Discrimination of single mutations in cancer-related gene fragments with a surface acoustic wave sensor

Recent Advances in SAW Sensors for Detection of Cancer Biomarkers

Surface acoustic wave (SAW) sensor technology is a promising approach to diagnosing cancer through the detection of cancer biomarkers due to its high sensitivity, potential label-free operation, and fast response times, and, fundamentally, because it is a non-invasive technique in comparison with the current traditional diagnostic techniques for cancer. This review focuses on this application, and for this purpose, the recent literature on cancer biomarkers detected by this advanced technology has been compiled, including that on volatile organic compounds (VOCs) from exhaled breath and larger biomolecules such as proteins, DNA, and microRNAs in body fluids, which demonstrates its great versatility. The conventional techniques for cancer biomarker detection in biofluids, such as ELISA, PCR, SPR, and UV absorbance, exhibit limitations including high costs, slow response times, a reduced sensitivity, the need for specialized instrumentation, and the requirement for highly trained personnel. Different SAW sensor configurations are discussed with attention paid to their specific properties, wave propagation modes, and suitability for different environments. Detailed studies are reviewed, highlighting biomarkers for lung, colorectal, prostate, breast, and ovarian cancer diagnostics, as well as the detection of circulating tumor cells and cancerous cell growth. This review identifies current challenges, including optimizing sensitivity, addressing environmental interferences, and the need for clinical validation. Finally, future research directions are proposed, emphasizing the use of VOC biomarkers and the integration of SAW technology into hybrid systems and microfluidic platforms to enable the creation of scalable, non-invasive diagnostic tools for the detection of cancer in early stages, and, in this way, to minimize the morbidity and mortality associated with this disease.

Sensitive Materials and Coating Technologies for Surface Acoustic Wave Sensors

Since their development, surface acoustic wave (SAW) devices have attracted much research attention due to their unique functional characteristics, which make them appropriate for the detection of chemical species. The scientific community has directed its efforts toward the development and integration of new materials as sensing elements in SAW sensor technology with a large area of applications, such as for example the detection of volatile organic compounds, warfare chemicals, or food spoilage, just to name a few. Thin films play an important role and are essential as recognition elements in sensor structures due to their wide range of capabilities. In addition, other requisites are the development and application of new thin film deposition techniques as well as the possibility to tune the size and properties of the materials. This review article surveys the latest progress in engineered complex materials, i.e., polymers or functionalized carbonaceous materials, for applications as recognizing elements in miniaturized SAW sensors. It starts with an overview of chemoselective polymers and the synthesis of functionalized carbon nanotubes and graphene, which is followed by surveys of various coating technologies and routes for SAW sensors. Different coating techniques for SAW sensors are highlighted, which provides new approaches and perspective to meet the challenges of sensitive and selective gas sensing.

Microfluidic Devices for Label-Free DNA Detection

Sensitive and specific DNA biomarker detection is critical for accurately diagnosing a broad range of clinical conditions. However, the incorporation of such biosensing structures in integrated microfluidic devices is often complicated by the need for an additional labelling step to be implemented on the device. In this review we focused on presenting recent advances in label-free DNA biosensor technology, with a particular focus on microfluidic integrated devices. The key biosensing approaches miniaturized in flow-cell structures were presented, followed by more sophisticated microfluidic devices and higher integration examples in the literature. The option of full DNA sequencing on microfluidic chips via nanopore technology was highlighted, along with current developments in the commercialization of microfluidic, label-free DNA detection devices.

Surface acoustic wave devices for chemical sensing and microfluidics: A review and perspective

Surface acoustic waves (SAWs), are electro-mechanical waves that form on the surface of piezoelectric crystals. Because they are easy to construct and operate, SAW devices have proven to be versatile and powerful platforms for either direct chemical sensing or for upstream microfluidic processing and sample preparation. This review summarizes recent advances in the development of SAW devices for chemical sensing and analysis. The use of SAW techniques for chemical detection in both gaseous and liquid media is discussed, as well as recent fabrication advances that are pointing the way for the next generation of SAW sensors. Similarly, applications and progress in using SAW devices as microfluidic platforms are covered, ranging from atomization and mixing to new approaches to lysing and cell adhesion studies. Finally, potential new directions and perspectives on the field as it moves forward are offered, with a specific focus on potential strategies for making SAW technologies for bioanalytical applications.

A surface acoustic wave biosensor synergizing DNA-mediated in situ silver nanoparticle growth for a highly specific and signal-amplified nucleic acid assay

An SAW biosensor harmonizes the surface mass effect for signal-amplified and sequence-specific DNA detection in blood serum.

Love Acoustic Wave-Based Devices and Molecularly-Imprinted Polymers as Versatile Sensors for Electronic Nose or Tongue for Cancer Monitoring

Cancer is a leading cause of death worldwide and actual analytical techniques are restrictive in detecting it. Thus, there is still a challenge, as well as a need, for the development of quantitative non-invasive tools for the diagnosis of cancers and the follow-up care of patients. We introduce first the overall interest of electronic nose or tongue for such application of microsensors arrays with data processing in complex media, either gas (e.g., Volatile Organic Compounds or VOCs as biomarkers in breath) or liquid (e.g., modified nucleosides as urinary biomarkers). Then this is illustrated with a versatile acoustic wave transducer, functionalized with molecularly-imprinted polymers (MIP) synthesized for adenosine-5'-monophosphate (AMP) as a model for nucleosides. The device including the thin film coating is described, then static measurements with scanning electron microscopy (SEM) and electrical characterization after each step of the sensitive MIP process (deposit, removal of AMP template, capture of AMP target) demonstrate the thin film functionality. Dynamic measurements with a microfluidic setup and four targets are presented afterwards. They show a sensitivity of 5 Hz·ppm(-1) of the non-optimized microsensor for AMP detection, with a specificity of three times compared to PMPA, and almost nil sensitivity to 3'AMP and CMP, in accordance with previously published results on bulk MIP.

Micro- and nano-structure based oligonucleotide sensors

This paper presents a review of micro- and nano-structure based oligonucleotide detection and quantification techniques. The characteristics of such devices make them very attractive for Point-of-Care or On-Site-Testing biosensing applications. Their small scale means that they can be robust and portable, their compatibility with modern CMOS electronics means that they can easily be incorporated into hand-held devices and their suitability for mass production means that, out of the different approaches to oligonucleotide detection, they are the most suitable for commercialisation. This review discusses the advantages of micro- and nano-structure based sensors and covers the various oligonucleotide detection techniques that have been developed to date. These include: Bulk Acoustic Wave and Surface Acoustic Wave devices, micro- and nano-cantilever sensors, gene Field Effect Transistors, and nanowire and nanopore based sensors. Oligonucleotide immobilisation techniques are also discussed.

The detection of multiple DNA targets with a single probe using a conformation-sensitive acoustic sensor

Acoustic sensing of DNA targets using a single probe that produces hybridization products of different conformations.

A dry membrane protection technique to allow surface acoustic wave biosensor measurements of biological model membrane approaches

Model membrane approaches have attracted much attention in biomedical sciences to investigate and simulate biological processes. The application of model membrane systems for biosensor measurements is partly restricted by the fact that the integrity of membranes critically depends on the maintenance of an aqueous surrounding, while various biosensors require a preconditioning of dry sensors. This is for example true for the well-established surface acoustic wave (SAW) biosensor SAM®5 blue. Here, a simple drying procedure of sensor-supported model membranes is introduced using the protective disaccharide trehalose. Highly reproducible model membranes were prepared by the Langmuir-Blodgett technique, transferred to SAW sensors and supplemented with a trehalose solution. Membrane rehydration after dry incorporation into the SAW device becomes immediately evident by phase changes. Reconstituted model membranes maintain their full functionality, as indicated by biotin/avidin binding experiments. Atomic force microscopy confirmed the morphological invariability of dried and rehydrated membranes. Approximating to more physiological recognition phenomena, the site-directed immobilization of the integrin VLA-4 into the reconstituted model membrane and subsequent VCAM-1 ligand binding with nanomolar affinity were illustrated. This simple drying procedure is a novel way to combine the model membrane generation by Langmuir-Blodgett technique with SAW biosensor measurements, which extends the applicability of SAM®5 blue in biomedical sciences.

High-performance surface acoustic wave immunosensing system on a PEG/aptamer hybridized surface

Label-free immunoassay systems have the advantages of procedural simplicity and a low construction cost of surfaces for immunosensing. When label-free immunoassay systems are considered, the nonspecific adsorption of unwanted materials should be eliminated unless it aids in the detection of error. PEG is well-known as a blocking agent for the prevention of the adsorption of nonspecific binding materials when coimmobilized with ligands for targets such as antibodies and oligonucleotides. The construction strategy for PEG/ligand coimmobilized surfaces is an important point in the preparation of a high-performance assays because the physiological condition of the ligand depends strongly on its interaction with the PEG chain. In this report, we investigate the interaction between thrombin and a thrombin-binding aptamer (TBA) on a PEG/TBA coimmobilized surface by using a shear horizontal surface acoustic wave (SAW) sensor. The thrombin-TBA binding property shows remarkable differences with changes in the PEG density and the distance from the gold surface to the aptamer.

Surface Acoustic Wave (SAW) biosensors: coupling of sensing layers and measurement

Surface acoustic wave (SAW) devices based on horizontally polarized surface shear waves enable direct and label-free detection of proteins in real time. Signal response changes result mainly from mass increase and viscoelasticity changes on the device surface. With an appropriate sensor configuration all types of binding reactions can be detected by determining resonant frequency changes of an oscillator. To create a biosensor, SAW devices have to be coated with a sensing layer binding specifically to the analyte. Intermediate hydrogel layers used within the coating have been proven to be very suitable to easily immobilize capture molecules or ligands corresponding to the analyte. However, aside from mass increase due to analyte binding, the SAW signal response in a subsequent binding experiment strongly depends on the morphology of the sensing layer, as this may lead to different relative changes of viscoelasticity. Bearing these points in mind, we present two basic biosensor coating procedures, one with immobilized capture molecule and a second with immobilized ligand, allowing reliable SAW biosensor signal responses in subsequent binding assays.

Synthesis of biotin-containing phosphoramidite linker with polyether spacer arm

A phosphoramidite linker unit, based on glycerol backbone and containing a biotin residue attached through a tetraethylene glycol spacer arm, was synthesized. DMTr-Glycidol and tetraethylene glycol were used as starting materials. After conversion of one of hydroxy groups in tetraethylene glycol into an amino group, the epoxy cycle in DMTr-glycidol was opened by this amino alcohol, resulting in the corresponding ether and some quantity of secondary amine. After attaching of biotin residue to the ether followed by phosphitylation, the desirable linker was obtained. The structure of the linker was confirmed by (1)H-(1)H COSY, (1)H-(13)C HSQC, (1)H-(13)C HMBC, (1)H-(15)N HSQC, and (1)H-(15)N HMBC spectra. The resulted phosphoramidite linker unit is suitable for use in common DNA synthesizers. This approach can be used for preparation of various modifiers containing reporter groups attached to the primary amino function using conventional procedures.

Aptamer modules as sensors and detectors

Aptamers comprise a range of molecular recognition scaffolds that can be engineered to bind to a legion of different proteins and other targets with excellent specificity and affinity. Because these non-natural oligonucleotides are accessible entirely synthetically, aptamers can be equipped with all sorts of reporter groups and can be coupled to many different carriers, surfaces, nanoparticles, or other biomolecules. They can be used in a highly modular fashion and often recognize their targets by a mechanism in which the aptamer undergoes considerable structural rearrangement, which can be exploited for transducing a binding event into a signal. As a consequence, aptamers have been adapted to a huge variety of "read-out configurations" and are increasingly used as capture agents in many different bioanalytical methods. But despite considerable success with these applications, many remaining challenges must still be overcome for the more widespread incorporation of aptasensors in clinical and environmental biosensing and diagnostics to take place. Some particularly noteworthy progress on this front is currently being made with aptasensor configurations that can be used for the multiplexed sensing of many analytes in parallel. In this Account, we describe some of the concepts involved in transducing the binding of a ligand into a signal through various physico-chemical interactions. Research in this area usually involves the combination of the molecular biology of proteins and nucleic acids with biotechnology, synthetic chemistry, physical chemistry, and surface physics. We begin with a brief introduction of the properties and characteristics that qualify aptamers as capture agents for many different analytes and their suitability as highly versatile biosensor components. We then address approaches that apply to surface acoustic wave configurations, drawing largely from our own contributions to aptasensor development, before moving on to describe previous and recent progress in multiplexed aptasensors. Obtaining proteome-wide profiles in cells, organs, organisms, or full populations requires the ability to accurately measure many different analytes in small sample volumes over a broad dynamic range. Multiplexed sensing is an invaluable tool in this endeavor. We discuss what we consider the biggest obstacles to the broader clinical use of aptasensor-based diagnostics and our perspective on how they can be surmounted. Finally,we explore the tremendous potential of aptamer-based sensors that can specifically discriminate between diseased and healthy cells. Progress in these areas will greatly expand the range of aptasensor applications, leading to enhanced diagnosis of diseases in clinical practice and, ultimately, improved patient care.

A microfluidics assisted porous silicon array for optical label-free biochemical sensing

A porous silicon (PSi) based microarray has been integrated with a microfluidic system, as a proof of concept device for the optical monitoring of selective label-free DNA-DNA interaction. A 4 × 4 square matrix of PSi one dimensional photonic crystals, each one of 200 μm diameter and spaced by 600 μm, has been sealed by a polydimethylsiloxane (PDMS) channels circuit. The PSi optical microarray elements have been functionalized by DNA single strands after sealing: the microfluidic circuit allows to reduce significantly the biologicals and chemicals consumption, and also the incubation time with respect to a not integrated device. Theoretical calculations, based on finite element method, taking into account molecular interactions, are in good agreement with the experimental results, and the developed numerical model can be used for device optimization. The functionalization process and the interaction between DNA probe and target has been monitored by spectroscopic reflectometry for each PSi element in the microchannels.

Biosensors in clinical chemistry - 2011 update

Research activity and applications of biosensors for measurement of analytes of clinical interest over the last eight years are reviewed. Nanotechnology has been applied to improve performance of biosensors using electrochemical, optical, mechanical and physical modes of transduction, and to allow arrays of biosensors to be constructed for parallel sensing. Biosensors have been proposed for measurement of cancer biomarkers, cardiac biomarkers as well as biomarkers for autoimmune disease, infectious disease and for DNA analysis. Novel applications of biosensors include measurements in alternate sample types, such as saliva. Biosensors based on immobilized whole cells have found new applications, for example to detect the presence of cancer and to monitor the response of cancer cells to chemotherapeutic agents. The number of research reports describing new biosensors for analytes of clinical interest continues to increase; however, movement of biosensors from the research laboratory to the clinical laboratory has been slow. The greatest impact of biosensors will be felt at point-of-care testing locations without laboratory support. Integration of biosensors into reliable, easy-to-use and rugged instrumentation will be required to assure success of biosensor-based systems at the point-of-care.

ADLOC: an aptamer-displacement assay based on luminescent oxygen channeling

Functional nucleic acids, such as aptamers and allosteric ribozymes, can sense their ligands specifically, thereby undergoing structural alterations that can be converted into a detectable signal. The direct coupling of molecular recognition to signal generation enables the production of versatile reporters that can be applied as molecular probes for various purposes, including high-throughput screening. Here we describe an unprecedented type of a nucleic acid-based sensor system and show that it is amenable to high-throughput screening (HTS) applications. The approach detects the displacement of an aptamer from its bound protein partner by means of luminescent oxygen channeling. In a proof-of-principle study we demonstrate that the format is feasible for efficient identification of small drug-like molecules that bind to a protein target, in this case to the Sec7 domain of cytohesin. We extended the approach to a new cytohesin-specific single chain DNA aptamer, C10.41, which exhibits a similar binding behavior to cytohesins but has the advantage of being more stable and easier to synthesize and to modify than the RNA-aptamer M69. The results obtained with both aptamers indicate the general suitability of the aptamer-displacement assay based on luminescent oxygen channelling (ADLOC) for HTS. We also analyzed the potential for false positive hits and identified from a library of 18,000 drug-like small molecules two compounds as strong singlet-oxygen quenchers. With full automation and the use of commercially available plate readers, we estimate that the ADLOC-based assay described here could be used to screen at least 100,000 compounds per day.

Kinetic binding analysis of aptamers targeting HIV-1 proteins by a combination of a microbalance array and mass spectrometry (MAMS)

An enhanced chip-based detection platform was developed by integrating a surface acoustic wave biosensor of the Love-wave type with protein identification by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-ToF MS). The system was applied to characterize the interaction of aptamers with their cognate HIV-1 proteins. The aptamers, which target two proteins of HIV-1, were identified using an automated in vitro selection platform. For aptamers S66A-C6 and S68B-C5, which target the V3 loop of the HIV-1 envelope protein gp120, KD values of 406 and 791 nM, respectively, were measured. Aptamer S69A-C15 was shown to bind HIV-1 reverse transcriptase (HIV-1 RT) with a KD value of 637 nM when immobilized on the biosensor surface. HIV-1 RT was identified with high significance using MALDI-ToF MS even in crude protein mixtures. The V3-loop of gp120 could be directly identified when using chip-bound purified protein samples. From crude protein mixtures, it could be identified indirectly with high significance via its fusion-partner glutathione-S-transferase (GST). Our data show that the combination of the selectivity of aptamers with a sensitive detection by MS enables the reliable and quantitative analysis of kinetic binding events of protein solutions in real time.

Aptamers and biosensors

The immobilization procedure to a biosensor surface has a major influence on the measurement results. To characterize the immobilization onto various biolayers, the interaction of DNA anti-thrombin aptamer with the protein thrombin was used as a model system. The aptamer was immobilized to a two-dimensional alkanethiol SAM via carboxylamide bonds and to a three-dimensional dextran matrix via streptavidin-biotin interaction. The calculated K (D) values of about 260 and 267 nM, respectively, were comparable, while the amount of bound analyte varied by a factor of 2, depending on the accessibility of the immobilized aptamer. Differences in the specificity were shown by use of the similar protein elastase.

A ZnO nanorod-based SAW oscillator system for ultraviolet detection

A high-precision ultraviolet (UV) detector combining ZnO nanostructure and a dual delay line surface acoustic wave (SAW) oscillator system is presented. The UV detector is made of ZnO nanorods on a 128 degrees YX-LiNbO(3)-based two-port SAW oscillator. The ZnO nanorod synthesized by chemical solution method is used as a UV sensing material. The center frequency of the SAW device is at 145 MHz. A dual delay line SAW oscillator system was constructed to eliminate external environmental fluctuations. Under illumination of a UV source consisting of an Xe lamp and a monochromator, frequency shifts of the UV detector were measured. A maximum frequency shift of over 40 kHz was observed under 365 nm illumination for several on-off cycles, indicating the ZnO nanorod-based detector was sensitive to UV light and with good repeatability. Moreover, frequency shifts reached a value of 19 kHz after 365 nm was turned on for 10 s, which implies a real-time high-sensitivity UV sensor was successfully fabricated. Results show a ZnO nanostructure-based SAW oscillator system is a promising candidate for a real-time, fast-response, high-precision UV detector.

Characterization of the Assaying Methods in Polymerization-Based Amplification of Surface Biomarkers

Polymerization-based amplification (PBA), which combines bio-recognition events with polymerization reactions on surfaces, provides visual, sensitive, and cost-effective detection of biological interactions, particularly at extremely low levels of the targeted biological moiety. This study characterizes assay parameters that enhance the utility of PBA to detect nucleic acid and protein biomarkers. Here, we successfully employ PBA on surfaces that contain uniform, high density, immobilized capture molecules, including three-dimensional nitrocellulose-coated substrates. Optimized assay and polymerization conditions are used to characterize the dynamic polymer film heights on glass substrates that result from solutions of KRAS proto-oncogene biomarker targets at concentrations between 5 nM and 500 pM. Differing aqueous monomer formulations are utilized to produce 20 nm films at the 500 pM DNA detection limit.