Three-mode electrochemical sensing of ultralow microRNA levels

Development of surface molecular-imprinted electrochemical sensor for palmitic acid with machine learning assistance

Palmitic acid (PA) is a kind of saturated high fatty acid, which is involved in physiological safety and food quality. A surface molecularly imprinted polymer (MIP) electrochemical sensor was prepared on MXene surface using dopamine (DA) as functional monomer. The electrode was modified with gold nanoparticles (AuNPs), ferrocene-graphene oxide-multiwalled carbon nanotubes (Fc-GO-MWCNT) composite to enhance the electroactive area and conductivity. The sensor was characterized by scanning electron microscope (SEM), energy-dispersive X-ray spectroscopy (EDS), electrochemical impedance spectroscopy (EIS) and Differential pulse voltammetry (DPV), respectively. The parameters concerning this assay and various regeneration conditions have been carefully studied. The sensor can detect PA in the range of 1 nM-1 mM (R2 = 0.995), the limit of detection (LOD) is 0.48 nM (S/N = 3), and the limit of quantification (LOQ) is 1.61 nM. The artificial neural network (ANN) model in machine learning is further used to analyze the data collected by the sensor. The results show that the back propagation (BP) neural network in ANN is more suitable for the intelligent analysis of PA. The practicality of the sensor was confirmed by detecting PA in pork samples. This is the first MIP-based electrochemical sensor for PA, and it has great potential in practical applications.

Ultrasensitive molecular imprinted electrochemical sensor for in vivo determination of glycine betaine in plants

Glycine betaine (GB) is a bioactive molecule protecting plants from abiotic stress. This study fabricated an ultrasensitive molecular imprinted polymer (MIP) electrochemical sensor to perform in vivo measurements of GB. Polydopamine (PDA) was formed on the carboxylated multi-walled carbon nanotubes (COOH-MWCNTs) by spontaneous polymerisation of dopamine (DA). Then MIP-coated MWCNTs were fabricated on a Au nanoparticles (NP) and thionine (Thi) modified screen-printed electrode (SPE). The MIP-COOH-MWCNTs/pThi/AuNPs/SPE exhibited an ultrasensitive GB detection response between 1 fmol/L and 10 mmol/L (R2 = 0.996) with a low detection limit (0.707 fmol/L, S/N = 3). In vivo measurement of GB in cucumber seedling leaves under different salinity stress conditions confirmed the practical applicability of the MIP sensor. Thus, this study proposed a novel and promising fabrication method for an electrochemical MIP sensor that has broad application prospects in precision agriculture.

Advanced Self-Powered Biofuel Cells with Capacitor and Nanogenerator for Biomarker Sensing

Self-powered biofuel cells (BFCs) have evolved for highly sensitive detection of biomarkers such as noncodon micro ribonucleic acids (miRNAs) in the presence of interfering substrates. Self-charging supercapacitive BFCs for in vivo and in vitro cellular microenvironments represent the most prevalent sensing mechanism for diagnosis. Therefore, self-powered biosensing (SPB) with a capacitor and contact separation with a triboelectric nanogenerator (TENG) offers electrochemical and colorimetric dual-mode detection via improved electrical signal intensity. In this review, we discuss three major components: stretchable self-powered BFC design, miRNA sensing, and impedance spectroscopy. A specific focus is given to 1) assembling of sensors for biomarkers, 2) electrical output signal intensification, and 3) role of supercapacitors and nanogenerators in SPBs. We outline the key features of stretchable SPBs and the sequence of miRNA sensing by SPBs. We have emphasized the need of a supercapacitor and nanogenerator for SPBs in the context of advanced assembly of the sensing unit. Finally, we outline the role of impedance spectroscopy in the detection and estimation of biomarkers. We highlight key challenges in SPBs for biomarker sensing, which needs improved sensing accuracy, integration strategies of electrochemical biosensing for in vitro and in vivo microenvironments, and the impact of miRNA sensing on cancer diagnostics. This article attempts a specific focus on the accuracy and limitations of sensing unit for miRNA biomarkers and associated tool for boosting electrical signal intensity for a potential big step further.

A dual-blocker aided and dual-label-free electrochemical biosensor based on mbHCR/rGO nanocomplexes for ultrasensitive DNA detection

Heterogeneous electrochemical DNA biosensors have attracted huge attention due to their enhanced signal sensitivity, compared to homogeneous biosensors. However, the high cost of probe labeling and the reduced recognition efficiency associated with current heterogeneous electrochemical biosensors confine their potential applications. In the present work, a dual-blocker assisted and dual-label-free heterogeneous electrochemical strategy based on multi-branched hybridization chain reaction (mbHCR) and reduced graphene oxide (rGO) was fabricated for ultrasensitive detection of DNA. The target DNA could trigger the mbHCR of two DNA hairpin probes, resulting in the generation of multi-branched long chain of DNA duplexes with bidirectional arms. One direction of the multi-branched arms in the mbHCR products were then bound to the label-free capture probe on the gold electrode through multivalent hybridization with enhanced recognition efficiency. The other direction of multi-branched arms in mbHCR product could adsorb rGO via π-π stacking interactions. Two DNA blockers were ingeniously designed to block the binding of excessive H1-pAT on electrode and to prevent the adsorption of rGO by residual unbound capture probes. As a result, with the electrochemical reporter methylene blue selectively intercalated into the long chain of DNA duplex and absorbed on rGO, a remarkable electrochemical signal rise was observed. Thus, a dual-blocker aided and dual-label-free electrochemical strategy for ultrasensitive DNA detection is readily realized with the merit of cost-effective. The as-developed dual-label-free electrochemical biosensor has great potential to be employed in nucleic acid related medical diagnostics.

Advances in Electrochemical Biosensor Technologies for the Detection of Nucleic Acid Breast Cancer Biomarkers

Breast cancer is the second leading cause of cancer deaths in women worldwide; therefore, there is an increased need for the discovery, development, optimization, and quantification of diagnostic biomarkers that can improve the disease diagnosis, prognosis, and therapeutic outcome. Circulating cell-free nucleic acids biomarkers such as microRNAs (miRNAs) and breast cancer susceptibility gene 1 (BRCA1) allow the characterization of the genetic features and screening breast cancer patients. Electrochemical biosensors offer excellent platforms for the detection of breast cancer biomarkers due to their high sensitivity and selectivity, low cost, use of small analyte volumes, and easy miniaturization. In this context, this article provides an exhaustive review concerning the electrochemical methods of characterization and quantification of different miRNAs and BRCA1 breast cancer biomarkers using electrochemical DNA biosensors based on the detection of hybridization events between a DNA or peptide nucleic acid probe and the target nucleic acid sequence. The fabrication approaches, the biosensors architectures, the signal amplification strategies, the detection techniques, and the key performance parameters, such as the linearity range and the limit of detection, were discussed.

Insight into Surface Electronic Effects on Pd Nanostructures as Efficient Electrocatalysts

Although the unique properties of nanomaterials have endowed enzyme-mimic catalysts with broad applications, the development of catalysts still relies on trial-and-error strategies without predictive indicators. Surface electronic structures have rarely been studied in enzyme-mimic catalysts. Herein, we present a platform for understanding the impact of surface electronic structures on electrocatalysis toward H₂O₂ decomposition, using the Pd icosahedra (Pd ico), Pd octahedra (Pd oct) and Pd cubic nanocrystals as electrocatalysts. The electronic properties on Pd were modulated with a correlation of surface orientation. We revealed the relationship between the electronic properties and electrocatalytic performance, in which the surface electron accumulation can boost the electrocatalytic activity of the enzyme-mimic catalysts. As a result, the Pd icodimer exhibits the highest electrocatalytic and sensing efficiency. This work offers new perspectives for the investigation of structure-activity relationships and provides an effective knob for utilizing the surface electronic structures to boost the catalytic performance for enzyme-mimics.

Primer exchange reaction-amplified protein-nucleic acid interactions for ultrasensitive and specific microRNA detection

Protein-nucleic acid interactions are not only fundamental to genetic regulation and cellular metabolism, but molecular basis to artificial biosensors. However, such interactions are generally weak and dynamic, making their specific and sensitive quantitative detection challenging. By using primer exchange reaction (PER)-amplified protein-nucleic acid interactions, we here design a universal and ultrasensitive electrochemical sensor to quantify microRNAs (miRNAs) in blood. This PER-miR sensor leverages specific recognition between S9.6 antibodies and miRNA/DNA hybrids to couple with PER-derived multi-enzyme catalysis for ultrasensitive miRNA detection. Surface binding kinetic analysis shows a rational K_d (8.9 nM) between the miRNA/DNA heteroduplex and electrode-attached S9.6 antibody. Based on such a favorable affinity, the programmable PER amplification enables the sensor to detect target miRNAs with sensitivity up to 90.5 aM, three orders of magnitude higher than that without PER in routine design, and with specificity of single-base resolution. Furthermore, the PER-miR sensor allows detecting multiple miRNAs in parallel, measuring target miRNA in lysates across four types of cell lines, and differentiating tumor patients from healthy individuals by directly analyzing the human blood samples (n = 40). These advantages make the sensor a promising tool to enable quantitative sensing of biomolecular interactions and precision diagnostics.

Unamplified and Real-Time Label-Free miRNA-21 Detection Using Solution-Gated Graphene Transistors in Prostate Cancer Diagnosis

The incidence of prostate cancer (PCa) in men globally increases as the standard of living improves. Blood serum biomarker prostate-specific antigen (PSA) detection is the gold standard assay that do not meet the requirements of early detection. Herein, a solution-gated graphene transistor (SGGT) biosensor for the ultrasensitive and rapid quantification detection of the early prostate cancer-relevant biomarker, miRNA-21 is reported. The designed single-stranded DNA (ssDNA) probes immobilized on the Au gate can hybridize effectively with the miRNA-21 molecules targets and induce the Dirac voltage shifts of SGGT transfer curves. The limit of detection (LOD) of the sensor can reach 10^-20  M without amplification and any chemical or biological labeling. The detection linear range is from 10^-20 to 10^-12  M. The sensor can realize real-time detection of the miRNA-21 molecules in less than 5 min and can well distinguish one-mismatched miRNA-21 molecule. The blood serum samples from the patients without RNA extraction and amplification are measured. The results demonstrated that the biosensor can well distinguish the cancer patients from the control group and has higher sensitivity (100%) than PSA detection (58.3%). Contrastingly, it can be found that the PSA level is not directly related to PCa.

Quantification of MicroRNAs or Viral RNAs with Microelectrode Sensors Enabled by Electrochemical Signal Amplification

Quantification of circulating microRNAs (miRNAs) or viral RNAs is of great significance because of their broad relevance to human health. Currently, quantitative reverse transcription polymerase chain reaction (qRT-PCR), as well as microarray and gene sequencing, are considered mainstream techniques for miRNA identification and quantitation and the gold standard for SARS-CoV2 detection in the COVID-19 pandemic. However, these laboratory techniques are challenged by the low levels and wide dynamic range (from aM to nM) of miRNAs in a physiological sample, as well as the difficulty in the implementation in point-of-care settings. Here, we describe a one-step label-free electrochemical sensing technique by assembling self-folded multi-stem DNA-redox probe structure on gold microelectrodes and introducing a reductant, tris(2-carboxyethyl) phosphine hydrochloride (TCEP), in the detection buffer solution to achieve ultrasensitive detection with a detection limit of 0.1 fM that can be further improved if needed.

The Future of Biomarkers in Veterinary Medicine: Emerging Approaches and Associated Challenges

Simple Summary

In this review we seek to outline the role of new technologies in biomarker discovery, particularly within the veterinary field and with an emphasis on ‘omics’, as well as to examine why many biomarkers-despite much excitement-have not yet made it to clinical practice. Further we emphasise the critical need for close collaboration between clinicians, researchers and funding bodies and the need to set clear goals for biomarker requirements and realistic application in the clinical setting, ensuring that biomarker type, method of detection and clinical utility are compatible, and adequate funding, time and sample size are available for all phases of development.

Abstract

New biomarkers promise to transform veterinary practice through rapid diagnosis of diseases, effective monitoring of animal health and improved welfare and production efficiency. However, the road from biomarker discovery to translation is not always straightforward. This review focuses on molecular biomarkers under development in the veterinary field, introduces the emerging technological approaches transforming this space and the role of ‘omics platforms in novel biomarker discovery. The vast majority of veterinary biomarkers are at preliminary stages of development and not yet ready to be deployed into clinical translation. Hence, we examine the major challenges encountered in the process of biomarker development from discovery, through validation and translation to clinical practice, including the hurdles specific to veterinary practice and to each of the ‘omics platforms–transcriptomics, proteomics, lipidomics and metabolomics. Finally, recommendations are made for the planning and execution of biomarker studies with a view to assisting the success of novel biomarkers in reaching their full potential.

A Review of the Nucleic Acid-Based Lateral Flow Assay for Detection of Breast Cancer from Circulating Biomarkers at a Point-of-Care in Low Income Countries

The current levels of breast cancer in African women have contributed to the high mortality rates among them. In South Africa, the incidence of breast cancer is also on the rise due to changes in behavioural and biological risk factors. Such low survival rates can be attributed to the late diagnosis of the disease due to a lack of access and the high costs of the current diagnostic tools. Breast cancer is asymptomatic at early stages, which is the best time to detect it and intervene to prevent high mortality rates. Proper risk assessment, campaigns, and access to adequate healthcare need to be prioritised among patients at an early stage. Early detection of breast cancer can significantly improve the survival rate of breast cancer patients, since therapeutic strategies are more effective at this stage. Early detection of breast cancer can be achieved by developing devices that are simple, sensitive, low-cost, and employed at point-of-care (POC), especially in low-income countries (LICs). Nucleic-acid-based lateral flow assays (NABLFAs) that combine molecular detection with the immunochemical visualisation principles, have recently emerged as tools for disease diagnosis, even for low biomarker concentrations. Detection of circulating genetic biomarkers in non-invasively collected biological fluids with NABLFAs presents an appealing and suitable method for POC testing in resource-limited regions and/or LICs. Diagnosis of breast cancer at an early stage will improve the survival rates of the patients. This review covers the analysis of the current state of NABLFA technologies used in developing countries to reduce the scourge of breast cancer.

Lifting the Veil: Characteristics, Clinical Significance, and Application of β-2-Microglobulin as Biomarkers and Its Detection with Biosensors

Because β-2-microglobulin (β₂M) is a surface protein that is present on most nucleated cells, it plays a key role in the human immune system and the kidney glomeruli to regulate homeostasis. The primary clinical significance of β₂M is in dialysis-related amyloidosis, a complication of end-stage renal disease caused by a gradual accumulation of β₂M in the blood. Therefore, the function of β₂M in kidney-related diseases has been extensively studied to evaluate its glomerular and tubular functions. Because increased β₂M shedding due to rapid cell turnover may indicate other underlying medical conditions, the possibility to use β₂M as a versatile biomarker rose in prominence across multiple disciplines for various applications. Therefore, this work has reviewed the recent use of β₂M to detect various diseases and its progress as a biomarker. While the use of state-of-the-art β₂M detection requires sophisticated tools, high maintenance, and labor cost, this work also has reported the use of biosensor to quantify β₂M over the past decade. It is hoped that a portable and highly efficient β₂M biosensor device will soon be incorporated in point-of-care testing to provide safe, rapid, and reliable test results.

Carbon dots hybrid for dual fluorescent detection of microRNA-21 integrated bioimaging of MCF-7 using a microfluidic platform

Background

MicroRNAs have short sequences of 20 ~ 25-nucleotides which are similar among family members and play crucial regulatory roles in numerous biological processes, such as in cell development, metabolism, proliferation, differentiation, and apoptosis.

Results

We reported a strategy for the construction of a dual-emission fluorescent sensor using carbon dots (CDs) and confirmed their applications for ratiometric microRNA-21 sensing and bioimaging of cancer cells in a microfluidic device. The composition of blue CDs (B-CDs) and yellow CDs (Y-CDs) depicts dual-emission behavior which is centered at 409 and 543 nm under an excitation wavelength of 360 nm. With increasing microRNA-21 concentration, the robust and specific binding of DNA probe functionalized B-CDs to complementary microRNA-21 target induced perturbations of probe structure and led to changing fluorescence intensity in both wavelengths. Consequently, the ratio of turn-on signal to turn-off signal is greatly altered. With monitoring of the inherent ratiometric fluorescence variation (ΔF_540nm/ΔF_410nm), as-prepared BY-CDs were established as an efficient platform for ratiometric fluorescent microRNA-21 sensing, with a wide linear range of 0.15 fM to 2.46 pM and a detection limit of 50 aM.

Conclusions

Furthermore, the proposed assay was applied for detecting microRNA-21 in dilute human serum samples with satisfactory recovery and also in MCF-7 cell lines in the range 3000 to 45,000 (cell mL⁻¹) with a detection limit (3 cells in 10 μL), demonstrating the potential of the assay for clinic diagnosis of microRNA-associated disease. More importantly, the images revealed that MCF-7 cells well labeled with BY-CDs could exhibit the applicability of the proposed microfluidic system as an effective cell trapping device in bioimaging.

Graphical Abstract

Supplementary Information

The online version contains supplementary material available at 10.1186/s12951-022-01274-3.

Accelerated Electron Transfer in Nanostructured Electrodes Improves the Sensitivity of Electrochemical Biosensors

Electrochemical biosensors hold the exciting potential to integrate molecular detection with signal processing and wireless communication in a miniaturized, low-cost system. However, as electrochemical biosensors are miniaturized to the micrometer scale, their signal-to-noise ratio degrades and reduces their utility for molecular diagnostics. Studies have reported that nanostructured electrodes can improve electrochemical biosensor signals, but since the underlying mechanism remains poorly understood, it remains difficult to fully exploit this phenomenon to improve biosensor performance. In this work, electrochemical aptamer biosensors on nanoporous electrode are optimized to achieve improved sensitivity by tuning pore size, probe density, and electrochemical measurement parameters. Further, a novel mechanism in which electron transfer is physically accelerated within nanostructured electrodes due to reduced charge screening, resulting in enhanced sensitivity is proposed and experimentally validated. In concert with the increased surface areas achieved with this platform, this newly identified effect can yield an up to 24-fold increase in signal level and nearly fourfold lower limit of detection relative to planar electrodes with the same footprint. Importantly, this strategy can be generalized to virtually any electrochemical aptamer sensor, enabling sensitive detection in applications where miniaturization is a necessity, and should likewise prove broadly applicable for improving electrochemical biosensor performance in general.

Efficient and Versatile Application of Fluorescence DNA-Conjugated CdTe Quantum Dots Nanoprobe for Detection of a Specific Target DNA of SARS Cov-2 Virus

Regarding the outbreak of the SARS Cov-2 virus pandemic worldwide, it seems necessary to provide new diagnostic methods to combat the virus. A fluorescence CdTe quantum dots-DNA (QDs-DNA) nanosensor was prepared for efficient detection of a specific target complementary DNA or RNA from the SARS Cov-2 virus using FRET experiment via forming a classic "sandwich" structure. The sequence of the complementary DNA (target DNA) is planned based on a substantial part of the SARS Cov-2 virus genome, and oligonucleotides of QDs-DNA nanoprobe are designed to complement it. The water-soluble CdTe QDs-DNA was prepared by replacing the thioglycolic acid (TGA) on the surface of QDs with capture DNA (thiolated DNA) through a ligand-exchange method. Subsequently, with the addition of complementary (target DNA) and quencher DNA (BHQ₂-labeled DNA) into the QDs-DNA conjugates, sandwiched hybrids were formed. The resulting assembly brings the BHQ₂-labeled DNA (as the acceptor), and the QDs (as the donor) into proximity, leading to quenching of fluorescence emission from the donor QDs through the FRET mechanism. In other words, a simple, highly sensitive, selective, and rapid approach was introduced to detect complementary DNA sequence from a specific part of the SARS Cov-2 virus genome with a detection limit of 2.52 × 10^-9 mol L^-1. Furthermore, the planned nanosensor was well used for the detection of RNA from SARS Cov-2 viruses in real samples with satisfactory analytical results, and the outcomes were compared with RT-PCR (Reverse Transcription Polymerase Chain Reaction) as the well-known standard method.

A novel DNA binding protein-based platform for electrochemical detection of miRNA

We present a novel amplification-free sandwich type platform assay for electrochemical detection of miRNA. The assay is based on T4 DNA polymerase mediated synthesis of the p53 binding DNA sequence at the 3' end of target miRNA. The resulting miRNA-DNA chimera is detected via an electrochemical sandwich hybridization assay where HRP-labelled p53 binds to its recognition sequence and an amperometric signal is generated by hydroquinone-mediated enzymatic reduction of H2O2. The limit of detection of our assay was estimated to be 22 fM with a linear dynamic range of 100 fM-1 nM. This new platform method of detecting miRNA shows superior performance to conventional electrochemical miRNA biosensors and has the potential for amplification-free analysis of miRNA with high specificity and sensitivity.

Understanding of Strain-Induced Electronic Structure Changes in Metal-Based Electrocatalysts: Using Pd@Pt Core-Shell Nanocrystals as an Ideal Platform

While metal-based electrocatalysts have garnered extensive attention owing to the large variety of enzyme-mimic properties, the search for such highly-efficient catalysts still relies on empirical explorations, owing to the lack of predictive indicators as well as the ambiguity of structure-activity relationships. Notably, surface electronic structures play a crucial role in metal-based catalysts yet remain unexplored in enzyme-mimics. Herein, the authors investigate the electronic structure as a possible indicator of electrocatalytic activities of H₂ O₂ decomposition and glucose oxidation using Pd@Pt core-shell nanocrystals as a well-defined platform. The electron densities of the Pd@Pt are modulated with the correlation of strain through precise control of surface orientation and the number of atomic layers. The close relationships between the electrocatalytic activities and the surface charge accumulation are found, in which the increase of the electron accumulation can enhance both the enzyme-mimic activities. As a result, the Pd@Pt_3L icosahedra with compressive strain in Pt shells exhibit the highest electrocatalytic activities for H₂ O₂ decomposition and glucose oxidation. Such systematic and comprehensive study provides the structure-activity relationships and paves a new way for the rational design of metal-based electrocatalysts. Especially, the charge accumulation degrees may serve as a general performance indicator for metal-based catalysts.

Utilization of chromogenic enzyme substrates for signal amplification in multiplexed detection of biomolecules using surface mass spectrometry

MicroRNAs (miRNAs) are important post-transcriptional gene regulators and can serve as potential biomarkers for many diseases. Most of the current miRNA detection techniques require purification from biological samples, amplification, labeling, or tagging, which makes quantitative analysis of clinically relevant samples challenging. Here we present a new strategy for the detection of miRNAs with uniformity over a large area based on signal amplification using enzymatic reactions and measurements using time-of-flight secondary ion mass spectrometry (ToF-SIMS), a sensitive surface analysis tool. This technique has high sequence specificity through hybridization with a hairpin DNA probe and allows the identification of single-base mismatches that are difficult to distinguish by conventional mass spectrometry. We successfully detected target miRNAs in biological samples without purification, amplification, or labeling of target molecules. In addition, by adopting a well-known chromogenic enzymatic reaction from the field of biotechnology, we extended the use of enzyme-amplified signal enhancement ToF (EASE-ToF) to protein detection. Our strategy has advantages with respect to scope, quantification, and throughput over the currently available methods, and is amenable to multiplexing based on the outstanding molecular specificity of mass spectrometry (MS). Therefore, our technique not only has the potential for use in clinical diagnosis, but also provides evidence that MS can serve as a useful readout for biosensing to perform multiplexed analysis extending beyond the limitations of existing technology.

Recent trends in application of nanomaterials for the development of electrochemical microRNA biosensors

The biology of the late twentieth century was marked by the discovery in 1993 of a new class of small non-coding ribonucleic acids (RNAs) which play major roles in regulating the translation and degradation of messenger RNAs. These small RNAs (18-25 nucleotides), called microRNAs (miRNAs), are implied in several biological processes such as differentiation, metabolic homeostasis, or cellular apoptosis and proliferation. The discovery in 2008 that the presence of miRNAs in body fluids could be correlated with cancer (prostate, breast, colon, lung, etc.) or other diseases (diabetes, heart diseases, etc.) has made them new key players as biomarkers. Therefore, miRNA detection is of considerable significance in both disease diagnosis and in the study of miRNA function. Until these days, more than 1200 miRNAs have been identified. However, traditional methods developed for conventional DNA does not apply satisfactorily for miRNA, in particular due to the low expression level of these miRNA in biofluids, and because they are very short strands. Electrochemical biosensors can provide this sensitivity and also offer the advantages of mass fabrication, low-cost, and potential decentralized analysis, which has wide application for microRNAs sensing, with many promising results already reported. The present review summarizes some newly developed electrochemical miRNA detection methods.

A sensitive spectrophotometric ellipsometry based Aptasensor for the vascular endothelial growth factor detection

A sensitive and selective, aptamer and spectroscopic ellipsometry based sensor is reported here for the early diagnosis of breast cancer, which is a common type of cancer following lung cancer. It was aimed to develop a single-step and label-free assay for the sensitive and selective detection of VEGF₁₆₅. To this end, two different aptamers and spectroscopic ellipsometry were used. In the presented study, by determining the appropriate aptamer immobilization conditions, the spectroscopic ellipsometry technique was successfully applied for the detection of VEGF₁₆₅ at the range of 1 pM-1000 pM in the buffer. Aptasensors have a detection limit of 5.81 pM and 4.29 pM, respectively.

Highly selective and antifouling electrochemical biosensors for sensitive MicroRNA assaying based on conducting polymer polyaniline functionalized with zwitterionic peptide

Ultrasensitive and low-fouling microRNA electrochemical biosensors were successfully constructed by introducing thiol-terminated antifouling molecules (peptide sequence, polyethylene glycol, or mercapto alcohol) onto the surface of polyaniline-modified electrodes. For the three kinds of antifouling materials investigated, the newly designed and synthesized peptide exhibited superior antifouling ability to others, and it could effectively reduce the nonspecific adsorption of proteins and even prevent the fouling effect of serum. Compared with microRNA biosensors without antifouling capability, or those modified with polyethylene glycol or mercapto alcohol, the biosensor modified with the designed zwitterionic peptide showed the highest specificity for single-base mismatch, three-base mismatch, and completely complementary microRNAs. Most interestingly, the experimental results indicated that the introduction of antifouling molecules to the sensing interfaces did not significantly change the sensitivity of the biosensor. The strategy of constructing antifouling biosensors based on newly synthesized zwitterionic peptides and conducting polymers can be promisingly extended to the development of other electrochemical sensors and biosensors without encountering biofouling. Graphical abstract Ultrasensitive and low-fouling microRNA electrochemical biosensors were constructed by introducing thiol-terminated antifouling molecules (peptide sequence, polyethylene glycol, or mercapto alcohol) onto the surface of polyaniline-modified electrodes. The biosensor modified with the designed zwitterionic peptide showed the highest specificity amongst four kinds of biosensors.

Necessity and Challenges of Sample Preconcentration in Analysis of Multiple MicroRNAs by Capillary Electrophoresis

Thousands of putative microRNA (miRNA)-based cancer biomarkers have been reported, but none has been validated for approval by the Food and Drug Administration. One of the reasons for this alarming discrepancy is the lack of a method that is sufficiently robust for carrying out validation studies, which may require analysis of samples from hundreds of patients across multiple institutions and pooling the results together. The capillary electrophoresis (CE)-based hybridization assay proved to be more robust than reversed transcription polymerase chain reaction (the current standard), but its limit of quantification (LOQ) exceeds 10 pM while miRNA concentrations in cell lysates are below 1 pM. Thus, CE-based separation must be preceded by on-column sample preconcentration. Here, we explain the challenges of sample preconcentration for CE-based miRNA analyses and introduce a preconcentration method that can suit CE-based miRNA analysis utilizing peptide nucleic acid (PNA) hybridization probes. The method combines field-amplified sample stacking (FASS) with isotachophoresis (ITP). We proved that FASS-ITP could retain and concentrate both near-neutral PNA with highly negatively charged PNA-miRNA hybrids. We demonstrated that preconcentration by FASS-ITP could be combined with the CE-based separation of the unreacted PNA probes from the PNA-miRNA hybrids and facilitate improvement in LOQ by a factor of 140, down to 0.1 pM. Finally, we applied FASS-ITP-CE for the simultaneous detection of two miRNAs in crude cell lysates and proved that the method was robust when used in complex biological matrices. The 140-fold improvement in LOQ and the robustness to biological matrices will significantly expand the applicability of CE-based miRNA analysis, bringing it closer to becoming a practical tool for validation of miRNA biomarkers.

An enzyme-free electrochemical biosensor based on target-catalytic hairpin assembly and Pd@UiO-66 for the ultrasensitive detection of microRNA-21

MicroRNA-21 (miR-21) has been widely investigated as important biomarkers for cancer diagnosis and treatment. Herein, a highly sensitive nonenzymatic electrochemical biosensor based on Pd@metal-organic frameworks (Pd@UiO-66) and target-catalytic hairpin assembly (CHA) with target recycling approach has been proposed for the detection of miR-21. The proposed biosensor integrates the efficient CHA strategy and excellent electrocatalytic performance of Pd@UiO-66 nanocomposites. The concentration of miRNA-21 is related to the amount of the adsorbed electrocatalyst, leading to the different electrochemical signals for readout towards paracetamol (AP). This biosensor shows a low limit of detection of 0.713 fM with the dynamic range of 20 fM -600 pM under the optimal experimental conditions, providing a powerful platform for detecting miR-21. Furthermore, the designed biochemical self-assembly strategy of this electrochemical biosensor is promising candidate for potential applications in the analysis of other important genetic biomarkers for early diagnosis of cancers.

Signal-off photoelectrochemical determination of miRNA-21 using aptamer-modified In2O3@Cu2MoS4 nanocomposite

In₂O₃@Cu₂MoS₄ nanocomposite with superior photoelectrochemical (PEC) performance is used for the first time as a photoactivity material, and a signal-off PEC biosensing platform for miRNA detection has been successfully constructed. Firstly, the Cu₂MoS₄ nanosheets are synthesized by a hydrothermal method, and then, the homogeneous In₂O₃ nanoparticles (In₂O₃ NPs) are synthesized by calcination in the air. The In₂O₃@Cu₂MoS₄ nanocomposite is constructed with the Cu₂MoS₄ nanosheets as matrix and In₂O₃ NPs as sensitizer through a layer-by-layer assembly strategy. The nanocomposite with a tight interface and the matched band structure restrains the electron-hole pair recombination. Under visible light (400-700 nm), the nanocomposite exhibits a strong initial signal. With the catalyzed hairpin assembly, dozens of PbS quantum dots (QDs) are introduced on the surface of an electrode, significantly reducing the photocurrent of n-type In₂O₃@Cu₂MoS₄. Since PbS QDs can compete with the nanocomposite for light energy and electron donors, the signal decreased. Under optimal conditions, the biosensor manifests a broad linear range (1 fM-1 nM) and a low detection limit of about 0.57 fM, at a working potential of 0 V (vs. Ag/AgCl). The recovery of spiked human serum is between 94.0 and 102%, and the relative standard deviation (RSD) is between 1.3 and 2.7%. Therefore, the as-fabricated biosensor exhibits a potential for the determination of miRNA-21 in practical applications.Graphical abstract The In₂O₃@Cu₂MoS₄ nanocomposite owns a strong anode photocurrent signal, which can be used as a photoactive material to construct a "signal-off" biosensor for the detection of miRNA in non-enzymatically catalyzed hairpin assembly (CHA) reaction.

rkDNA-graphene oxide as a simple probe for the rapid detection of miRNA21

In this study we developed a novel diagnostic tool for the detection of miRNA21, based on the fluorescent nucleotide morpholine naphthalimide deoxyuridine (dUrkTP). We incorporated dUrkTP into DNA through primer extension to obtain rkDNA displaying high fluorescence. We then used lambda exonuclease, a specific nuclease for 3́-monophosphate-containing DNA, to separate rkDNA from its complementary sequence. The fluorescence of the free rkDNA was quenched dramatically upon interacting with graphene oxide (GO). Our rkDNA-GO fluorescence probing system exhibited high sensitivity and selectivity for the detection of miRNA21. This inexpensive probing system, employing simple primer extension and exonuclease degradation, required only 30 min to detect its target miRNA. This strategy appears suitable for the detection of diverse types of miRNA.

A plasmonic nanoledge array sensor for detection of anti-insulin antibodies of type 1 diabetes biomarker

Here we present a plasmonic nanoledge device with high sensitivity and selectivity used to detect protein biomarkers simply by functionalizing the device, which specifically binds to particular biomolecule or biomarkers. We employ this plasmonic nanoledge device for the detection of anti-insulin antibodies of type 1 diabetes (T1D) in buffer and human serum at the range of pg ml^-1 to 100 ng ml^-1. The signal transduction is based on the extraordinary optical transmission (EOT) through the nanoledge array and the optical spectral changes with the biological binding reaction between the surface functionalized insulin with anti-insulin antibody. Control experiments indicate little interferences from the human serum background and addition of other proteins such as bovine serum albumin (BSA) and epidermal growth factor (EGF) at 20 ng ml^-1. The high sensitivity, specificity and easy adaptability of the plasmonic device offer new opportunities in biosensing and diagnostic applications for T1D.

Ultrasensitive analysis of microRNAs with gold nanoparticle-decorated molybdenum disulfide nanohybrid-based multilayer nanoprobes

The nanoprobe-based signal amplification strategy is a powerful way to ultrasensitively detect biomolecules. Herein, a gold nanoparticle-decorated molybdenum disulfide (MoS₂-AuNP)-based multilayer nanoprobe (MLNP) was designed for ultrasensitive analysis of microRNA-21 (miRNA-21). The MLNP-amplified electrochemical biosensor exhibited an ultrawide dynamic range (10 aM-1 μM) and an ultralow detection limit (38 aM) for target miRNA-21 analysis. Furthermore, this biosensor can determine miRNA-21 expression in cell lysates of 100 human cervical cancer (HeLa) cells. Our results demonstrate that MoS₂-AuNP nanocomposites have great potential in constructing biosensors for target molecule analysis.

Impediometric Electrochemical Sensor Based on The Inspiration of Carnation Italian Ringspot Virus Structure to Detect an Attommolar of miR

Electrochemical sensors are the tools to detect the accurate and sensitive miRs. There is the challenge to increase the power and sensitivity of the surface for the electrochemical sensor. We design a virus-like hallow structure of cuco2o4 that it holds the large amounts of p19 protein by mimicking of inherent virus (Carnation italian ringspot virus) to detect 21mir with the limit of detection (LOD = 1aM). The electrochemical measurements are performed between the potentials at -0.3 V and +0.3 V with 1 mM [Fe(CN)6] -3/-4. After dropping the cuco2o4 on the SCPE (screen carbon printed electrode), the sensor is turned on due to the high electrochemical properties. Then, p19 proteins move into the hallow structure and inhibit the exchange of electrochemical reactions between the shells and the sensor is turned off. Then, adding the duplexes of RNA/miRs cause to increase the electrochemical property of p19 due to the change of p19 conformation and the system is turned on, again. So, for the first time, a virus-like hallow structure has been used to detect the 21miR in the human serum, MCF-7, Hella cells, with high sensitivity, specificity, and reproducibility in few minutes.

MicroRNA Biomarkers for Infectious Diseases: From Basic Research to Biosensing

In the pursuit of improved diagnostic tests for infectious diseases, several classes of molecules have been scrutinized as prospective biomarkers. Small (18–22 nucleotide), non-coding RNA transcripts called microRNAs (miRNAs) have emerged as promising candidates with extensive diagnostic potential, due to their role in numerous diseases, previously established methods for quantitation and their stability within biofluids. Despite efforts to identify, characterize and apply miRNA signatures as diagnostic markers in a range of non-infectious diseases, their application in infectious disease has advanced relatively slowly. Here, we outline the benefits that miRNA biomarkers offer to the diagnosis, management, and treatment of infectious diseases. Investigation of these novel biomarkers could advance the use of personalized medicine in infectious disease treatment, which raises important considerations for validating their use as diagnostic or prognostic markers. Finally, we discuss new and emerging miRNA detection platforms, with a focus on rapid, point-of-care testing, to evaluate the benefits and obstacles of miRNA biomarkers for infectious disease.

DNA-Driven Two-Layer Core-Satellite Gold Nanostructures for Ultrasensitive MicroRNA Detection in Living Cells

It is a significant challenge to achieve controllable self-assembly of superstructures for biological applications in living cells. Here, a two-layer core-satellite assembly is driven by a Y-DNA, which is designed with three nucleotide chains that hybridized through complementary sequences. The two-layer core-satellite nanostructure (C₃₀ S₅ S₁₀ NS) is constructed using 30 nm gold nanoparticles (Au NPs) as the core, 5 nm Au NPs as the first satellite layer, and 10 nm Au NPs as the second satellite layer, resulting in a very strong circular dichroism (CD) and surface-enhanced Raman scattering. After optimization, the yield is up to 85%, and produces a g-factor of 0.16 × 10^-2 . The hybridization of the target microRNA (miRNA) with the molecular probe causes a significant drop in the CD and Raman signals, and this phenomenon is used to detect the miRNA in living cells. The CD signal has a good linear range of 0.011-20.94 amol ng_RNA^-1 and a limit of detection (LOD) of 0.0051 amol ng_RNA^-1 , while Raman signal with the range of 0.052-34.98 amol ng_RNA^-1 and an LOD of 2.81 × 10^-2 amol ng_RNA^-1 . This innovative dual-signal method can be used to quantify biomolecules in living cells, opening the way for ultrasensitive, highly accurate, and reliable diagnoses of clinical diseases.

RNA secondary structured logic gates for profiling the microRNA cancer biomarkers

Deregulation of microRNAs expression is symptomatic of cancer disease and occurs before the awareness of cancer signs. Early detection of cancer disease can improve or drop the disease entirely. DNA computing is an emerging field of detecting microRNAs based on toehold-mediated strand displacement reactions, which is a more efficient method than the commonly used method like real-time PCR. Accuracy and cost of diagnostic applications are essential criteria that are achieved by using the DNA logic gates based on the DNA computing method. In this study, the authors proposed the multi-input liver cancer biosensor with the RNA secondary structure motifs as the computational module and two approaches are suggested.

Single Functionalized pRNA/Gold Nanoparticle for Ultrasensitive MicroRNA Detection Using Electrochemical Surface-Enhanced Raman Spectroscopy

Controlling the selective one-to-one conjugation of RNA with nanoparticles is vital for future applications of RNA nanotechnology. Here, the monofunctionalization of a gold nanoparticle (AuNP) with a single copy of RNA is developed for ultrasensitive microRNA-155 quantification using electrochemical surface-enhanced Raman spectroscopy (EC-SERS). A single AuNP is conjugated with one copy of the packaging RNA (pRNA) three-way junction (RNA 3WJ). pRNA 3WJ containing one strand of the 3WJ is connected to a Sephadex G100 aptamer and a biotin group at each arm (SEPapt/3WJ/Bio) which is then immobilized to the Sephadex G100 resin. The resulting complex is connected to streptavidin-coated AuNP (STV/AuNP). Next, the STV/AuNP-Bio/3WJa is purified and reassembled with another 3WJ to form a single-labeled 3WJ/AuNP. Later, the monoconjugate is immobilized onto the AuNP-electrodeposited indium tin oxide coated substrate for detecting microRNA-155 based on EC-SERS. Application of an optimum potential of +0.2 V results in extraordinary amplification (≈7 times) of methylene blue (reporter) SERS signal compared to the normal SERS signal. As a result, a highly sensitive detection of 60 × 10-18 m microRNA-155 in 1 h in serum based on monoconjugated AuNP/RNA is achieved. Thus, the monofunctionalization of RNA onto nanoparticle can provide a new methodology for biosensor construction and diverse RNA nanotechnology development.

A photocleavable and mass spectrometric DNA-peptide probe enables fast and specific enzyme-free detection of microRNA

MiRNAs are known to be involved in a series of diseases, including breast cancer, and they have the potential to serve as diagnostic/prognostic markers and therapeutic targets. A prerequisite for miRNAs to be applied in clinical practice is the quantitative profiling of their expression. However, the majority of current assays used in miRNA detection are highly enzyme-dependent. In this study, a novel enzyme-free assay was developed that relies on stacking hybridization and a photocleavable DNA-PL-peptide probe, which contains a reporter peptide (AVLGVDPFR), a photocleavable o-nitrobenzyl derivative linker and a detection DNA sequence that is complementary to a part of the target miRNA (e.g., miR-21, miR-125a or miR-200c). Stacking hybridization enabled the DNA-PL-peptide probe to capture DNA in a contiguous tandem arrangement to generate a long DNA single strand complementary to the target miRNA. Then, photolysis was initiated to rapidly release the reporter peptide, and the reporter peptide was ultimately monitored by liquid chromatography-tandem mass spectrometry (LC-MS/MS). In this experiment, the parameters linked with photorelease, binding, conjugation and hybridization were characterized. The results showed that the assay time was significantly shortened, and the detection specificity was improved. After validation of the assay, the target miRNA level was determined in human breast cells and tissue samples. The results demonstrated that photocleavable materials coupled with mass spectrometric detection have great potential in clinical practice.

Rapid and sensitive electrochemical detection of microRNAs by gold nanoparticle-catalyzed silver enhancement

Using the proposed method the microRNA assay was successfully carried out in less than 70 min and the detection limit was as low as 15 fM.

MicroRNAs in ovarian cancer and recent advances in the development of microRNA-based biosensors

Ovarian cancer is the most aggressive of all gynaecological malignancies and is the leading cause of cancer-associated mortality worldwide.

CRISPR/Cas13a-Powered Electrochemical Microfluidic Biosensor for Nucleic Acid Amplification-Free miRNA Diagnostics

Noncoding small RNAs, such as microRNAs, are becoming the biomarkers of choice for multiple diseases in clinical diagnostics. A dysregulation of these microRNAs can be associated with many different diseases, such as cancer, dementia, and cardiovascular conditions. The key for effective treatment is an accurate initial diagnosis at an early stage, improving the patient's survival chances. In this work, the first clustered regularly interspaced short palindromic repeats (CRISPR)/Cas13a-powered microfluidic, integrated electrochemical biosensor for the on-site detection of microRNAs is introduced. Through this unique combination, the quantification of the potential tumor markers microRNA miR-19b and miR-20a is realized without any nucleic acid amplification. With a readout time of 9 min and an overall process time of less than 4 h, a limit of detection of 10 pm is achieved, using a measuring volume of less than 0.6 µL. Furthermore, the feasibility of the biosensor platform to detect miR-19b in serum samples of children, suffering from brain cancer, is demonstrated. The validation of the obtained results with a standard quantitative real-time polymerase chain reaction method shows the ability of the electrochemical CRISPR-powered system to be a low-cost, easily scalable, and target amplification-free tool for nucleic acid based diagnostics.

A Dynamic DNA Machine via Free Walker Movement on Lipid Bilayer for Ultrasensitive Electrochemiluminescent Bioassay

Herein, an ultrasensitive electrochemiluminescent (ECL) strategy was proposed based on a highly efficient dynamic DNA machine based on microRNA triggered free movement on the lipid bilayer interface. Typically, the lipid bilayer is constructed on the electrode surface modified with nafion@ECL luminophore and gold nanoparticles to immobilize the DNA walker labeled with cholesterol and hairpin nucleotides labeled with cholesterol and ferrocene (Fc), based on the cholesterol-lipid interaction. On this state, Fc was close to the ECL luminophore, performing a quenched ECL emission. In the presence of target microRNA 21, it could trigger the entropy beacon-based DNA amplification to convert microRNA to massive special DNA sequences, which could further hybridize with the blocking DNA on DNA walker to reactivate the DNA walker and thus trigger the DNA walker-based amplification to make Fc to be far from the ECL luminophore, performing a recovered ECL emission related with the concentration of microRNA 21. Compared with the conventional DNA walker immobilized on the interface via chemical bonds or physical adsorption, a higher reaction efficiency could be achieved due to the free movements of DNA walker and its substrates on the interface. As expected, satisfactory performances for the detection of microRNA 21 were achieved with a detection limit of 0.4 fM and quantitative estimation in cells. Furthermore, this dynamic DNA machine-based ECL strategy could be readily expanded for the detection of other biomarkers for clinical diagnosis.