Rapid and label-free nanomechanical detection of biomarker transcripts in human RNA

Folded flexure MOEMS for the detection of PSA and hepatitis DNA as biosensor for prostate cancer and viruses

Micro-opto-electro-mechanical systems (MOEMS) biosensors are employed in various applications such as disease monitoring, drug investigation, detection of pollutants, and biological fluid studies. In this paper, a novel MOEMS biosensor based on a differential folded-flexure structure is introduced. The designed device is employed to detect prostate-specific antigen (PSA) protein and Hepatitis DNA. The target molecules cause a mechanical deflection in the folded-flexure; subsequently, the transmitted optical power across the finger, attached to the flexure, is modulated in proportion to the input concentration. Then, a photodiode power sensor measures the modulated optical power, where the output of the sensor is simply a current related to the target molecules' concentrations. The employed readout circuit operates at a wavelength of λ = 1550 nm with a laser power of 1 µW. The dimensions of the proposed biosensor are considered to be 365 × 340 × 2 μm³, making this sensor small enough and suitable for integration. The designed biosensor provides notable features of mechanical deflection sensitivities of 0.2053 nm/(ng/ml) and 7.2486 nm/nM, optical transmittance sensitivities of 0.535504 × 10-3 1/(ng/ml) and 18.91 × 10-3 1/nM, total output sensitivities of 0.5398 (mA/W)/(ng/ml) and 19.059 (mA/W)/nM, and measurement ranges of 0-1000 ng/ml and 0-28.33 nM for PSA and Hepatitis DNA, respectively. The proposed system is a sensitive and powerful sensor that can play an important role in diagnosing many diseases.

A Genosensor Based on the Modification of a Microcantilever: A Review

When the free end of a microcantilever is modified by a genetic probe, this sensor can be used for a wider range of applications, such as for chemical analysis, biological testing, pharmaceutical screening, and environmental monitoring. In this paper, to clarify the preparation and detection process of a microcantilever sensor with genetic probe modification, the core procedures, such as probe immobilization, complementary hybridization, and signal extraction and processing, are combined and compared. Then, to reveal the microcantilever's detection mechanism and analysis, the influencing factors of testing results, the theoretical research, including the deflection principle, the establishment and verification of a detection model, as well as environmental influencing factors are summarized. Next, to demonstrate the application results of the genetic-probe-modified sensors, based on the classification of detection targets, the application status of other substances except nucleic acid, virus, bacteria and cells is not introduced. Finally, by enumerating the application results of a genetic-probe-modified microcantilever combined with a microfluidic chip, the future development direction of this technology is surveyed. It is hoped that this review will contribute to the future design of a genetic-probe-modified microcantilever, with further exploration of the sensitive mechanism, optimization of the design and processing methods, expansion of the application fields, and promotion of practical application.

Rapid Bacteria Detection from Patients' Blood Bypassing Classical Bacterial Culturing

Sepsis is a life-threatening condition mostly caused by a bacterial infection resulting in inflammatory reaction and organ dysfunction if not treated effectively. Rapid identification of the causing bacterial pathogen already in the early stage of bacteremia is therefore vital. Current technologies still rely on time-consuming procedures including bacterial culturing up to 72 h. Our approach is based on ultra-rapid and highly sensitive nanomechanical sensor arrays. In measurements we observe two clearly distinguishable distributions consisting of samples with bacteria and without bacteria respectively. Compressive surface stress indicates the presence of bacteria. For this proof-of-concept, we extracted total RNA from EDTA whole blood samples from patients with blood-culture-confirmed bacteremia, which is the reference standard in diagnostics. We determined the presence or absence of bacterial RNA in the sample through 16S-rRNA hybridization and species-specific probes using nanomechanical sensor arrays. Via both probes, we identified two clinically highly-relevant bacterial species i.e., Escherichia coli and Staphylococcus aureus down to an equivalent of 20 CFU per milliliter EDTA whole blood. The dynamic range of three orders of magnitude covers most clinical cases. We correctly identified all patient samples regarding the presence or absence of bacteria. We envision our technology as an important contribution to early and sensitive sepsis diagnosis directly from blood without requirement for cultivation. This would be a game changer in diagnostics, as no commercial PCR or POCT device currently exists who can do this.

Recent Advances in Nanomechanical Membrane-Type Surface Stress Sensors towards Artificial Olfaction

Nanomechanical sensors have gained significant attention as powerful tools for detecting, distinguishing, and identifying target analytes, especially odors that are composed of a complex mixture of gaseous molecules. Nanomechanical sensors and their arrays are a promising platform for artificial olfaction in combination with data processing technologies, including machine learning techniques. This paper reviews the background of nanomechanical sensors, especially conventional cantilever-type sensors. Then, we focus on one of the optimized structures for static mode operation, a nanomechanical Membrane-type Surface stress Sensor (MSS), and discuss recent advances in MSS and their applications towards artificial olfaction.

Multimodal real-time frequency tracking of cantilever arrays in liquid environment for biodetection: Comprehensive setup and performance analysis

We present a nanomechanical platform for real-time quantitative label-free detection of target biomolecules in a liquid environment with mass sensitivity down to few pg. Newly fabricated arrays of up to 18 cantilevers are integrated in a micromachined fluidic chamber, connected to software-controlled fluidic pumps for automated sample injections. We discuss two functionalization approaches to independently sensitize the interface of different cantilevers. A custom piezo-stack actuator and optical readout system enable the measurement of resonance frequencies up to 2 MHz. We implement a new measurement strategy based on a phase-locked loop (PLL), built via in-house developed software. The PLL allows us to track, within the same experiment, the evolution of resonance frequency over time of up to four modes for all the cantilevers in the array. With respect to the previous measurement technique, based on standard frequency sweep, the PLL enhances the estimated detection limit of the device by a factor of 7 (down to 2 pg in 5 min integration time) and the time resolution by more than threefold (below 15 s), being on par with commercial gold-standard techniques. The detection limit and noise of the new setup are investigated via Allan deviation and standard deviation analysis, considering different resonance modes and interface chemistries. As a proof-of-concept, we show the immobilization and label-free in situ detection of live bacterial cells (E. coli), demonstrating qualitative and quantitative agreement in the mechanical response of three different resonance modes.

Rapid and Ultrasensitive Detection of Mutations and Genes Relevant to Antimicrobial Resistance in Bacteria

The worldwide emergence of multidrug-resistant (MDR) bacteria is associated with significant morbidity, mortality, and healthcare costs. Rapid and accurate diagnostic methods to detect antibiotic resistance are critical for antibiotic stewardship and infection control measurements. Here a cantilever nanosensor-based diagnostic assay is shown to detect single nucleotide polymorphisms (SNPs) and genes associated with antibiotic resistance in Gram negative (Pseudomonas aeruginosa) and positive (Enterococcus faecium) bacteria, representing frequent causes for MDR infections. Highly specific RNA capture probes for SNPs (ampRD135G or ampRG154R ) or resistance genes (vanA, vanB, and vanD) allow to detect the binding of bacterial RNA within less than 5 min. Serial dilutions of bacterial RNA indicate an unprecedented sensitivity of 10 fg µL-1 total RNA corresponding to less than ten bacterial cells for SNPs and 1 fg µL-1 total RNA for vanD detection equivalent to single bacterial cell sensitivity.

A suspended graphene-based optical interferometric surface stress sensor for selective biomolecular detection

Graphene-based sensors are of great interest in research due to their high specific surface area and high electron mobility that make them suitable for numerous advanced applications. In this paper, selective molecular detection using an antigen-antibody reaction on suspended graphene with a cavity-sealing structure was demonstrated. The suspended graphene sealed nanocavities in a pre-patterned Si substrate, which increased robustness and allowed the use of wet chemical processes for surface functionalization of the suspended graphene to achieve selective molecular binding. The selectivity was evaluated by nanomechanical deflection induced by molecular adsorption on the suspended graphene, resulting in spectral shifts in the optical interference between the suspended graphene and Si substrate. The chemically functionalized suspended graphene enables the analysis of intermolecular interactions and molecular kinetics by colorimetry using optical interference.

Pixel-based biosensor for enhanced control: silicon nanowires monolithically integrated with field-effect transistors in fully depleted silicon on insulator technology

Silicon nanowires (SiNWs) are a widely used technology for sensing applications. Complementary metal-oxide-semiconductor (CMOS) integration of SiNWs advances lab-on-chip (LOC) technology and offers opportunities for read-out circuit integration, selective and multiplexed detection. In this work, we propose novel scalable pixel-based biosensors exploiting the integration of SiNWs with CMOS in fully-depleted silicon-on-insulator technology. A detailed description of the wafer-scale fabrication of SiNW pixels using the CMOS compatible sidewall-transfer-lithography as an alternative to widely investigated time inefficient e-beam lithography is presented. Each 60 nm wide SiNWs sensor is monolithically connected to a control transistor and novel on-chip fluid-gate forming an individual pixel that can be operated in two modes: biasing transistor frontgate (V _G) or substrate backgate (V _BG). We also present the first electrical results of single N and P-type SiNW pixels. In frontgate mode, N and P-type SiNW pixels exhibit subthreshold slope (SS) ≈ 70-80 mV/dec and I _on/I _off ≈ 10⁵. The N-type and P-type pixels have an average threshold voltage, Vth of -1.7 V and 0.85 V respectively. In the backgate mode, N and P-type SiNW pixels exhibit SS ≈ 100-150 mV/dec and I _on/I _off ≈ 10⁶. The N and P-type pixels have an average V _th of 5 V and -2.5 V respectively. Further, the influence of the backgate and frontgate voltage on the switching characteristics of the SiNW pixels is also studied. In the frontgate mode, the V _th of the SiNW pixels can be tuned at 0.2 V for 1 V change in V _BG for N-type or at -0.2 V for -1 V change in V _BG for P-type pixels. In the backgate mode, it is found that for stable operation of the pixels, the V _G of the N and P-type transistors must be in the range 0.5-2.5 V and 0 V to -2.5 V respectively.

Regulatory-sequence mechanical biosensor: A versatile platform for investigation of G-quadruplex/label-free protein interactions and tunable protein detection

Mechanical biosensors can be used to quantitatively explore DNA-protein binding mechanisms by detecting targets at low concentrations or measuring force in single-molecule force spectroscopy. However, restrictions in single-molecule manipulation and labelling protocols have hindered the application for bulk analysis of label-free protein detection. Here, we present the integration of molecular force measurement and finely tunable detection of label-free proteins into one mechanical sensor. Regulatory-sequence force spectroscopy was obtained to investigate the binding force of DNA G-quadruplexes (GQ) and label-free protein. The dual control of regulatory sequences and mechanical forces induces the structure switching from DNA duplex to GQ/protein complex. It exhibits a synergistic effect, enabling the rational fine-tuning of the dynamic range for biosensing protein concentrations over eight orders of magnitude. Furthermore, this method was exploited to estimate the stability of the human telomeric DNA GQ by Ku protein and ligand methylpyridostatin. The results revealed that human telomeric GQ has two different binding sites for Ku protein and ligand. Force spectroscopy integrating label-free force measurement and tunable target detection holds great promise for use in biosensing, drug screening, targeted therapies, DNA nanotechnology, and fields in which GQ are of rapidly increasing importance.

Enhanced Sensitivity in Nanopore Sensing of Cancer Biomarkers in Human Blood via Click Chemistry

Cancer biomarkers are expected to be indicative of the occurrence of certain cancer diseases before the tumors form and metastasize. However, many biomarkers can only be acquired in extremely low concentrations, which are often beyond the limit of detection (LOD) of current instruments and technologies. A practical strategy for nanopore sensing of cancer biomarkers in raw human blood down to the femtomolar level is developed here. This strategy first converts the detection of cancer biomarkers to the quantification of copper ions by conducting a sandwich assay involving copper oxide nanoparticles. The released Cu²⁺ is then taken to catalyze the "click" reaction which ligates a host-guest modified DNA probe. Finally, this DNA probe is subjected to single-channel recordings to afford the translocation events that can be used to derive the concentrations of the original biomarkers. Due to the amplification effects of nanoparticle loadings and the "click" reaction, the LOD of this strategy can be as low as the subfemtomolar level. Further, the acid treatment step could effectively eliminate the interferences from plasma proteins in raw human blood and make the strategy highly suitable for the detection of cancer biomarkers in clinical samples.

Ultrasensitive detection of long non-coding RNAs based on duplex-specific nuclease-actuated cyclic enzymatic repairing-mediated signal amplification

We develop a new method for sensitive detection of long noncoding RNAs using duplex-specific nuclease-actuated cyclic enzymatic repairing-mediated signal amplification.

Hyaluronate-Functionalized Graphene for Label-Free Electrochemical Cytosensing

Electrochemical sensors for early tumor cell detection are currently an important area of research, as this special region directly improves the efficiency of cancer treatment. Functional graphene is a promising alternative for selective recognition and capture of target cancer cells. In our work, an effective cytosensor of hyaluronate-functionalized graphene (HG) was prepared through chemical reduction of graphene oxide. The as-prepared HG nanostructures were characterized with Fourier transform infrared spectroscopy and transmission electron microscopy coupled with cyclic voltammograms and electrochemical impedance spectroscopy, respectively. The self-assembly of HG with ethylene diamine, followed by sodium hyaluronate, enabled the fabrication of a label-free electrochemical impedance spectroscopy cytosensor with high stability and biocompatibility. Finally, the proposed cytosensor exhibited satisfying electrochemical behavior and cell-capture capacity for human colorectal cancer cells HCT-116, and also displayed a wide linear range, from 5.0 × 10² cells∙mL-1 to 5.0 × 10⁶ cells∙mL-1, and a low detection limit of 100 cells∙mL-1 (S/N = 3) for quantification. This work paves the way for graphene applications in electrochemical cytosensing and other bioassays.

Modified cantilever arrays improve sensitivity and reproducibility of nanomechanical sensing in living cells

Mechanical signaling involved in molecular interactions lies at the heart of materials science and biological systems, but the mechanisms involved are poorly understood. Here we use nanomechanical sensors and intact human cells to provide unique insights into the signaling pathways of connectivity networks, which deliver the ability to probe cells to produce biologically relevant, quantifiable and reproducible signals. We quantify the mechanical signals from malignant cancer cells, with 10 cells per ml in 1000-fold excess of non-neoplastic human epithelial cells. Moreover, we demonstrate that a direct link between cells and molecules creates a continuous connectivity which acts like a percolating network to propagate mechanical forces over both short and long length-scales. The findings provide mechanistic insights into how cancer cells interact with one another and with their microenvironments, enabling them to invade the surrounding tissues. Further, with this system it is possible to understand how cancer clusters are able to co-ordinate their migration through narrow blood capillaries.

Samadhan Patil et al. report a new method for improving the sensitivity and reproducibility of mechanobiological measurements in malignant cancer cells. Their findings provide insight into the interaction of cells with each other and the microenvironment and may impact our understanding of metastasis.

Metal (Au, Pt) Nanoparticle-Latex Nanocomposites as Probes for Immunochromatographic Test Strips with Enhanced Sensitivity

The development of a sensitive and rapid diagnostic test for early detection of infectious viruses is urgently required to defend against pandemic and infectious diseases including seasonal influenza. In this study, we developed noble metal (Au, Pt) nanoparticle-latex nanocomposite particles for use as probes for immunochromatographic test (ICT) strips. The nanocomposite particles were conjugated with monoclonal antibody (mAb) to detect an influenza A (H1N1) antigen. For comparison, Au nanoparticles conjugated with mAb were also prepared. The lowest detectable concentrations of the influenza A antigen were found to be 6.25 × 10^-3 and 2.5 × 10^-2 HAU/mL for Au nanoparticle-latex and Pt nanoparticle-latex nanocomposite particles, respectively, whereas it was 4.0 × 10^-1 HAU/mL for Au nanoparticles. These results clearly demonstrated that the nanocomposite probes were more sensitive than conventional nanoparticle-based probes for ICT. To expand the versatility of the nanocomposite probes, the surfaces of the probes were functionalized with biotinylated proteins to enable modification of their surfaces with desired biotinylated antibodies through biotin-avidin binding.

Towards personalised rapid label free miRNA detection for cancer and liver injury diagnostics in cell lysates and blood based samples

Advances in prevention, diagnosis and therapy are coupled to innovation and development of new medical tools, leading to improved patient prognosis. We developed an automatic biosensor platform that could provide a non-invasive, rapid and personalised diagnosis using nanomechanical cantilever sensors. miRNA are involved in gene expression and are extractable biomarkers for multiple diseases. We detected specific expression patterns of miRNA relevant to cancer and adverse drug effects directly in cell lysates or blood based samples using only a few microliters of sample within one hour. Specific miRNA hybridisation to the upper cantilever surface induces physical bending of the sensor which is detected by monitoring the position of a laser that reflects from the sensors surface. Internal reference sensors negate environmental and nonspecific effects. We showed that the sensitivity of label free cantilever nanomechanical sensing of miRNA surpasses that of surface plasmon resonance by more than three orders of magnitude. A cancer associated miRNA expression profile from cell lysates and one associated with hepatocytes derived from necrotic liver tissue in blood-based samples has been successfully detected. Our label free mechanical approach displays the capability to perform in relevant clinical samples while also obtaining comparable results to PCR based techniques. Without the need to individually extend, amplify or label each target allowing multitarget analysis from one sample.

Application of nanotechnology in biosensors for enhancing pathogen detection

Rapid detection and identification of pathogenic microorganisms is fundamental to minimizing the spread of infectious disease, and informing clinicians on patient treatment strategies. This need has led to the development of enhanced biosensors that utilize state of the art nanomaterials and nanotechnology, and represent the next generation of diagnostics. A primer on nanoscale biorecognition elements such as, nucleic acids, antibodies, and their synthetic analogs (molecular imprinted polymers), will be presented first. Next the application of various nanotechnologies for biosensor transduction will be discussed, along with the inherent nanoscale phenomenon that leads to their improved performance and capabilities in biosensor systems. A future outlook on characterization and quality assurance, nanotoxicity, and nanomaterial integration into lab-on-a-chip systems will provide the closing thoughts. This article is categorized under: Diagnostic Tools > Diagnostic Nanodevices Diagnostic Tools > Biosensing.

A Review on Surface Stress-Based Miniaturized Piezoresistive SU-8 Polymeric Cantilever Sensors

In the last decade, microelectromechanical systems (MEMS) SU-8 polymeric cantilevers with piezoresistive readout combined with the advances in molecular recognition techniques have found versatile applications, especially in the field of chemical and biological sensing. Compared to conventional solid-state semiconductor-based piezoresistive cantilever sensors, SU-8 polymeric cantilevers have advantages in terms of better sensitivity along with reduced material and fabrication cost. In recent times, numerous researchers have investigated their potential as a sensing platform due to high performance-to-cost ratio of SU-8 polymer-based cantilever sensors. In this article, we critically review the design, fabrication, and performance aspects of surface stress-based piezoresistive SU-8 polymeric cantilever sensors. The evolution of surface stress-based piezoresistive cantilever sensors from solid-state semiconductor materials to polymers, especially SU-8 polymer, is discussed in detail. Theoretical principles of surface stress generation and their application in cantilever sensing technology are also devised. Variants of SU-8 polymeric cantilevers with different composition of materials in cantilever stacks are explained. Furthermore, the interdependence of the material selection, geometrical design parameters, and fabrication process of piezoresistive SU-8 polymeric cantilever sensors and their cumulative impact on the sensor response are also explained in detail. In addition to the design-, fabrication-, and performance-related factors, this article also describes various challenges in engineering SU-8 polymeric cantilevers as a universal sensing platform such as temperature and moisture vulnerability. This review article would serve as a guideline for researchers to understand specifics and functionality of surface stress-based piezoresistive SU-8 cantilever sensors.

The Role of Nanomechanics in Healthcare

Nanomechanics has played a vital role in pushing our capability to detect, probe, and manipulate the biological species, such as proteins, cells, and tissues, paving way to a deeper knowledge and superior strategies for healthcare. Nanomechanical characterization techniques, such as atomic force microscopy, nanoindentation, nanotribology, optical tweezers, and other hybrid techniques have been utilized to understand the mechanics and kinetics of biospecies. Investigation of the mechanics of cells and tissues has provided critical information about mechanical characteristics of host body environments. This information has been utilized for developing biomimetic materials and structures for tissue engineering and artificial implants. This review summarizes nanomechanical characterization techniques and their potential applications in healthcare research. The principles and examples of label-free detection of cancers and myocardial infarction by nanomechanical cantilevers are discussed. The vital importance of nanomechanics in regenerative medicine is highlighted from the perspective of material selection and design for developing biocompatible scaffolds. This review interconnects the advancements made in fundamental materials science research and biomedical technology, and therefore provides scientific insight that is of common interest to the researchers working in different disciplines of healthcare science and technology.

Optical-Interferometry-Based CMOS-MEMS Sensor Transduced by Stress-Induced Nanomechanical Deflection

We developed a Fabry-Perot interferometer sensor with a metal-oxide-semiconductor field-effect transistor (MOSFET) circuit for chemical sensing. The novel signal transducing technique was performed in three steps: mechanical deflection, transmittance change, and photocurrent change. A small readout photocurrent was processed by an integrated source follower circuit. The movable film of the sensor was a 350-nm-thick polychloro-para-xylylene membrane with a diameter of 100 µm and an air gap of 300 nm. The linearity of the integrated source follower circuit was obtained. We demonstrated a gas response using 80-ppm ethanol detected by small membrane deformation of 50 nm, which resulted in an output-voltage change with the proposed high-efficiency transduction.

Focal molography is a new method for the in situ analysis of molecular interactions in biological samples

Focal molography is a next-generation biosensor that visualizes specific biomolecular interactions in real time. It transduces affinity modulation on the sensor surface into refractive index modulation caused by target molecules that are bound to a precisely assembled nanopattern of molecular recognition sites, termed the 'mologram'. The mologram is designed so that laser light is scattered at specifically bound molecules, generating a strong signal in the focus of the mologram via constructive interference, while scattering at nonspecifically bound molecules does not contribute to the effect. We present the realization of molograms on a chip by submicrometre near-field reactive immersion lithography on a light-sensitive monolithic graft copolymer layer. We demonstrate the selective and sensitive detection of biomolecules, which bind to the recognition sites of the mologram in various complex biological samples. This allows the label-free analysis of non-covalent interactions in complex biological samples, without a need for extensive sample preparation, and enables novel time- and cost-saving ways of performing and developing immunoassays for diagnostic tests.

Optomechanical devices for deep plasma cancer proteomics

Most of the cancer deaths could be avoided by early detection of the tumor when it is confined to its primary site and it has not metastasized. To this aim, one of the most promising strategies is the discovery and detection of protein biomarkers shed by the young tumor to the bloodstream. Proteomic technologies, mainly mass spectrometry and multiplexed immunoassays, have rapidly developed during last years with improved limits of detection and multiplexing capability. Unfortunately, these developments together major investments and large international efforts have not resulted into new useful protein biomarkers. Here, we analyze the potential and limitations of current proteomic technologies for detecting protein biomarkers released into circulation by the tumor. We find that these technologies can hardly probe the deepest region of the plasma proteome, at concentrations below the pg/mL level, where protein biomarkers for early cancer detection may exist. This clearly indicates the need of incorporating novel ultrasensitive techniques to the proteomic tool-box that can cover the inaccessible regions of the plasma proteome. We here propose biological detectors based on nanomechanical systems for discovery and detection of cancer protein biomarkers in plasma. We review the modes of operation of these devices, putting our focus on recent developments on nanomechanical sandwich immunoassays and nanomechanical spectrometry. The first technique enables reproducible immunodetection of proteins at concentrations well below the pg/mL level, with a limit of detection on the verge of 10 ag/mL. This technology can potentially detect low abundance tumor-associated proteins in plasma at the very early stages of the tumor. The second technique enables the identification of individual intact proteins by two physical coordinates, the mass and stiffness, instead of the mass-to-charge ratio of the protein constituents. This technology enormously simplifies the identification of proteins and it can provide useful information on interactions and posttranslational modifications, that otherwise is lost in mass spectrometry.

Stroke-associated pattern of gene expression previously identified by machine-learning is diagnostically robust in an independent patient population

Our group recently employed genome-wide transcriptional profiling in tandem with machine-learning based analysis to identify a ten-gene pattern of differential expression in peripheral blood which may have utility for detection of stroke. The objective of this study was to assess the diagnostic capacity and temporal stability of this stroke-associated transcriptional signature in an independent patient population. Publicly available whole blood microarray data generated from 23 ischemic stroke patients at 3, 5, and 24 h post-symptom onset, as well from 23 cardiovascular disease controls, were obtained via the National Center for Biotechnology Information Gene Expression Omnibus. Expression levels of the ten candidate genes (ANTXR2, STK3, PDK4, CD163, MAL, GRAP, ID3, CTSZ, KIF1B, and PLXDC2) were extracted, compared between groups, and evaluated for their discriminatory ability at each time point. We observed a largely identical pattern of differential expression between stroke patients and controls across the ten candidate genes as reported in our prior work. Furthermore, the coordinate expression levels of the ten candidate genes were able to discriminate between stroke patients and controls with levels of sensitivity and specificity upwards of 90% across all three time points. These findings confirm the diagnostic robustness of the previously identified pattern of differential expression in an independent patient population, and further suggest that it is temporally stable over the first 24 h of stroke pathology.

Blood Droplet-Based Cancer Diagnosis via Proteolytic Activity Measurement in Cancer Progression

Matrix metalloproteinase (MMP) is a key marker and target molecule for cancer diagnosis, as MMP is able to cleave peptide chains resulting in degradation of extracellular matrix (ECM), a necessary step for cancer development. In particular, MMP2 has recently been recognized as an important biomarker for lung cancer. Despite the important role of detecting MMP molecules in cancer diagnosis, it is a daunting task to quantitatively understand a correlation between the status of cancer development and the secretion level of MMP in a blood droplet. Here, we demonstrate a nanoscale cancer diagnosis by nanomechanical quantitation of MMP2 molecules under cancer progression with using a blood droplet of lung cancer patients. Specifically, we measured the frequency dynamics of nanomechanical biosensor functionalized with peptide chains mimicking ECM in response to MMP2 secreted from tumors in lung with different metastasis level. It is shown that the frequency shift of the biosensor, which exhibits the detection sensitivity below 1 nM, enables the quantitation of the secretion level of MMP2 molecules during the progression of cancer cells or tumor growth. More importantly, using a blood droplet of lung cancer patients, nanomechanical biosensor is shown to be capable of depicting the correlation between the secretion level of MMP2 molecules and the level of cancer metastasis, which highlights the cantilever-based MMP2 detection for diagnosis of lung cancer. Our finding will broaden the understanding of cancer development activated by MMP and allow for a fast and point-of-care cancer diagnostics.

Fast Diagnostics of BRAF Mutations in Biopsies from Malignant Melanoma

According to the American skin cancer foundation, there are more new cases of skin cancer than the combined incidence of cancers of the breast, prostate, lung, and colon each year, and malignant melanoma represents its deadliest form. About 50% of all cases are characterized by a particular mutation BRAF(V600E) in the BRAF (Rapid Acceleration of Fibrosarcoma gene B) gene. Recently developed highly specific drugs are able to fight BRAF(V600E) mutated tumors but require diagnostic tools for fast and reliable mutation detection to warrant treatment efficiency. We completed a preliminary clinical trial applying cantilever array sensors to demonstrate identification of a BRAF(V600E) single-point mutation using total RNA obtained from biopsies of metastatic melanoma of diverse sources (surgical material either frozen or fixated with formalin and embedded in paraffin). The method is faster than the standard Sanger or pyrosequencing methods and comparably sensitive as next-generation sequencing. Processing time from biopsy to diagnosis is below 1 day and does not require PCR amplification, sequencing, and labels.

Oligonucleotide-based label-free detection with optical microresonators: strategies and challenges

This review targets diversified oligonucleotide-based biodetection techniques, focusing on the use of microresonators of whispering gallery mode (WGM) type as optical biosensors mostly integrated with lab-on-a-chip systems. On-chip and microfluidics combined devices along with optical microresonators provide rapid, robust, reproducible and multiplexed biodetection abilities in considerably small volumes. We present a detailed overview of the studies conducted so far, including biodetection of various oligonucleotide biomarkers as well as deoxyribonucleic acids (DNAs), ribonucleic acids (RNAs) and proteins. We particularly advert to chemical surface modifications for specific and selective biosensing.

Spatially Multiplexed Micro-Spectrophotometry in Bright Field Mode for Thin Film Characterization

Thickness characterization of thin films is of primary importance in a variety of nanotechnology applications, either in the semiconductor industry, quality control in nanofabrication processes or engineering of nanoelectromechanical systems (NEMS) because small thickness variability can strongly compromise the device performance. Here, we present an alternative optical method in bright field mode called Spatially Multiplexed Micro-Spectrophotometry that allows rapid and non-destructive characterization of thin films over areas of mm² and with 1 μm of lateral resolution. We demonstrate an accuracy of 0.1% in the thickness characterization through measurements performed on four microcantilevers that expand an area of 1.8 mm² in one minute of analysis time. The measured thickness variation in the range of few tens of nm translates into a mechanical variability that produces an error of up to 2% in the response of the studied devices when they are used to measure surface stress variations.

Droplet-based Biosensing for Lab-on-a-Chip, Open Microfluidics Platforms

Low cost, portable sensors can transform health care by bringing easily available diagnostic devices to low and middle income population, particularly in developing countries. Sample preparation, analyte handling and labeling are primary cost concerns for traditional lab-based diagnostic systems. Lab-on-a-chip (LoC) platforms based on droplet-based microfluidics promise to integrate and automate these complex and expensive laboratory procedures onto a single chip; the cost will be further reduced if label-free biosensors could be integrated onto the LoC platforms. Here, we review some recent developments of label-free, droplet-based biosensors, compatible with "open" digital microfluidic systems. These low-cost droplet-based biosensors overcome some of the fundamental limitations of the classical sensors, enabling timely diagnosis. We identify the key challenges that must be addressed to make these sensors commercially viable and summarize a number of promising research directions.

Synchronization and Phase Noise Reduction in Micromechanical Oscillator Arrays Coupled through Light

Synchronization of many coupled oscillators is widely found in nature and has the potential to revolutionize timing technologies. Here, we demonstrate synchronization in arrays of silicon nitride micromechanical oscillators coupled in an all-to-all configuration purely through an optical radiation field. We show that the phase noise of the synchronized oscillators can be improved by almost 10 dB below the phase noise limit for each individual oscillator. These results open a practical route towards synchronized oscillator networks.

Decoupling competing surface binding kinetics and reconfiguration of receptor footprint for ultrasensitive stress assays

Cantilever arrays have been used to monitor biochemical interactions and their associated stress. However, it is often necessary to passivate the underside of the cantilever to prevent unwanted ligand adsorption, and this process requires tedious optimization. Here, we show a way to immobilize membrane receptors on nanomechanical cantilevers so that they can function without passivating the underlying surface. Using equilibrium theory, we quantitatively describe the mechanical responses of vancomycin, human immunodeficiency virus type 1 antigens and coagulation factor VIII captured on the cantilever in the presence of competing stresses from the top and bottom cantilever surfaces. We show that the area per receptor molecule on the cantilever surface influences ligand-receptor binding and plays an important role on stress. Our results offer a new way to sense biomolecules and will aid in the creation of ultrasensitive biosensors.

Micro- and nanodevices integrated with biomolecular probes

Understanding how biomolecules, proteins and cells interact with their surroundings and other biological entities has become the fundamental design criterion for most biomedical micro- and nanodevices. Advances in biology, medicine, and nanofabrication technologies complement each other and allow us to engineer new tools based on biomolecules utilized as probes. Engineered micro/nanosystems and biomolecules in nature have remarkably robust compatibility in terms of function, size, and physical properties. This article presents the state of the art in micro- and nanoscale devices designed and fabricated with biomolecular probes as their vital constituents. General design and fabrication concepts are presented and three major platform technologies are highlighted: microcantilevers, micro/nanopillars, and microfluidics. Overview of each technology, typical fabrication details, and application areas are presented by emphasizing significant achievements, current challenges, and future opportunities.

A Micro-Preconcentrator Combined Olfactory Sensing System with a Micromechanical Cantilever Sensor for Detecting 2,4-Dinitrotoluene Gas Vapor

Preventing unexpected explosive attacks and tracing explosion-related molecules require the development of highly sensitive gas-vapor detection systems. For that purpose, a micromechanical cantilever-based olfactory sensing system including a sample preconcentrator was developed to detect 2,4-dinitrotoluene (2,4-DNT), which is a well-known by-product of the explosive molecule trinitrotoluene (TNT) and exists in concentrations on the order of parts per billion in the atmosphere at room temperature. A peptide receptor (His-Pro-Asn-Phe-Ser-Lys-Tyr-Ile-Leu-His-Gln-Arg) that has high binding affinity for 2,4-DNT was immobilized on the surface of the cantilever sensors to detect 2,4-DNT vapor for highly selective detection. A micro-preconcentrator (µPC) was developed using Tenax-TA adsorbent to produce higher concentrations of 2,4-DNT molecules. The preconcentration was achieved via adsorption and thermal desorption phenomena occurring between target molecules and the adsorbent. The µPC directly integrated with a cantilever sensor and enhanced the sensitivity of the cantilever sensor as a pretreatment tool for the target vapor. The response was rapidly saturated within 5 min and sustained for more than 10 min when the concentrated vapor was introduced. By calculating preconcentration factor values, we verified that the cantilever sensor provides up to an eightfold improvement in sensing performance.

Sensing with Advanced Computing Technology: Fin Field-Effect Transistors with High-k Gate Stack on Bulk Silicon

Field-effect transistors (FETs) form an established technology for sensing applications. However, recent advancements and use of high-performance multigate metal-oxide semiconductor FETs (double-gate, FinFET, trigate, gate-all-around) in computing technology, instead of bulk MOSFETs, raise new opportunities and questions about the most suitable device architectures for sensing integrated circuits. In this work, we propose pH and ion sensors exploiting FinFETs fabricated on bulk silicon by a fully CMOS compatible approach, as an alternative to the widely investigated silicon nanowires on silicon-on-insulator substrates. We also provide an analytical insight of the concept of sensitivity for the electronic integration of sensors. N-channel fully depleted FinFETs with critical dimensions on the order of 20 nm and HfO2 as a high-k gate insulator have been developed and characterized, showing excellent electrical properties, subthreshold swing, SS ∼ 70 mV/dec, and on-to-off current ratio, Ion/Ioff ∼ 10(6), at room temperature. The same FinFET architecture is validated as a highly sensitive, stable, and reproducible pH sensor. An intrinsic sensitivity close to the Nernst limit, S = 57 mV/pH, is achieved. The pH response in terms of output current reaches Sout = 60%. Long-term measurements have been performed over 4.5 days with a resulting drift in time δVth/δt = 0.10 mV/h. Finally, we show the capability to reproduce experimental data with an extended three-dimensional commercial finite element analysis simulator, in both dry and wet environments, which is useful for future advanced sensor design and optimization.

Influence of disordered packing pattern on elastic modulus of single-stranded DNA film on substrate

Determining mechanical properties of single-stranded DNA film grafted on gold surface is critical for analysis and design of DNA-microcantilever biosensors. However, it remains an open issue to quantify the relations among the disordered packing patterns of DNA chains, the mechanical properties of DNA film and the resultant biodetection signals. In this paper, first, the bending experiment of microcantilever is carried out to provide the basic data for a refined multi-scale model of microcantilever deflection induced by ssDNA immobilization. In the model, the complicated interactions in DNA film (consisting of DNA, water molecules and salt ions) are simplified as effective interactions among coarse-grained soft cylinders, which can reveal the varieties of DNA structure in the circumstances of different lengths and salt concentrations; Ohshima's distribution of net charge density is employed to incorporate compositional variations of salt ions along the thickness direction into the Strey's mesoscopic empirical potential on molecular interactions in DNA solutions, and the related model parameters for ssDNA film on substrate are obtained from the curve fitting with our microcantilever bending experiment. Second, the effect of nanoscopic distribution of DNA chains on elastic modulus of ssDNA film is studied by a thought experiment of uniaxial compression, and the disordered patterns of DNA chains are generated by Monte Carlo method. Simulation results point out that nanoscale ssDNA film shows size effect, gradient and diversity in elastic modulus and can achieve maximum stiffness by preferring a disordered and energetically favorable packing pattern collectively induced by electrostatic force, hydration force and configurational entropy.

Design of surface modifications for nanoscale sensor applications

Nanoscale biosensors provide the possibility to miniaturize optic, acoustic and electric sensors to the dimensions of biomolecules. This enables approaching single-molecule detection and new sensing modalities that probe molecular conformation. Nanoscale sensors are predominantly surface-based and label-free to exploit inherent advantages of physical phenomena allowing high sensitivity without distortive labeling. There are three main criteria to be optimized in the design of surface-based and label-free biosensors: (i) the biomolecules of interest must bind with high affinity and selectively to the sensitive area; (ii) the biomolecules must be efficiently transported from the bulk solution to the sensor; and (iii) the transducer concept must be sufficiently sensitive to detect low coverage of captured biomolecules within reasonable time scales. The majority of literature on nanoscale biosensors deals with the third criterion while implicitly assuming that solutions developed for macroscale biosensors to the first two, equally important, criteria are applicable also to nanoscale sensors. We focus on providing an introduction to and perspectives on the advanced concepts for surface functionalization of biosensors with nanosized sensor elements that have been developed over the past decades (criterion (iii)). We review in detail how patterning of molecular films designed to control interactions of biomolecules with nanoscale biosensor surfaces creates new possibilities as well as new challenges.

Rapid discrimination of DNA strands using an opto-calorimetric microcantilever sensor

A rapid technique for quantitative detection and discrimination of DNA strands without using immobilized probe molecules is demonstrated using an opto-calorimetric, self-powered sensor based on a Pb(Zr(0.52)Ti(0.48))O3 (PZT) microcantilever. Microcalorimetric infrared (IR) spectroscopy provides excellent chemical selectivity based on the unique molecular vibrational characteristics of each nucleotide in the mid IR region. The piezoelectric and pyroelectric properties of the PZT microcantilever were exploited in the quantitative detection and discrimination of adsorbed DNA strands with their spectral characteristics. We report the unique spectral characteristics of different DNA nucleotides that are monitored by wavelength-dependent temperature variations for different relative molar ratio of each nucleotide. This approach offers a fast, label-free technique which is highly sensitive and selective for the detection of single nucleotide differences in DNA strands and has the potential to be used as a rapid prescreening biosensor for various biomolecules.

Hydration induced stress on DNA monolayers grafted on microcantilevers

Surface tethered single-stranded DNA films are relevant biorecognition layers for oligonucleotide sequence identification. Also, hydration induced effects on these films have proven useful for the nanomechanical detection of DNA hybridization. Here, we apply nanomechanical sensors and atomic force microscopy to characterize in air and upon varying relative humidity conditions the swelling and deswelling of grafted single stranded and double stranded DNA films. The combination of these techniques validates a two-step hybridization process, where complementary strands first bind to the surface tethered single stranded DNA probes and then slowly proceed to a fully zipped configuration. Our results also demonstrate that, despite the slow hybridization kinetics observed for grafted DNA onto microcantilever surfaces, ex situ sequence identification does not require hybridization times typically longer than 1 h, while quantification is a major challenge.

Highly sensitive amplicon-based transcript quantification by semiconductor sequencing

Background

In clinical and basic research custom panels for transcript profiling are gaining importance because only project specific informative genes are interrogated. This approach reduces costs and complexity of data analysis and allows multiplexing of samples. Polymerase-chain-reaction (PCR) based TaqMan assays have high sensitivity but suffer from a limited dynamic range and sample throughput. Hence, there is a gap for a technology able to measure expression of large gene sets in multiple samples.

Results

We have adapted a commercially available mRNA quantification assay (AmpliSeq-RNA) that measures mRNA abundance based on the frequency of PCR amplicons determined by high-throughput semiconductor sequencing. This approach allows for parallel, accurate quantification of about 1000 transcripts in multiple samples covering a dynamic range of five orders of magnitude. Using samples derived from a well-characterized stem cell differentiation model, we obtained a good correlation (r = 0.78) of transcript levels measured by AmpliSeq-RNA and DNA-microarrays. A significant portion of low abundant transcripts escapes detection by microarrays due to limited sensitivity. Standard quantitative RNA sequencing of the same samples confirms expression of low abundant genes with an overall correlation coefficient of r = 0.87. Based on digital AmpliSeq-RNA imaging we show switches of signaling cascades at four time points during differentiation of stem cells into cardiomyocytes.

Conclusions

The AmpliSeq-RNA technology adapted to high-throughput semiconductor sequencing allows robust transcript quantification based on amplicon frequency. Multiplexing of at least 900 parallel PCR reactions is feasible because sequencing-based quantification eliminates artefacts coming from off-target amplification. Using this approach, RNA quantification and detection of genetic variations can be performed in the same experiment.

Effect of non-specific species competition from total RNA on the static mode hybridization response of nanomechanical assays of oligonucleotides

We investigate here the nanomechanical response of microcantilever sensors in real-time for detecting a range of ultra-low concentrations of oligonucleotides in a complex background of total cellular RNA extracts from cell lines without labeling or amplification. Cantilever sensor arrays were functionalized with probe single stranded DNA (ssDNA) and reference ssDNA to obtain a differential signal. They were then exposed to complementary target ssDNA strands that were spiked in a fragmented total cellular RNA background in biologically relevant concentrations so as to provide clinically significant analysis. We present a model for prediction of the sensor behavior in competitive backgrounds with parameters that are indicators of the change in nanomechanical response with variation in the target and background concentration. For nanomechanical assays to compete with current technologies it is essential to comprehend such responses with eventual impact on areas like understanding non-coding RNA pharmacokinetics, nucleic acid biomarker assays and miRNA quantification for disease monitoring and diagnosis to mention a few. Additionally, we also achieved a femtomolar sensitivity limit for online oligonucleotide detection in a non-competitive environment with these sensors.