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

Ultrasensitive detection of vital biomolecules based on a multi-purpose BioMEMS for Point of care testing: digoxin measurement as a case study

Rapid and label-free detection of very low concentrations of biomarkers in disease diagnosis or therapeutic drug monitoring is essential to prevent disease progression in Point of Care Testing. For this purpose, we propose a multi-purpose optical Bio-Micro-Electro-Mechanical-System (BioMEMS) sensing platform which can precisely measure very small changes of biomolecules concentrations in plasma-like buffer samples. This is realized by the development of an interferometric detection method on highly sensitive MEMS transducers (cantilevers). This approach facilitates the precise analysis of the obtained results to determine the analyte type and its concentrations. Furthermore, the proposed multi-purpose platform can be used for a wide range of biological assessments in various concentration levels by the use of an appropriate bioreceptor and the control of its coating density on the cantilever surface. In this study, the present system is prepared for the identification of digoxin medication in its therapeutic window for therapeutic drug monitoring as a case study. The experimental results represent the repeatability and stability of the proposed device as well as its capability to detect the analytes in less than eight minutes for all samples. In addition, according to the experiments carried out for very low concentrations of digoxin in plasma-like buffer, the detection limit of LOD = 300 fM and the maximum sensitivity of S = 5.5 × 1012 AU/M are achieved for the implemented biosensor. The present ultrasensitive multi-purpose BioMEMS sensor can be a fully-integrated, cost-effective device to precisely analyze various biomarker concentrations for various biomedical applications.

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.

A label-free biomarkers detection platform relied on a bilayer long-wave infrared metamaterials BioNEMS sensor

A novel approach based on optical Biological-Nano-Electro-Mechanical-Systems (BioNEMS) sensor is presented in this paper to provide highly sensitive and precise detection of biomolecules. The proposed BioNEMS sensor is relied on a bi-layer metamaterials structure, tuned by its wavelength. The presented biosensor consists of a BioNEMS membrane coated by Complementary Split Ring Resonators and an array of Split Ring Resonators cells on the substrate. While the immobilized bioreceptors adsorb the biomarkers (i.e. mRNA or protein), it causes a bending of the suspended membrane. This is due to the differential surface stress which is induced on the Nano-Electro-Mechanical-Systems structure. As a consequence, the coupling strength of two complementary metamaterial layers and thus the electromagnetic response of the biosensor are changed. Furthermore, the proposed device is designed and analyzed by numerical and analytical approaches in order to obtain its functional characteristics as follows: detection sensitivity of 21 967 nm/RIU, figure of merit of 327.8 RIU^-1", mechanical sensitivity of 2.6μm/Nm^-1" and resonant frequency of 4.92 kHz. According to the obtained results, the functional characteristics of the proposed label-free biosensor show its high potential for highly sensitive and accurate molecule detections, disease diagnosis as well as drug delivery tests for Lab-On-Chip systems.

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.

Nanotechnological immunoassay for rapid label-free analysis of candidate malaria vaccines

Malaria is a life-threatening epidemic disease with half of the world's population at risk. Although its incidence rate has fallen since 2010, this ratio dramatically stalled between 2014 and 2018. New fast and optimized tools in vaccine analysis and seroconversion testing are critically needed. We developed a clinical diagnostic device based on piezo-actuated nanoresonators that perform as quantitative in situ calibrated nano-bio sensors for specific detection of multiple target molecules in serum samples. The immunoassay successfully diagnoses humoral immune responses induced by malaria vaccine candidates and reveals the timeline and stage of the infection. We applied the newly developed strategy to a variety of different samples, from pure antibody/vaccine solutions, to blood samples from clinical trials on both naïve and pre-exposed malaria volunteers from sub-Saharan countries. Our nanomechanical assay provides a direct one-step label-free quantitative immunoassay that is on par with the gold-standard, multi-step enzyme-linked immunosorbent assay (ELISA). We achieve a limit of detection of few pg ml-1, or sub-pM concentrations. The 6 μl sample volume allows more than 50 experiments from one finger prick. Furthermore, we simultaneously detected multiple analytes by differential functionalization of multiple sensors in parallel. The inherent differential read-out with in situ controls reduces false positive results. Due to the faster turnaround time, the minimal volume required and the automatized handling system, this technique has great potential for miniaturization and routine diagnostics in pandemic emergencies.

Delivery of MSCs with a Hybrid β-Sheet Peptide Hydrogel Consisting IGF-1C Domain and D-Form Peptide for Acute Kidney Injury Therapy

Purpose

By providing a stem cell microenvironment with particular bioactive constituents in vivo, synthetic biomaterials have been progressively successful in stem cell-based tissue regeneration by enhancing the engraftment and survival of transplanted cells. Designs with bioactive motifs to influence cell behavior and with D-form amino acids to modulate scaffold stability may be critical for the development and optimization of self-assembling biomimetic hydrogel scaffolds for stem cell therapy.

Materials and Methods

In this study, we linked naphthalene (Nap) covalently to a short D-form peptide (Nap-^DF^DFG) and the C domain of insulin-like growth factor-1 (IGF-1C) as a functional hydrogel-based scaffolds, and we hypothesized that this hydrogel could enhance the therapeutic efficiency of human placenta-derived mesenchymal stem cells (hP-MSCs) in a murine acute kidney injury (AKI) model.

Results

The self-assembling peptide was constrained into a classical β-sheet structure and showed hydrogel properties. Our results revealed that this hydrogel exhibited increased affinity for IGF-1 receptor. Furthermore, cotransplantation of the β-IGF-1C hydrogel and hP-MSCs contributed to endogenous regeneration post-injury and boosted angiogenesis in a murine AKI model, leading to recovery of renal function.

Conclusion

This hydrogel could provide a favorable niche for hP-MSCs and thereby rescue renal function in an AKI model by promoting cell survival and angiogenesis. In conclusion, by covalently linking the desired functional groups to D-form peptides to create functional hydrogels, self-assembling β-sheet peptide hydrogels may serve as a promising platform for tissue-engineering and stem cell therapy.

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Thin Film Analysis by Nanomechanical Infrared Spectroscopy

There is a fundamental need for techniques for thin film characterization. The current options for obtaining infrared (IR) spectra typically suffer from low signal-to-noise-ratios (SNRs) for sample thicknesses confined to a few nanometers. We present nanomechanical infrared spectroscopy (NAM-IR), which enables the measurement of a complete infrared fingerprint of a polyvinylpyrrolidone (PVP) layer as thin as 20 nm with an SNR of 307. Based on the characterization of the given NAM-IR setup, a minimum film thickness of only 160 pm of PVP can be analyzed with an SNR of 2. Compared to a conventional attenuated total reflectance Fourier transform infrared spectroscopy (ATR-FTIR) system, NAM-IR yields an SNR that is 43 times larger for a 20 nm-thick PVP layer and requires only a fraction of the acquisition time. These results pave the way for NAM-IR as a highly sensitive, fast, and practical tool for IR analysis of polymer thin films.

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.

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.

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.

Epitope Binning Assay Using an Electron Transfer-Modulated Aptamer Sensor

Surface plasmon resonance and quartz crystal microbalance are workhorses of protein-DNA interaction research for over 20 years, providing ways to quantitatively determine the protein-DNA binding. However, the cost, necessary technical expertise, and severe nonspecific adsorption poses barriers to their use. Convenient and effective techniques for the measurement of protein-DNA binding affinity and the epitope binning between DNA and proteins for developing highly sensitive detection platform remain challenging. Here, we develop a binding-induced alteration in electron transfer kinetics of the redox reporter labeled (methylene blue) on DNA aptamer to measure the binding affinity between prostate-specific antigen (PSA) and aptamer. We demonstrate that the binding of PSA to aptamer decreases the electron transfer rate of methylene blue for ∼45%. Further, we identify the best pairwise selection of aptamers for developing sandwich assay by sorting from 10 pairwise modes with the PSA detection limit of 500 ng/mL. Our study provides promising ways to analyze the binding affinity between ligand and receptor and to sort pairwise between aptamers or antibodies for the development of highly sensitive sandwich immunoassays.

Nanomechanical sensors for direct and rapid characterization of sperm motility based on nanoscale vibrations

Infertility, whether of male or female origin, is a critical challenge facing the low birth rate and aging population throughout the world, and semen analysis is a cornerstone of the diagnostic evaluation of the male contribution to infertility. This means that tools which can characterize sperm properties in an effective manner are very much needed. The conventional approaches are essentially image-based, which have a limited value for analyzing sperm properties. Here, we show that an assay using nanomechanical sensors can detect sperm motility based on nanomotion. We use microcantilever sensors to directly characterize the mechanical response of the sperm based on the fluctuations of microcantilevers. We applied this methodology to sperms exposed to different chemical or physical agents. Real-time nanomechanical fluctuations showed that living sperms produced smaller fluctuations after treatment with inhibitory chemicals, and larger fluctuations after treatment with stimulatory chemicals. Our preliminary experiments suggest that the frequency of fluctuation is associated with sperm motility. This technique offers a brand-new perspective in the characterization of the sperm. By combining conventional measurements, reproductive medicine doctors and researchers should now be able to achieve unprecedented depth in the sperm properties.

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.

Advances in biosensing strategies for HIV-1 detection, diagnosis, and therapeutic monitoring

HIV-1 is a major global epidemic that requires sophisticated clinical management. There have been remarkable efforts to develop new strategies for detecting and treating HIV-1, as it has been challenging to translate them into resource-limited settings. Significant research efforts have been recently devoted to developing point-of-care (POC) diagnostics that can monitor HIV-1 viral load with high sensitivity by leveraging micro- and nano-scale technologies. These POC devices can be applied to monitoring of antiretroviral therapy, during mother-to-child transmission, and identification of latent HIV-1 reservoirs. In this review, we discuss current challenges in HIV-1 diagnosis and therapy in resource-limited settings and present emerging technologies that aim to address these challenges using innovative solutions.

Lab-on-chip systems for integrated bioanalyses

Biomolecular detection systems based on microfluidics are often called lab-on-chip systems. To fully benefit from the miniaturization resulting from microfluidics, one aims to develop 'from sample-to-answer' analytical systems, in which the input is a raw or minimally processed biological, food/feed or environmental sample and the output is a quantitative or qualitative assessment of one or more analytes of interest. In general, such systems will require the integration of several steps or operations to perform their function. This review will discuss these stages of operation, including fluidic handling, which assures that the desired fluid arrives at a specific location at the right time and under the appropriate flow conditions; molecular recognition, which allows the capture of specific analytes at precise locations on the chip; transduction of the molecular recognition event into a measurable signal; sample preparation upstream from analyte capture; and signal amplification procedures to increase sensitivity. Seamless integration of the different stages is required to achieve a point-of-care/point-of-use lab-on-chip device that allows analyte detection at the relevant sensitivity ranges, with a competitive analysis time and cost.