Towards a real-time, label-free, diamond-based DNA sensor

Diamonds for Life: Developments in Sensors for Biomolecules

Diamond-based electrodes and biosensors are interesting in analytics because of their particular set of properties, namely: large potential window, chemical inertness, low baseline current, stability, and transparency. Diamond-based electrodes and biosensors were shown to detect biological molecules such as neurotransmitters and proteins, respectively. In this review, we summarise the different types of diamond electrodes and biosensors based on their type of detection (electrochemical or optical), functionalisation, and target analyte. The last section presents a discussion on the different analytical responses obtained with electrodes or biosensors, according to the type of analyte. Electrodes work quite well for detecting small molecules with redox properties, whereas biosensors are more suited for detecting molecules with a high molecular weight, such as DNA and proteins.

The Effect of Surface Treatment on Structural Properties of CVD Diamond Layers with Different Grain Sizes Studied by Raman Spectroscopy

Extensive Raman spectroscopy studies combined with scanning electron microscopy (SEM) and X-ray photoelectron spectroscopy (XPS) measurements were performed to investigate structural and chemical changes in diamond layers deposited by chemical vapour deposition (CVD) upon post-growth treatment with hydrogen. The aim of this study is to characterize the changes in micro-structural properties of diamond layers with different grain sizes and different contents of sp2 carbon phase. Hydrogenation or oxidization of diamond layer surface is often performed to modify its properties; however, it can also strongly affect the surface structure. In this study, the impact of hydrogenation on the structure of diamond layer surface and its chemical composition is investigated. Owing to their polycrystalline nature, the structural properties of CVD diamond layers can strongly differ within the same layer. Therefore, in this project, in order to compare the results before and after hydrogen treatment, the diamond layers are subjected to Raman spectroscopy studies in the vicinity of a T-shape marker fabricated on the surface of each diamond layer studied.

Enhancing the Performance of DNA Surface-Hybridization Biosensors through Target Depletion

DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not significantly vary while hybridizing to the surface-bound probes. If the target is initially at low concentrations and/or if the number of probes is very large, and they have high affinity for the target, the DNA in solution may become depleted. In this paper we analyze the equilibrium and kinetics of hybridization of DNA biosensors in the case of strong target depletion, by extending the Langmuir adsorption model. We focus, in particular, on the detection of a small amount of a single-nucleotide "mutant" sequence (concentration c₂) in a solution, which differs by one or more nucleotides from an abundant "wild-type" sequence (concentration c₁ ≫ c₂). We show that depletion can give rise to a strongly enhanced sensitivity of the biosensors. Using representative values of rate constants and hybridization free energies, we find that in the depletion regime one could detect relative concentrations c₂/c₁ that are up to 3 orders of magnitude smaller than in the conventional approach. The kinetics is surprisingly rich and exhibits a nonmonotonic adsorption with no counterpart in the no-depletion case. Finally, we show that, alongside enhanced detection sensitivity, this approach offers the possibility of sample enrichment, by substantially increasing the relative amount of the mutant over the wild-type sequence.

A Label-Free Impedimetric DNA Sensor Based on a Nanoporous SnO₂ Film: Fabrication and Detection Performance

Nanoporous SnO₂ thin films were elaborated to serve as sensing electrodes for label-free DNA detection using electrochemical impedance spectroscopy (EIS). Films were deposited by an electrodeposition process (EDP). Then the non-Faradic EIS behaviour was thoroughly investigated during some different steps of functionalization up to DNA hybridization. The results have shown a systematic decrease of the impedance upon DNA hybridization. The impedance decrease is attributed to an enhanced penetration of ionic species within the film volume. Besides, the comparison of impedance variations upon DNA hybridization between the liquid and vapour phase processes for organosilane (APTES) grafting on the nanoporous SnO₂ films showed that vapour-phase method is more efficient. This is due to the fact that the vapour is more effective than the solution in penetrating the nanopores of the films. As a result, the DNA sensors built from vapour-treated silane layer exhibit a higher sensitivity than those produced from liquid-treated silane, in the range of tested target DNA concentration going to 10 nM. Finally, the impedance and fluorescence response signals strongly depend on the types of target DNA molecules, demonstrating a high selectivity of the process on nanoporous SnO₂ films.

The heat-transfer method: a versatile low-cost, label-free, fast, and user-friendly readout platform for biosensor applications

In recent years, biosensors have become increasingly important in various scientific domains including medicine, biology, and pharmacology, resulting in an increased demand for fast and effective readout techniques. In this Spotlight on Applications, we report on the recently developed heat-transfer method (HTM) and illustrate the use of the technique by zooming in on four established bio(mimetic) sensor applications: (i) mutation analysis in DNA sequences, (ii) cancer cell identification through surface-imprinted polymers, (iii) detection of neurotransmitters with molecularly imprinted polymers, and (iv) phase-transition analysis in lipid vesicle layers. The methodology is based on changes in heat-transfer resistance at a functionalized solid-liquid interface. To this extent, the device applies a temperature gradient over this interface and monitors the temperature underneath and above the functionalized chip in time. The heat-transfer resistance can be obtained by dividing this temperature gradient by the power needed to achieve a programmed temperature. The low-cost, fast, label-free and user-friendly nature of the technology in combination with a high degree of specificity, selectivity, and sensitivity makes HTM a promising sensor technology.

Heat-transfer-based detection of SNPs in the PAH gene of PKU patients

Conventional neonatal diagnosis of phenylketonuria is based on the presence of abnormal levels of phenylalanine in the blood. However, for carrier detection and prenatal diagnosis, direct detection of disease-correlated mutations is needed. To speed up and simplify mutation screening in genes, new technologies are developed. In this study, a heat-transfer method is evaluated as a mutation-detection technology in entire exons of the phenylalanine hydroxylase (PAH) gene. This method is based on the change in heat-transfer resistance (R_th) upon thermal denaturation of dsDNA (double-stranded DNA) on nanocrystalline diamond. First, ssDNA (single-stranded DNA) fragments that span the size range of the PAH exons were successfully immobilized on nanocrystalline diamond. Next, it was studied whether an R_th change could be observed during the thermal denaturation of these DNA fragments after hybridization to their complementary counterpart. A clear R_th shift during the denaturation of exon 5, exon 9, and exon 12 dsDNA was observed, corresponding to lengths of up to 123 bp. Finally, R_th was shown to detect prevalent single-nucleotide polymorphisms, c.473G>A (R158Q), c.932T>C (p.L311P), and c.1222C>T (R408W), correlated with phenylketonuria, displaying an effect related to the different melting temperatures of homoduplexes and heteroduplexes.

Combining electrochemical impedance spectroscopy and surface plasmon resonance into one simultaneous read-out system for the detection of surface interactions

In this article we describe the integration of impedance spectroscopy (EIS) and surface plasmon resonance (SPR) into one surface analytic device. A polydimethylsiloxane (PDMS) flow cell is created, matching the dimensions of a commercially available sensor chip used for SPR measurements. This flow cell allowed simultaneous measurements between an EIS and a SPR setup. After a successful integration, a proof of principle study was conducted to investigate any signs of interference between the two systems during a measurement. The flow cell was rinsed with 10 mM Tris-HCl and 1× PBS buffer in an alternating manner, while impedance and shifts of the resonance angle were monitored. After achieving a successful proof of principle, a usability test was conducted. It was assessed whether simultaneous detection occurred when: (i) Protein A is adsorbed to the gold surface of the chip; (ii) The non-occupied zone is blocked with BSA molecules and (iii) IgG1 is bound to the Protein A. The results indicate a successful merge between SPR and EIS.

Heat-transfer resistance at solid-liquid interfaces: a tool for the detection of single-nucleotide polymorphisms in DNA

In this article, we report on the heat-transfer resistance at interfaces as a novel, denaturation-based method to detect single-nucleotide polymorphisms in DNA. We observed that a molecular brush of double-stranded DNA grafted onto synthetic diamond surfaces does not notably affect the heat-transfer resistance at the solid-to-liquid interface. In contrast to this, molecular brushes of single-stranded DNA cause, surprisingly, a substantially higher heat-transfer resistance and behave like a thermally insulating layer. This effect can be utilized to identify ds-DNA melting temperatures via the switching from low- to high heat-transfer resistance. The melting temperatures identified with this method for different DNA duplexes (29 base pairs without and with built-in mutations) correlate nicely with data calculated by modeling. The method is fast, label-free (without the need for fluorescent or radioactive markers), allows for repetitive measurements, and can also be extended toward array formats. Reference measurements by confocal fluorescence microscopy and impedance spectroscopy confirm that the switching of heat-transfer resistance upon denaturation is indeed related to the thermal on-chip denaturation of DNA.

Nano-structured nickel oxide based DNA biosensor for detection of visceral leishmaniasis (Kala-azar)

Sol-gel synthesized nickel oxide (NiO) film deposited onto indium tin oxide (ITO) coated glass plate has been utilized for the development of sensitive and stable DNA biosensor and demonstrated for diagnosis of visceral leishmaniasis also known as Kala-azar. Leishmania specific sensor is developed by immobilizing 23mer DNA sequence (oligonucleotide) identified from 18S rRNA gene sequences from Leishmania donovani. Characterization studies like X-Ray Diffraction and Scanning Electron Microscopy revealed the formation of nano-structured NiO, while immobilization of single strand (ss)-DNA of Leishmania was supported by UV-visible, Fourier Transform Infrared Spectroscopy and Scanning Electron Microscopy techniques. Response studies of ss-DNA/NiO/ITO bioelectrode are carried out using differential pulsed voltammetry in presence of methylene blue redox dye as a redox mediator. A linear response is obtained in the wide concentration range of 2 pg ml(-1) to 2 μg ml(-1) of complementary target genomic DNA (disease DNA) within the variation of 10% for 5 sets of studies. The observed results hold promise not only for diagnosis of Kala-azar patients but also hold enormous potential of the nano-NiO based probe for development of stable and sensitive biosensors.

Rapid assessment of the stability of DNA duplexes by impedimetric real-time monitoring of chemically induced denaturation

In this article, we report on the electronic monitoring of DNA denaturation by NaOH using electrochemical impedance spectroscopy in combination with fluorescence imaging as a reference technique. The probe DNA consisting of a 36-mer fragment was covalently immobilized on nanocrystalline-diamond electrodes and hybridized with different types of 29-mer target DNA (complementary, single-nucleotide defects at two different positions, and a non-complementary random sequence). The mathematical separation of the impedimetric signals into the time constant for NaOH exposure and the intrinsic denaturation-time constants gives clear evidence that the denaturation times reflect the intrinsic stability of the DNA duplexes. The intrinsic time constants correlate with calculated DNA-melting temperatures. The impedimetric method requires minimal instrumentation, is label-free and fast with a typical time scale of minutes and is highly reproducible. The sensor electrodes can be used repetitively. These elements suggest that the monitoring of chemically induced denaturation at room temperature is an interesting approach to measure DNA duplex stability as an alternative to thermal denaturation at elevated temperatures, used in DNA-melting experiments and single nucleotide polymorphism (SNP) analysis.

Nanocrystalline diamond impedimetric aptasensor for the label-free detection of human IgE

Like antibodies, aptamers are highly valuable as bioreceptor molecules for protein biomarkers because of their excellent selectivity, specificity and stability. The integration of aptamers with semiconducting materials offers great potential for the development of reliable aptasensors. In this paper we present an aptamer-based impedimetric biosensor using a nanocrystalline diamond (NCD) film as a working electrode for the direct and label-free detection of human immunoglobulin E (IgE). Amino (NH(2))-terminated IgE aptamers were covalently attached to carboxyl (COOH)-modified NCD surfaces using carbodiimide chemistry. Electrochemical impedance spectroscopy (EIS) was applied to measure the changes in interfacial electrical properties that arise when the aptamer-functionalized diamond surface was exposed to IgE solutions. During incubation, the formation of aptamer-IgE complexes caused a significant change in the capacitance of the double-layer, in good correspondence with the IgE concentration. The linear dynamic range of IgE detection was from 0.03 μg/mL to 42.8 μg/mL. The detection limit of the aptasensor reached physiologically relevant concentrations (0.03 μg/mL). The NCD-based aptasensor was demonstrated to be highly selective even in the presence of a large excess of IgG. In addition, the aptasensor provided reproducible signals during six regeneration cycles. The impedimetric aptasensor was successfully tested on human serum samples, which opens up the potential of using EIS for direct and label-free detection of IgE levels in blood serum.

DNA sensors with diamond as a promising alternative transducer material

Bio-electronics is a scientific field coupling the achievements in biology with electronics to obtain higher sensitivity, specificity and speed. Biosensors have played a pivotal role, and many have become established in the clinical and scientific world. They need to be sensitive, specific, fast and cheap. Electrochemical biosensors are most frequently cited in literature, often in the context of DNA sensing and mutation analysis. However, many popular electrochemical transduction materials, such as silicon, are susceptible to hydrolysis, leading to loss of bioreceptor molecules from the surface. Hence, increased attention has been shifted towards diamond, which surpasses silicon on many levels.

Topographical and functional characterization of the ssDNA probe layer generated through EDC-mediated covalent attachment to nanocrystalline diamond using fluorescence microscopy

The covalent attachment method for DNA on nanocrystalline diamond (NCD), involving the introduction of COOH functionalities on the surface by photoattachment of 10-undecenoic acid (10-UDA), followed by the 1-ethyl-3-(3-dimethylaminopropyl)-carbodiimide (EDC)-mediated coupling to NH 2-labeled ssDNA, is evaluated in terms of stability, density, and functionality of the resulting biological interface. This is of crucial importance in DNA biosensor development. The covalent nature of DNA attachment will infer the necessary stability and favorable orientation to the ssDNA probe molecules. Using confocal fluorescence microscopy, the influence of buffer type for the removal of excess 10-UDA and ssDNA, the probe ssDNA length, the probe ssDNA concentration, and the presence of the COOH-linker on the density and functionality of the ssDNA probe layer were investigated. It was determined that the most homogeneously dense and functional DNA layer was obtained when 300 pmol of short ssDNA was applied to COOH-modified NCD samples, while H-terminated NCD was resistant for DNA attachment. Exploiting this surface functionality dependence of the DNA attachment efficiency, a shadow mask was applied during the photochemical introduction of the COOH-functionalities, leaving certain regions on the NCD H-terminated. The subsequent DNA attachment resulted in a fluorescence pattern corresponding to the negative of the shadow mask. Finally, NCD surfaces covered with mixtures of the 10-UDA linker molecule and a similar molecule lacking the COOH functionality, functioning as a lateral spacer, were examined for their suitability in preventing nonspecific adsorption to the surface and in decreasing steric hindrance. However, purely COOH-modified NCD samples, patterned with H-terminated regions and treated with a controlled amount of probe DNA, proved the most efficient in fulfilling these tasks.

Label-free DNA sensor by boron-doped diamond electrode using an ac impedimetric approach

An electrochemical biosensor using a boron-doped diamond (BDD) electrode is described for differentiating between gene sequences according to DNA hybridization events using an ac impedimetric approach. BDD electrodes were dipped into a 1% solution of polyethylenimine (PEI) to adsorb a thin layer of positively charged PEI on the surface of BDD, then PEI-modified BDD electrodes were used to immobilize negatively charged single-stranded PCR fragments from Exon 7 of human p53 gene. Alternating current impedimetric measurements were first performed on these systems in phosphate buffered saline (PBS) and then upon exposure to single-stranded DNA (ssDNA). When the ssDNA-immobilized BDD electrode and solution ssDNA were completely complementary, a large drop in impedance was measured. Complementary DNA could be clearly detected at concentrations down to 10 (-19) g mL (-1) at a fixed frequency (10 Hz). Higher concentrations of DNA gave faster hybridization with saturation occurring at levels above 1.0 pg mL (-1.) Responses were much lower upon exposure to noncDNA, even at higher concentrations. The results show it is possible to directly detect target DNA at a fixed frequency and without additional labeling.

Structural and optical properties of DNA layers covalently attached to diamond surfaces

Label-free detection of DNA molecules on chemically vapor-deposited diamond surfaces is achieved with spectroscopic ellipsometry in the infrared and vacuum ultraviolet range. This nondestructive method has the potential to yield information on the average orientation of single as well as double-stranded DNA molecules, without restricting the strand length to the persistence length. The orientational analysis based on electronic excitations in combination with information from layer thicknesses provides a deeper understanding of biological layers on diamond. The pi-pi* transition dipole moments, corresponding to a transition at 4.74 eV, originate from the individual bases. They are in a plane perpendicular to the DNA backbone with an associated n-pi* transition at 4.47 eV. For 8-36 bases of single- and double-stranded DNA covalently attached to ultra-nanocrystalline diamond, the ratio between in- and out-of-plane components in the best fit simulations to the ellipsometric spectra yields an average tilt angle of the DNA backbone with respect to the surface plane ranging from 45 degrees to 52 degrees . We comment on the physical meaning of the calculated tilt angles. Additional information is gathered from atomic force microscopy, fluorescence imaging, and wetting experiments. The results reported here are of value in understanding and optimizing the performance of the electronic readout of a diamond-based label-free DNA hybridization sensor.