires Templated self-assembly Nanoelectronics Molecular combing 

1 Introduction

In nanotechnology, self-assembly is a valuable strategy where the design, manufacture, and control on the scale of a few nanometers are governed by molecular and supramolecular affinities (like structural and chemical properties). In particular, the exceptional recognition properties of DNA make it an ideal candidate to encode instructions for such nanoscale assembly to create scaffolds (1, 2) and to incorporate other materials in the self-assembly process (3). In nanoelectronics, it is highly desirable to utilize DNA not only as a positioning scaffold but also for electrical interconnections. Since DNA transport properties are still under discussion (4), it is pragmatically envisioned to develop a method where electronic conduction is ensured by a metallic coating selectively deposited onto the DNA strand.

During the past 10 years, numerous methods to metalize DNA scaffolds have been developed (5). Different metals have been used in the metallization process based on silver (6, 7) or copper (8) ions, gold nanoparticles (9, 10), platinum (11, 12, 13, 14, 15, 16, 17, 18), or palladium (19, 20, 21, 22, 23, 24) complexes.

Recently, Pd metallization appeared of particular interest (25) since it has been shown to be the best choice for electrodes connecting single-wall carbon nanotubes (SWNTs). SWNTs occupy a special place within molecular electronics (26) and a particular attention is given to methods that can lead to the self-assembling and electrical connection of these nanoobjects. In the DNA-directed vision, the metallization process should be the last step of the fabrication process to use the DNA recognition properties as long as possible. Therefore, the most proficient scenario consists of DNA already deposited in the definitive circuit arrangement onto the substrate, where the final metallization can take place. The ultimate goal of the metallization process is to obtain thin metallic nanowires, while minimizing parasitic metal cluster nucleation and growth on the surrounding surface. In addition, attention should be devoted to both structural and conductive homogeneity of the obtained nanowires; these two issues are crucial for the use of DNA scaffolding in a circuit. Neither a big resistance value nor a large desorption of nanostructures during the process are acceptable.

Here, we present a protocol to metallize DNA with Pd. The DNA is first combed on a surface to facilitate the evaluation of the yield and uniformity of the metallization process. The surface is SiO2, the standard for micro and nanoelectronics, and it is passivated by a silanization process to minimize the parasitic metallization. The chosen silane is hexamethyldisilazane (HMDS). After the deposition of the DNA nanoobjects to be metallized (as for the case of combed DNA for which we here give instructions) a thin DNA-templated wire of palladium oxide is then grown with a strong preference over precipitation on the substrate ­surface. Reduction of the oxide to metal makes the obtained nanowires conductive.

One of the main advantage of this method is that it allows to have uniform metallization and preserve samples against large desorption. This is not always the case for other published protocols where cycling of different solutions is needed and where fast reduction kinetics are employed. It is worth to note that these two aspects are generally difficult to control to achieve a good homogeneity of the nanowire geometry and properties.

In Subheading 3.1, we describe the surface treatment of SiO2 substrates with hexamethyldisilazane (HMDS); this is performed in order to limit parasitic metallization of the substrate when DNA strands are metalized.

Subheading 3.2 explains the surface characterization procedure for testing the above-mentioned surface treatment: contact-angle measurement.

The contact angle (θ) at the liquid–vapor interface is a widely used characterization method to evaluate the degree of wettability of the surfaces. It is defined as the angle between the tangent to a liquid droplet deposited on a planar solid surface and the solid surface itself. In a first approximation, the relation between the contact angle and the interfacial tensions of the three phases (vapor, liquid, and solid) can be described by the Young’s equation (see Fig. 1).
Fig. 1.

Definition of the contact angle. On a hydrophilic substrate θ is small, while it gets larger (larger than a right angle) on a hydrophobic surface.

In the case of a water droplet, the contact angle characterizes the hydrophobicity of the surface: in our case, it helps to monitor the presence of CH3 groups introduced by the silanization.

Subheading 3.3 describes how to obtain substrates with adsorbed combed DNA, which are ideal for the verification and optimization of the metallization procedure. The combing principle and setups are well described in literature (27, 28).

Subheading 3.4 describes the protocol for the mineralization and the metallization of the surface-adsorbed DNA molecules. The rationale of this protocol is the following (and it is described in Fig. 2): after depositing DNA on the substrate, a selective precipitation of the oxidized form of Pd on DNA is realized, toward the formation of a nanowire, according to the following reaction (29, 30, 31):
Fig. 2.

Scheme of the metallization by precipitation/reduction approach. (a) The palladium oxides precipitate onto the DNA scaffold. A palladium oxide nanowire is obtained. (b) the palladium oxide nanowire is converted to a metallic palladium one by a reducing agent.

$$ {K}_{2}PdC{l}_{4}+{H}_{2}O\to PdO\downarrow \text{ + }2HCl\text{ + }2KCl.$$

Here, the final diameter, continuity, and uniformity of the nanowire are realized. At this stage, however, the nanowire is nonconducting. The reduction of oxides with metallic behavior is then performed, only when the nanowire is completely formed.

2 Materials

  1. 1.

    Deionized (DI) water, 18.2 MΩ resistivity (Millipore).

     
  2. 2.

    Si/SiO2 subtrates: As doped Si n type <100> orientation with 150 nm of SiO2 (Siltronix).

     
  3. 3.

    Hexamethyldisilazane (CH3)3 SiNHSi(CH3)3 HMDS (99.9% purity, Sigma-Aldrich).

     
  4. 4.

    Piranha solution: 1:3 by volume mixture of 30% hydrogen peroxide and concentrated sulfuric acid. (Caution: Piranha solution reacts violently with organic materials and should be handled with extreme care.)

     
  5. 5.
    Dipotassium tetrachloropalladium complex (K2PdCl4) (Sigma-Aldrich): the K2PdCl4 solution is prepared at 20 mM and let hydrolyze during 2 weeks at 4°C. The hydrolization degree is checked by measuring the pH of the solution in analogy of what is done for Pt complexes (18). See Fig. 3 for the pH trend over time.
    Fig. 3.

    Evolution of pH vs. time of Pd complexes solution. It indicates the degree of hydrolysis.

     
  6. 6.

    Lambda phage DNA, methylated, from Escherichia coli (Sigma-Aldrich).

     
  7. 7.

    ULSI (ultra large-scale integration) grade acetone (Sigma-Aldrich).

     
  8. 8.

    MES–NaCl buffer: 10 mM MES buffer (Sigma), 50 mM NaCl, pH 5.5.

     
  9. 9.

    Hydrogen gas, pure (compressed).

     
  10. 10.

    Lambda DNA solution: 7 ng/μl λ-DNA (Sigma) in MES–NaCl buffer.

     

3 Methods

3.1 Silanization of SiO2 with Hexamethyldisilazane

  1. 1.

    A 2-in. silicon wafer (with a 1,500  Å surface layer of SiO2) is treated with piranha solution for 1 h, then carefully rinsed with deionized water.

     
  2. 2.

    A step of RIE (reactive ion etching) in a O2 plasma is then performed to increase the reactivity of the surface (i.e., the density of surface silanols). The parameters for the RIE are 130 V, 2 min, 5 mbar.

     
  3. 3.

    The wafer is then baked for 15 min at 170°C to achieve dehydration, thus preventing HMDS from reacting with water.

     
  4. 4.

    The substrate is put in a sealed glass chamber (500 ml) with a small open glass container with 100 μl of HMDS for 30 min (in air).

     
  5. 5.

    The wafer is carefully rinsed with deionized water then with acetone (see Note 1).

     

The HMDS monolayer formed can then be characterized by two methods.

3.2 Surface Contact-Angle Measurement

We measure the contact angle by using the simple experimental setup schematized in Fig. 4.
Fig. 4.

Scheme of contact-angle measurement setup.

  1. 1.

    Place the solid substrate on a plane goniometer.

     
  2. 2.

    Deposit a 10 μL water droplet on the surface with the aid of a micropipette.

     
  3. 3.

    Shine white light on the droplet by using a lamp and record the image of the droplet on the surface by using a CCD camera.

     
  4. 4.
    Evaluate the contact angle from the picture (as shown graphically in Fig. 5). As an example, we report in Fig. 6 the measured contact angle vs. the HMDS silanization time (see Note 2).
    Fig. 5.

    Example of recorded image for contact-angle measurement.

    Fig. 6.

    Pilot of the contact angle on HMDS–SiO2 as a function of the time of silylation.

     
  5. 5.

    AFM imaging can also be performed at this stage in order to test the flatness and cleanliness of the surface (see Note 3).

     

3.3 DNA Combing on HMDS-Coated Silicon

  1. 1.
    Dip coat the substrate in a λ-phage DNA solution in MES–NaCl pH 5.5 by applying a meniscus receding speed of ∼100 μm/s. We used a combing setup as schematized in Fig. 7.
    Fig. 7.

    Scheme of combing technique by receding meniscus.

     
  2. 2.
    Evaluate the results of combing by AFM imaging of the dry substrate. In Fig. 8, an AFM image of the combed DNA is shown.
    Fig. 8.

    λ-DNA combed onto a HMDS/SiO2 substrate.

     

3.4 DNA Mineralization and Metallization

  1. 1.

    The sample with the combed DNA is immersed in the ­precipitation solution contained in a microtube. Then, it is incubated at 45°C for 42 h, in a thermostat (see Notes 4 and 5).

     
  2. 2.

    The sample is then removed from the microtube, carefully rinsed with deionized water and dried with nitrogen.

     
  3. 3.

    Reduce the nanowires by placing the sample in a static 1 bar hydrogen atmosphere overnight at 400°K (see Note 6).

     
  4. 4.

    XPS analysis can be used at this stage to verify the extent of reduction (see Note 7).

     
  5. 5.
    SEM or AFM imaging can give insight on the quality and homogeneity of the nanowires. In Fig. 9, we report, respectively, AFM (Fig. 9a) and SEM images (Fig. 9b) before and after the process. It is possible to evaluate that nearly no DNA desorption and breakage is induced by the process. Higher resolution micrographs can be analyzed in order to evaluate the nanowire thickness and homogeneity (25).
    Fig. 9.

    Micrographs of the sample surface before and after the metallization process. (a) AFM phase image of a 13  ×  13 μm2 area after combing and prior to metallization. (b) SEM image of a 20  ×  15 μm2 area of the same sample after metallization.

     

4 Notes

  1. 1.

    This rinsing step is intended to remove any physisorbed layer or hydrolyzed silane, from the reaction of HMDS with any residual water.

     
  2. 2.

    We note that the contact angle value saturates around 80° indicating a limitation in the number of the grafted trimethylsilyl (TMS) groups. This phenomenon has already been observed and it can be explained by a reached equilibrium between the grafting process and the partial destruction of TMS by the released ammonia following Belyakova et al. (32).

     
  3. 3.

    AFM tapping-mode phase imaging (such as that showed in Fig. 8) is useful in evidencing the presence of HMDS layers (especially easy to visualize on patterned substrates) as the height of the HMDS molecules covering the surface is below 3Å and a low contrast is commonly obtained in height or amplitude images.

     
  4. 4.

    During the incubation time, the PdO deposits onto DNA in a very slow and progressive way, allowing the control of morphology of the PdO nanowire from coarse discontinuous to continuous. In this way, it is possible to obtain extremely regular, thin, and continuous nanowires down to a diameter of 20–25 nm. At the end of this step of PdO deposition, the nanowires are completely formed and similar in terms of size and shape. Thanks to the surface passivation, the precipitation process is selective and extremely well templated by the DNA scaffold. Only limited parasitic precipitation on the substrate is observed for the typical duration of experiments yielding the desired nanowires.

     
  5. 5.

    The temperature and time of incubation are key parameters of the reaction to control the homogeneity of synthesized nanowires. Those reported are the results of parameter optimization in our conditions and adjustments might be necessary (see also ref. 25).

     
  6. 6.

    For the reduction step, two reducing agents were studied: dimethylamine borane (DMAB) and hydrogen. The DMAB reduction can be performed by 15 min immersion of the sample in a 20 mM DMAB solution. In this case, XPS measurement demonstrated that only first layer of Pd is reduced, but in our hands, hydrogen gas gave the best results (for reduction H2 no form of oxidized Pd can be detected).

     
  7. 7.

    It should be noted that XPS analysis is a surface technique and only the first few nanometers can be characterized. Therefore, any conclusion cannot be done for the more internal core of the nanowire. However, the metallic character of the nanowire was also confirmed by electrical measurements. The resistivity of single nanowires was determined by us from the I/V curves and was found to be 3  ×  10−6 Ωm which is one order of magnitude higher than that of bulk Pd (1.05  ×  10−7 Ωm) (see also ref. 25).

     

Notes

Acknowledgments

This work was partially funded by the NUCAN-NMP Strep 013775 project and the French Ministry of Research through the ACI Bio-NT project.

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Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Khoa Nguyen
  • Stephane Campidelli
  • Arianna Filoramo
    • 1
  1. 1.Laboratoire d’Electronique MoléculaireCEA SaclayGif-sur-Yvette CedexFrance

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