Article pubs.acs.org/JPCC
Role of Alumina Coatings for Selective and Controlled Bonding of DNA on Technologically Relevant Oxide Surfaces Théo Calais,†,‡ Benoit Playe,§ Jean-Marie Ducéré,†,‡ Jean-François Veyan,§ Sara Rupich,§ Anne Hemeryck,†,‡ Mehdi Djafari Rouhani,†,‡ Carole Rossi,†,‡ Yves J. Chabal,§ and Alain Estève*,†,‡ †
CNRS, Laboratoire d’analyse et d’architectures des systèmes, 7 avenue du Colonel Roche, F-31400 Toulouse, France Université de Toulouse, LAAS, F-31400 Toulouse, France § Department of Materials Science and Engineering, University of Texas at Dallas, Richardson, Texas 75080, United States ‡
S Supporting Information *
ABSTRACT: DNA immobilization on surfaces is crucial to a number of applications. However, detailed understanding of DNA/surface chemistry remains poorly documented, especially on oxide surfaces, due to the complexity of such large molecules. This work focuses on a simpler molecule, 2-deoxythymidine-5-monophosphate (dTMP), which contains all the chemical elements of DNA. It confirms that adsorption of dTMP onto OH-terminated SiO2 surfaces does not result in a chemical bond (dTMP readily washes off) and instead shows that dTMP chemically adsorbs on Al2O3 surfaces. We combine first-principles calculations, X-ray photoelectron spectroscopy (XPS) and Fourier transform infrared (FTIR) spectroscopy to determine the bonding configuration of dTMP onto alumina surfaces controllably grown by atomic layer deposition. We demonstrate that dTMP covalently reacts with alumina. Calculations indicate that covalent bonding of all dTMP polar groups (sugar ring, phosphate group, and thymine) is thermodynamically favored. Spectroscopic data and theory-based assignments of vibrational modes show that the bonding takes place primarily through both the thymine and phosphate groups. The reactivity and the tendency for dTMP to lie flat on the surface lead to an irreversible and disorganized dTMP layering. Studies of dTMP adsorption as a function of Al2O3 thickness show that the density of grafted dTMP can be controlled, with measurable amounts even above the Al2O3 monolayer coverage. These findings provide technological directions for DNA-based nanotechnologies to graft DNA on surfaces that would otherwise be unreactive. architectures.22,23 Grafting DNA on other surfaces, such as on CuO and Al nanoparticles, has also successfully been performed for nanoenergetic applications.12 Recently, developments to spatially control immobilization (via either electrostatic or covalent interactions) of individual DNA nanostructures such as origamis onto silicon has focused attention and stressed many issues to achieve proper self-organization and integration into larger on-chip nanosystems.24,25 However, apart from work done on gold or modified-silicon dioxide surfaces,26−28 there has been few quantitative analyses to unravel the bonding of DNA on other surfaces of technological interest, thus impeding further developments.29−31 The knowledge remains qualitative, relying more on empirical observations such as the use of thiol (for metallic surfaces20) or carboxylic acid or biotin/streptavidin (for oxides and semiconductor surfaces),12,32 which directly impacts the control and reproducibility of the experimental results. For instance, there is a qualitative recognition that DNA does not
1. INTRODUCTION For the past decade, DNA has attracted increasing interest for nanotechnologies because of its ability to self-organize at the molecular scale,1−5 making it one of the most versatile nanoobjects for applications in several potential fields (medicine, nanoelectronic, environment, energy, etc.).6−12 Controlled DNA sequences are able not only to program the assembly of 1D, 2D, and 3D objects of almost any shape but also to interact selectively with almost any other molecular object, biological or not.13−18 Obviously, the control of DNA−surface interactions and related spatial self-organization is critically important for developing specific applications, such as the integration of DNA into MEMS (microelectromechanical systems). Most of the fundamental studies of DNA adsorption have been done on gold surfaces, due to the availability of thiolmodified DNA and the well-known sulfur affinity to gold.19 This has led to a number of applications at the intersection of physics, chemistry, and biology. For instance, thiol-terminated DNA strands have been used to graft DNA onto gold surfaces for the fabrication of nucleic microarrays20,21 or on gold nanoparticles for demonstrating the DNA ability to produce well organized and programmable 2D and 3D hybrid © XXXX American Chemical Society
Received: July 15, 2015 Revised: September 17, 2015
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DOI: 10.1021/acs.jpcc.5b06820 J. Phys. Chem. C XXXX, XXX, XXX−XXX
Article
The Journal of Physical Chemistry C
concentration dependence. With the support of DFT modeling, it provides detailed bonding information and thermodynamic insight, which suggests a powerful modification of glass surfaces for enhanced DNA adsorption without the need for organic functionalization, which greatly simplifies the process and opens new avenues for technology.
bind directly and covalently to oxidized silicon surfaces, leading to the need to functionalize surfaces, for instance, with amineterminated organic layers typically using silane chemistry to graft to the SiO2 surfaces.33−37 It is therefore important to address DNA bonding to oxide surfaces to open new fields of application. In order to unravel the chemical bonding of DNA, a simplified model molecule is chosen, 2-deoxythymidine-5monophosphate (dTMP), because its simple molecular structure comprises all basic elements of a DNA chain (see Figure 1). The small size of dTMP, compared with regular
2. MATERIALS AND METHODS 2.1. Materials. We used standard thymidine 5′-monophosphate disodium salt hydrate abbreviated dTMP supplied by Sigma-Aldrich. Sodium chloride (NaCl, Sigma-Aldrich) was used to prepare control solutions to understand the effect of salt on the investigated surfaces. Other chemicals were as follows: acetone (Fisher), ammonium hydroxide (40%, Aldrich), dichloromethane (Fisher), hydrofluoric acid (49%, CMOS grade, JT Baker), hydrogen peroxide (30%, CMOS grade, JT Baker), methanol (Fisher), sulfuric acid (98%, Aldrich), trimethylaluminum (TMA). Nanopure deionized water (dH2O) with a resistivity of 18.2 MΩ.cm was obtained via a Millipore system and deoxygenated via N2 purge prior to use. Single-crystal phosphorus doped n-type Si(100) CZ and FZ wafers with resistivity 20−60 Ω·cm, thickness of 500−550 μm, and thermal oxide thickness of 5−10 nm were acquired from Atecom and used as substrates. 2.2. Surface Preparation. Prior to the H-terminated preparation, FZ silicon substrates were cleaned by 10 min sonication in dichloromethane, acetone, and then methanol. The oxide was subsequently regrown by immersion in “SC1 solution” consisting of 4:1:1 H2O/H2O2/NH4OH (by volume) for 15 min at 80 °C, followed by “SC2 solution” consisting of 4:1:1 H2O/H2O2/HCl for 15 min at 80 °C. Substrates were etched by a 20 s immersion in HF for 1 min 30 s and finally immersed in a second SC1 solution. After this step, a FTIR analysis of the surface is processed to determine a reference before the H-termination obtained by etching the surface in NH4F for 15 min. A second IR spectrum is then taken to determine the quality of the H-terminated silicon surface before dTMP deposition. For the deposition of dTMP on silicon surfaces with a thermal oxide, oxidized CZ silicon substrates were cleaned by a “Piranha” treatment (2:1 solution of concentrated H2SO4: 30% H2O2 by volume) at 80 °C for 30 min. (Note that piranha must be handled with care as it is extremely oxidizing, reacts violently with organics, and should be stored in vented containers to avoid pressure buildup). Finally, prior to the deposition of alumina films by ALD, CZ silicon surfaces were cleaned using a “Piranha” treatment. After this treatment, the substrates were etched by a 20 s immersion in HF, after which an oxide was regrown by immersion in SC1 solution for 15 min at 80 °C and followed by SC2 solution. After these cleaning steps, a 2 nm-thick Al2O3 film was deposited with a Cambridge Nanotech Savannah 100 atomic layer deposition system in a cleanroom using 20 cycles of TMA and H2O. The thickness (∼2 nm) was measured with a Horiba Jobin UVISEL spectroscopic ellipsometer. Alumina surfaces were finally cleaned before reaction with dTMP by 10 min sonication in dichloromethane, acetone, and then methanol. 2.3. dTMP Attachment Procedure. Several solutions of 50 mM dTMP were prepared by dissolution of 5 mg of dTMP in 273 μL of dH2O. dTMP attachment reactions were conducted by immersing clean alumina, oxidized silicon, or H-terminated silicon substrates (5.7 cm2) in a 50 μM dTMP solution prepared by dilution of 1.5 μL of the stock solution
Figure 1. Chemical representation of 2-deoxythymidine-5-monophosphate (dTMP).
DNA, makes it possible to derive much more precise information and synergies from spectroscopy and atomicscale modeling, avoiding the potential interference of noninteracting parts of longer DNA strands. Recognizing that bonding may involve more than just the chemical groups (e.g., DNA structure), the present work combines spectroscopic studies (infrared absorption spectroscopy and X-ray photoelectron spectroscopy) with first-principles DFT-based (density functional theory) modeling to unravel the bonding mechanism of dTMP to three types of surfaces: hydrophobic H-terminated silicon, hydrophilic OH-terminated SiO2, and Al2O3-coated silicon surfaces. The addition of a thin Al2O3 film on silicon is done using atomic layer deposition (ALD), which makes it possible to deposit conformal ultrathin films with monolayer precision, that is, to chemically modify silicon oxide surfaces. For this surface, we explore a coverage range from chemically modified SiO 2 (i.e., using a couple ALD cycles of trimethylaluminum (TMA) and H2O) to thicker stoichiometric Al2O3 films (obtained with 20 cycles of TMA and H2O) in order to determine the role of such coating layer on dTMP bonding. We briefly show that there is no chemical bonding on the first two types of surfaces, and therefore focus most of the work on Al2O3-coated surfaces. Such a coating is attractive both for its compatibility with conventional micro- and nanofabrication techniques and for the simplicity to deposit thin alumina films using ALD, which is a technique compatible with microelectronics processing, as well as with treatment of large area glass. It is a good candidate to modify silicon or glass surfaces for the purpose of DNA attachment. The main finding of this work is that dTMP chemisorbs on Al2O3 surfaces, even on ultrathin layers. In fact, we find that the density of adsorbed dTMP can be controlled by the amount of Al2O3 deposited (i.e., thickness of the Al2O3 layer), down to a single Al2O3 monolayer, illustrating the role of alumina coatings to activate and control DNA adsorption on oxides. This study includes the determination of processing parameters and incubation time as well as the temperature and dTMP B
DOI: 10.1021/acs.jpcc.5b06820 J. Phys. Chem. C XXXX, XXX, XXX−XXX
Article
The Journal of Physical Chemistry C
of 19.057 × 16.503 × 34 Å3 with a surface area of 3.145 nm2. Al and O atoms of the bottom layer of the slab are kept frozen during relaxation in order to mimic bulk presence. The bottom layer is passivated with 16 dissociated water molecules (H, OH on O and Al atoms respectively). In order to mimic a hydrated alumina surface, 16 water molecules have been adsorbed and further dissociated on the slab surface. This structure results from a low activated as well as exothermic process and reaches the full coverage of each aluminum surface atom with OH groups (see Supporting Information S1).43,44 Our resulting hydrated model-surface is thus a periodic cell of Al96O176H64, surmounted by a vacuum space and repeated in the three directions. Dissociative adsorption of dTMP on hydrated surfaces was performed by substitution of n water molecules by one dTMP molecule (as shown in eq 1). The number of water molecules depends on the initial position of dTMP on the surface. Ten dTMP configurations have been investigated to capture all possible ways for dTMP to form single or multiple covalent and hydrogen bonds with the substrate (see Supporting Information S1).
with 1.5 mL of dH2O. The temperature of incubation was controlled at 30 °C by immersing the glassware in an oil bath. The interior of the glassware was maintained in a nitrogen environment during the reaction. After the attachment reaction, substrates were delicately dried with nitrogen flow and immediately analyzed by FTIR on an instrument located in a N2 glovebox. All XPS measurements were performed after the FTIR measurements so as not to complicate the analysis in case transport back and forth to the XPS would contaminate the substrates. 2.4. IR Measurements. Attenuated total reflectance (ATR) was used to obtain the IR spectra of dTMP in the liquid state. ATR spectra were obtained with a Thermo Nicolet iS50 FTIR. All measurements on thin films were performed in transmission (∼70° incidence) at 4 cm−1 resolution using a Thermo Nicolet 6700 FTIR spectrometer equipped with a DTGS detector located inside a N2 glovebox (
