Rapid assessment of the stability of DNA duplexes by impedimetric real-time monitoring of chemically induced denaturation

Bioanalytical sensors using the heat-transfer method HTM and related techniques

This review provides an overview on bio- and chemosensors based on a thermal transducer platform that monitors the thermal interface resistance R th between a solid chip and the supernatant liquid. The R th parameter responds in a surprisingly strong way to molecular-scale changes at the solid-liquid interface, which can be measured thermometrically, using for instance thermocouples in combination with a controllable heat source. In 2012, the effect was first observed during on-chip denaturation experiments on complementary and mismatched DNA duplexes that differ in their melting temperature. Since then, the concept is addressed as heat-transfer method, in short HTM, and numerous applications of the basic sensing principle were identified. Functionalizing the chip with bioreceptors such as molecularly imprinted polymers makes it possible to detect neurotransmitters, inflammation markers, viruses, and environmental pollutants. In combination with aptamer-type receptors, it is also possible to detect proteins at low concentrations. Changing the receptors to surface-imprinted polymers has opened up new possibilities for quantitative bacterial detection and identification in complex matrices. In receptor-free variants, HTM was successfully used to characterize lipid vesicles and eukaryotic cells (yeast strains, cancer cell lines), the latter showing spontaneous detachment under influence of the temperature gradient inherent to HTM. We will also address modifications to the original HTM technique such as M-HTM, inverted HTM, thermal wave transport analysis TWTA, and the hot-wire principle. The article concludes with an assessment of the possibilities and current limitations of the method, together with a technological forecast.

Passivated Impedimetric Sensors for Immobilization-Free Pathogen Detection by Isothermal Amplification and Melt Curve Analysis

The ongoing SARS-CoV-2 pandemic demonstrates that the capacity of centralized clinical diagnosis laboratories represents a significant limiting factor in the global fight against the newly emerged virus. Scaling up these capacities also requires simple and robust methods for virus diagnosis to be easily driven by untrained personnel in a point-of-care (POC) environment. The use of impedance sensors reduces the complexity and costs of diagnostic instruments and increases automation of diagnosis processes. We present an impedance point-of-care system (IMP-POCS) that uses interdigitated electrodes surrounded by an integrated heating meander to monitor loop-mediated isothermal amplification (LAMP) and melt curve analysis (MCA) consecutively in a short time. MCA permits distinguishing false- from true-positive results and significantly raises the validity of pathogen detection. Conclusively, the herein-developed miniaturized total analysis system (µTAS) represents a powerful and promising tool for providing reliable, low-cost alternatives to standard clinical diagnosis.

Recent Advances in Chain Conformation and Bioactivities of Triple-Helix Polysaccharides

Natural polysaccharides derived from renewable biomass sources are regarded as environmentally friendly and sustainable polymers. As the third most abundant biomacromolecule in nature, after proteins and nucleic acids, polysaccharides are also closely related with many different life activities. In particular, β-glucans are one of the most widely reported bioactive polysaccharides and are usually considered as biological response modifiers. Among them, β-glucans with triple-helix conformation have been the hottest and most well-researched polysaccharides at present, especially lentinan and schizophyllan, which are clinically used as cancer therapies in some Asian countries. Thus, creation of these active triple-helix polysaccharides is beneficial to the research and development of sustainable "green" biopolymers in the fields of food and life sciences. Therefore, full fundamental research of triple-helix polysaccharides is essential to discover more applications for polysaccharides. In this Review, the recent research progress of chain conformations, bioactivities, and structure-function relationships of triple-helix β-glucans is summarized. The main contents include the characterization methods of the macromolecular conformation, proof of triple helices, bioactivities, and structure-function relationships. We believe that the governments, enterprises, universities, and institutes dealing with the survival and health of human beings can expect the development of natural bioproducts in the future. Hence, a deep understanding of β-glucans with triple-helix chain conformation is necessary for application of natural medicines and biologics for a sustainable world.

Enhancing the Performance of DNA Surface-Hybridization Biosensors through Target Depletion

DNA surface-hybridization biosensors utilize the selective hybridization of target sequences in solution to surface-immobilized probes. In this process, the target is usually assumed to be in excess, so that its concentration does not significantly vary while hybridizing to the surface-bound probes. If the target is initially at low concentrations and/or if the number of probes is very large, and they have high affinity for the target, the DNA in solution may become depleted. In this paper we analyze the equilibrium and kinetics of hybridization of DNA biosensors in the case of strong target depletion, by extending the Langmuir adsorption model. We focus, in particular, on the detection of a small amount of a single-nucleotide "mutant" sequence (concentration c₂) in a solution, which differs by one or more nucleotides from an abundant "wild-type" sequence (concentration c₁ ≫ c₂). We show that depletion can give rise to a strongly enhanced sensitivity of the biosensors. Using representative values of rate constants and hybridization free energies, we find that in the depletion regime one could detect relative concentrations c₂/c₁ that are up to 3 orders of magnitude smaller than in the conventional approach. The kinetics is surprisingly rich and exhibits a nonmonotonic adsorption with no counterpart in the no-depletion case. Finally, we show that, alongside enhanced detection sensitivity, this approach offers the possibility of sample enrichment, by substantially increasing the relative amount of the mutant over the wild-type sequence.

Molecular drug susceptibility testing and strain typing of tuberculosis by DNA hybridization

In Mycobacterium tuberculosis (Mtb) the detection of single nucleotide polymorphisms (SNPs) is of high importance both for diagnostics, since drug resistance is primarily caused by the acquisition of SNPs in multiple drug targets, and for epidemiological studies in which strain typing is performed by SNP identification. To provide the necessary coverage of clinically relevant resistance profiles and strain types, nucleic acid-based measurement techniques must be able to detect a large number of potential SNPs. Since the Mtb problem is pressing in many resource-poor countries, requiring low-cost point-of-care biosensors, this is a non-trivial technological challenge. This paper presents a proof-of-concept in which we chose simple DNA-DNA hybridization as a sensing principle since this can be transferred to existing low-cost hardware platforms, and we pushed the multiplex boundaries of it. With a custom designed probe set and a physicochemical-driven data analysis it was possible to simultaneously detect the presence of SNPs associated with first- and second-line drug resistance and Mtb strain typing. We have demonstrated its use for the identification of drug resistance and strain type from a panel of phylogenetically diverse clinical strains. Furthermore, reliable detection of the presence of a minority population (<5%) of drug-resistant Mtb was possible.

Label-free real-time optical monitoring of DNA hybridization using SiN Mach-Zehnder interferometer-based integrated biosensing platform

We report on the label-free real-time optical monitoring of DNA hybridization upon exposure to a flow of complementary DNA at different concentrations. The biosensor is composed of a silicon nitride integrated unbalanced Mach-Zehnder interferometer (MZI), with an integrated arrayed waveguide grating as a spectral filter. This MZI has been shown to have both sufficient multiplexing capability and limit of detection on the order of 10  -  6 RIU. Probe DNA, consisting of a 36-mer fragment is covalently immobilized on the silicon nitride integrated biosensor. The wavelength shift is monitored upon complementary DNA targets being flown over the sensor. Concentrations of 1 pM can be easily detected. Also, an alternative route to modify the sensor surface with carboxylic groups using the photochemical reaction of fatty acids is proposed and preliminary XPS results are presented. Moreover, preliminary results for DNA obtained from a rolling circle amplification (RCA-DNA) process and spiked in a realistic amplification buffer are presented.

Micro-patterned molecularly imprinted polymer structures on functionalized diamond-coated substrates for testosterone detection

Molecularly imprinted polymers (MIPs) can selectively bind target molecules and can therefore be advantageously used as a low-cost and robust alternative to replace fragile and expensive natural receptors. Yet, one major challenge in using MIPs for sensor development is the lack of simple and cost-effective techniques that allow firm fixation as well as controllable and consistent receptor material distribution on the sensor substrate. In this work, a convenient method is presented wherein microfluidic systems in conjunction with in situ photo-polymerization on functionalized diamond substrates are used. This novel strategy is simple, efficient, low-cost and less time consuming. Moreover, the approach ensures a tunable and consistent MIP material amount and distribution between different sensor substrates and thus a controllable active sensing surface. The obtained patterned MIP structures are successfully tested as a selective sensor platform to detect physiological concentrations of the hormone disruptor testosterone in buffer, urine and saliva using electrochemical impedance spectroscopy. The highest added testosterone concentration (500 nM) in buffer resulted in an impedance signal of 10.03 ± 0.19% and the lowest concentration (0.5 nM) led to a measurable signal of 1.8 ± 0.15% for the MIPs. With a detection limit of 0.5 nM, the MIP signals exhibited good linearity between a 0.5 nM and 20 nM concentration range. Apart from the excellent and selective recognition offered by these MIP structures, they are also stable during and after the dynamic sensor measurements. Additionally, the MIPs can be easily regenerated by a simple washing procedure and are successfully tested for their reusability.

Thermodynamic framework to assess low abundance DNA mutation detection by hybridization

The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine.

The heat-transfer method: a versatile low-cost, label-free, fast, and user-friendly readout platform for biosensor applications

In recent years, biosensors have become increasingly important in various scientific domains including medicine, biology, and pharmacology, resulting in an increased demand for fast and effective readout techniques. In this Spotlight on Applications, we report on the recently developed heat-transfer method (HTM) and illustrate the use of the technique by zooming in on four established bio(mimetic) sensor applications: (i) mutation analysis in DNA sequences, (ii) cancer cell identification through surface-imprinted polymers, (iii) detection of neurotransmitters with molecularly imprinted polymers, and (iv) phase-transition analysis in lipid vesicle layers. The methodology is based on changes in heat-transfer resistance at a functionalized solid-liquid interface. To this extent, the device applies a temperature gradient over this interface and monitors the temperature underneath and above the functionalized chip in time. The heat-transfer resistance can be obtained by dividing this temperature gradient by the power needed to achieve a programmed temperature. The low-cost, fast, label-free and user-friendly nature of the technology in combination with a high degree of specificity, selectivity, and sensitivity makes HTM a promising sensor technology.

Heat-transfer-based detection of SNPs in the PAH gene of PKU patients

Conventional neonatal diagnosis of phenylketonuria is based on the presence of abnormal levels of phenylalanine in the blood. However, for carrier detection and prenatal diagnosis, direct detection of disease-correlated mutations is needed. To speed up and simplify mutation screening in genes, new technologies are developed. In this study, a heat-transfer method is evaluated as a mutation-detection technology in entire exons of the phenylalanine hydroxylase (PAH) gene. This method is based on the change in heat-transfer resistance (R_th) upon thermal denaturation of dsDNA (double-stranded DNA) on nanocrystalline diamond. First, ssDNA (single-stranded DNA) fragments that span the size range of the PAH exons were successfully immobilized on nanocrystalline diamond. Next, it was studied whether an R_th change could be observed during the thermal denaturation of these DNA fragments after hybridization to their complementary counterpart. A clear R_th shift during the denaturation of exon 5, exon 9, and exon 12 dsDNA was observed, corresponding to lengths of up to 123 bp. Finally, R_th was shown to detect prevalent single-nucleotide polymorphisms, c.473G>A (R158Q), c.932T>C (p.L311P), and c.1222C>T (R408W), correlated with phenylketonuria, displaying an effect related to the different melting temperatures of homoduplexes and heteroduplexes.

Combining electrochemical impedance spectroscopy and surface plasmon resonance into one simultaneous read-out system for the detection of surface interactions

In this article we describe the integration of impedance spectroscopy (EIS) and surface plasmon resonance (SPR) into one surface analytic device. A polydimethylsiloxane (PDMS) flow cell is created, matching the dimensions of a commercially available sensor chip used for SPR measurements. This flow cell allowed simultaneous measurements between an EIS and a SPR setup. After a successful integration, a proof of principle study was conducted to investigate any signs of interference between the two systems during a measurement. The flow cell was rinsed with 10 mM Tris-HCl and 1× PBS buffer in an alternating manner, while impedance and shifts of the resonance angle were monitored. After achieving a successful proof of principle, a usability test was conducted. It was assessed whether simultaneous detection occurred when: (i) Protein A is adsorbed to the gold surface of the chip; (ii) The non-occupied zone is blocked with BSA molecules and (iii) IgG1 is bound to the Protein A. The results indicate a successful merge between SPR and EIS.

Targeted resequencing of HIV variants by microarray thermodynamics

Within a single infected individual, a virus population can have a high genomic variability. In the case of HIV, several mutations can be present even in a small genomic window of 20–30 nucleotides. For diagnostics purposes, it is often needed to resequence genomic subsets where crucial mutations are known to occur. In this article, we address this issue using DNA microarrays and inputs from hybridization thermodynamics. Hybridization signals from multiple probes are analysed, including strong signals from perfectly matching (PM) probes and a large amount of weaker cross-hybridization signals from mismatching (MM) probes. The latter are crucial in the data analysis. Seven coded clinical samples (HIV-1) are analyzed, and the microarray results are in full concordance with Sanger sequencing data. Moreover, the thermodynamic analysis of microarray signals resolves inherent ambiguities in Sanger data of mixed samples and provides additional clinically relevant information. These results show the reliability and added value of DNA microarrays for point-of-care diagnostic purposes.

Optimizing the thermal read-out technique for MIP-based biomimetic sensors: towards nanomolar detection limits

In previous work, the novel heat-transfer method (HTM) for the detection of small molecules with Molecularly Imprinted Polymers (MIP)-type receptors was presented. In this study we focus on optimization of this sensor performance, with as final aim to lower the detection limit by reducing the noise level. It was determined that the noise originates foremost from the power supply, which can be controlled by varying the PID parameters. Therefore, the effect of the individual parameters was evaluated by tuning P, I and D separately at a temperature of 37 °C, giving a first indication of the optimal configuration. Next, a temperature profile was programmed and the standard deviation of the heat-transfer resistance over the entire regime was studied for a set of parameters. The optimal configuration, P1-I6-D0, reduced the noise level with nearly a factor of three compared to the original parameters of P10-I5-D0. With the optimized settings, the detection of L-nicotine in buffer solutions was studied and the detection limit improved significantly from 100 nM to 35 nM. Summarizing, optimization of the PID parameters and thereby improving the detection limit is a key parameter for first applications of the HTM-method for MIP receptors in analytical research.

A microfluidic-based frequency-multiplexing impedance sensor (FMIS)

We present a novel technology for the simultaneous and simple impedimetric screening of multiple microfluidic channels with only one electrode pair. We have exploited the frequency dimension to distinguish between up to three channels. Each 'sub-sensor' possesses its corresponding measurement frequency where the sample-specific dielectric properties can be probed. We have shown the validity of our frequency-multiplexing impedance sensor (FMIS) by comparison with conventional 'single sensors'. Our highly sensitive FMIS was proven suitable for life science applications through usage as a cell-based toxicology platform. We are confident that our technology might find great utility in parallelized cell-based analysis systems as well as in biomedical devices where size limitations and spatially distributed probing are important parameters.

Probing hybridization parameters from microarray experiments: nearest-neighbor model and beyond

In this article, it is shown how optimized and dedicated microarray experiments can be used to study the thermodynamics of DNA hybridization for a large number of different conformations in a highly parallel fashion. In particular, free energy penalties for mismatches are obtained in two independent ways and are shown to be correlated with values from melting experiments in solution reported in the literature. The additivity principle, which is at the basis of the nearest-neighbor model, and according to which the penalty for two isolated mismatches is equal to the sum of the independent penalties, is thoroughly tested. Additivity is shown to break down for a mismatch distance below 5 nt. The behavior of mismatches in the vicinity of the helix edges, and the behavior of tandem mismatches are also investigated. Finally, some thermodynamic outlying sequences are observed and highlighted. These sequences contain combinations of GA mismatches. The analysis of the microarray data reported in this article provides new insights on the DNA hybridization parameters and can help to increase the accuracy of hybridization-based technologies.

Heat-transfer resistance at solid-liquid interfaces: a tool for the detection of single-nucleotide polymorphisms in DNA

In this article, we report on the heat-transfer resistance at interfaces as a novel, denaturation-based method to detect single-nucleotide polymorphisms in DNA. We observed that a molecular brush of double-stranded DNA grafted onto synthetic diamond surfaces does not notably affect the heat-transfer resistance at the solid-to-liquid interface. In contrast to this, molecular brushes of single-stranded DNA cause, surprisingly, a substantially higher heat-transfer resistance and behave like a thermally insulating layer. This effect can be utilized to identify ds-DNA melting temperatures via the switching from low- to high heat-transfer resistance. The melting temperatures identified with this method for different DNA duplexes (29 base pairs without and with built-in mutations) correlate nicely with data calculated by modeling. The method is fast, label-free (without the need for fluorescent or radioactive markers), allows for repetitive measurements, and can also be extended toward array formats. Reference measurements by confocal fluorescence microscopy and impedance spectroscopy confirm that the switching of heat-transfer resistance upon denaturation is indeed related to the thermal on-chip denaturation of DNA.