UV cross-linking of unmodified DNA on glass surfaces

Surface Functionalization with (3-Glycidyloxypropyl)trimethoxysilane (GOPS) as an Alternative to Blending for Enhancing the Aqueous Stability and Electronic Performance of PEDOT:PSS Thin Films

Organic mixed ionic-electronic conductors, such as poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS), are essential materials for the fabrication of bioelectronic devices due to their unique ability to couple and transport ionic and electronic charges. The growing interest in bioelectronic devices has led to the development of organic electrochemical transistors (OECTs) that can operate in aqueous solutions and transduce ionic signals of biological origin into measurable electronic signals. A common challenge with OECTs is maintaining the stability and performance of the PEDOT:PSS films operating under aqueous conditions. Although the conventional approach of blending the PEDOT:PSS dispersions with a cross-linker such as (3-glycidyloxypropyl)trimethoxysilane (GOPS) helps to ensure strong adhesion of the films to device substrates, it also impacts the morphology and thus electrical properties of the PEDOT:PSS films, which leads to a significant reduction in the performance of OECTs. In this study, we instead functionalize only the surface of the device substrates with GOPS to introduce a silane monolayer before spin-coating the PEDOT:PSS dispersion on the substrate. In all cases, having a GOPS monolayer instead of a blend leads to increased electronic performance metrics, such as three times higher electronic conductivity, volumetric capacitance, and mobility-capacitance product [μC*] value in OECT devices, ultimately leading to a record value of 406 ± 39 F cm-1 V-1 s-1 for amorphous PEDOT:PSS. This increased performance does not come at the expense of operational stability, as both the blend and surface functionalization show similar performance when subjected to pulsed gate bias stress, long-term electrochemical cycling tests, and aging over 150 days. Overall, this study establishes a novel approach to using GOPS as a surface monolayer instead of a blended cross-linker, for achieving high-performance organic mixed ionic-electronic conductors that are stable in water for bioelectronics.

Covalently Attaching Hollow Silica Nanoparticles on a COC Surface for the Fabrication of a Three-Dimensional Protein Microarray

Compared to traditional two-dimensional (2D) biochips, three-dimensional (3D) biochips exhibit the advantages of higher probe density and detection sensitivity due to their designable surface microstructure as well as enlarged surface area. In the study, we proposed an approach to prepare a 3D protein chip by deposition of a monolayer of functionalized hollow silica nanoparticles (HSNs) on an activated cyclic olefin copolymer (COC) substrate. First, the COC substrate was chemically modified through the photografting technique to tether poly[3-(trimethoxysilyl) propyl methacrylate] (PTMSPMA) brushes on it. Then, a monolayer of HSNs was deposited on the modified COC and covalently attached via a condensation reaction between the hydrolyzed pendant siloxane groups of PTMSPMA and the Si-OH groups of HSNs. The roughness of the COC substrate significantly increased to 50.3 nm after depositing a monolayer of HSNs (ranging from 100 to 700 nm), while it only caused a negligible reduction in the light transmittance of COC. The HSN-modified COC was further functionalized with epoxide groups by a silane coupling agent for binding proteins. Immunoglobulin G could be effectively immobilized on this substrate with the highest immobilization efficiency of 75.2% and a maximum immobilization density of 1.236 μg/cm², while the highest immobilization efficiency on a 2D epoxide group-modified glass slide was only 57.4%. Moreover, immunoassay results confirmed a competitive limit of detection (LOD) (1.06 ng/mL) and a linear detection range (1-100 ng/mL) of the 3D protein chip. This facile and effective approach for fabricating nanoparticle-based 3D protein microarrays has great potential in the field of biorelated detection.

A Model System for Sensitive Detection of Viable E. coli Bacteria Combining Direct Viability PCR and a Novel Microarray-Based Detection Approach

We established an innovative approach that included direct, viability, and nested PCR for rapid and reliable identification of the fecal indicator organism Escherichia coli (E. coli). Direct PCR enabled successful amplification of the target uidA gene, omitting a prior DNA isolation or purification step. Furthermore, we applied viability PCR (v-PCR) to ensure the detection of only relevant viable bacterial cells. The principle involves the binding of propidium monoazide (PMA), a selective nucleic acid intercalating dye, to accessible DNA of heat killed bacteria cells and, consequently, allows viable and heat killed E. coli cells to be discriminated. To ensure high sensitivity, direct v-PCR was followed by a nested PCR step. The resulting amplicons were analyzed by a rapid 30 min microarray-based DNA hybridization assay for species-specific DNA detection of E. coli. A positive signal was indicated by enzymatically generated silver nanoparticle deposits, which served as robust endpoint signals allowing an immediate visual readout. The presented novel protocol allows the detection of 1 × 101 viable E. coli cells per PCR run.

Optimization of GOPS-Based Functionalization Process and Impact of Aptamer Grafting on the Si Nanonet FET Electrical Properties as First Steps towards Thrombin Electrical Detection

Field effect transistors (FETs) based on networks of randomly oriented Si nanowires (Si nanonets or Si NNs) were biomodified using Thrombin Binding Aptamer (TBA-15) probe with the final objective to sense thrombin by electrical detection. In this work, the impact of the biomodification on the electrical properties of the Si NN-FETs was studied. First, the results that were obtained for the optimization of the (3-Glycidyloxypropyl)trimethoxysilane (GOPS)-based biofunctionalization process by using UV radiation are reported. The biofunctionalized devices were analyzed by atomic force microscopy (AFM) and scanning transmission electron microscopy (STEM), proving that TBA-15 probes were properly grafted on the surface of the devices, and by means of epifluorescence microscopy it was possible to demonstrate that the UV-assisted GOPS-based functionalization notably improves the homogeneity of the surface DNA distribution. Later, the electrical characteristics of 80 devices were analyzed before and after the biofunctionalization process, indicating that the results are highly dependent on the experimental protocol. We found that the TBA-15 hybridization capacity with its complementary strand is time dependent and that the transfer characteristics of the Si NN-FETs obtained after the TBA-15 probe grafting are also time dependent. These results help to elucidate and define the experimental precautions that must be taken into account to fabricate reproducible devices.

KRAS mutation screening by chip-based DNA hybridization--a further step towards personalized oncology

The use of predictive biomarkers can help to improve therapeutic options for the individual cancer patient. For the treatment of colon cancer patients with anti-EGFR-based drugs, the KRAS mutation status has to be determined to pre-select responders that will benefit from this medication. Amongst others, array-based tests have been established for profiling of the KRAS mutation status. Within this article we describe an on-chip hybridization technique to screen therapeutic relevant KRAS codon 12 mutations. The DNA chip-based platform enables the reliable discrimination of selected mutations by allele-specific hybridization. Here, silver deposits represent robust endpoint signals that allow for a simple naked eye rating. With the here presented assay concept a precise identification of heterozygous and homozygous KRAS mutations, even against a background of up to 95% wild-type DNA, was realizable. The applicability of the test was successfully proven for various cancer cell lines as well as clinical tumour samples. Thus, the chip-based DNA hybridization technique seems to be a promising tool for KRAS mutation analysis to further improve personalized cancer treatment.

DNA hybridization assay at individual, biofunctionalized zinc oxide nanowires

Reliable and efficient identification of DNA is a major goal in on-site diagnostics. One dimensional nanostructures like nanowires (NW) represent potential sensor structures due to their extreme surface-to-bulk ratio, enabling enhanced biomolecule binding which results in optimal signals. While silicon NW are already well studied, NW made from other materials with promising properties like ZnO are not yet established as NW sensor material for bioanalytics. Here we demonstrate the DNA functionalization of ZnO NW even at the single NW level and their successful application in a DNA hybridization assay.

Surface functionalization chemistries on highly sensitive silica-based sensor chips

The surfaces of silica-based sensor chips, designed for evanescent-field-coupled waveguide-mode sensors, were functionalized using various surface chemistries. The immobilization of molecular entities on the functionalized silica surfaces was monitored using various microscopic techniques (scanning electron, fluorescence, and atomic force microscopies). Further, gold nanoparticle-based signal enhancement analyses were performed with protein conjugation on different functionalized surfaces using a waveguide-mode sensor. Based on these analyses, the sensor surfaces modified with glutaraldehyde (Glu) and carbonyldiimidazole were found to be good for molecules of different sizes. In addition, it can be inferred that the Glu-modified surface may be suitable for small molecules with diameters around 5 nm owing to its surface roughness. The modified surface with carbonyldiimidazole is suitable for the direct immobilization of larger molecules especially for biomolecular assemblies without intermediate chemical modifications.

The morphology of silver nanoparticles prepared by enzyme-induced reduction

Silver nanoparticles were synthesized by an enzyme-induced growth process on solid substrates. In order to customize the enzymatically grown nanoparticles (EGNP) for analytical applications in biomolecular research, a detailed study was carried out concerning the time evolution of the formation of the silver nanoparticles, their morphology, and their chemical composition. Therefore, silver-nanoparticle films of different densities were investigated by using scanning as well as transmission electron microscopy to examine their structure. Cross sections of silver nanoparticles, prepared for analysis by transmission electron microscopy were additionally studied by energy-dispersive X-ray spectroscopy in order to probe their chemical composition. The surface coverage of substrates with silver nanoparticles and the maximum particle height were determined by Rutherford backscattering spectroscopy. Variations in the silver-nanoparticle films depending on the conditions during synthesis were observed. After an initial growth state the silver nanoparticles exhibit the so-called desert-rose or nanoflower-like structure. This complex nanoparticle structure is in clear contrast to the auto-catalytically grown spherical particles, which maintain their overall geometrical appearance while increasing their diameter. It is shown, that the desert-rose-like silver nanoparticles consist of single-crystalline plates of pure silver. The surface-enhanced Raman spectroscopic (SERS) activity of the EGNP structures is promising due to the exceptionally rough surface structure of the silver nanoparticles. SERS measurements of the vitamin riboflavin incubated on the silver nanoparticles are shown as an exemplary application for quantitative analysis.

Development of highly fluorescent silica nanoparticles chemically doped with organic dye for sensitive DNA microarray detection

Increasing the sensitivity in DNA microarray hybridization can significantly enhance the capability of microarray technology for a wide range of research and clinical diagnostic applications, especially for those with limited sample biomass. To address this issue, using reverse microemulsion method and surface chemistry, a novel class of homogenous, photostable, highly fluorescent streptavidin-functionalized silica nanoparticles was developed, in which Alexa Fluor 647 (AF647) molecules were covalently embedded. The coating of bovine serum albumin on the resultant fluorescent particles can greatly eliminate nonspecific background signal interference. The thus-synthesized fluorescent nanoparticles can specifically recognize biotin-labeled target DNA hybridized to the microarray via streptavidin-biotin interaction. The response of this DNA microarray technology exhibited a linear range within 0.2 to 10 pM complementary DNA and limit of detection of 0.1 pM, enhancing microarray hybridization sensitivity over tenfold. This promising technology may be potentially applied to other binding events such as specific interactions between proteins.

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. I. Covalent immobilization of oligonucleotide probes onto the nylon]

The features of UV-induced immobilization of oligonucleotides on a nylon membranes and the effectiveness of enzymatic labeling of immobilized probes at heterophase detection of nucleic acids are studied. Short terminal oligothymidilate (up to 10 nt) sequences are suggested to attach to the probe via a flexible ethylene glycol based linker. The presence of such fragment enhances the intensity of immobilization and reduces UV-dependent degradation of the targeted (sequence-specific) part of the probe by reducing the dose needed for the immobilization of DNA. The optimum dose of UV-irradiation is determined to be ~0.4 J/cm(2) at the wavelength 254 nm. This dose provides high level of hybridization signal for immobilized probes with various nucleotide composition of the sequence specific moiety. The amide groups of the polyamide are shown to play the key role in the photoinduced immobilization of nucleic acids, whereas the primary amino groups in the structure of PA is not the center responsible for the covalent binding of DNA by UV-irradiation, as previously believed. Various additives in the soaking solution during the membrane of UV-dependent immobilization of probes are shown to influence its effectiveness. The use of alternative to UV-irradiation system of radical generation are shown to provide the immobilization of oligonucleotides onto the nylon membrane.

[Oligonucleotide derivatives in the nucleic acid hybridization analysis. II. Isothermal signal amplification in process of DNA analysis by minisequencing]

The isothermal amplification of reporter signal via limited probe extension (minisequencing) upon hybridization of nucleic acids has been studied. The intensity of reporter signal has been shown to increase due to enzymatic labeling of multiple probes upon consecutive hybridization with one DNA template both in homophase and heterophase assays using various kinds of detection signal: radioisotope label, fluorescent label, and enzyme-linked assay. The kinetic scheme of the process has been proposed and kinetic parameters for each step have been determined. The signal intensity has been shown to correlate with physicochemical characteristics of both complexes: probe/DNA and product/DNA. The maximum intensity has been observed at minimal difference between the thermodynamic stability of these complexes, provided the reaction temperature has been adjusted near their melting temperature values; rising or lowering the reaction temperature reduces the amount of reporting product. The signal intensity has been shown to decrease significantly upon hybridization with the DNA template containing single-nucleotide mismatches. Limited probe extension assay is useful not only for detection of DNA template but also for its quantitative characterization.

Towards multiple readout application of plasmonic arrays

In order to combine the advantages of fluorescence and surface-enhanced Raman spectroscopy (SERS) on the same chip platform, a nanostructured gold surface with a unique design, allowing both the sensitive detection of fluorescence light together with the specific Raman fingerprint of the fluorescent molecules, was established. This task requires the fabrication of plasmonic arrays that permit the binding of molecules of interest at different distances from the metallic surface. The most efficient SERS enhancement is achieved for molecules directly adsorbed on the metallic surface due to the strong field enhancement, but where, however, the fluorescence is quenched most efficiently. Furthermore, the fluorescence can be enhanced efficiently by careful adjustment of the optical behavior of the plasmonic arrays. In this article, the simultaneous application of SERS and fluorescence, through the use of various gold nanostructured arrays, is demonstrated by the realization of a DNA detection scheme. The results shown open the way to more flexible use of plasmonic arrays in bioanalytics.