A multi-scale model for the analysis of the inhomogeneity of elastic properties of DNA biofilm on microcantilevers

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.

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.

Relay-type sensing mode: A strategy to push the limit on nanomechanical sensor sensitivity based on the magneto lever

Ultrasensitive molecular detection and quantization are crucial for many applications including clinical diagnostics, functional proteomics, and drug discovery; however, conventional biochemical sensors cannot satisfy the stringent requirements, and this has resulted in a long-standing dilemma regarding sensitivity improvement. To this end, we have developed an ultrasensitive relay-type nanomechanical sensor based on a magneto lever. By establishing the link between very weak molecular interaction and five orders of magnitude larger magnetic force, analytes at ultratrace level can produce a clearly observable mechanical response. Initially, proof-of-concept studies showed an improved detection limit up to five orders of magnitude when employing the magneto lever, as compared with direct detection using probe alone. In this study, we subsequently demonstrated that the relay-type sensing mode was universal in application ranging from micromolecule to macromolecule detection, which can be easily extended to detect enzymes, DNA, proteins, cells, viruses, bacteria, chemicals, etc. Importantly, we found that, sensitivity was no longer subject to probe affinity when the magneto lever was sufficiently high, theoretically, even reaching single-molecule resolution.

ELECTRONIC SUPPLEMENTARY MATERIAL

Supplementary material (experimental section) is available in the online version of this article at 10.1007/s12274-022-5049-0.

Anomalous Elastic Properties of Attraction-Dominated DNA Self-Assembled 2D Films and the Resultant Dynamic Biodetection Signals of Microbeam Sensors

The condensation of DNA helices has been regularly found in cell nucleus, bacterial nucleoids, and viral capsids, and during its relevant biodetections the attractive interactions between DNA helices could not be neglected. In this letter, we theoretically characterize the elastic properties of double-stranded DNA (dsDNA) self-assembled 2D films and their multiscale correlations with the dynamic detection signals of DNA-microbeams. The comparison of attraction- and repulsion-dominated DNA films shows that the competition between attractive and repulsive micro-interactions endows dsDNA films in multivalent salt solutions with anomalous elastic properties such as tensile surface stresses and negative moduli; the occurrence of the tensile surface stress for the attraction-dominated DNA self-assembled film reveals the possible physical mechanism of the condensation found in organism. Furthermore, dynamic analyses of a hinged-hinged DNA-microbeam reveal non-monotonous frequency shifts due to attraction- or repulsion-dominated dsDNA adsorptions and dynamic instability occurrence during the detections of repulsion-dominated DNA films. This dynamic instability implies the existence of a sensitive interval of material parameters in which DNA adsorptions will induce a drastic natural frequency shift or a jump of vibration mode even with a tiny variation of the detection conditions. These new insights might provide us some potential guidance to achieve an ultra-highly sensitive biodetection method in the future.

The pH-dependent elastic properties of nanoscale DNA films and the resultant bending signals for microcantilever biosensors

The diverse mechanical properties of nanoscale DNA films on solid substrates have a close correlation with complex detection signals of micro-/nano-devices. This paper is devoted to formulating several multiscale models to study the effect of pH-dependent ionic inhomogeneity on the graded elastic properties of nanoscale DNA films and the resultant bending deflections of microcantilever biosensors. First, a modified inverse Debye length is introduced to improve the classical Poisson-Boltzmann equation for the electrical potential of DNA films to consider the inhomogeneous effect of hydrogen ions. Second, the graded characteristics of the particle distribution are taken into consideration for an improvement in Parsegian's mesoscopic potential for both attraction-dominated and repulsion-dominated films. Third, by the improved interchain interaction potential and the thought experiment about the compression of a macroscopic continuum DNA bar, we investigate the diversity of the elastic properties of single-stranded DNA (ssDNA) films due to pH variations. The relevant theoretical predictions quantitatively or qualitatively agree well with the relevant DNA experiments on the electrical potential, film thickness, condensation force, elastic modulus, and microcantilever deflections. The competition between attraction and repulsion among the fixed charges and the free ions endows the DNA film with mechanical properties such as a remarkable size effect and a non-monotonic behavior, and a negative elastic modulus is first revealed in the attraction-dominated ssDNA film. There exists a transition between the pH-sensitive parameter interval and the pH-insensitive one for the bending signals of microcantilevers, which is predominated by the initial stress effect in the DNA film.

Effect of surface charge state on the surface stress of a microcantilever

The surface charge state at a liquid-solid interface is important to the variations in the physical/chemical properties of adsorbate film such as surface stress and the ensuing tip deflection of the microcantilever. The well-known Stoney's equation, derived more than 100 years ago, conceals the film electrical properties with the replacement of substrate deformation induced by adsorptions of particles. This implicit expression provides a shortcut to circumvent the difficulty in identifying some film properties, however, it limits the capacity to ascertain the relation between surface stress variation and the surface charge state. In this paper, we present an analytical expression to quantify the cantilever deflection/surface stress and the film potential difference by combining the piezoelectric theory and Poisson-Boltzmann equation for electrolyte solution. This updated version indicates that the two linear correlations between surface stress and surface charge density or the bias voltage are not contradictory, but two aspects of one thing under different conditions. Based on Parsegian's mesoscopic interaction potential, a multiscale prediction for the piezoelectric coefficient of double-stranded DNA (dsDNA) film is done, and the results show that the distinctive size effect with variations in salt concentration and nucleotide number provides us with an opportunity to obtain a more sensitive potential-actuated microcantilever sensor by careful control of packing conditions.

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.

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.