DNA On Silicon Devices: On-Chip Synthesis, Hybridization, and Charge Transfer (original) (raw)
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Synthesis and characterization of DNA-modified silicon (111) surfaces
Journal of The American Chemical Society, 2000
surfaces are modified by attachment of oligodeoxynucleotides and characterized with respect to DNA surface density, chemical stability, and DNA hybridization binding specificity. Surface functionalization employs the reaction of ω-unsaturated alkyl esters with the Si(111) surface using UV irradiation. Cleavage of the ester using potassium tert-butoxide yields a carboxyl-modified surface, which serves as a substrate for the attachment of DNA by means of an electrostatically adsorbed layer of polylysine and attachment of thiol-modified DNA using a heterobifunctional cross-linker. The resultant DNA-modified surfaces are shown to exhibit excellent specificity and chemical stability under the conditions of DNA hybridization. This work provides an avenue for the development of devices in which the exquisite binding specificity of biomolecular recognition is directly coupled to semiconductor devices.
Assessment of porous silicon substrate for well-characterised sensitive DNA chip implement
Biosensors & Bioelectronics
A biochip approach based on porous silicon as substrate is presented. The goal is to enhance the sensitivity of the biochip by increasing the specific surface area on the support. The elaboration of porous silicon layers has been optimized to guarantee good accessibility for large biomolecule targets. Oligonucleotide probes are synthesised directly on the surface using phosphoramidite chemistry. The high specific surface area of porous silicon allows the direct characterisation, by infrared spectroscopy, of the porous layer formation and the functionalisation steps. The monolayer grafting and derivatisation protocol is additionally characterized by wettability and fluorescence microscopy. The surface modification of porous layers (i.e. thermal oxidation and chemical derivatisation) ensures the stability of the structure against strong chemical reagents used during the direct oligonucleotide synthesis. Finally the protocol is successfully transferred to a flat Si/SiO 2 substrate, and validated by biological target specific recognition during hybridisation tests. In particular, radioactive measurements show a 10-fold enhancement of the oligonucleotide surface density on the porous silicon substrate compared to the flat thermal silica.
A short route of covalent biofunctionaliztion of silicon surfaces
Sensors and Actuators B-chemical, 2011
Covalently attached organic monolayers on etched Si(1 1 1) surfaces were prepared by heating solutions of 1-alkenes and 1-alkynes in a refluxing mesitylene. Surface modification was monitored by measurement of the static water contact angle, X-ray photoelectron spectroscopy (XPS), infrared reflection absorption spectroscopy (IRRAS), and atomic force microscopy (AFM). Flat and clean N-hydroxysuccinimide (NHS)ester-terminated/1-decyl mixed monolayers were covalently attached in one step onto a silicon surface. This procedure allows a mild and rapid functionalization of the surface by substitution of the NHSester moieties with amines at room temperature. The NHS-ester groups were shown to be fully intact onto the surface. The surface reactivity of the NHS-ester moieties toward amines was qualitatively and quantitatively evaluated via the reaction with methoxytetraethyleneglycolamine (TEGamine) and finally functionalized with single strand and complete DNA molecules.
Molecular devices formed by direct monolayer attachment to silicon
Solid-State Electronics, 2004
We present the results of studies of solution-based attachment of long-chain aliphatic molecules to hydrogen-terminated SiAE1 1 1ae surfaces formed to determine the electrical properties of hybrid silicon-molecular nanoelectronic devices. We have applied an improved solution-based method for the direct attachment of organic molecules to Si. In this method, ultraviolet radiation is used to assist the covalent attachment of alcohols to the hydrogen-terminated SiAE1 1 1ae surface to successfully form molecular monolayers. To determine the quality of these organic monolayers, they were physically and chemically characterized with infrared spectroscopy, spectroscopic ellipsometry, and contact angle measurements. The electrical properties of these organic films were probed by using current-voltage (IV ) and capacitance voltage (CV ) measurements obtained from a metal-organic-silicon test structure fabricated by post-monolayer metal deposition. Devices containing monolayers of differing chain length have been studied, and the expected decrease in accumulation capacitance with longer molecules (which form thicker films) was observed. The measured CV 's are in agreement with traditional theory for a metal-insulator-semiconductor capacitor.
Physica E: Low-dimensional Systems and Nanostructures, 2009
The hybrid nanoelectronics, i.e., organic molecules deposited on Si exhibiting electronic functionalities is expected to extend the scaling limits of Si microelectronics down to few nanometers. In this review, first we make an overview of the organic molecules exhibiting various functionalities, such as, dielectric, diode, memory and transistor. We then review the literature on electrochemical grafting of organic molecules to Si, which have been carried out using terminal vinyl (CQC), ethynyl (CRC), halide (Cl, Br, I), tetraalkylammonium salt, diazonium salt and silane as reactant. It has been demonstrated that electrochemistry not only allows grafting of molecules on Si but also provides very useful information on the characteristics of the grafted layers. The electronic functionalities of various electrografted molecules are discussed. An additional advantage of the electrochemical process is that monolayer patterns with spatial resolution in a wide range, i.e. from nanometer to millimeter, can be easily prepared. The recent advances made in the spatial patterning of monolayers using electrochemical lithography are briefly reviewed.
Nucleic Acids Research, 2006
Unoxidized crystalline silicon, characterized by high purity, high homogeneity, sturdiness and an atomically flat surface, offers many advantages for the construction of electronic miniaturized biosensor arrays upon attachment of biomolecules (DNA, proteins or small organic compounds). This allows to study the incidence of molecular interactions through the simultaneous analysis, within a single experiment, of a number of samples containing small quantities of potential targets, in the presence of thousands of variables. A simple, accurate and robust methodology was established and is here presented, for the assembling of DNA sensors on the unoxidized, crystalline Si(100) surface, by loading controlled amounts of a monolayer DNA-probe through a two-step procedure. At first a monolayer of a spacer molecule, such as 10-undecynoic acid, was deposited, under optimized conditions, via controlled cathodic electrografting, then a synthetic DNA-probe was anchored to it, through amidation in aqueous solution. The surface coverage of several DNA-probes and the control of their efficiency in recognizing a complementary target-DNA upon hybridization were evaluated by fluorescence measurements. The whole process was also monitored in parallel by Atomic Force Microscopy (AFM).
Direct electrical detection of hybridization at DNA-modified silicon surfaces
Biosensors and Bioelectronics, 2004
Electrochemical impedance spectroscopy was used to investigate the changes in interfacial electrical properties that arise when DNA-modified Si(1 1 1) surfaces are exposed to solution-phase DNA oligonucleotides with complementary and non-complementary sequences. The n-and p-type silicon(1 1 1) samples were covalently linked to DNA molecules via direct Si-C linkages without any intervening oxide layer. Exposure to solutions containing DNA oligonucleotides with the complementary sequence produced significant changes in both real and imaginary components of the electrical impedance, while exposure to DNA with non-complementary sequences generated negligible responses. These changes in electrical properties were corroborated with fluorescence measurements and were reproduced in multiple hybridization-denaturation cycles. The ability to detect DNA hybridization is strongly frequency-dependent. Modeling of the response and comparison of results on different silicon bulk doping shows that the sensitivity to DNA hybridization arises from DNA-induced changes in the resistance of the silicon substrate and the resistance of the molecular layers.
An AFM investigation of oligonucleotides anchored on unoxidized crystalline silicon surfaces
Biomolecular Engineering, 2007
Carboxylic terminated monolayers have been covalently attached on phosphorous doped crystalline (1 0 0) silicon surfaces using a cathodic electro grafting technique. The functionalization concentration and efficiency have been evaluated with different techniques. In particular, topographic images, performed with an atomic force microscope, were used to optimize the protocol in order to obtain a surface whose characteristics of uniformity and reproducibility are ideal for a bio-electronic device. Phase lag images of the functionalized surfaces were also performed, and show non-topographic structures that have been interpreted as areas of different molecule self-orientation.
Chemistry of Materials, 2002
Silicon is arguably the most important material in modern technology and there has been much recent interest in chemically modifying its surface. 1,2 Linford and co-workers 3 recently published a new method of simultaneously preparing alkyl monolayers on silicon and patterning silicon by scribing it with a diamond-tipped rod while it is wet with 1-alkenes or 1-alkynes. They proposed that scribing creates highly active Si species that condense with unsaturated molecules. Here, we report that monolayers on Si can also be produced and Si surfaces concomitantly patterned by scribing Si that is wet with 1-chloro-, 1-bromo-, and 1-iodoalkanes. 4 As before, 3 this process takes place under ambient conditions, without the need to degas reagents. A dry Si surface with its thin (10-20 Å) native oxide layer is simply wet with an alkyl halide and the surface is scribed. We propose that surface species on scribed silicon, which may include SidSi (double) bonds and Si dangling bonds (Si • ), as are present on Si(100)-(2 × 1) and Si(111)-(7 × 7), respectively, 2 react with alkyl halides to produce Si-X (X is Cl, Br, or I) and Si-alkyl species. This process is shown below for Si • : homolytic scission of a C-X bond is followed by condensation of Si • with an alkyl radical.