Immobilization of homooligonucleotide probe layers onto Si/SiO(2) substrates: characterization by electrochemical impedance measurements and radiolabelling

Application strategies of peptide nucleic acids toward electrochemical nucleic acid sensors

Peptide nucleic acids (PNAs) have attracted tremendous interest in the fabrication of highly sensitive electrochemical nucleic acid biosensors due to their higher stability and increased sensitivity than common DNA probes. The neutral pseudopeptide backbone of PNAs not only makes the PNA/DNA duplexes more stable but also provides many opportunities to construct ultrasensitive nucleic acid sensors. This review presents the details of various protocols for the construction of PNA-based electrochemical nucleic acid sensors. The crucial factors, origin, and development of PNA, immobilization methods of PNA probes and signal generation mechanisms, are discussed. This review aims to provide a reference for ultrasensitive PNA electrochemical biosensor preparation.

pH driven addressing of silicon nanowires onto Si3N4/SiO2 micro-patterned surfaces

pH was used as the main driving parameter for specifically immobilizing silicon nanowires onto Si3N4 microsquares at the surface of a SiO2 substrate. Different pH values of the coating aqueous solution enabled to experimentally distribute nanowires between silicon nitride and silicon dioxide: at pH 3 nanowires were mainly anchored on Si3N4; they were evenly distributed between SiO2 and Si3N4 at pH 2.8; and they were mainly anchored on SiO2 at pH 2. A theoretical model based on DLVO theory and surface protonation/deprotonation equilibria was used to study how, in adequate pH conditions, Si nanowires could be anchored onto specific regions of a patterned Si3N4/SiO2 surface. Instead of using capillary forces, or hydrophilic/hydrophobic contrast between the two types of materials, the specificity of immobilization could rely on surface electric charge contrasts between Si3N4 and SiO2. This simple and generic method could be used for addressing a large diversity of nano-objects onto patterned substrates.

Epoxy-terminated self-assembled monolayers containing internal urea or amide groups

We report the synthesis of new coupling agents with internal amide or urea groups possessing an epoxy-terminal group and trimethoxysilyl-anchoring group. The structural characterizations of the corresponding self-assembled monolayers (SAMs) were performed by polarization modulation infrared reflection adsorption spectroscopy (PM-IRRAS). The molecular assembly is mainly based on the intermolecular hydrogen-bonding between adjacent amide or urea groups in the monolayers. Because of the steric hindrance of amide or urea groups, the distance between the alkyl chains is too large to establish van der Waals interactions, inducing their disorder. The reactivity of the epoxy-terminal groups was successfully investigated through reaction with a fluorescent probe. We show that SAMs containing internal urea or amide groups exhibited a higher density of accessible epoxide groups than the corresponding long-chain (C22) glycidyl-terminated SAM.

Optimizing radiolabeling amine-functionalized silica nanoparticles using SarAr-NCS for applications in imaging and radiotherapy

Silica nanoparticles functionalized with amine groups and in the size range of approximately 60-94 nm were produced by combining sol-gel processing and emulsion technology. Hexa-aza cage ligand SarAr-NCS was conjugated to the silica nanoparticles and subsequently radiolabeled with a solution of (57)Co(2+)-doped carrier Co(2+). The number of Co(2+) ions bound to the silica particles at pH 7 was used to determine the average number of available SarAr-NCS ligands conjugated to a silica particle. For organically modified silica particles of 94.0 and 59.5 nm diameter, the maximum number of metal binding sites was determined to be 11700 and 3270 sites per particle, respectively. For silica particles (63.5 nm peak diameter) produced using an water-in-oil emulsion, the calculated average was 4480 on the particle surface. The number of SarAr-NCS conjugated on the particles was easily controlled, potentially providing for a range of products for applications in the risk assessment of particles and theranostic imaging or radiotherapy when radiolabeled with a suitable radioisotope such as (64)Cu or (67)Cu.

Manipulation of interfacial amine density in epoxy-amine systems as studied by near-edge X-ray absorption fine structure (NEXAFS)

In this work, we investigate the ability to tune the quantity of surface amine functional groups in the interfacial region of epoxy-diamine composites using NEXAFS, a technique that is extremely sensitive to surface composition. Thereby, we employ a model surface (silicon wafer with the native oxide present) and, after deposition of an epoxy functionalized silane, we immersed the wafers in various diamines, followed by reaction with a diepoxy acting as a molecular probe. These results show that the number of available surface amines depends on the diamine chosen, wherein smaller molecular weight diamines provide more reaction sites. Subsequent experiments with mixtures of diamines undergoing competitive adsorption show that the amine quantity can be tailored by choice of the diamine mixture. Further experiments of diamine treated 3-(glycidoxypropyl) trimethoxysilane layers in a reacting epoxy/diamine showed that the surface reaction site density differences observed for adsorption experiments persisted in the reacting epoxy, implying that the surface reaction rate (and by extension, the surface amine concentration) dictate interfacial cross-link density up to the point of gelation.

Route to smooth silica-based surfaces decorated with novel self-assembled monolayers (SAMs) containing glycidyl-terminated very long hydrocarbon chains

Novel glycidyl-terminated organosilicon coupling agents possessing a trialkoxysilyl head group and a very long hydrocarbon chain (C22) were synthesized. Their ability to afford densely packed self-assembled monolayers (SAMs) grafted on silica-based surfaces was investigated. Transmission FT-IR spectra showed that the most regular films were obtained by using trichloracetic acid as the catalyst (10 M%). Atomic force microscopy (AFM) and optical ellipsometry were consistent with well ordered monolayers exhibiting a marked decrease of the surface roughness. Epifluorescence microscopy revealed that these SAMs possessed a better surface reactivity than monolayers obtained with the commercially available (3-glycidoxypropyl) trimethoxysilane (GPTS) upon grafting of a fluorescent probe (dansylcadaverin). Moreover, direct attachment of fluorescent antibodies (RAG-TRITC) through covalent binding led to higher mean fluorescence intensities, showing that these new SAMs possess high potential for the immobilization of biological molecules.

PM IRRAS investigation of thin silica films deposited on gold. Part 1. Theory and proof of concept

Polarization modulation infrared reflection absorption spectroscopy (PM IRRAS) was successfully used for the first time to characterize an optically transparent thin oxide film. SiO2 layers of 7 nm thickness were synthesized by plasma enhanced chemical vapor deposition (PECVD) on 200 nm thick gold covered glass slides. Despite the fact that silica is transparent and absorptive to IR radiation when deposited in the form of thin films on a gold surface, it preserves the high metallic reflectivity for the IR light. At grazing angles of incidence of the IR beam, the enhancement of the normal component of the electric field at the interface is comparable to that of Au alone. In addition, the analysis of the structure of a 1,2-dimyristoyl-sn-glycero-3-phosphocholine (DMPC) lipid monolayer deposited using the Langmuir-Blodgett technique is demonstrated.

Investigation into the effect that probe immobilisation method type has on the analytical signal of an EIS DNA biosensor

The analytical performance of an enhanced surface area electrolyte insulator semiconductor (EIS) device was investigated for DNA sensor development. The work endeavored to advance EIS performance by monitoring the effect of DNA probe layers have on the impedimetric signal during target hybridisation detection. Two universally employed covalent chemistries, direct and spacer-mediated attachment of amino modified probe molecules to amino-functionalised surfaces were investigated. Relative areal densities of immobilised probe were measured on planar and enhanced surface area substrates using epi-fluorescence microscopy. The reproducibility of the each immobilisation method was seen to have a direct effect on the reproducibility of the impedimetric signal. The sensitivity and selectivity was seen to be dependent on the type of immobilisation method. Real time, impedimetric detection of target DNA hybridisation concentrations as low as 25 and 1 nM were possible. The impact that probe concentration had on the impedimetric signal for selective and non-selective interactions was also investigated.

Direct electrical detection of antigen–antibody binding on diamond and silicon substrates using electrical impedance spectroscopy

The integration of biological molecules with semiconducting materials such as silicon and diamond has great potential for the development of new types of bioelectronic devices, such as biosensors and bioactuators. We have investigated the electrical properties of the antibody-antigen modified diamond and silicon surfaces using electrical impedance spectroscopy (EIS). Frequency dependent measurements at the open-circuit potential show: (a) significant changes in impedance at frequency >10(4) Hz when the surface immobilized IgG was exposed to anti-IgG, and (b) only little or no change when exposed to anti-IgM. Mott-Schottky measurements at high frequency (200 kHz) show that the impedance is dominated by the space charge layer of the semiconducting substrates. Silicon surfaces modified in a similar manner to the diamond surface are compared; n-type and p-type samples show complementary behavior, as expected for a field effect. We also show it is possible to directly observe antigen-antibody interaction at a fixed frequency in real time, and with no additional labeling.

DNA hybridization detection on electrical microarrays using coulostatic pulse technique

We demonstrated a novel application of transient coulostatic pulse technique for the detection of label free DNA hybridization on nm-sized gold interdigitated ultramicroelectrode arrays (Au-IDA) made in silicon technology. The array consists of eight different positions with an Au-IDA pair at each position arranged on the Si-based Biochip. Immobilization of capture probes onto the Au-IDA was accomplished by self-assembling of thiol-modified oligonucleotides. Target hybridization was indicated by a change in the magnitude of the time dependant potential relaxation curve in presence of electroactive Fe(CN)(6)(3-) in the phosphate buffer solution. While complementary DNA hybridization showed 50% increase in the relaxation potential, the non-complementary DNA showed a negligible change. A constant behaviour was noted for all positions. The dsDNA specific intercalating molecule, methylene blue, was found to be enhancing the discrimination effect. The changes in the relaxation potential curves were further corroborated following the ELISA like experiments using ExtraAvidine alkaline phosphatase labelling and redox recycling of para-aminophenol phosphate at IDAs. The coulostatic pulse technique was shown to be useful for identifying DNA sequences from brain tumour gene CK20, human herpes simplex virus, cytomegalovirus, Epstein-Barr virus and M13 phage. Compared to the hybridization of short chain ONTs (27 mers), the hybridization of long chain M13 phage DNA showed three times higher increase in the relaxation curves. The method is fast enough to monitor hybridization interactions in milli or microsecond time scales and is well suitable for miniaturization and integration compared to the common impedance techniques for developing capacitative DNA sensors.

Charging behavior of single-stranded DNA polyelectrolyte brushes

DNA monolayers are widely used in fundamental and applied genomics and are versatile experimental models for elucidating the behavior of charged polymers at interfaces. The physical behavior of these systems is to a large extent governed by their internal ionic microenvironment, which is investigated here for layers of end-tethered, single-stranded DNA oligonucleotides (DNA brushes). Retention of counterions by the DNA brush manifests as lowered susceptibility of the interfacial capacitance to external salt conditions. A physical model based on concepts adapted from polymer science was used to further elucidate the connection between monolayer organization and its charging behavior. The data indicate a reorganization of the monolayer with changes in ionic strength and strand coverage that is consistent with that expected for a polyelectrolyte brush. A method for electrochemical quantification of strand coverage, based on shift of reduction potential for redox counterions associated with the DNA monolayer, is also described. These results provide guidance for development of label-free electrochemical diagnostics employing DNA monolayers and formulate a description of monolayer behavior within a polymer science framework.

DNA Covalent Immobilization onto Screen-Printed Electrode Networks for Direct Label-Free Hybridization Detection of p53 Sequences

A new electrochemical biochip for the detection of DNA sequences was developed. The entire biochip-i.e., working, reference, and counter electrodes-was constructed based on the screen-printing technique and exhibits eight working electrodes that could be individually addressed and grafted through a simple electrochemical procedure. Screen-printed electrode networks were functionalized electrochemically with 1-ethyl-3-(3dimethylaminopropyl)carbodidiimide according to a simple procedure. Single-stranded DNA with a C6-NH(2) linker at the 5'-end was then covalently bound to the surface to act as probe for the direct, nonlabeled, detection of complementary strands in a conductive liquid medium. In the present system, the study was focused on a particular codon (273) localized in the exon 8 of the p53 gene (20 mer, TTGAGGTGCATGTTTGTGCC). The integrity of the immobilized probes and its ability to capture target sequences was monitored through chemiluminescent detection following the hybridization of a peroxidase-labeled target. The grafting of the probe at the electrode surface was shown to generate significant shifts of the Nyquist curves measured in the 10-kHz to 80-Hz range. These variations of the faradaic impedance were found to be related to changes of the double layer capacitance of the electrochemical system's equivalent circuit. Similarly, hybridization of complementary strands was monitored through the measurements of these shifts, which enabled the detection of target sequences from 1 to 200 nM. Discrimination between complementary, noncomplementary, and single-nucleotide mismatch targets was easily accomplished.

Assessment of porous silicon substrate for well-characterised sensitive DNA chip implement

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 bio-molecule 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.

Synthetic oligonucleotides: AFM characterisation and electroanalytical studies

One of the most important steps in designing more sensitive and stable DNA based biosensors is the immobilisation procedure of the nucleic acid probes on the transducer surface, while maintaining their conformational flexibility. MAC Mode AFM images in air demonstrated that the oligonucleotide sequences adsorb spontaneously on the electrode surface, showing the existence of pores in the adsorbed layer that reveal big parts of the electrode surface, which enables non-specific adsorption of other molecules on the uncovered areas. The electrostatic immobilisation onto a glassy carbon electrode followed by hybridisation with a complementary sequence and control with a non-complementary sequence was studied using differential pulse voltammetry and electrochemical impedance spectroscopy. Changes in the oxidation currents of guanosine and adenosine were observed after hybridisation events as well as after control experiments. Modification of the double layer capacitance that took place after hybridisation or control experiments showed that non-specific adsorption of complementary or non-complementary sequences occur allowing the formation of a mixed multilayer.

Surface characterization of 3-glycidoxypropyltrimethoxysilane films on silicon-based substrates

Silane coupling agents are commonly used to activate surfaces for subsequent immobilization of biomolecules. The homogeneity and surface morphology of silane films is important for controlling the structural order of immobilized single-stranded DNA probes based on oligonucleotides. The surfaces of silicon wafers and glass slides with covalently attached 3-glycidoxypropyltrimethoxysilane (GOPS) have been characterized by using angularly dependent X-ray photoelectron spectroscopy (XPS), time-of-flight secondary-ion mass spectrometry (ToF-SIMS), atomic force microscopy (AFM), scanning electron microscopy (SEM), and monochromatic and spectroscopic ellipsometry. XPS and ToF-SIMS data provided evidence of complete surface coverage by GOPS. Data from angularly resolved XPS and ellipsometry methods suggested that the GOPS films were of monolayer thickness. AFM and SEM data indicated the presence of films that consisted of nodules approximately 50-100 nm in diameter. Modeling suggested that the nodules may lead to a nanoscale structural morphology that might influence the hybridization kinetics and thermodynamics of immobilized oligonucleotides.

Label-free impedance detection of oligonucleotide hybridisation on interdigitated ultramicroelectrodes using electrochemical redox probes

The direct detection of oligodeoxynucleotide (ODN) hybridisation using electrochemical impedance spectroscopy was made on interdigitated array (IDA) gold (Au) ultramicroelectrodes manufactured by silicon technology. The immobilisation of single stranded ODNs (ssODNs) was accomplished by self-assembling of thiol-modified ODNs onto an Au-electrode surface. Faradaic impedance was measured in the presence of K(3)[Fe(CN)(6)]. Double strand formation was identified by a decrease of approximately 50% in impedance in the low frequency region in the presence of K(3)[Fe(CN)(6)], compared to the spectrum of single stranded ODN. The frequency dependent diffusion of Fe(CN)(6)(3-) ions through defects in the ODN monolayer determines the impedance of Au-ssODN surface. The influence of DNA intercalator methylene blue on the impedance of both, single and double strands, was examined along with K(3)[Fe(CN)(6)] and confirmed by cyclic voltammetry. The layer densities and the hybridisation have been further corroborated by chronoamperometric redox recycling of para-aminophenol (p-AP) in ELISA like experiments. It can be concluded, that a performed impedance spectroscopy did not change the layer density. The impedance spectroscopy at ultramicroelectrodes combined with faradaic redox reactions enhances the impedimetric detection of DNA hybridisation on IDA platforms.

Electrical detection of biomolecular interactions with metal–insulator–semiconductor diodes

We report the label-free detection of DNA hybridization using a metal-insulator-semiconductor (MIS) diode or capacitor. Upon immobilization of single-stranded DNA on the gold gate of a MIS capacitor, the capacitance versus voltage characteristics show a significant shift in the direction of negative voltages as expected from the immobilization of negative charges on the gate. The hybridization with the complementary strand gives rise to a further significant shift in the same direction as before, which is consistent with the increase of negative charges on the gate brought about by the hybridization. Fluorescence studies indicate that the immobilization and hybridization of DNA can be electrostatically promoted by electric fields externally applied to the MIS capacitors. The MIS diode detection method is applicable to all biomolecular interactions that affect the surface dipole at the interface between the metal gate and the electrolyte and can be extended to other chemical and biochemical systems such as proteins and cells.

Formation and characterization of DNA microarrays at silicon nitride substrates

A versatile method for direct, covalent attachment of DNA microarrays at silicon nitride layers, previously deposited by chemical vapor deposition at silicon wafer substrates, is reported. Each microarray fabrication process step, from silicon nitride substrate deposition, surface cleaning, amino-silanation, and attachment of a homobifunctional cross-linking molecule to covalent immobilization of probe oligonucleotides, is defined, characterized, and optimized to yield consistent probe microarray quality, homogeneity, and probe-target hybridization performance. The developed microarray fabrication methodology provides excellent (high signal-to-background ratio) and reproducible responsivity to target oligonucleotide hybridization with a rugged chemical stability that permits exposure of arrays to stringent pre- and posthybridization wash conditions through many sustained cycles of reuse. Overall, the achieved performance features compare very favorably with those of more mature glass based microarrays. It is proposed that this DNA microarray fabrication strategy has the potential to provide a viable route toward the successful realization of future integrated DNA biochips.

Direct electrical detection of hybridization at DNA-modified silicon surfaces

Electrochemical impedance spectroscopy was used to investigate the changes in interfacial electrical properties that arise when DNA-modified Si(111) surfaces are exposed to solution-phase DNA oligonucleotides with complementary and non-complementary sequences. The n- and p-type silicon(111) 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.

Frequency dependent and surface characterization of DNA immobilization and hybridization

The hybridization of oligomeric DNA was investigated using the frequency dependent techniques of quartz crystal microbalance (QCM) and electrochemical impedance spectroscopy (EIS). Synthetic 5'-amine-terminated single stranded oligonucleotides (ssDNA) were immobilized on the surface of the oxidized platinum driving electrodes of AT-cut quartz QCM crystals using 3-glycidoxypropyl-trimethoxysilane. Similar ssDNA coupling was accomplished on the exposed glass surface between the metallic digits of microlithographically fabricated interdigitated microsensor electrodes (IMEs). Confirmation of this covalent coupling surface chemistry was achieved using Fourier transform infrared spectroscopy-attenuated total reflectance (FTIR-ATR). Substantial changes in resonant frequency values (0.012% decrease) and electrochemical impedance values (both real and imaginary components) (35.4 and 42.1% increase in impedance magnitude at 1.0 Hz in buffer and deionized water, respectively) were observed resulting from hybridization of the attached ssDNA upon exposure to its complement under appropriate hybridization conditions. Non-complementary (random) oligomer sequence demonstrated a modest change in resonant frequency and a non-detectable change in impedance. Microarray glass slide surfaces modified with 3-glycidoxypropyltrimethoxysilane (GPS), shown to be advantageous in the design and use of microarrays of amine-terminated ssDNA, is confirmed to arise from direct covalent coupling of the DNA to the surface with little non-specific adsorption. The possibility to detect the binding state of DNA in the vicinity of an electrode, without a direct connection between the measurement electrode and the DNA is hereby reported. The potential for development of label-free, low-density DNA microarrays is demonstrated and is being pursued.

Impedance-based detection of DNA sequences using a silicon transducer with PNA as the probe layer

Electrochemical impedance measurements were used for the detection of single-strand DNA sequences using a peptide nucleic acid (PNA) probe layer immobilized onto Si/SiO2 chips. An epoxysilane layer is first immobilized onto the Si/SiO2 surface. The immobilization procedure consists of an epoxide/amine coupling reaction between the amino group of the PNA linker and the epoxide group of the silane. A 20-nucleotide sequence of PNA was used. Impedance measurements allow for the detection of the changes in charge distribution at the oxide/solution interface following modifications to the oxide surface. Due to these modifications, there are significant shifts in the semiconductor's flat-band potential after immobilization and hybridization. The results obtained using this direct and rapid approach are supported by fluorescence measurements according to classical methods for the detection of nucleic acid sequences.