A homogeneous fluorescence sensing platform with water-soluble carbon nanoparticles for detection of microRNA and nuclease activity

Carbon-Based Fluorescent Nano-Biosensors for the Detection of Cell-Free Circulating MicroRNAs

Currently, non-communicable diseases (NCDs) have emerged as potential risks for humans due to adopting a sedentary lifestyle and inaccurate diagnoses. The early detection of NCDs using point-of-care technologies significantly decreases the burden and will be poised to transform clinical intervention and healthcare provision. An imbalance in the levels of circulating cell-free microRNAs (ccf-miRNA) has manifested in NCDs, which are passively released into the bloodstream or actively produced from cells, improving the efficacy of disease screening and providing enormous sensing potential. The effective sensing of ccf-miRNA continues to be a significant technical challenge, even though sophisticated equipment is needed to analyze readouts and expression patterns. Nanomaterials have come to light as a potential solution as they provide significant advantages over other widely used diagnostic techniques to measure miRNAs. Particularly, CNDs-based fluorescence nano-biosensors are of great interest. Owing to the excellent fluorescence characteristics of CNDs, developing such sensors for ccf-microRNAs has been much more accessible. Here, we have critically examined recent advancements in fluorescence-based CNDs biosensors, including tools and techniques used for manufacturing these biosensors. Green synthesis methods for scaling up high-quality, fluorescent CNDs from a natural source are discussed. The various surface modifications that help attach biomolecules to CNDs utilizing covalent conjugation techniques for multiple applications, including self-assembly, sensing, and imaging, are analyzed. The current review will be of particular interest to researchers interested in fluorescence-based biosensors, materials chemistry, nanomedicine, and related fields, as we focus on CNDs-based nano-biosensors for ccf-miRNAs detection applications in the medical field.

An amphiprotic paper-based electrode for glucose detection based on layered carbon nanotubes with silver and polystyrene particles

In this work, a flexible amphiprotic amino-bonded carbon nanotube-Ag nanoparticle/polystyrene (CNT-NH₂-Ag/PS) paper electrode was fabricated to measure glucose in human body fluids by a combination of vacuum filtration and high temperature baking. The front side of the fabricated paper electrode was hydrophobic and conductive, whereas its back side was hydrophilic and nonconductive. In the fabrication process, the coating sequence of CNT-NH₂, Ag and PS was critical to determine the performance of the resulting CNT-NH₂-Ag/PS electrode besides other parameters (e.g., amount of soluble starch, PS and Ag nanoparticles, type and amount of CNT-NH₂, and electrode sensing area). Based on a series of experimental observations, the possible mechanism of glucose detection on the paper electrode was proposed, in which glucose was more favorable to migrate to the hydrophilic back side of the paper and interact with the active species (e.g., O₂^-) on the electrode surface. The electrochemical results showed that the CNT-NH₂-Ag/PS paper electrode maintained stable electrochemical properties even after five cycles of use and 60 days of storage in air. The amphiprotic paper electrode demonstrated excellent sensing performance for glucose with a linear range of 1 μM to 1000 μM, a low detection limit of 0.2 μM, and a sensitivity of 31 333.0 μA mM^-1 cm^-2. The fabricated paper electrode was also successfully applied to detect different levels of glucose in complex human body fluids such as saliva, urine, and serum. These features make this type of paper electrode promising for glucose measurement.

Optical Biosensors for the Detection of Rheumatoid Arthritis (RA) Biomarkers: A Comprehensive Review

A comprehensive review of optical biosensors for the detection of biomarkers associated with rheumatoid arthritis (RA) is presented here, including microRNAs (miRNAs), C-reactive protein (CRP), rheumatoid factor (RF), anti-citrullinated protein antibodies (ACPA), interleukin-6 (IL-6) and histidine, which are biomarkers that enable RA detection and/or monitoring. An overview of the different optical biosensors (based on fluorescence, plasmon resonances, interferometry, surface-enhanced Raman spectroscopy (SERS) among other optical techniques) used to detect these biomarkers is given, describing their performance and main characteristics (limit of detection (LOD) and dynamic range), as well as the connection between the respective biomarker and rheumatoid arthritis. It has been observed that the relationship between the corresponding biomarker and rheumatoid arthritis tends to be obviated most of the time when explaining the mechanism of the optical biosensor, which forces the researcher to look for further information about the biomarker. This review work attempts to establish a clear association between optical sensors and rheumatoid arthritis biomarkers as well as to be an easy-to-use tool for the researchers working in this field.

Polymethacrylate Sphere-Based Assay for Ultrasensitive miRNA Detection

Although microRNAs (miRNAs) have emerged as increasingly important target analytes, their biorecognition remains challenging due to their small size, high sequence homology, and low abundance in clinical samples. Nanospheres and microspheres have also gained increasing attention in biosensor applications due to their high specific surface area and the wide variety of compositions available. In this study, chemically designed and synthesized microspheres with active functional groups were used to promote effective miRNA immobilization resulting in better biorecognition. Upon conjugation with fluorescence-labeled complimentary probes, acylate-based spheres have indirectly detected MiR159, offering significantly enhanced analytical sensitivity, specificity, and accuracy while yielding a considerably low limit of detection (LOD) of 40 picomolar. Furthermore, MiR159 presence, which is known to be inversely correlated to breast cancer incidence and progression, was successfully detected in a competitive assay, which is promising for upgrading the current assay to clinical use.

An allosteric switch-based hairpin for label-free chemiluminescence detection of ribonuclease H activity and inhibitors

To assay enzyme activities and screen its inhibitors, we demonstrated a novel label-free chemiluminescent (CL) aptasensor for the sensitive detection of RNase H activity based on hairpin technology. The specific hairpin structure was a DNA-RNA chimeric strand, which contained a streptavidin aptamer sequence and a blocked RNA sequence. RNase H could specifically recognize and cleave the RNA sequence of the DNA-RNA hybrid stem, liberating the streptavidin aptamer which could be accumulated by streptavidin-coated magnetic microspheres (SA-MP). Then the CL signal was generated due to an instantaneous derivatization reaction between the specific CL reagent 3,4,5-trimethoxyphenyl-glyoxal (TMPG) and the guanine (G) nucleotides in the SA aptamer. This novel assay method exhibited a good linear relationship in the range of 0.1-10 U mL-1 under the optimized conditions. Our results suggested that the developed system was a promising platform for monitoring the RNase H activity and showed great potential in biomedical studies and drug screening.

RNA chaperone assisted intramolecular annealing reaction towards oligouridylated RNA detection in cancer cells

Proximity induced intramolecular nucleotide strand displacement, which can be simply performed in a single tube or in a complex cellular environment, is one of the key mechanisms for the detection of biological targets, especially for significant genetic molecules. The host factor for RNA phage Qb replication (Hfq), with two distinct single stranded RNA binding sites, has excellent properties as an affinity ligand in a proximity induced reaction. In this research, a versatile RNA chaperone-Hfq assisted RNA annealing strategy for the sensitive detection of the intermediate product, oligouridylated RNA, in a genetic regulation process was developed. Benefiting from the high binding affinity of Hfq for the probe and the target, the sensitive determination of oligouridylated RNA in cell lysis and human cervical cancer (HeLa) cells was successfully achieved. This study has also revealed that the Hfq assisted RNA annealing strategy can be further extended and applied in specific microRNA analysis, and RNA related tumorigenicity and disease diagnosis.

Recent advances in nanomaterial-based electrochemical and optical sensing platforms for microRNA assays

This review describes recent efforts in the application of nanomaterials as sensing elements in electrochemical and optical miRNAs assays.

Synchronous sensing of three conserved sequences of Zika virus using a DNAs@MOF hybrid: experimental and molecular simulation studies

A metal–organic framework of Cu(ii) has been prepared and impregnated with three dye-labeled DNA sequences. The hybrid material formed is capable of synchronous detection of three conserved Zika virus RNA sequences.

MnO2 Nanotube-Based NanoSearchlight for Imaging of Multiple MicroRNAs in Live Cells

Sensitive assay and imaging of multiple low-abundance microRNAs (miRNAs) in living cells remain a grand challenge. Herein, based on polyelectrolyte-induced reduction, a facile approach has been proposed to synthesize novel MnO2 nanotubes. Owing to the remarkably strong fluorescence quenching ability, low cytotoxicity, and excellent colloid stability, the as-prepared MnO2 nanotubes showed great potential for simultaneous detection and imaging of multiple miRNAs in vitro and in situ in living cells for the first time. Besides, MnO2 nanotubes can be reduced to Mn2+ by intracellular acid pH or glutathione, which may serve as an activatable contrast reagent for MRI. Therefore, the MnO2 nanotube-based probes, termed "NanoSearchlight", provide a promising, multimodal imaging tool for precise and accurate diagnosis and prognosis of cancers.

Nanotechnology-Enhanced No-Wash Biosensors for in Vitro Diagnostics of Cancer

In vitro biosensors have been an integral component for early diagnosis of cancer in the clinic. Among them, no-wash biosensors, which only depend on the simple mixing of the signal generating probes and the sample solution without additional washing and separation steps, have been found to be particularly attractive. The outstanding advantages of facile, convenient, and rapid response of no-wash biosensors are especially suitable for point-of-care testing (POCT). One fast-growing field of no-wash biosensor design involves the usage of nanomaterials as signal amplification carriers or direct signal generating elements. The analytical capacity of no-wash biosensors with respect to sensitivity or limit of detection, specificity, stability, and multiplexing detection capacity is largely improved because of their large surface area, excellent optical, electrical, catalytic, and magnetic properties. This review provides a comprehensive overview of various nanomaterial-enhanced no-wash biosensing technologies and focuses on the analysis of the underlying mechanism of these technologies applied for the early detection of cancer biomarkers ranging from small molecules to proteins, and even whole cancerous cells. Representative examples are selected to demonstrate the proof-of-concept with promising applications for in vitro diagnostics of cancer. Finally, a brief discussion of common unresolved issues and a perspective outlook on the field are provided.

Aptamer-mediated universal enzyme assay based on target-triggered DNA polymerase activity

We herein describe an innovative method for a universal fluorescence turn-on enzyme assay, which relies on the target enzyme-triggered DNA polymerase activity. In the first target recognition step, the target enzyme is designed to destabilize detection probe derived from an aptamer specific to DNA polymerase containing the overhang sequence and the complementary blocker DNA, which consequently leads to the recovery of DNA polymerase activity inhibited by the detection probe. This target-triggered polymerase activity is monitored in the second signal transduction step based on primer extension reaction coupled with TaqMan probe. Utilizing this design principle, we have successfully detected the activities of two model enzymes, exonuclease I and uracil DNA glycosylase with high sensitivity and selectivity. Since this strategy is composed of separated target recognition and signal transduction modules, it could be universally employed for the sensitive determination of numerous different target enzymes by simply redesigning the overhang sequence of detection probe, while keeping TaqMan probe-based signal transduction module as a universal signaling tool.

Circulating RNAs as new biomarkers for detecting pancreatic cancer

Pancreatic cancer remains difficult to treat and has a high mortality rate. It is difficult to diagnose early, mainly due to the lack of screening imaging modalities and specific biomarkers. Consequently, it is important to develop biomarkers that enable the detection of early stage tumors. Emerging evidence is accumulating that tumor cells release substantial amounts of RNA into the bloodstream that strongly resist RNases in the blood and are present at sufficient levels for quantitative analyses. These circulating RNAs are upregulated in the serum and plasma of cancer patients, including those with pancreatic cancer, compared with healthy controls. The majority of RNA biomarker studies have assessed circulating microRNAs (miRs), which are often tissue-specific. There are few reports of the tumor-specific upregulation of other types of small non-coding RNAs (ncRNAs), such as small nucleolar RNAs and Piwi-interacting RNAs. Long ncRNAs (lncRNAs), such as HOTAIR and MALAT1, in the serum/plasma of pancreatic cancer patients have also been reported as diagnostic and prognostic markers. Among tissue-derived RNAs, some miRs show increased expression even in pre-cancerous tissues, and their expression profiles may allow for the discrimination between a chronic inflammatory state and carcinoma. Additionally, some miRs and lncRNAs have been reported with significant alterations in expression according to disease progression, and they may thus represent potential candidate diagnostic or prognostic biomarkers that may be used to evaluate patients once detection methods in peripheral blood are well established. Furthermore, recent innovations in high-throughput sequencing techniques have enabled the discovery of unannotated tumor-associated ncRNAs and tumor-specific alternative splicing as novel and specific biomarkers of cancers. Although much work is required to clarify the release mechanism, origin of tumor-specific circulating RNAs, and selectivity of carrier complexes, and technical advances must also be achieved, such as creating a consensus normalization protocol for quantitative data analysis, circulating RNAs are largely unexplored and might represent novel clinical biomarkers.

An electrochemiluminescent microRNA biosensor based on hybridization chain reaction coupled with hemin as the signal enhancer

In this study, a new universal biosensor based on luminol anodic electrochemiluminescence (ECL) for the detection of microRNA-155 was constructed by using hydrogen peroxide (H2O2) as a co-reactant and hemin as a catalyzer for signal amplification. The bare glassy carbon electrode (GCE) was first electrodeposited with Au nanoparticles (AuNPs). Then, helper DNA, which was partly complementary with the hairpin DNA chains, was assembled on the prepared GCE. Target microRNA-155 and the hairpin hybridization chains could create a formation of extended double-stranded DNA (dsDNA) polymers through the displacement of hybridization chains and the hybridization chain reaction (HCR). The HCR-generated dsDNA polymers give rise to the intercalation of a lot of hemin which could catalyze the oxidation of H2O2, leading to a remarkably amplified ECL signal output. The proposed biosensor showed a wide linear range from 5 fM to 50 pM with a relatively low detection limit of 1.67 fM for microRNA-155 detection. With excellent selectivity, good stability and high sensitivity, the proposed biosensor is promising in the development of a high-throughput assay of microRNA-155.

Hybrids of Nucleic Acids and Carbon Nanotubes for Nanobiotechnology

Recent progress in the combination of nucleic acids and carbon nanotubes (CNTs) has been briefly reviewed here. Since discovering the hybridization phenomenon of DNA molecules and CNTs in 2003, a large amount of fundamental and applied research has been carried out. Among thousands of papers published since 2003, approximately 240 papers focused on biological applications were selected and categorized based on the types of nucleic acids used, but not the types of CNTs. This survey revealed that the hybridization phenomenon is strongly affected by various factors, such as DNA sequences, and for this reason, fundamental studies on the hybridization phenomenon are important. Additionally, many research groups have proposed numerous practical applications, such as nanobiosensors. The goal of this review is to provide perspective on biological applications using hybrids of nucleic acids and CNTs.

A self-assembling magnetic resonance beacon for the detection of microRNA-1

A self-assembling magnetic resonance beacon was used to visualize the microRNA-1 expression-dependent change in magnetic resonance signal intensity.

Target-responsive DNA/RNA nanomaterials for microRNA sensing and inhibition: the jack-of-all-trades in cancer nanotheranostics?

microRNAs (miRNAs) show high potential for cancer treatment, however one of the most significant bottlenecks in enabling miRNA effect is the need for an efficient vehicle capable of selective targeting to tumor cells without disrupting normal cells. Even more challenging is the ability to detect and silence multiple targets simultaneously with high sensitivity while precluding resistance to the therapeutic agents. Focusing on the pervasive role of miRNAs, herein we review the multiple nanomaterial-based systems that encapsulate DNA/RNA for miRNA sensing and inhibition in cancer therapy. Understanding the potential of miRNA detection and silencing while overcoming existing limitations will be critical to the optimization and clinical utilization of this technology.

Synthesis of polyethyleneimine capped carbon dots for preconcentration and slurry sampling analysis of trace chromium in environmental water samples

Carbon dots capped with polyethyleneimine (CD-PEI) were synthesized and applied in selective separation and preconcentration of trace Cr(VI). Dispersed particle extraction (DPE) slurry sampling with flame atomic absorption spectrometry (FAAS) was used to selectively and sensitively determine Cr(VI) in water samples. The as-synthesized CD-PEI was confirmed by Fourier transform infrared spectroscopy, high-resolution transmission electron microscopy, elemental analysis, fluorescence and zeta potential measurement. The adsorption of Cr(VI) on CD-PEI was evaluated. Its isothermal adsorption was studied and fitted in the Langmuir model. Nearly 85% of Cr(VI) was adsorbed within 10 min showed that the CD-PEI exhibited fairly fast kinetics for the sorption of Cr(VI). Experimental conditions, including the content and size of CD-PEI, sample pH, adsorption time, sample volume, slurry volume and interfering ions, were further optimized to obtain efficient preconcentration and high-precision determination of Cr(VI). CD-PEI with small size turned to be a good candidate for the preparation of slurry. CD-PEI served not only as a promising adsorbent for separation and preconcentration of Cr, but also a signal-enhancing agent in FAAS. The method achieved an enhancement factor of 30 and a detection limit (S/N=3) of 0.21 µg L(-1) Cr(VI) with a consumption of 14.0 mL sample and an adsorption time of 5 min, which provided two times of signal enhancement. The RSD for 11 replicate measurements of 5.0 µg L(-1) Cr(VI) was 2.8%. The possible signal enhancement mechanism was proposed. The developed method has been applied to determine trace Cr(VI) in a variety of water samples.

Nanotechnology-based strategies for the detection and quantification of microRNA

MicroRNAs (miRNAs) are important regulators of gene expression, and many pathological conditions, including cancer, are characterized by altered miRNA expression levels. Therefore, accurate and sensitive quantification of miRNAs may result in correct disease diagnosis establishing these small noncoding RNA transcripts as valuable biomarkers. Aiming at overcoming some limitations of conventional quantification strategies, nanotechnology is currently providing numerous significant alternatives to miRNA sensing. In this review an up-to-date account of nanotechnology-based strategies for miRNA detection and quantification is given. The topics covered are: nanoparticle-based approaches in solution, sensing based on nanostructured surfaces, combined nanoparticle/surface sensing approaches, and single-molecule approaches.

Noninvasive micromarkers

BACKGROUND

The recent revolutionary advances made in genome-wide sequencing technology have transformed biology and molecular diagnostics, allowing new sRNA (small RNA) classes to be discovered as potential disease-specific biological indicators. Cell-free microRNAs (miRNAs) have been shown to exist stably in a wide spectrum of body fluids and their expression profiles have been shown to reflect an assortment of physiological conditions, underscoring the utility of this new class of molecules to function as noninvasive biomarkers of disease.

CONTENT

We summarize information on the known mechanisms of miRNA protection and release into extracellular space and compile the current literature on extracellular miRNAs that have been investigated as biomarkers of 20 different cancers, 11 organ damage conditions and 10 diverse disease states. We also discuss the various strategies involved in the miRNA biomarker discovery workflow and provide a critical opinion on the impediments faced by this advancing field that need to be overcome in the laboratory.

SUMMARY

The field of miRNA-centered diagnostics is still in its infancy, and basic questions with regard to the exact role of miRNAs in the pathophysiology of diseases, and the mechanisms of their release from affected cells into biological fluids are yet to be completely understood. Nevertheless, these noninvasive micromarkers have immense potential in translational medicine not only for use in monitoring the efficacy and safety of therapeutic regimens but also to guide the diagnosis of diseases, to determine the risk of developing diseases or conditions, and more importantly, to inform treatment options.