Direct detection of a BRAF mutation in total RNA from melanoma cells using cantilever arrays

Biosensors for melanoma skin cancer diagnostics

Skin cancer is a critical global public health concern, with melanoma being the deadliest variant, correlated to 80% of skin cancer-related deaths and a remarkable propensity to metastasize. Despite notable progress in skin cancer prevention and diagnosis, the limitations of existing methods accentuate the demand for precise diagnostic tools. Biosensors have emerged as valuable clinical tools, enabling rapid and reliable point-of-care (POC) testing of skin cancer. This review offers insights into skin cancer development, highlights essential cutaneous melanoma biomarkers, and assesses the current landscape of biosensing technologies for diagnosis. The comprehensive analysis in this review underscores the transformative potential of biosensors in revolutionizing melanoma skin cancer diagnosis, emphasizing their critical role in advancing patient outcomes and healthcare efficiency. The increasing availability of these approaches supports direct diagnosis and aims to reduce the reliance on biopsies, enhancing POC diagnosis. Recent advancements in biosensors for skin cancer diagnosis hold great promise, with their integration into healthcare expected to enhance early detection accuracy and reliability, thereby mitigating socioeconomic disparities.

DNA storage-from natural biology to synthetic biology

Natural DNA storage allows cellular differentiation, evolution, the growth of our children and controls all our ecosystems. Here, we discuss the fundamental aspects of DNA storage and recent advances in this field, with special emphasis on natural processes and solutions that can be exploited. We point out new ways of efficient DNA and nucleotide storage that are inspired by nature. Within a few years DNA-based information storage may become an attractive and natural complementation to current electronic data storage systems. We discuss rapid and directed access (e.g. DNA elements such as promotors, enhancers), regulatory signals and modulation (e.g. lncRNA) as well as integrated high-density storage and processing modules (e.g. chromosomal territories). There is pragmatic DNA storage for use in biotechnology and human genetics. We examine DNA storage as an approach for synthetic biology (e.g. light-controlled nucleotide processing enzymes). The natural polymers of DNA and RNA offer much for direct storage operations (read-in, read-out, access control). The inbuilt parallelism (many molecules at many places working at the same time) is important for fast processing of information. Using biology concepts from chromosomal storage, nucleic acid processing as well as polymer material sciences such as electronical effects in enzymes, graphene, nanocellulose up to DNA macramé , DNA wires and DNA-based aptamer field effect transistors will open up new applications gradually replacing classical information storage methods in ever more areas over time (decades).

Nanomechanical assay for ultrasensitive and rapid detection of SARS-CoV-2 based on peptide nucleic acid

The massive global spread of the COVID-19 pandemic makes the development of more effective and easily popularized assays critical. Here, we developed an ultrasensitive nanomechanical method based on microcantilever array and peptide nucleic acid (PNA) for the detection of severe acute respiratory syndrome-coronavirus-2 (SARS-CoV-2) RNA. The method has an extremely low detection limit of 0.1 fM (10⁵ copies/mL) for N-gene specific sequence (20 bp). Interestingly, it was further found that the detection limit of N gene (pharyngeal swab sample) was even lower, reaching 50 copies/mL. The large size of the N gene dramatically enhances the sensitivity of the nanomechanical sensor by up to three orders of magnitude. The detection limit of this amplification-free assay method is an order of magnitude lower than RT-PCR (500 copies/mL) that requires amplification. The non-specific signal in the assay is eliminated by the in-situ comparison of the array, reducing the false-positive misdiagnosis rate. The method is amplification-free and label-free, allowing for accurate diagnosis within 1 h. The strong specificity and ultra-sensitivity allow single base mutations in viruses to be distinguished even at very low concentrations. Also, the method remains sensitive to fM magnitude lung cancer marker (miRNA-155). Therefore, this ultrasensitive, amplification-free and inexpensive assay is expected to be used for the early diagnosis of COVID-19 patients and to be extended as a broad detection tool.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material (experimental section, N gene sequences and all nucleic acid sequences used in the study, Figs. S1-S6, and Tables S1-S3) is available in the online version of this article at 10.1007/s12274-022-4333-3.

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.

Models of adsorption-induced deformation: ordered materials and beyond

Adsorption-induced deformation is a change in geometrical dimensions of an adsorbent material caused by gas or liquid adsorption on its surface. This phenomenon is universal and sensitive to adsorbent properties, which makes its prediction a challenging task. However, the pure academic interest is complemented by its importance in a number of engineering applications with porous materials characterization among them. Similar to classical adsorption-based characterization methods, the deformation-based ones rely on the quality of the underlying theoretical framework. This fact stimulates the recent development of qualitative and quantitative models toward the more detailed description of a solid material, e.g. account of non-convex and corrugated pores, calculations of adsorption stress in realistic three-dimension solid structures, the extension of the existing models to new geometries, etc. The present review focuses on the theoretical description of adsorption-induced deformation in micro and mesoporous materials. We are aiming to cover recent theoretical works describing the deformation of both ordered and disordered porous bodies.

Amplification-Free Identification and Determination of Nucleic Acids by Surface Plasmon Resonance and Surface-Enhanced Raman Spectroscopy

This review discusses contemporary approaches to designing sensory systems for the identification and determination of nucleic acids (NAs) without amplifying target molecules. Here we summarize the data about methods based on surface plasmon resonance and surface-enhanced Raman spectroscopy, as well as their possibilities, limitations, and prospects for further development.

Nanomechanical sensor for rapid and ultrasensitive detection of tumor markers in serum using nanobody

Early cancer diagnosis requires ultrasensitive detection of tumor markers in blood. To this end, we develop a novel microcantilever immunosensor using nanobodies (Nbs) as receptors. As the smallest antibody (Ab) entity comprising an intact antigen-binding site, Nbs achieve dense receptor layers and short distances between antigen-binding regions and sensor surfaces, which significantly elevate the generation and transmission of surface stress. Owing to the inherent thiol group at the C-terminus, Nbs are covalently immobilized on microcantilever surfaces in directed orientation via one-step reaction, which further enhances the stress generation. For microcantilever-based nanomechanical sensor, these advantages dramatically increase the sensor sensitivity. Thus, Nb-functionalized microcantilevers can detect picomolar concentrations of tumor markers with three orders of magnitude higher sensitivity, when compared with conventional Ab-functionalized microcantilevers. This proof-of-concept study demonstrates an ultrasensitive, label-free, rapid, and low-cost method for tumor marker detection. Moreover, interestingly, we find Nb inactivation on sensor interfaces when using macromolecule blocking reagents. The adsorption-induced inactivation is presumably caused by the change of interfacial properties, due to binding site occlusion upon complex coimmobilization formations. Our findings are generalized to any coimmobilization methodology for Nbs and, thus, for the construction of high-performance immuno-surfaces.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material (experimental section, HER2 detection using anti-HER2-mAb-functionalized microcantilevers) is available in the online version of this article at 10.1007/s12274-021-3588-4.

Carbon Based Nanodots in Early Diagnosis of Cancer

Detection of cancer at an early stage is one of the principal factors associated with successful treatment outcome. However, current diagnostic methods are not capable of making sensitive and robust cancer diagnosis. Nanotechnology based products exhibit unique physical, optical and electrical properties that can be useful in diagnosis. These nanotech-enabled diagnostic representatives have proved to be generally more capable and consistent; as they selectively accumulated in the tumor site due to their miniscule size. This article rotates around the conventional imaging techniques, the use of carbon based nanodots viz Carbon Quantum Dots (CQDs), Graphene Quantum Dots (GQDs), Nanodiamonds, Fullerene, and Carbon Nanotubes that have been synthesized in recent years, along with the discovery of a wide range of biomarkers to identify cancer at early stage. Early detection of cancer using nanoconstructs is anticipated to be a distinct reality in the coming years.

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.

Ultrasensitive Detection of RNA with Single-Base Resolution by Coupling Electrochemical Sensing Strategy with Chimeric DNA Probe-Aided Ligase Chain Reaction

Accurate and sensitive detection of single-base mutations in RNAs is of great value in basic studies of life science and medical diagnostics. However, the current available RNA detection methods are challenged by heterogeneous clinical samples in which trace RNA mutants usually existed in a large pool of normal wild sequences. Thus, there is still great need for developing the highly sensitive and highly specific methods in detecting single-base mutations of RNAs in heterogeneous clinical samples. In the present study, a new chimeric DNA probe-aided ligase chain reaction-based electrochemical method (cmDNA-eLCR) was developed for RNA mutation detection through the BSA-based carrier platform and the horseradish peroxidase-hydrogen peroxide-tetramethylbenzidine (HRP-H₂O₂-TMB) system. The denaturing polyacrylamide gel electrophoresis and a fluorophore-labeled probe was ingeniously designed to demonstrate the advantage of cmDNA in ligation to normal DNA templated by RNA with the catalysis of T4 RNA ligase 2 as well as its higher selectivity than DNA ligase system. Finally, the proposed cmDNA-eLCR, compared with the traditional eLCR, showed excellent performance in discriminating single base-mismatched sequences, where the signal response for mismatched targets at a high concentration could overlap completely with that for the blank control. Besides, this cmDNA-eLCR assay had a wide linear range crossing six orders of magnitude from 1.0 × 10^-15 to1.0 × 10^-10 M with a limit of detection as low as 0.6 fM. Furthermore, this assay was applied to detect RNA in real sample with a satisfactory result, thereby demonstrating its great potential in diagnosis of RNA-related diseases.

Evaluation of the expression levels of BRAFV600E mRNA in primary tumors of thyroid cancer using an ultrasensitive mutation assay

Background

The BRAF^V600E gene encodes for the mutant BRAF^V600E protein, which triggers downstream oncogenic signaling in thyroid cancer. Since most currently available methods have focused on detecting BRAF^V600E mutations in tumor DNA, there is limited information about the level of BRAF^V600E mRNA in primary tumors of thyroid cancer, and the diagnostic relevance of these RNA mutations is not known.

Methods

Sixty-two patients with thyroid cancer and non-malignant thyroid disease were included in the study. Armed with an ultrasensitive technique for mRNA-based mutation analysis based on a two step RT-qPCR method, we analysed the expression levels of the mutated BRAF^V600E mRNA in formalin-fixed paraffin-embedded samples of thyroid tissues. Sanger sequencing for detection of BRAF^V600E DNA was performed in parallel for comparison and normalization of BRAF^V600E mRNA expression levels.

Results

The mRNA-based mutation detection assay enables detection of the BRAF^V600E mRNA transcripts in a 10,000-fold excess of wildtype BRAF counterparts. While BRAF^V600E mutations could be detected by Sanger sequencing in 13 out of 32 malignant thyroid cancer FFPE tissue samples, the mRNA-based assay detected mutations in additionally 5 cases, improving the detection rate from 40.6 to 56.3%. Furthermore, we observed a surprisingly large, 3-log variability, in the expression level of the BRAF^V600E mRNA in FFPE samples of thyroid cancer tissue.

Conclusions

The expression levels of BRAF^V600E mRNA was characterized in the primary tumors of thyroid cancer using an ultrasensitive mRNA-based mutation assay. Our data inspires further studies on the prognostic and diagnostic relevance of the BRAF^V600E mRNA levels as a molecular biomarker for the diagnosis and monitoring of various genetic and malignant diseases.

Micro/Nano fabricated cantilever based biosensor platform: A review and recent progress

Recent trends in biosensing research have motivated scientists and research professionals to investigate the development of miniaturized bioanalytical devices to make them portable, label-free and smaller in size. The performance of the cantilever-based devices which is one of the very important domains of sensitive field level detection has improved significantly with the development of new micro/nanofabrication technologies and surface functionalization techniques. The cantilevers have scaled down to Nano from micro-level and have become exceptionally sensitive and also have some anomalous associated properties due to the scale. In this review we have discussed about fundamental principles of cantilever operation, detection methods, and previous, present and future approaches of study through cantilever-based sensing platform. Other than that, we have also discussed the past major bio-sensing efforts through micro/nano cantilevers and about recent progress in the field.

Silicon Microcantilever Sensors to Detect the Reversible Conformational Change of a Molecular Switch, Spiropyan

The high sensitivity of silicon microcantilever sensors has expanded their use in areas ranging from gas sensing to bio-medical applications. Photochromic molecules also represent promising candidates for a large variety of sensing applications. In this work, the operating principles of these two sensing methods are combined in order to detect the reversible conformational change of a molecular switch, spiropyran. Thus, arrays of silicon microcantilever sensors were functionalized with spiropyran on the gold covered side and used as test microcantilevers. The microcantilever deflection response was observed, in five sequential cycles, as the transition from the spiropyran (SP) (CLOSED) to the merocyanine (MC) (OPEN) state and vice-versa when induced by UV and white light LED sources, respectively, proving the reversibility capabilities of this type of sensor. The microcantilever deflection direction was observed to be in one direction when changing to the MC state and in the opposite direction when changing back to the SP state. A tensile stress was induced in the microcantilever when the SP to MC transition took place, while a compressive stress was observed for the reverse transition. These different type of stresses are believed to be related to the spatial conformational changes induced in the photochromic molecule upon photo-isomerisation.

High-Performance Nucleic Acid Sensors for Liquid Biopsy Applications

Circulating tumour nucleic acids (ctNAs) are released from tumours cells and can be detected in blood samples, providing a way to track tumors without requiring a tissue sample. This "liquid biopsy" approach has the potential to replace invasive, painful, and costly tissue biopsies in cancer diagnosis and management. However, a very sensitive and specific approach is required to detect relatively low amounts of mutant sequences linked to cancer because they are masked by the high levels of wild-type sequences. This review discusses high-performance nucleic acid biosensors for ctNA analysis in patient samples. We compare sequencing- and amplification-based methods to next-generation sensors for ctDNA and ctRNA (including microRNA) profiling, such as electrochemical methods, surface plasmon resonance, Raman spectroscopy, and microfluidics and dielectrophoresis-based assays. We present an overview of the analytical sensitivity and accuracy of these methods as well as the biological and technical challenges they present.

Nanomechanical detection of Escherichia coli infection by bacteriophage T7 using cantilever sensors

Viruses that infect bacteria (bacteriophages) are a promising alternative treatment for bacterial diseases, especially in the case of antibiotic resistance. Due to a renewed interest in phage therapies, development of rapid and specific detection methods for bacteria/bacteriophage interaction are gaining attention for proper diagnosis and treatment. This paper describes a new method to detect the interaction between Escherichia coli and bacteriophage T7 in a sensitive and quantitative way, using the nanomechanical motion of bacteria adhered to a cantilever surface. Our approach combines both deflection and dynamic frequency-domain characterization. The device was able to determine the viability of a low amount of living bacteria attached to the cantilever, and was used to monitor T7 interaction with E. coli over a wide range of virus concentrations up to 109 PFU ml-1. The nanomechanical assay described here requires no protein labeling and can be performed in a single reaction without additional reagents. The system was able to detect the interaction between a few thousand particles through the fluctuation of mechanical energy over a broad range of frequencies. The presented data provides the basis for more detailed studies of the sequence of molecular events that contribute to the motion of the device.

T cell-induced CSF1 promotes melanoma resistance to PD1 blockade

Colony-stimulating factor 1 (CSF1) is a key regulator of monocyte/macrophage differentiation that sustains the protumorigenic functions of tumor-associated macrophages (TAMs). We show that CSF1 is expressed in human melanoma, and patients with metastatic melanoma have increased CSF1 in blood compared to healthy subjects. In tumors, CSF1 expression correlated with the abundance of CD8⁺ T cells and CD163⁺ TAMs. Human melanoma cell lines consistently produced CSF1 after exposure to melanoma-specific CD8⁺ T cells or T cell-derived cytokines in vitro, reflecting a broadly conserved mechanism of CSF1 induction by activated CD8⁺ T cells. Mining of publicly available transcriptomic data sets suggested co-enrichment of CD8⁺ T cells with CSF1 or various TAM-specific markers in human melanoma, which was associated with nonresponsiveness to programmed cell death protein 1 (PD1) checkpoint blockade in a smaller patient cohort. Combination of anti-PD1 and anti-CSF1 receptor (CSF1R) antibodies induced the regression of BRAF^V600E -driven, transplant mouse melanomas, a result that was dependent on the effective elimination of TAMs. Collectively, these data implicate CSF1 induction as a CD8⁺ T cell-dependent adaptive resistance mechanism and show that simultaneous CSF1R targeting may be beneficial in melanomas refractory to immune checkpoint blockade and, possibly, other T cell-based therapies.

Amplification-free SERS analysis of DNA mutation in cancer cells with single-base sensitivity

Accurate and sensitive identification of DNA mutations in tumor cells is critical to the diagnosis, prognosis and personalized therapy of cancer. Conventional polymerase chain reaction (PCR)-based methods are limited by the complicated amplification process. Herein, an amplification-free surface enhanced Raman spectroscopy (SERS) approach which directly detects point mutations in cancer cells has been proposed. A highly sensitive and uniform SERS substrate was fabricated using gold@silver core-shell nanorods, achieving an enhancement factor of 1.85 × 106. By combining the SERS-active nanosubstrate with molecular beacon probes, the limit of detection reached as low as 50 fM. To enable parallel analysis and automated operation, the SERS sensor was integrated into a microfluidic chip. This novel chip-based assay was able to differentiate between mutated and wild-type KRAS genes among a variety of other nucleic acids from cancer cells in 40 min. Owing to the simple operation and fast analysis, the SERS-based DNA assay chip could potentially provide insights into clinical cancer theranostics in an easy and inexpensive manner at the point of care.

Hofmann Metal-Organic Framework Monolayer Nanosheets as an Axial Coordination Platform for Biosensing

Two-dimensional (2D) nanomaterials are remarkably attractive platform candidates for signal transduction through fluorescence resonance energy transfer or photo-induced electron-transfer pathway. In this work, a 2D Hofmann metal organic framework (hMOF) monolayer nanosheet was developed as an axial coordination platform for DNA detection via a ligand-to-metal charge-transfer quenching mechanism. Through modulating the position of phosphonate groups of rigid ligands, a layer-structured hMOF was synthesized. The single crystals showed that the adjacent layers were linked via hydrogen bonds between diethyl 4-pyridylphosphonate and the solvent. Furthermore, the 2D hMOF monolayer nanosheets were obtained easily via a top-down method. More significantly, the quenching mechanism was identified as an axial coordination between the open Fe²⁺ sites of hMOF nanosheets and fluorophores with 91% quenching efficiency, constituting an excellent signal transduction strategy. The smart use of hMOF monolayer nanosheets as an axial coordination platform could lead to promising applications in signal switching or/and sensing devices.

Anomalous interfacial stress generation during sodium intercalation/extraction in MoS2 thin-film anodes

Although the generation of mechanical stress in the anode material is suggested as a possible reason for electrode degradation and fading of storage capacity in batteries, only limited knowledge of the electrode stress and its evolution is available at present. Here, we show real-time monitoring of the interfacial stress of a few-layer MoS₂ system under the sodiation/desodiation process using microcantilever electrodes. During the first sodiation with a voltage plateau of 1.0 to 0.85 V, the MoS₂ exhibits a compressive stress (2.1 Nm^-1), which is substantially smaller than that measured (9.8 Nm^-1) during subsequent plateaus at 0.85 to 0.4 V due to the differential volume expansion of the MoS₂ film. The conversion reaction to Mo below 0.1 V generates an anomalous compressive stress of 43 Nm^-1 with detrimental effects. These results also suggest the existence of a separate discharge stage between 0.6 and 0.1 V, where the generated stress is only approximately one-third of that observed below 0.1 V. This approach can be adapted to help resolve the localized stress in a wide range of electrode materials, to gain additional insights into mechanical effects of charge storage, and for long-lifetime battery design.

Novel Membrane Detector Based on Smart Nanogels for Ultrasensitive Detection of Trace Threat Substances

A novel membrane detector is developed by a facile strategy combining commercialized membrane and smart nanogels for ultrasensitive and highly selective real-time detection of trace threat substances. On the basis of nanogel filtration and polydopamine adhesion, the membrane detector is fabricated by simply immobilizing smart nanogels onto the multiple pores of a commercialized membrane as the nanosensors and nanovalves. This is demonstrated by incorporating Pb²⁺-responsive poly( N-isopropylacrylamide- co-acryloylamidobenzo-18-crown-6) nanogels in the straight pores of a commercialized polycarbonate membrane for ultrasensitive and highly selective real-time detection of trace Pb²⁺. When selectively recognizing the Pb²⁺ in solution, the smart nanogels in the membrane pores swell, which lead to trans-membrane flux change. Quantitative detection of Pb²⁺ concentration can be achieved by simply measuring the flow rate of the trans-membrane flow. Due to the multiple nanochannels of nanogel-immobilized pores in the membrane for Pb²⁺ sensing and flux regulating, ultrasensitive and highly selective real-time detection of trace Pb²⁺ with concentration as low as 10^-10 mol L^-1 can be achieved. The nanogel-immobilized membrane detector offers a flexible platform to create versatile new membrane detectors by incorporating diverse smart nanogels for ultrasensitive and highly selective real-time detection of different trace threat substances.

A Clamp-Based One-Step Droplet Digital Reverse Transcription PCR (ddRT-PCR) for Precise Quantitation of Messenger RNA Mutation in Single Cells

Precise detection of the low copy numbers of messenger RNA (mRNA) mutation in single cells is of great significance but still remains challenging. Herein, by integrating the outstanding features of a rationally designed peptide nucleic acid (PNA) clamp for highly selective discrimination of single-nucleotide variation, and droplet digital PCR for ultrasensitive and precise quantification, we have developed a robust one-step droplet digital reverse transcription PCR (ddRT-PCR) method which enables precise mRNA mutation detection in single cells with ultrahigh specificity to clearly discern as low as 0.01% mutated mRNA in a high background of wild-type mRNA. Because of its outstanding single-molecule level sensitivity and ultrahigh specificity, this ddRT-PCR method holds great promise for studying cellular heterogeneity at the single cell level, as well as for the precise quantification of mutant mRNAs in complex plasma or serum for liquid biopsy.

Theoretical Analysis for Bending of Single-Stranded DNA Adsorption on Microcantilever Sensors

An energy-based model is presented to establish the bending deformation of microcantilever beams induced by single-stranded DNA (ssDNA) adsorption. The total free energy of the DNA-microcantilever sensor was obtained by considering the excluded-volume energy and the polymer stretching energy of DNA chains from mean-field theory, and the mechanical energy of three non-biological layers. The radius of curvature and deflection of the cantilever were determined through the minimum principle of energy. The efficiency of the present model was confirmed through comparison with experimental data. The effects of length, grafting density, salt concentration, thickness, and elastic modulus of substrate on tip deflections are also discussed in this paper. These factors can significantly affect the deflections of the biosensor. This work demonstrates that it is useful to develop a theoretical model for the label-free nanomechanical detection technique.

Fe-Au Nanoparticle-Coupling for Ultrasensitive Detections of Circulating Tumor DNA

Effectiveness of cancer therapy relies heavily on the efficient early diagnosis. Circulating tumor DNA (ctDNA) detection is one of the most clinically meaningful liquid biopsy approaches for the noninvasive cancer early diagnosis, which, unfortunately, cannot be applied as a routine diagnostic tool till a number of obstacles, for example, unsatisfactory specificity and sensitivity, and extremely high costs, are overcome. Here, the first paradigm of nanomaterial's application in the extremely specific, ultrasensitive, and yet economical ctDNA detections is reported based on a facile nanoparticle-coupling strategy without amplification, with which polymerase chain reaction (PCR)-introduced bias and other shortcomings are successfully circumvented. Aiming at seven Kirsten rat sarcoma-2 virus (KRAS) point mutations, the present strategy exhibits high specificity and an ultrahigh sensitivity of detecting as low as 0.1 pg mL^-1 of KRAS point mutation without prior PCR amplification. Discriminating KRAS gene mutations in lung adenocarcinoma patients at an extremely low detection limit equivalent to 0.12% mutation relative to wild-type gene is successful. It is envisioned that this nanoparticle-coupling approach could be routinely applied clinically for ultra-early diagnosis and monitoring of diverse malignant tumors, thus facilitating the fight against cancer.

Fast demodulated white-light interferometry-based fiber-optic Fabry-Perot cantilever microphone

We demonstrate a highly sensitive and stable fiber-optic Fabry-Perot cantilever microphone based on fast demodulated white-light interferometry. The cavity length of the low-finesse Fabry-Perot interferometry is absolutely measured by realizing a high-speed demodulation method utilizing a full spectrum, with the advantages of both high resolution and large dynamic range. An acoustic test demonstrates high sensitivities and linear responsivities at frequencies below 2 kHz. The pressure responsivity and the noise-limited minimum detectable acoustic pressure level are measured to be 211.2 nm/Pa and 5  μPa/Hz^1/2, respectively, at the frequency of 1 kHz. Comparative experimental results show that the signal-to-noise ratio is over 10 times higher than a reference condenser microphone.

Identifying DNA mismatches at single-nucleotide resolution by probing individual surface potentials of DNA-capped nanoparticles

Here, we demonstrate a powerful method to discriminate DNA mismatches at single-nucleotide resolution from 0 to 5 mismatches (χ₀ to χ₅) using Kelvin probe force microscopy (KPFM). Using our previously developed method, we quantified the surface potentials (SPs) of individual DNA-capped nanoparticles (DCNPs, ∼100 nm). On each DCNP, DNA hybridization occurs between ∼2200 immobilized probe DNA (pDNA) and target DNA with mismatches (tDNA, ∼80 nM). Thus, each DCNP used in the bioassay (each pDNA-tDNA interaction) corresponds to a single ensemble in which a large number of pDNA-tDNA interactions take place. Moreover, one KPFM image can scan at least dozens of ensembles, which allows statistical analysis (i.e., an ensemble average) of many bioassay cases (ensembles) under the same conditions. We found that as the χ_n increased from χ₀ to χ₅ in the tDNA, the average SP of dozens of ensembles (DCNPs) was attenuated owing to fewer hybridization events between the pDNA and the tDNA. Remarkably, the SP attenuation vs. the χ_n showed an inverse-linear correlation, albeit the equilibrium constant for DNA hybridization exponentially decreased asymptotically as the χ_n increased. In addition, we observed a cascade reaction at a 100-fold lower concentration of tDNA (∼0.8 nM); the average SP of DCNPs exhibited no significant decrease but rather split into two separate states (no-hybridization vs. full-hybridization). Compared to complementary tDNA (i.e., χ₀), the ratio of no-hybridization/full-hybridization within a given set of DCNPs became ∼1.6 times higher in the presence of tDNA with single mismatches (i.e., χ₁). The results imply that our method opens new avenues not only in the research on the DNA hybridization mechanism in the presence of DNA mismatches but also in the development of a robust technology for DNA mismatch detection.

A high accuracy cantilever array sensor for early liver cancer diagnosis

Early liver cancer diagnosis has clinical significance in treating cancer. Joint detection of multiple biomarkers has been considered as an effective and reliable method for early cancer diagnosis. In this work, a novel biosensor based on microcantilever array was batch-fabricated for multiple liver cancer biomarkers detection with high sensitivity, high accuracy, high throughput, and high specification. A micro-cavity was designed in the free end of the cantilever for local reaction between antibody and antigen, which can dramatically reduce the effect of adsorption-induced stiffness coefficient k variation. Furthermore,the pillar arrays in the micro-cavity were designed for increasing detection upper limit. A linear relationship between the relative frequency shift and the antigen concentration was observed for three liver cancer biomarkers, alpha-fetoprotein (AFP), γ-glutamyltranspeptidase II (GGT-2), and hepatocyte growth factor (HGF). Slight cross-reaction response to different antigens ensures high specificity of the sensor. These features will promote clinical application of the cantilever sensors in early cancer diagnosis.

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.

Nanolock-Nanopore Facilitated Digital Diagnostics of Cancer Driver Mutation in Tumor Tissue

Cancer driver mutations are clinically significant biomarkers. In precision medicine, accurate detection of these oncogenic changes in patients would enable early diagnostics of cancer, individually tailored targeted therapy, and precise monitoring of treatment response. Here we investigated a novel nanolock-nanopore method for single-molecule detection of a serine/threonine protein kinase gene BRAF V600E mutation in tumor tissues of thyroid cancer patients. The method lies in a noncovalent, mutation sequence-specific nanolock. We found that the nanolock formed on the mutant allele/probe duplex can separate the duplex dehybridization procedure into two sequential steps in the nanopore. Remarkably, this stepwise unzipping kinetics can produce a unique nanopore electric marker, with which a single DNA molecule of the cancer mutant allele can be unmistakably identified in various backgrounds of the normal wild-type allele. The single-molecule sensitivity for mutant allele enables both binary diagnostics and quantitative analysis of mutation occurrence. In the current configuration, the method can detect the BRAF V600E mutant DNA lower than 1% in the tumor tissues. The nanolock-nanopore method can be adapted to detect a broad spectrum of both transversion and transition DNA mutations, with applications from diagnostics to targeted therapy.

Optomechanical proposal for monitoring microtubule mechanical vibrations

Microtubules provide the mechanical force required for chromosome separation during mitosis. However, little is known about the dynamic (high-frequency) mechanical properties of microtubules. Here, we theoretically propose to control the vibrations of a doubly clamped microtubule by tip electrodes and to detect its motion via the optomechanical coupling between the vibrational modes of the microtubule and an optical cavity. In the presence of a red-detuned strong pump laser, this coupling leads to optomechanical-induced transparency of an optical probe field, which can be detected with state-of-the art technology. The center frequency and line width of the transparency peak give the resonance frequency and damping rate of the microtubule, respectively, while the height of the peak reveals information about the microtubule-cavity field coupling. Our method opens the new possibilities to gain information about the physical properties of microtubules, which will enhance our capability to design physical cancer treatment protocols as alternatives to chemotherapeutic drugs.

Ultrasensitive Detection of Cancer Prognostic miRNA Biomarkers Based on Surface Plasmon Enhanced Light Scattering

The development of simple yet ultrasensitive biosensing approaches for the detection of cancer prognostic microRNA is an important step toward their successful clinical implementation. We demonstrate the relevance for the detection of circulating miRNA of a novel signal amplification scheme based on surface plasmon resonance enhanced light scattering (SP-LS). In addition to experimental optimization carried out using gold nanoparticle (AuNP) tags conjugated with a monoclonal antibody with high affinity for RNA*DNA hybrid duplexes, simulation modeling was conducted to obtain insights about SP-LS biosensing. SP-LS enabled the detection of miRNA-122 at subpicomolar concentrations within 30 min, and a limit of detection of 2 attomoles (60 fM, 50 μL) was determined. MiRNA-122 could also be reliably detected in a high concentration background of nontarget miRNA. The proposed SP-LS miRNA detection approach could be readily applied to other miRNA targets of diagnostic importance and further developed to allow for multiplex measurements of miRNA panels. The promising results obtained in this study and advantageous features of SP-LS warrant further development and its application to clinical samples.

Surface mediated cooperative interactions of drugs enhance mechanical forces for antibiotic action

The alarming increase of pathogenic bacteria that are resistant to multiple antibiotics is now recognized as a major health issue fuelling demand for new drugs. Bacterial resistance is often caused by molecular changes at the bacterial surface, which alter the nature of specific drug-target interactions. Here, we identify a novel mechanism by which drug-target interactions in resistant bacteria can be enhanced. We examined the surface forces generated by four antibiotics; vancomycin, ristomycin, chloroeremomycin and oritavancin against drug-susceptible and drug-resistant targets on a cantilever and demonstrated significant differences in mechanical response when drug-resistant targets are challenged with different antibiotics although no significant differences were observed when using susceptible targets. Remarkably, the binding affinity for oritavancin against drug-resistant targets (70 nM) was found to be 11,000 times stronger than for vancomycin (800 μM), a powerful antibiotic used as the last resort treatment for streptococcal and staphylococcal bacteria including methicillin-resistant Staphylococcus aureus (MRSA). Using an exactly solvable model, which takes into account the solvent and membrane effects, we demonstrate that drug-target interactions are strengthened by pronounced polyvalent interactions catalyzed by the surface itself. These findings further enhance our understanding of antibiotic mode of action and will enable development of more effective therapies.

Direct-write nanoscale printing of nanogranular tunnelling strain sensors for sub-micrometre cantilevers

The sensitivity and detection speed of cantilever-based mechanical sensors increases drastically through size reduction. The need for such increased performance for high-speed nanocharacterization and bio-sensing, drives their sub-micrometre miniaturization in a variety of research fields. However, existing detection methods of the cantilever motion do not scale down easily, prohibiting further increase in the sensitivity and detection speed. Here we report a nanomechanical sensor readout based on electron co-tunnelling through a nanogranular metal. The sensors can be deposited with lateral dimensions down to tens of nm, allowing the readout of nanoscale cantilevers without constraints on their size, geometry or material. By modifying the inter-granular tunnel-coupling strength, the sensors' conductivity can be tuned by up to four orders of magnitude, to optimize their performance. We show that the nanoscale printed sensors are functional on 500 nm wide cantilevers and that their sensitivity is suited even for demanding applications such as atomic force microscopy.

Reducing the size of cantilever-based sensors increases the sensitivity and detection speed of techniques such as atomic force microscopy. Here, the authors demonstrate a nanomechanical readout method that can be easily scaled down in size by using electron co-tunnelling through a nanogranular metal.

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.