Studies of Functional Nucleic Acids Modified Light Addressable Potentiometric Sensors: X-ray Photoelectron Spectroscopy, Biochemical Assay, and Simulation

A novel aptamer-G-quadruplex/hemin self-assembling color system: rapid visual diagnosis of invasive fungal infections

BACKGROUND

The clinical symptoms of invasive fungal infections (IFI) are nonspecific, and early clinical diagnosis is challenging, resulting in high mortality rates. This study reports the development of a novel aptamer-G-quadruplex/hemin self-assembling color system (AGSCS) based on (1 → 3)-β-D-glucans' detection for rapid, specific and visual diagnosis of IFI.

METHODS

We screened high affinity and specificity ssDNA aptamers binding to (1 → 3)-β-D-glucans, the main components of cell wall from Candida albicans via Systematic Evolution of Ligands by EXponential enrichment. Next, a comparison of diagnostic efficiency of AGSCS and the (1 → 3)-β-D-glucans assay ("G test") with regard to predicting IFI in 198 clinical serum samples was done.

RESULTS

Water-soluble (1 → 3)-β-D-glucans were successfully isolated from C. albicans ATCC 10,231 strain, and these low degree of polymerization glucans (< 1.7 kD) were targeted for aptamer screening with the complementary sequences of G-quadruplex. Six high affinity single stranded DNA aptamers (A1, A2, A3, A4, A5 and A6) were found. The linear detection range for (1 → 3)-β-D-glucans stretched from 1.6 pg/mL to 400 pg/mL on a microplate reader, and the detection limit was 3.125 pg/mL using naked eye observation. Using a microplate reader, the sensitivity and specificity of AGSCS for the diagnosis of IFI were 92.68% and 89.65%, respectively, which was higher than that of the G test.

CONCLUSION

This newly developed visual diagnostic method for detecting IFI showed promising results and is expected to be developed as a point-of-care testing kit to enable quick and cost effective diagnosis of IFI in the future.

Light-Addressable Electrochemical Sensors toward Spatially Resolved Biosensing and Imaging Applications

The light-addressable electrochemical sensor (LAES) is a recently emerged bioanalysis technique combining electrochemistry with the photoelectric effect in a semiconductor. In an LAES, a semiconductor substrate is illuminated locally to generate charge carriers in a well-defined area, thereby confining the electrochemical process to a target site. Benefiting from the unique light addressability, an LAES can not only detect multiple analytes in parallel within a single sensor plate but also act as a bio(chemical) imaging sensor to visualize the two-dimensional distribution of specific analytes. An LAES usually has three working modes: a potentiometric mode using light-addressable potentiometric sensors (LAPS) and an impedance mode using scanning photoinduced impedance microscopy (SPIM), while an amperometric mode refers to light-addressable electrochemistry (LAE) and photoelectrochemical (PEC) sensing. In this review, we describe the detection principles of each mode of LAESs and the concept of light addressability. In addition, we highlight the recent progress and advance of LAESs in spatial resolution, sensor system design, multiplexed detection, and bio(chemical) imaging applications. An outlook on current research challenges and future prospects is also presented.

The Light-Addressable Potentiometric Sensor and Its Application in Biomedicine towards Chemical and Biological Sensing

The light-addressable potential sensor (LAPS) was invented in 1988 and has developed into a multi-functional platform for chemical and biological sensing in recent decades. Its surface can be flexibly divided into multiple regions or pixels through light addressability, and each of them can be sensed independently. By changing sensing materials and optical systems, the LAPS can measure different ions or molecules, and has been applied to the sensing of various chemical and biological molecules and cells. In this review, we firstly describe the basic principle of LAPS and the general configuration of a LAPS measurement system. Then, we outline the most recent applications of LAPS in chemical sensing, biosensing and cell monitoring. Finally, we enumerate and analyze the development trends of LAPS from the aspects of material and optical improvement, hoping to provide a research and application perspective for chemical sensing, biosensing and imaging technology.

In-Situ Monitoring of Real-Time Loop-Mediated Isothermal Amplification with QCM: Detecting Listeria monocytogenes

Functionalized DNA sequences are promising sensing elements to combine with transducers for bio-sensing specific target microbes. As an application example, this paper demonstrates in situ detection of loop-mediated isothermal amplification products by hybridizing them with thiolated-ssDNA covalently anchored on the electrodes of a quartz crystal microbalance (QCM). Such hybridization leads to a frequency signal, which is suitable for monitoring real-time LAMP amplification based on mass-sensing: it detects interactions between the complementary nucleobases of LAMP products in solution and the thiolated-ssDNA probe sequence on the gold surface. Target DNA LAMP products cause irreversible frequency shifts on the QCM surfaces during hybridization in the kHz range, which result from both changes in mass and charge on the electrode surface. In order to confirm the LAMP assay working in the QCM sensing system at elevated temperature, the sky blue of positive LAMP products solution was achieved by using the Hydroxy Naphthol Blue (HNB) and agarose gel electrophoresis. Since on-QCM sensing of DNA hybridization leads to irreversible sensor responses, this work shows characterization by X-ray photoelectron spectroscopy (XPS) core spectra of S2p, N1s, Mg1s, P2p and C1s. XPS results confirmed that indeed both DNA and by-products of LAMP attached to the surface. Listeria monocytogenes DNA served to study in-situ detection of amplified LAMP products on DNA-functionalized surfaces.

Biosensing with DNAzymes

This article provides a comprehensive review of biosensing with DNAzymes, providing an overview of different sensing applications while highlighting major progress and seminal contributions to the field of portable biosensor devices and point-of-care diagnostics. Specifically, the field of functional nucleic acids is introduced, with a specific focus on DNAzymes. The incorporation of DNAzymes into bioassays is then described, followed by a detailed overview of recent advances in the development of in vivo sensing platforms and portable sensors incorporating DNAzymes for molecular recognition. Finally, a critical perspective on the field, and a summary of where DNAzyme-based devices may make the biggest impact are provided.

Interfacing aptamers, nanoparticles and graphene in a hierarchical structure for highly selective detection of biomolecules in OECT devices

In several biomedical applications, the detection of biomarkers demands high sensitivity, selectivity and easy-to-use devices. Organic electrochemical transistors (OECTs) represent a promising class of devices combining a minimal invasiveness and good signal transduction. However, OECTs lack of intrinsic selectivity that should be implemented by specific approaches to make them well suitable for biomedical applications. Here, we report on a biosensor in which selectivity and a high sensitivity are achieved by interfacing, in an OECT architecture, a novel gate electrode based on aptamers, Au nanoparticles and graphene hierarchically organized to optimize the final response. The fabricated biosensor performs state of the art limit of detection monitoring biomolecules, such as thrombin-with a limit of detection in the picomolar range (≤ 5 pM) and a very good selectivity even in presence of supraphysiological concentrations of Bovine Serum Albumin (BSA-1mM). These accomplishments are the final result of the gate hierarchic structure that reduces sterich indrance that could contrast the recognition events and minimizes false positive, because of the low affinity of graphene towards the physiological environment. Since our approach can be easily applied to a large variety of different biomarkers, we envisage a relevant potential for a large series of different biomedical applications.

Possibility of Combining Carbon Dots and Liquid Exfoliated Graphene as a Carbon-Based Light Addressable Potentiometric Sensor

A light addressable potentiometric sensor (LAPS) is a versatile sensing platform for bioassay. However, the lack of carbon-based LAPS (C-LAPS) is a bottleneck for its sustainable development in a carbon electronic era. Herein, a study of C-LAPS based on the combinations of carbon dots (CDs) and liquid exfoliated graphene (LEG) is presented. Devices of C-LAPS are first fabricated by self-assembling the hydrothermally synthesized CDs and the cosolvent ultrasonic delaminated LEG on poly(diallyldimethylammonium chloride) (PDDA)-modified indium tin oxide (ITO) glasses. According to the stacking orders of CDs and LEG, C-LAPS are named as CDs/LEG@PDDA/ITO and LEG/CDs@PDDA/ITO. Then, their electronic and photoelectronic features are measured and compared with the pure CD- and pure LEG-decorated ITO electrodes. Furthermore, working mechanisms are proposed by means of the classical theories of energy band bending and built-in electric field at the heterojunction of CDs and LEG. The resemblances of CDs/LEG@PDDA/ITO-based C-LAPS with Si-based LAPS (Si-LAPS) are confirmed from the points of view of production and separation of the photogenerated carriers, the formation of photocurrent, and the distinction with LEG/CDs@PDDA/ITO. Finally, its feasibility for biological application is justified by using the immune reaction of 5-methylcytosine (5mC) and its antibody (anti-5mC) as a proof of concept. The improved linear responses are evidenced by the comparisons with Si-LAPS' results. Conclusively, the proposed C-LAPS is believed to be a candidate for traditional semiconductor-based LAPS, with the merit of solution-processable. Meanwhile, the theoretical deductions about C-LAPS' principle can also pave the way for developing similar carbon-based sensors.

A label-free lead(II) ion sensor based on surface plasmon resonance and DNAzyme-gold nanoparticle conjugates

Detection of lead(II) (Pb²⁺) ions in water is important for the protection of human health and environment. The growing demand for onsite detection still faces challenges for sensitive and easy-to-use methods. In this work, a novel surface plasmon resonance (SPR) biosensor based on GR-5 DNAzyme and gold nanoparticles (AuNPs) was developed. Thiolated DNAzyme was immobilized on the gold surface of the sensor chip followed by anchoring the substrate-functionalized AuNPs through the DNAzyme-substrate hybridization. The coupling between the localized surface plasmon (LSP) of AuNPs and the surface plasmon polaritons (SPP) on the gold sensor surface was used to improve the sensitivity. The substrate cleavage in the presence of Pb²⁺ ions was catalyzed by DNAzyme, leading to the removal of AuNPs and the diminished LSP-SPP coupling. The optimal detection limit was 80 pM for the sensor fabricated with 1 μM DNAzyme, corresponding to two or three orders of magnitude lower than the toxicity levels of Pb²⁺ in drinking water defined by WHO and USEPA. By tuning the surface coverage of DNAzyme, the sensitivity and dynamic range could be controlled. This sensor also featured high selectivity to Pb²⁺ ions and simple detection procedure. Successful detection of Pb²⁺ ions in groundwater indicates that this method has the prospect in the onsite detection of Pb²⁺ ions in water. Given the variety of AuNPs and metal-specific DNAzymes, this detection strategy would lead to the development of more sensitive and versatile heavy metal sensors. Graphical abstract.

Meso-tetra(4-carboxyphenyl)porphine-Enhanced DNA Methylation Sensing Interface on a Light-Addressable Potentiometric Sensor

DNA methylation (DNAm) sensors are an emerging branch in the discipline of sensors. It is believed to be able to promote the next generation of epigenetics-based diagnostic technology. Differing from the traditional biochemical sensors that aimed at individual molecules, the challenge in DNAm sensors is how to determine the amount of 5-methylcytosine (5mC) in a continuous nucleotide sequence. Here, we report a comparative study about meso-tetra(4-carboxyphenyl)porphine (TCPP)-based DNAm sensing interfaces on a light-addressable potentiometric sensor (LAPS), depending on TCPP's postures that are flat in the π-conjugated TCPP layer on reduced-graphene-oxide-decorated LAPS (#1) and stand-up in the covalently anchored TCPP on glutaraldehyde (GA)-treated LAPS (#2), along with the blank one (only GA-treated LAPS, #3). These DNAm sensing interfaces are also distinct from the traditional biosensing interface on LAPS, that is: it is not functionalized by the sensing indicator (5mC antibody, in this case) but by the target nucleotide sequence. The surface characterization techniques such as Raman spectra, scanning electron microscopy, and X-ray photoelectron spectroscopy are conducted to prove the decorations, as well as the anchored nucleotides. It is found that, though all of them can detect as low as one 5mC in the target sequence, the enhanced DNAm sensitivity is obtained by #2, which is evidenced by the higher output-voltage changing ratio for the 5mC site of #2 than those of #1 and #3. Furthermore, the underlying causes for the improved sensitivity in #2 are proposed, according to the conformational and electronic properties of TCPP molecules. Conclusively, TCPP's synergetic function, including the molecular configuration and the activate (carboxyl) groups on its peripheral substituents, to improve the DNAm sensing interface on LAPS is investigated and demonstrated. This can shed light on a new approach for DNA methylation detection, with the merits of low cost, independence on bisulfite conversion, and polymerase chain reaction.

Reduced Carboxylate Graphene Oxide based Field Effect Transistor as Pb2+ Aptamer Sensor

Aptamer functionalized graphene field effect transistor (apta-GFET) is a versatile bio-sensing platform. However, the chemical inertness of graphene is still an obstacle for its large-scale applications and commercialization. In this work, reduced carboxyl-graphene oxide (rGO-COOH) is studied as a self-activated channel material in the screen-printed apta-GFETs for the first time. Examinations are carefully executed using lead-specific-aptamer as a proof-of-concept to demonstrate its functions in accommodating aptamer bio-probes and promoting the sensing reaction. The graphene-state, few-layer nano-structure, plenty of oxygen-containing groups and enhanced LSA immobilization of the rGO-COOH channel film are evidenced by X-ray photoelectron spectroscopy, Raman spectrum, UV-visible absorbance, atomic force microscopy and scanning electron microscope. Based on these characterizations, as well as a site-binding model based on solution-gated field effect transistor (SgFET) working principle, theoretical deductions for rGO-COOH enhanced apta-GFETs’ response are provided. Furthermore, detections for disturbing ions and real samples demonstrate the rGO-COOH channeled apta-GFET has a good specificity, a limit-of-detection of 0.001 ppb, and is in agreement with the conventional inductively coupled plasma mass spectrometry method. In conclusion, the careful examinations demonstrate rGO-COOH is a promising candidate as a self-activated channel material because of its merits of being independent of linking reagents, free from polymer residue and compatible with rapidly developed print-electronic technology.

Porous Graphene Oxide Enhanced Aptamer Specific Circulating-Tumor-Cell Sensing Interface on Light Addressable Potentiometric Sensor: Clinical Application and Simulation

The circulating-tumor-cell (CTC) specific aptamer is believed to be a power recognition factor to realize clinical CTC assay. However, the limited sensing range is still one of the challenges in its real application. The porous-graphene-oxide (PGO) enhanced aptamer specific CTC sensing interface is studied on the platform of light-addressable-potentiometric-sensor (LAPS) to provide a clinical available method for CTC detection. The underlying mechanism of this sensing interface on LAPS is modeled and simulated. It is confirmed to be a promising candidate for CTC assay by the linear responding for 5-5000 spiked cells, as well as the satisfactory sensitivity for clinical samples.

Simultaneous Monitoring of Amyloid-β (Aβ) Oligomers and Fibrils for Effectively Evaluating the Dynamic Process of Aβ Aggregation

Herein, we provide a proof of concept for a novel strategy that targets the assessment of the aggregation of amyloid-β (Aβ) by simultaneously determining its oligomers (Aβo) and fibrils (Aβf) in one analytical system. By fabricating and combining two immunosensors for Aβo and Aβf, respectively, we constructed a two-channel electrochemical system. The ratio of Aβf to Aβo was calculated and taken as a possible criterion for evaluating the extent of aggregation. Thereby, the presence of and transformation between oligomers and fibrils were accurately probed by incubating the Aβ monomer for different times and then calculating the ratios of Aβf to Aβo. The applicability of this method was further validated by tracking the dynamic progress of Aβ aggregation in the cerebrospinal fluid and tissues of Alzheimer's disease (AD) rats, which revealed that the ratio of Aβf to Aβo in rat brain gradually increased with the progression of AD, which was indicative of the severity of peptide aggregation during this process. Overall, this study represents the first example of a quantitative strategy for precisely evaluating the aggregation process that is related to pathological events in AD brain.