Single-Molecule Sensor for High-Confidence Detection of miRNA

LRET-Based Simultaneous Detection of Dual miRNAs via Multitrap Optical Tweezers Assisted Suspension Array Tagged by Two Different Luminescent Quenchable UCNPs Combining CRISPR/Cas12a Amplification

Nowadays, optical tweezers play a vital role not only in optical manipulation but also in bioassay. As principal optical trapping objects, microbeads can combine optical tweezers with suspension array technology, with amply focused laser beams and adequately concentrated tags contributing to highly sensitive detection. In view of the inefficiency of conventional single-trap optical tweezers, multitrap systems are developed. Here, green- and blue-emitting core-shell-shell upconversion nanoparticles (UCNPs) are adopted to encode microbeads and determine dual miRNAs, with the internal shells leading the luminescence process to facilitate quenching through luminescence resonance energy transfer (LRET). Utilizing the trans cleavage of CRISPR/Cas12a, quenched luminescence signals are recovered and amplified, causing further enhanced detection sensitivity. Ultimately, limits of detection (LOD) of 17 and 22 aM are obtained with excellent specificities verified. Furthermore, dual miRNAs from MCF-7, A549, and MCF-10A cells are extracted and detected, with results consistent with those obtained by PCR. Notably, miR-155 in MCF-7 and A549 cells is detectable at the single-cell level. Thus, the differences in the measured miRNA levels between MCF-7 and MCF-10A cells imply the potential of this method to discriminate breast cancer cells from epithelial cells despite the difficulty in distinguishing different cancer cells due to similar miRNA levels.

Pitfalls and challenges of peptide nucleic acid immobilisation on carbon surfaces for sequence-specific capturing of nucleic acid biomarkers

Nucleic acid sensors based on a peptide nucleic acid (PNA) probe have seen a surge in interest since their discovery in the 1990s, and after the patent protecting them expired in 2013. The appeal of PNA as capture and/or sensing probes as an alternative to standard DNA or RNA oligonucleotides originates from their superior chemical stability and affinity for complementary oligonucleotides, as well as their increased responsiveness to single base mismatches. The implementation of PNA probes onto optical and electrochemical sensors has showed great promise although progress has been hampered by issues mostly associated with surface chemistry, probe accessibility and non-specific binding. Herein, we report on a systematic comparison between various PNA immobilisation strategies on carbon substrates based on both covalent and non-covalent chemistries. Besides the use of standard electrochemical techniques to characterise the extent of surface modification, the ability of immobilised PNAs to engage in chemical interactions with freely diffusing molecules was also investigated. Using original chemical tags, this study provides a unique insight into the impact of immobilisation chemistries on PNA's (bio)availability. Rapid immobilisation of biotinylated PNA oligomers on screen-printed carbon electrode (SPCE) coated with adsorbed polystreptavidin (pSA) demonstrated highest efficiency and ease in the preparation process. An original nucleic acid sensor using this immobilisation chemistry is reported that is based on a sandwich assay between a surface bound PNA capture probe and a freely diffusing electrochemically active PNA sensing probe.

Insight of Employing Molecular Junctions for Sensor Applications

Molecular junctions (MJs) exhibit distinct charge transport properties and have the potential to become the next generation of electronic devices. Advancing molecular electronics for practical uses, such as sensors, is crucial to propel its progress to the next level. In this review, we discussed how MJs can serve as a sensor for detecting a wide range of analytes with exceptional sensitivity and specificity. The primary advances and potential of molecular junctions for the various kinds of sensors including photosensors, explosives (DNTs, TNTs), cancer biomarker detection (DNA, mRNA), COVID detection, biogases (CO, NO, NH), environmental pH, practical chemicals, and water pollutants are listed and examined here. The fundamental ideas of molecular junction formation as well as the sensing mechanism have been examined here. This review demonstrates that MJ-based sensors hold significant promise for real-time and on-site detection. It provides valuable insights into current research and outlines potential future directions for advancing molecular junction-based sensors for practical applications.

A Smartphone-Mediated "All-In-One" Biosensing Chip for Visual and Value-Assisted Detection

A smartphone-mediated self-powered biosensor is fabricated for miRNA-141 detection based on the CRISPR/Cas12a cross-cutting technique and a highly efficient nanozyme. As a novel nanozyme and a signal-amplified coreaction accelerator, the AuPtPd@GDY nanozyme exhibits an excellent ability to catalyze cascade color reactions and high conductivity to enhance the electrochemical signal for miRNA-141 assays. After CRISPR/Cas12a cross-cutting of S2-glucose oxidase (S2-GOD), the electrochemical signal is weakened, and miRNA-141 is detected by monitoring the decrease in the signal. On the other hand, a cascade reaction among glucose, H2O2, and TMB is catalyzed by GOD and AuPtPd@GDY, respectively, resulting in a color change of the solution, which senses miRNA-141. The self-powered biosensor enables value-assisted and visual detection of miRNA-141 with limits of detection of 3.1 and 15 aM, respectively. Based on the dual-modal self-powered sensing system, a smartphone-mediated "all-in-one" biosensing chip is designed to achieve the real-time and intelligent monitoring of miRNA-141. This work provides a new approach to design multifunctional biosensors to realize the visualization and portable detection of tumor biomarkers.

Ultra-stable and highly-bright CsPbBr3 perovskite/silica nanocomposites for miRNA detection based on digital single-nanoparticle counting

Single-nanoparticle counting (SNPC) based on fluorescent tag (FT) stands out for its capacity to achieve amplification-free and sensitive detection of biomarkers. The stability and luminescence of FT are important to the sensitivity and reliability of SPNC. In this work, we developed novel perovskite/silica nanocomposites by in-situ nanoconfined growth of CsPbBr3 nanocrystals inside mesoporous structure of silica nanoparticles. PbBr(OH) was formed in an alkaline-assisted reaction triggered by water on the surface of CsPbBr3 nanocrystals. The as-obtained nanocomposites, featuring dual protection from silica matrix and PbBr(OH), exhibited high absolute photoluminescence quantum yield (PLQY) of 86.5% and demonstrated outstanding PL stability confronting with water, heat, ultrasound and UV-irradiation, which is desired by SNPC-based biosensor. Thereafter, these nanocomposites were used to construct an operationally friendly SNPC assay for the amplification-free quantification of cancer-associated miRNA. Quantitative detection of miRNA could be accomplished by directly counting the number of nanocomposites using a flow cytometer in this assay. This strategy did not ask for multiple washing steps and demonstrated specific and sensitive detection of miRNA 21, which exhibited a dynamic range of 1-1000 pM and limit of detection of 79 amol. The employment of highly stable perovskite/silica nanocomposites improved the test reliability and stability of SNPC, revealing the vast potential of perovskites in biosensing.

Computational generation and characterization of IsdA-binding aptamers with single-molecule FRET analysis

Staphylococcus aureus is a major foodborne bacterial pathogen. Early detection of S. aureus is crucial to prevent infections and ensure food quality. The iron-regulated surface determinant protein A (IsdA) of S. aureus is a unique surface protein necessary for sourcing vital iron from host cells for the survival and colonization of the bacteria. The function, structure, and location of the IsdA protein make it an important protein for biosensing applications relating to the pathogen. Here, we report an in-silico approach to develop and validate high-affinity binding aptamers for the IsdA protein detection using custom-designed in-silico tools and single-molecule Fluorescence Resonance Energy Transfer (smFRET) measurements. We utilized in-silico oligonucleotide screening methods and metadynamics-based methods to generate 10 aptamer candidates and characterized them based on the Dissociation Free Energy (DFE) of the IsdA-aptamer complexes. Three of the aptamer candidates were shortlisted for smFRET experimental analysis of binding properties. Limits of detection in the low picomolar range were observed for the aptamers, and the results correlated well with the DFE calculations, indicating the potential of the in-silico approach to support aptamer discovery. This study showcases a computational SELEX method in combination with single-molecule binding studies deciphering effective aptamers against S. aureus IsdA, protein. The established approach demonstrates the ability to expedite aptamer discovery that has the potential to cut costs and predict binding efficacy. The application can be extended to designing aptamers for various protein targets, enhancing molecular recognition, and facilitating the development of high-affinity aptamers for multiple uses.

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.

Multiple miRNA Detection through a Suspended Microbead Array Encoded by Triple-Color Upconversion Luminescent Nanotags via Bi-Beam Splitter Hybrid-Multitrap Optical Tweezers

In recent years, optical tweezers have become a novel tool for biodetection, and to improve the inefficiency of a single trap, the development of multitraps is required. Herein, we constructed a set of hybrid multitrap optical tweezers with the balance of stability and flexibility by the combination of two different beam splitters, a diffraction optical element (DOE) and galvano mirrors (GMs), to capture polystyrene (PS) microbeads in aqueous solutions to create an 18-trap suspended array. A sandwich hybridization strategy of DNA-miRNA-DNA was adopted to detect three kinds of target miRNAs associated with triple negative breast cancer (TNBC), in which different upconversion nanoparticles (UCNPs) with red, green, and blue emissions were applied as luminescent tags to encode the carrier PS microbeads to further indicate the levels of the targets. With encoded luminescent microbeads imaged by a three-channel microscopic system, the biodetection displayed high sensitivity with low limits of detection (LODs) of 0.27, 0.32, and 0.33 fM and exceptional linear ranges of 0.5 fM to 1 nM, 0.7 fM to 1 nM, and 1 fM to 1 nM for miR-343-3p, miR-155, and miR-199a-5p, respectively. In addition, this bead-based assay method was demonstrated to have the potential for being applied in patients' serum by satisfactory standard addition recovery experiment results.

FRET-Based Single-Molecule Detection of Pathogen Protein IsdA Using Computationally Selected Aptamers

Iron-regulated surface determinant protein A (IsdA) is a key surface protein found in the foodborne bacteria─Staphylococcus aureus (S. aureus)─which is known to be critical for bacterial survival and colonization. S. aureus is pathogenic and has been linked to foodborne diseases; thus, early detection is critical to prevent diseases caused by this bacterium. Despite IsdA being a specific marker for S. aureus and several detection methods have been developed for sensitive detection of this bacteria such as cell culture, nucleic acids amplification, and other colorimetric and electrochemical methods, the detection of S. aureus through IsdA is underdeveloped. Here, by combining computational generation of target-guided aptamers and fluorescence resonance energy transfer (FRET)-based single-molecule analysis, we presented a widely applicable and robust detection method for IsdA. Three different RNA aptamers specific to the IsdA protein were identified and their ability to switch a FRET construct to a high-FRET state in the presence of protein was verified. The presented approach demonstrated the detection of IsdA down to picomolar levels (×10^-12 M, equivalent to ∼1.1 femtomoles IsdA) with a dynamic range extending to ∼40 nM. The FRET-based single-molecule technique that we reported here is capable of detecting the foodborne pathogen protein IsdA with high sensitivity and specificity and has a broader application in the food industry and aptamer-based sensing field by enabling quantitative detection of a wide range of pathogen proteins.

The deleted in oral cancer (DOC1 aka CDK2AP1) tumor suppressor gene is downregulated in oral squamous cell carcinoma by multiple microRNAs

Cyclin-dependent kinase 2-associated protein 1 (CDK2AP1; also known as deleted in oral cancer or DOC1) is a tumor suppressor gene known to play functional roles in both cell cycle regulation and in the epigenetic control of embryonic stem cell differentiation, the latter as a core subunit of the nucleosome remodeling and histone deacetylation (NuRD) complex. In the vast majority of oral squamous cell carcinomas (OSCC), expression of the CDK2AP1 protein is reduced or lost. Notwithstanding the latter (and the DOC1 acronym), mutations or deletions in its coding sequence are extremely rare. Accordingly, CDK2AP1 protein-deficient oral cancer cell lines express as much CDK2AP1 mRNA as proficient cell lines. Here, by combining in silico and in vitro approaches, and by taking advantage of patient-derived data and tumor material in the analysis of loss of CDK2AP1 expression, we identified a set of microRNAs, namely miR-21-5p, miR-23b-3p, miR-26b-5p, miR-93-5p, and miR-155-5p, which inhibit its translation in both cell lines and patient-derived OSCCs. Of note, no synergistic effects were observed of the different miRs on the CDK2AP1-3-UTR common target. We also developed a novel approach to the combined ISH/IF tissue microarray analysis to study the expression patterns of miRs and their target genes in the context of tumor architecture. Last, we show that CDK2AP1 loss, as the result of miRNA expression, correlates with overall survival, thus highlighting the clinical relevance of these processes for carcinomas of the oral cavity.

Rapid Detection of Ag(I) via Size-Induced Photoluminescence Quenching of Biocompatible Green-Emitting, l-Tryptophan-Scaffolded Copper Nanoclusters

Atomically precise metal nanoclusters capped with small molecules like amino acids are highly favored due to their specific interactions and easy incorporation into biological systems. However, they are rarely explored due to the challenge of surface functionalization of nanoclusters with small molecules. Herein, we report the synthesis of a green-emitting (λex = 380 nm, λem = 500 nm), single-amino-acid (l-tryptophan)-scaffolded copper nanocluster (Trp-Cu NC) via a one-pot route under mild reaction conditions. The synthesized nanocluster can be used for the rapid detection of a heavy metal, silver (Ag(I)), in the nanomolar concentration range in real environmental and biological samples. The strong green photoluminescence intensity of the nanocluster quenched significantly upon the addition of Ag(I) due to the formation of bigger nanoparticles, thereby losing its energy quantization. A notable color change from light yellow to reddish-brown can also be observed in the presence of Ag(I), allowing its visual colorimetric detection. Portable paper strips fabricated with the Trp-Cu NC can be reliably used for on-site visual detection of Ag(I) in the micromolar concentration range. The Trp-Cu NC possesses excellent biocompatibility, making it a suitable nanoprobe for cell imaging; thus, it can act as an in vivo biomarker. The nanocluster showed a significant spectral overlap with anticancer drug doxorubicin and thus can be used as an effective fluorescence resonance energy transfer (FRET) pair. FRET results can reveal important information regarding the attachment of the drug to the nanocluster and hence its role as a potential drug carrier for targeted drug delivery within the human body.

microRNA Detection via Nanostructured Biochips for Early Cancer Diagnostics

MicroRNA (miRNA) are constituted of approximately 22 nucleotides and play an important role in the regulation of many physiological functions and diseases. In the last 10 years, an increasing interest has been recorded in studying the expression profile of miRNAs in cancer. Real time-quantitative polymerase chain reaction (RT-qPCR), microarrays, and small RNA sequencing represent the gold standard techniques used in the last 30 years as detection methods. The advent of nanotechnology has allowed the fabrication of nanostructured biosensors which are widely exploited in the diagnostic field. Nanostructured biosensors offer many advantages: (i) their small size allows the construction of portable, wearable, and low-cost products; (ii) the large surface-volume ratio enables the loading of a great number of biorecognition elements (e.g., probes, receptors); and (iii) direct contact of the recognition element with the analyte increases the sensitivity and specificity inducing low limits of detection (LOD). In this review, the role of nanostructured biosensors in miRNA detection is explored, focusing on electrochemical and optical sensing. In particular, four types of nanomaterials (metallic nanoparticles, graphene oxide, quantum dots, and nanostructured polymers) are reported for both detection strategies with the aim to show their distinct properties and applications.

Target recognition initiated self-dissociation based DNA nanomachine for sensitive and accurate MicroRNA (miRNA) detection

As a valuable biomarker for various tumor, sensitive and reliable quantitative determination of microRNA (miRNA) is crucial for both disease diagnosis and cancer treatment. Herein, we depict a novel simple and sensitive miRNA detection approach by exploiting an elegantly designed target recognition initiated self-dissociation based DNA nanomachine. In this nanomachine, target recognition assists the formation of active DNAzyme secondary conformation, and the active DNAzyme generates a nicking site in H probe, initiating the self-assembly of H probe. With the reflexed sequences as primer, dual signal recycles are formed under the cooperation of DNA polymerase and Nb.BbvCI. Eventually, the method exhibits a high sensitivity with the limit of detection as low as 12 fM. In addition, the method is also demonstrated with a high selectivity that can distinguish one mismatched base pair. We believe the established approach can be a robust tool for the early-diagnosis of a variety of cancers and also in anticancer drug development.

Iron Oxide Nanoparticles: A Review on the Province of Its Compounds, Properties and Biological Applications

Materials science and technology, with the advent of nanotechnology, has brought about innumerable nanomaterials and multi-functional materials, with intriguing yet profound properties, into the scientific realm. Even a minor functionalization of a nanomaterial brings about vast changes in its properties that could be potentially utilized in various applications, particularly for biological applications, as one of the primary needs at present is for point-of-care devices that can provide swifter, accurate, reliable, and reproducible results for the detection of various physiological conditions, or as elements that could increase the resolution of current bio-imaging procedures. In this regard, iron oxide nanoparticles, a major class of metal oxide nanoparticles, have been sweepingly synthesized, characterized, and studied for their essential properties; there are 14 polymorphs that have been reported so far in the literature. With such a background, this review's primary focus is the discussion of the different synthesis methods along with their structural, optical, magnetic, rheological and phase transformation properties. Subsequently, the review has been extrapolated to summarize the effective use of these nanoparticles as contrast agents in bio-imaging, therapeutic agents making use of its immune-toxicity and subsequent usage in hyperthermia for the treatment of cancer, electron transfer agents in copious electrochemical based enzymatic or non-enzymatic biosensors and bactericidal coatings over biomaterials to reduce the biofilm formation significantly.

Highly Selective FRET-Aided Single-Molecule Counting of MicroRNAs Labeled by Splinted Ligation

MicroRNAs (miRNAs) are short non-coding RNAs that play an important role in regulating gene expression. Since miRNAs are abnormally expressed in various cancers, they are considered to be promising biomarkers for early cancer diagnosis. However, the short length and strong sequence similarity among miRNAs make their reliable quantification very challenging. We developed a highly selective amplification-free miRNA detection method based on Förster resonance energy transfer (FRET)-aided single-molecule counting. miRNAs were selectively labeled with FRET probes using splinted ligation. When imaged with a single-molecule FRET setup, the miRNA molecules were accurately identified by the probe's FRET. miRNA concentrations were estimated from the count of molecules. The high sensitivity of the method in finding sparse molecules enabled us to achieve a limit of detection of 31-56 amol for miR-125b, miR-100, and miR-99a. Single nucleotide mismatch could be discriminated with a very high target-to-mismatch ratio. The method accurately measured the high expression of miR-125b in gastric cancer cells, which agreed well with previous reports. The high sensitivity and accuracy of this technique demonstrated its clinical potential as a robust miRNA detection method.

Ratiometric Fluorescence Detection of Colorectal Cancer-Associated Exosomal miR-92a-3p with DSN-Assisted Signal Amplification by a MWCNTs@Au NCs Nanoplatform

The detection of miRNA shows great promise in disease diagnosis. In this work, a ratiometric fluorescent biosensor based on multi-walled carbon nanotubes@gold nanoclusters (MWCNTs@Au NCs) and duplex-specific nuclease (DSN)-assisted signal amplification was fabricated for miRNA detection. Colorectal cancer (CRC)-associated miR-92a-3p extracted from exosomes was selected as the target. MWCNTs@Au NCs performs the dual functions of fluorescence quencher and internal fluorescence reference. In the absence of miR-92a-3p, an Atto-425-modified single-stranded DNA probe is adsorbed on MWCNTs@Au NCs, resulting in the quenching of Atto-425. In the presence of miR-92a-3p, the duplex is formed by hybridization of the probe and miR-92a-3p and leaves the MWCNTs@Au NCs, resulting in the fluorescence recovery of Atto-425. DSN can cleave the probe and result in the release of miR-92a-3p. The released miR-92a-3p can hybridize with other probes to form a signal amplification cycle. The fluorescence of MWCNTs@Au NCs remains stable and constitutes a ratiometric fluorescence system with that of Atto-425. A detection concentration interval of 0.1–10 pM and a limit of detection of 31 fM was obtained under optimized measurement conditions. In addition, the accuracy of the biosensor was validated by detecting the concentration of miR-92a-3p extracted from clinical exosome samples.