Microelectrode miRNA sensors enabled by enzymeless electrochemical signal amplification

Ulcerative colitis: clinical biomarkers, therapeutic targets, and emerging treatments

Ulcerative colitis (UC) is one of the two forms of inflammatory bowel disease. It affects 5 million people globally, and is a chronic and recurring inflammation of the gastrointestinal tract with clinical presentation of abdominal pain, chronic diarrhea, rectal bleeding, and weight loss. The cause and the etiology of UC remain poorly understood. There is no cure and no 'gold standard diagnostic' for UC. The existing treatments are ineffective, and UC patients have a lower life expectancy with a risk of colorectal cancer. Recent studies in pathophysiology, clinical presentation, and biomarkers have significantly improved our understanding of UC. In this review we summarize recent advances in identifying novel clinical biomarkers, diagnostics, treatment targets, and emerging therapeutics. These insights are expected to assist in developing effective treatments for UC.

New nanosensor fabricated on single nanopore electrode filled with prussian blue and graphene quantum dots coated by polypyrrole for hydrogen peroxide sensing

Hydrogen peroxide (H2O2) is a common oxidant that plays an important role in many biological processes and is also an important medium analysis in various fields. In this work, a new electrochemical nanosensor capable of detecting and quantifying hydrogen peroxide was introduced. This nanosensor was fabricated by electrodepositing prussian blue (PB)/graphene quantum dots (GQDs)/polypyrrole (PPy) on single nanopore electrode etched from single gold nanoelectrode. This prepapred nanosensor exhibits good electrochemical response to hydrogen peroxide with high sensitivity and stability, with a linear response in the 2.0 and 80 μM by using amperometric method and differential pulse voltammetry (DPV) method. The limit of detections are 0.33 μM (S/N = 3) for amperometric method and 0.67 μM (S/N = 3) for differential pulse voltammetry (DPV) method, respectively. This nanosensor can be used for the determination of hydrogen peroxide in human urine, and can serve as a new electrochemical platform to monitor H2O2 release from single living cells due to its small overal dimension and high sensitivity.

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.

Silver nano-reporter enables simple and ultrasensitive profiling of microRNAs on a nanoflower-like microelectrode array on glass

MicroRNAs (miRNAs) are small non-coding RNAs with ~ 22 nucleotides, playing important roles in the post-transcriptional regulation of gene expression. The expression profiles of many miRNAs are closely related to the occurrence and progression of cancer and can be used as biomarkers for cancer diagnosis and prognosis. However, their intrinsic properties, such as short length, low abundance and high sequence homology, represent great challenges in miRNA detection of clinical samples. To overcome these challenges, we developed a simple, ultrasensitive detection platform of electrochemical miRNAs chip (e-miRchip) with a novel signal amplification strategy using silver nanoparticle reporters (AgNRs) for multiplexed, direct, electronic profiling of miRNAs. A two-step hybridization strategy was used to detect miRNAs, where the target miRNA hybridizes with a stem-loop probe to unlock the probe first, and the opened stem-loop can further hybridize with AgNRs for signaling amplification. To enhance the detection sensitivity, the gold nanoflower electrodes (GNEs) were constructed in the microaperture arrays of the e-miRchips by electroplating. With the optimal size of the GNEs, the e-miRchip showed excellent performance for miR-21 detection with a detection limit of 0.56 fM and a linear range extended from 1 fM to 10 pM. The e-miRchip also exhibited good specificity in differentiating the 3-base mismatched sequences of the target miRNA. In addition, the e-miRchip was able to directly detect miR-21 expression in the total RNA extracts or cell lysates collected from lung cancer cells and normal cells. This work demonstrated the developed e-miRchip as an efficient and promising miniaturized point-of-care diagnostic device for the early diagnosis and prognosis of cancers.

Graphical Abstract

Ultrasenstive SERS biosensor based on Zn2+ from ZnO nanoparticle assisted DNA enzyme amplification for detection of miRNA

In this work, a simple and sensitive SERS biosensor was proposed for ultrasensitive detecting miRNA 122 based on ZnO nanoparticle amplification strategy and the full utilization of DNA chain. Firstly, ZnO@S1/S2 and CoFe₂O₄@S3 complexes can flock together with the assistance of target miRNA. Accompanied with the incremental amount of miRNA, the quantity of ZnO@S1/S2 would increase. Therefore, a significant amplification capability can be obtained by converting ZnO complexes into Zn²⁺ with the assistance of HCl. In this case, the DNA chain S2 can be obtained by the ZnO dissolving. In addition, through a clever design, the obtained Zn²⁺ can be further utilized to induce DNA enzyme cycle amplification to cleave S5 into DNA chain which was similar with DNA S2. This step greatly avoided the waste of DNA chains and improved the utilization efficiency of DNA chains. The S2 and abundant S2 analogues can complement with S4 on the Raman sensing interface to imbed lots of Raman probe DOX for obtaining strong Raman signal. By this way, with the increased number of miRNA, the S2 and abundant S2 analogues would increase, so the amount of DOX would increase to produce strong Raman signal to quantitatively detect target miRNA. As a result, this SERS biosensor based on Zn⁺ amplification and high utilization efficiency of DNA chain can obtain a low detection limit of 6.82 aM and wide linear range from 10 aM to 10 pM, which shown great potential in the clinical application and medical diagnosis.

Wash-Free, Sandwich-Type Protein Detection Using Direct Electron Transfer and Catalytic Signal Amplification of Multiple Redox Labels

Direct electron transfer (DET) between a redox label and an electrode has been used for sensitive and selective sandwich-type detection without a wash step. However, applying DET is still highly challenging in protein detection, and a single redox label per probe is insufficient to obtain a high electrochemical signal. Here, we report a wash-free, sandwich-type detection of thrombin using DET and catalytic signal amplification of multiple redox labels. The detection scheme is based on (i) the redox label-catalyzed oxidation of a reductant, (ii) the conjugation of multiple redox labels per probe using a poly-linker, (iii) the low nonspecific adsorption of the conjugated poly-linker due to uncharged, reduced redox labels, and (iv) a facile DET using long, flexible poly-linker and spacer DNA. Amine-reactive phenazine ethosulfate and NADH were used as the redox label and reductant, respectively. N₃-terminated polylysine was used as the poly-linker for the conjugation between an aptamer probe and multiple redox labels. Approximately 11 redox labels per probe and rapid catalytic NADH oxidation enable high signal amplification. Thrombin in urine could be detected without a wash step with a detection limit of ∼50 pM, which is practically promising for point-of-care testing of proteins.

Gold dispersed hierarchical flower-like copper oxide microelectrodes for the sensitive detection of glucose and lactic acid in human serum and urine

Herein, we report self-supported gold dispersed copper oxide microflowers (Au@CuO MFs) on copper microelectrodes (CME) as a sensitive platform for the sensing of glucose and lactic acid in human serum...

Electrochemical Beacon Method to Quantify 10 Attomolar Nucleic Acids with a Semilog Dynamic Range of 7 Orders of Magnitude

Change in the dynamics of single-stranded DNA or RNA probes tethered to an Au electrode on immunospecific binding to the analyte is a versatile approach to quantify a variety of molecules, such as heavy metal ions, pesticides, proteins, and nucleic acids (NAs). A widely studied approach is the electrochemical beacon method where the redox of a dye attached to the probe decreases as its proximity to the underlying electrode changes on binding. The limit of quantification (LOQ) defined by the semilog dependence of the signal on target concentration is in the picomolar range. Here, a method was studied where, by differential reflectivity, multiple reactions were measured on a monolith electrode. An alternative contrast mechanism was discovered, which led to an approach to enhance the LOQ to 10 aM and increase the dynamic range to 7 orders of magnitude using similar probes and binding conditions. Quantitative analysis on sequences with the G-C fraction ranging from 37 to 72% was performed. The approach will allow for the development of a label-free, enzyme-free microarray to detect biomolecules including NAs and proteins on a single electrode at quantification from 10 aM to 0.1 nM with high specificity.

Cross-triggered and cascaded recycling amplification system for electrochemical detection of circulating microRNA in human serum

A cross-triggered and cascaded recycling amplification system was developed for electrochemical sensing of microRNA 122 based on the DNAzyme/multicomponent nucleic acid enzyme cleavage technique and a dumbbell-shaped probe. The linear range and detection limit were obtained to be 1 fM-100 pM and 0.34 fM, respectively. Compared with some reported studies, the proposed system can achieve the selective detection of endogenous miRNA in liver injury patients and healthy human serums with the advantages of high sensitivity, low cost, and easy manipulation, which are significant for disease diagnosis as well as the fundamental research of molecular biology.

Dual-signaling amplification strategy for glutathione sensing by using single gold nanoelectrodes

A new nanosensor for glutathione (GSH) detection by use of single nanoelectrodes has been developed through a dual-signaling ratiometric amplification strategy. Ag nanoparticles (Ag NPs) metalized DNA1 was modified on an Au nanoelectrode surface. Due to the strong affinity between Ag NP and GSH, Ag NPs could be removed by the addition of GSH. The remaining metalized DNA1 could hardly form a double strand, while the de-metalized DNA1 could hybrid with DNA2 and DNA3 to form a complex structure to adsorb methylene blue (MB), and then the electrochemical signal of differential pulse voltammetry (DPV) from MB oxidation could be observed. With the addition of GSH, the peak current of MB oxidation at about -0.27 V (I_MB) increases, while the signal of Ag oxidation at about 0.1 V (I_Ag) decreases. It was found that there had a linear relationship between the ratio of dual-signal (I_MB/I_Ag) and the GSH concentrations, which could be used to detect GSH. The ratiometric nanosensor is label-free, easy to operate, and can eliminate inherent system errors. Considering the advantages of nanoelectrodes, such as low IR drop, fast response, and small overall dimension, this developed nanosensor can be used for GSH detection living systems (e.g., cell lysate).

Strategies for Biomolecular Analysis and Continuous Physiological Monitoring

Portable devices capable of rapid disease detection and health monitoring are crucial to decentralizing diagnostics from clinical laboratories to the patient point-of-need. Although technologies have been developed targeting this challenge, many require the use of reporter molecules or reagents that complicate the automation and autonomy of sensors. New work in the field has targeted reagentless approaches to enable breakthroughs that will allow personalized monitoring of a wide range of biomarkers on demand. This Perspective focuses on the ability of reagentless platforms to revolutionize the field of sensing by allowing rapid and real-time analysis in resource-poor settings. First, we will highlight advantages of reagentless sensing techniques, specifically electrochemical detection strategies. Advances in this field, including the development of wearable and in situ sensors capable of real-time monitoring of biomarkers such as nucleic acids, proteins, viral particles, bacteria, therapeutic agents, and metabolites, will be discussed. Reagentless platforms which allow for wash-free, calibration free-detection with increased dynamic range are highlighted as a key technological advance for autonomous sensing applications. Furthermore, we will highlight remaining challenges which must be overcome to enable widespread use of reagentless devices. Finally, future prospects and potential breakthroughs in precision medicine that will arise as a result of further development of reagentless sensing approaches are discussed.

DNA Nanosieve-Based Regenerative Electrochemical Biosensor Utilizing Nucleic Acid Flexibility for Accurate Allele Typing in Clinical Samples

Herein, an interface-based DNA nanosieve that has the ability to differentiate ssDNA from dsDNA has been demonstrated for the first time. The DNA nanosieve could be readily built through thiol-DNA's self-assembly on the gold electrode surface, and its cavity size was tunable by varying the concentration of thiol-DNAs. Electrochemical chronocoulometry using [Ru(NH₃)₆]³⁺ as redox revealed that the average probe-to-probe separation in the 1 μM thiol-DNA-modified gold electrode was 10.6 ± 0.3 nm so that the rigid dsDNA with a length of ∼17 nm could not permeate the nanosieve, whereas the randomly coiled ssDNA could enter it due to its high flexibility, which has been demonstrated by square wave voltammetry and methylene blue labels through an upside-down hybridization format. After combining the transiently binding characteristic of a short DNA duplex and introducing a regenerative probe (the counterpart of ssDNA), a highly reproducible nanosieve-based E-DNA model was obtained with a relative standard deviation (RSD) as low as 2.7% over seven cycles. Finally, we built a regenerative nanosieve-based E-DNA sensor using a ligation cycle reaction as an ssDNA amplification strategy and realized one-sensor-based continuous measurement to multiple clinical samples with excellent allele-typing performance. This work holds great potential in low-cost and high-throughput analysis between biosensors and biochips and also opens up a new avenue in nucleic acid flexibility-based DNA materials for future applications in DNA origami and molecular logic gates.

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.

Multiplexed and single-cell detection of microRNA with plasmonic nanoparticle assemblies

We present a label-free, low cost, and miniatured biosensing platform based on the disassembly of core-satellite plasmonic nanoparticle assemblies. The rapid and selective detection of an exemplary nucleic acid biomarker, has-miRNA-210-3p, was achieved via the strand displacement nucleic acid reaction. Target binding leads to dehybridization of the DNA linkers and changes in the scattering properties of nanostructures as monitored by darkfield microscopy. We demonstrate the ability to detect microRNA expunged from single cells and the potential to multiplex discrete assemblies to enable diverse biological applicability. The work may help translate the applicability of microRNA as diagnostic biomarkers, quantitate their abundance in the microenvironment, and facilitate the study of their correlation or causation to other biomolecules at the single-cell level.

Paper-Based Microfluidic Sensors for Onsite Environmental Detection: A Critical Review

A newly developed research topic, fabricated paper-based microfluidic sensors, was discussed in the field of low-cost environmental detection. Distinguished with the traditional dipstick or lateral-flow setups, these paper-based microfluidic sensors can serve as a tool for onsite quantitative and semi-quantitative measurements, without risks to cause environmental pollution. They have attracted increasing interest since the first easy-fabricated paper-based setup reported by Whitesides group in 2007. Most of the publications utilized paper-based sensors in clinical detection. In recent years, some groups started to use these sensors in environmental measurement, leading to precise, easy operation, low-cost, and eco-friendly methods for onsite detection. In this review, paper-based microfluidic sensors were briefly introduced, followed by literatures review and discussion for future perspectives.

Single gold nanoclusters: Formation and sensing application for isonicotinic acid hydrazide detection

Nano-sized electrodes have their special advantages for sensing applications, such as small overall dimension, fast response and low background current. In this work, single gold nanoclusters (AuNCs) were controllably prepared on single Pt nanoelectrode surface by electrodeposition method. The AuNCs covered Pt nanoelectrode (AuNCs/PtNE) had steady-state voltammetric response in redox species solution, which was similar to micro-/nano-sized electrodes. It was interesting to find isonicotinic acid hydrazide (INH, also known as isoniazid) showed good electrochemical response on AuNCs/PtNE surface, which had investigated carefully by square wave voltammetry (SWV) and chronoamperometry. Moreover, the prepared single AuNCs/PtNEs showed the capability for INH sensing with good sensitivity, reproducibility and selectivity, which was demonstrated for INH detection in human urine samples.

Electrochemical Biosensors for Detection of MicroRNA as a Cancer Biomarker: Pros and Cons

Cancer is the second most fatal disease in the world and an early diagnosis is important for a successful treatment. Thus, it is necessary to develop fast, sensitive, simple, and inexpensive analytical tools for cancer biomarker detection. MicroRNA (miRNA) is an RNA cancer biomarker where the expression level in body fluid is strongly correlated to cancer. Various biosensors involving the detection of miRNA for cancer diagnosis were developed. The present review offers a comprehensive overview of the recent developments in electrochemical biosensor for miRNA cancer marker detection from 2015 to 2020. The review focuses on the approaches to direct miRNA detection based on the electrochemical signal. It includes a RedOx-labeled probe with different designs, RedOx DNA-intercalating agents, various kinds of RedOx catalysts used to produce a signal response, and finally a free RedOx indicator. Furthermore, the advantages and drawbacks of these approaches are highlighted.

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.

Electrochemical nano-genosensor for highly sensitive detection of miR-21 biomarker based on SWCNT-grafted dendritic Au nanostructure for early detection of prostate cancer

MicroRNAs (miRNAs) appear as a novel reliable candidate in biomarkers for early diagnosis of cancer. Due to their roles in various types of cancer, their potential as a diagnostic biomarker is getting more attention. Here, a novel electrochemical biosensor for detection of miR-21 was demonstrated, through combining the advantages of electrochemical methods and nanomaterials with the selectivity of oligonucleotides, based on thiolated receptor probe-functionalized dendritic gold nanostructures (den-Au) via the self-assembly monolayer (SAM) process which grafted on the single-wall carbon nanotubes (SWCNTs) platform on the surface of the fluorine-doped tin oxide (FTO) electrode. Cadmium ions (Cd²⁺) were used as signal units and also signal amplification substance which labeled before on miR-21 target. The oxidation signal of Cd²⁺ as a signal unit was measured by differential pulse voltammetry (DPV) technique that had a very wide linear relationship with the concentration of miR-21 target (0.01 fmol L^-1 to 1 μmol L^-1) and low experimental detection limit of 0.01 fmol L^-1. Furthermore, fabricated biosensor showed acceptable performance in human serum samples and also good selectivity indiscriminate between the complementary target and non-complementary one, so this nano-genosensor can clinically be used for prostate cancer diagnosis through the detection of miR-21 in human serum samples.

Gold Nanoparticles-Based Multipedal DNA Walker for Ratiometric Detection of Circulating Tumor Cell

Sensitive and accurate quantification of circulating tumor cell (CTC) can provide new insights for early diagnosis and prognosis of cancers. Herein, we have developed a multipedal DNA walker for ultrasensitive detection of CTC for the first time. Generally, a number of walker strands are simply modified on gold nanoparticle (AuNPs). The integrated aptamer sequence can specially interact with the transmembrane receptor protein of CTC and facilitate the enrichment of AuNPs on the surface of cells. After a low speed centrifugation, the complex of CTC and AuNPs could be precipitated and the supernate represents decreased UV-vis absorbance response of AuNPs. On the other hand, since multiple walker strands are modified on a single AuNP, hybridization with several tracks on the electrode occurs simultaneously for the following nicking endonuclease-catalyzed cleaving. Experimental results verify that the rate of multipedal walking is much faster. In addition, TCEP-mediated electrochemical amplification is employed to further enhance the electrochemical signal. By comparing the variations of electrochemical and UV-vis absorbance responses, ultrahigh sensitivity for CTC assay is achieved. The limit of detection is down to 1 cell/mL. The results of selectivity confirmation and blood sample test are also satisfactory. This AuNPs-based multipedal DNA walker offers a speedy analysis of CTC and shows great potential use for early clinical diagnosis and treatment of cancers.

Ultrasensitive detection of miRNA via one-step rolling circle-quantitative PCR (RC-qPCR)

A novel microRNA (miRNA) quantification method has been developed using one-step rolling circle-quantitative PCR (RC-qPCR) analysis. Vent (exo-) DNA polymerase is firstly utilized to combine a rolling circle amplification (RCA) and qPCR in one step with high sensitivity and specificity in our RC-qPCR assay. Before performing the RC-qPCR, a padlock probe is ligated only when it is perfectly hybridized with miRNA. This ligation-based miRNA assay is highly specific for mature miRNAs, discriminating among related miRNAs that differ by as little as one nucleotide. It exhibits a dynamic range of seven orders of magnitude with a detection limit of 500 aM, and could be also used for the quantification of other small RNA molecules such as short interfering RNAs (siRNAs).

Amperometric sensing of hydrazine by using single gold nanopore electrodes filled with Prussian Blue and coated with polypyrrole and carbon dots

A nanoprobe for hydrazine sensing is described that is making use of a single gold nanopore electrode (SAuNPEs) that was modified by electro-deposition of Prussian Blue (PB) and then coated with a thin membrane of polypyrrole and carbon dots in order to enhance stability and catalytic activity. Best operated at a low potential of 0.3 V vs. Ag/AgCl, the nanosensor display good electrocatalytic activity towards the oxidation of hydrazine, with a linear response in the 0.5-80 μM hydrazine concentration range and a 0.18 μM detection limit (at S/N = 3). The method was applied to the determination of hydrazine in human urine. Graphical abstract Schematic presentation of the electrocatalytic oxidation of hydrazine using a single gold nanopore electrode that was modified by electro-deposition of Prussian Blue and then coated with a thin membrane of polypyrrole and carbon dots.

A signal amplification strategy and sensing application using single gold nanoelectrodes

In this work, a label-free electrochemical apta-nanosensor was fabricated on a single gold nanodisk electrode (AuNDE) for thrombin sensing with high sensitivity via a novel signal amplification strategy. This recognition platform was fabricated via self-assembly of helper DNA (HP-DNA), thrombin-binding aptamer (TBA) and gold nanoparticle (AuNP)-DNA complexes to form a sandwich structure on the AuNDE surface. A novel signal amplification strategy via designed AuNP-DNA complexes was introduced using Ru(NH3)63+ as the signal reporter based on the electrostatic interaction. In the presence of thrombin, the strong interaction between the TBA and target led to the dissociation of sandwich DNA complexes from the AuNDE, which resulted in the reduction current of Ru(NH3)63+. This proposed sensing platform showed a wide detection range of 0.1 pM-5 nM and a low detection limit of 0.02 pM. Considering the small overall dimensions and high sensitivity, this nanosensor can be potentially applied for bioanalysis in living biosystems.

A novel ratiometric SERS biosensor with one Raman probe for ultrasensitive microRNA detection based on DNA hydrogel amplification

A ratiometric SERS biosensor with DNA hydrogel-captured glucose oxidase amplification method was fabricated to detect microRNA 122.

Sandwich DNA Hybridization Fluorescence Resonance Energy-Transfer Strategy for miR-122 Detection by Core-Shell Upconversion Nanoparticles

An upconversion nanoparticle (UCNP)-based fluorescence resonance energy-transfer (FRET) strategy is normally restricted by the complicated preparations, low energy-transfer efficiency, and the challenge on improving specificity. Herein, simple DNA-functionalized UCNPs were designed as energy donors for constructing a FRET-based probe to detect the liver-specific microRNA 122 (miR-122). To improve FRET efficiency, UCNPs were constructed with confined core-shell structures, in which emitting ions were precisely located in the thin shell to make them close enough to external energy acceptors. Subsequently, capture DNA was simply functionalized on the outer surface of UCNPs based on ligand exchange that contributed to shortening the energy-transfer distance without extra modification. To gain high specificity, the donor-to-acceptor distance of FRET was controlled by a sandwich DNA hybridization structure using two shorter DNAs with designed complementary sequences (capture DNA and dye-labeled report DNA) to capture the longer target of miR-122. Therefore, the sensitive detection of miR-122 was achieved based on the decreased signals of UCNPs and the increased signals of the dye labeled on reported DNA. With good biocompatibility, this method has been further applied to cancer cell imaging and in vivo imaging, which opened up a new avenue to the sensitive detection and imaging of microRNA in biological systems.

Ratiometric electrochemical assay for sensitive detecting microRNA based on dual-amplification mechanism of duplex-specific nuclease and hybridization chain reaction

We propose a ratiometric electrochemical assay for detecting microRNA (miRNA) on the basis of dual-amplification mechanism by using distinguishable electrochemical signals from thionine (Thi) and ferrocene (Fc). The thiol-modified and ferrocene-labeled hairpin capture probes (CP) are first immobilized on an Au electrode via Au-S reaction. The target miRNA hybridizes with CP and unfolding the hairpin structure of CP to form miRNA-DNA duplexes. Then, kamchatka crab duplex specific nuclease (DSN) specifically cleaves the DNA in miRNA-DNA duplexes, leading to the release of miRNA and another cleaves cycle, meanwhile, numerous Fc leaves away from the electrode surface and leads to the signal-off of Fc. The residual fragment on electrode surface acts as a HCR primer to form dsDNA polymers through in situ HCR with the presence of the primer and two probes (HDNA and HDNA'), resulting in the capture of numerous DNA/Au NPs/Thi and the signal-on of Thi. The dual-amplification mechanism significantly amplifies the decrease of Fc signal and the increase of Thi signal for ratiometric readout (I_Thi/I_Fc), thus providing a sensitive method for the selective detection of miR-141 with a detection limit down to 11aM. The dual-signal ratiometric outputs have an intrinsic self-calibration to the effects from system, which is promising to be applied in biosensing and clinical diagnosis.

A reusable ratiometric electrochemical biosensor on the basis of the binding of methylene blue to DNA with alternating AT base sequence for sensitive detection of adenosine

We develop a reusable ratiometric electrochemical biosensor on the basis of the binding of methylene blue (MB) to DNA with alternating AT base sequence for sensitive detection of adenosine. We design a strand 1 with MB-modified thymine (T) base in the proximal 3' termini as the capture probe for its immobilization on the gold electrode and a 3' termini ferrocene (Fc)-modified aptamer for the recognition of adenosine. The hybridization of strand 1 with the aptamer leads to the formation of a double-stranded DNA (dsDNA) and consequently the away of MB from the electrode surface and the close of Fc to the electrode surface, generating a small value of I_MB/I_Fc (I_MB and I_Fc are the peak currents of MB and Fc, respectively). In the presence of adenosine, its binding with the aptamer induces the release of Fc from the electrode surface and the close of MB to the electrode surface, generating a large value of I_MB/I_Fc. As a result, adenosine may be accurately quantified by the measurement of ratiometric signal (I_MB/I_Fc). This ratiometric electrochemical biosensor can be simply fabricated and exhibits high sensitivity with a limit of detection of as low as 90.8pM and a large dynamic range from 0.1nM to 100μM. Moreover, this biosensor demonstrates good performance with excellent selectivity, regeneration capability, high reliability and good reproducibility, and may become a universal platform for the detection of various biomolecules which can be recognized by aptamers, holding great potential for further applications in biomedical research and clinical diagnosis.

Multiplexed Electrochemical Detection of MiRNAs from Sera of Glioma Patients at Different Stages via the Novel Conjugates of Conducting Magnetic Microbeads and Diblock Oligonucleotide-Modified Gold Nanoparticles

MicroRNAs (miRNAs) serve as diagnostic and prognostic biomarkers for a wide variety of cancers. Via the novel conjugates of gold nanoparticle-coated magnetic microbeads (AuNP-MMBs) and the diblock oligonucleotide (ODN)-modified AuNPs, multiplexed electrochemical assay of miRNAs was performed. The hybridization to target miRNAs leads to the conformational change of the hairpin-structured ODN probes, and the attachment of the diblock ODN-modified AuNPs was achieved. By examining the oxidation peak currents of methylene blue (MB) and ferrocene (Fc) moieties residing on the diblock ODNs, simultaneous quantification of miRNA-182 and miRNA-381 was conducted. The detection signals were significantly enhanced due to the numerous MB and Fc tags on the AuNPs. The proposed assay was highly selective for discriminating miRNAs with similar sequences, and detection limits of 0.20 fM and 0.12 fM for miRNA-182 and miRNA-381, respectively, were achieved. The feasibility of the method for sensitive determination of miRNA-182 and miRNA-381 from serum samples of glioma patients at different stages was demonstrated. The sensing protocol thus holds great potential for early diagnosis and treatment of cancer patients.

Electrochemical aptamer-based nanosensor fabricated on single Au nanowire electrodes for adenosine triphosphate assay

In this work, single Au nanowire electrodes (AuNWEs) were fabricated by laser-assisted pulling/hydrofluoric acid (HF) etching process, which then were characterized by transmission electron microscopy (TEM), electrochemical method and finite-element simulation. The as-prepared single AuNWEs were used to construct electrochemical aptamer-based nanosensors (E-AB nanosensors) based on the formation of Au-S bond that duplex DNA tagged with methylene blue (MB) was modified on the surface of electrode. In the presence of adenosine triphosphate (ATP), the MB-labeled aptamer dissociated from the duplex DNA due to the strong specific affinity between aptamer and target, which lead to the reduction of MB electrochemical signals. Moreover, BSA was employed to further passivate electrode surface bonding sites for the stable of the sensor. The as-prepared E-AB nanosensor has been used for ATP assay with excellent sensitivity and selectivity, even in a complex system like cerebrospinal fluid of rat brain. Considering the unique properties of good stability, larger surface area and smaller overall dimensions, this E-AB nanosensor should be an ideal platform for widely sensing applications in living bio-system.

Isothermal amplification detection of miRNA based on the catalysis of nucleases and voltammetric characteristics of silver nanoparticles

MiRNAs are a fascinating kind of biomolecule due to their vital functions in gene regulation and potential value as biomarkers for serious diseases including cancers. Exploiting convenient and sensitive methods for miRNA expression assays is imperative. In this study, we employ an exonuclease (RecJ_f) and a nicking endonuclease (Nt.BbvCI) to catalyse isothermal reactions for the amplified detection of miRNA. The degree of cyclical enzymatic amplification depends on the initial target miRNA level, which can determine the density of DNA probes bound on the electrode surface. Since DNA probes with an amino group at the 3' end are able to locate silver nanoparticles on the electrode, which provide intense stripping responses, the sensitive quantification of miRNA can be achieved. The proposed method has a limit of detection as low as 35 aM, with remarkable specificity, which offers a new approach for investigating miRNA networks and for clinical diagnosis applications.

A Quasi-direct LC-MS/MS-based Targeted Proteomics Approach for miRNA Quantification via a Covalently Immobilized DNA-peptide Probe

MicroRNAs (miRNAs) play a vital role in regulating gene expression and are associated with a variety of cancers, including breast cancer. Their distorted and unique expression is a potential marker in clinical diagnoses and prognoses. Thus, accurate determination of miRNA expression levels is a prerequisite for their applications. However, the assays currently available for miRNA detection typically require pre-enrichment, amplification and labeling steps, and most of the assays are only semi-quantitative. Therefore, we developed a quasi-direct liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based targeted proteomics approach to quantify target miRNA by innovatively converting the miRNA signal into the mass response of a reporter peptide via a covalently immobilized DNA-peptide probe. Specifically, the probe containing the targeted proteomics-selected substrate/reporter peptide, GDRAVQLGVDPFR/AVQLGVDPFR, and the DNA sequence complementary to the target miRNA (i.e., miR-21) was first immobilized on APMTS modified silica nanoparticles using PDITC. After the immobilized probe was recognized and hybridized with the target miRNA, the excess probe was degraded using MBN and followed by a trypsin digestion of the hybrids. The reporter peptide was released and quantified using LC-MS/MS. The obtained LOQ was 5 pM. Finally, the developed assay was used for the quantitative analysis of miR-21 in breast cells and tissue samples.

A Combination of DNA-peptide Probes and Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS): A Quasi-Targeted Proteomics Approach for Multiplexed MicroRNA Quantification

The distorted and unique expression of microRNAs (miRNAs) in cancer makes them an attractive source of biomarker. There is much evidence indicating that a panel of miRNAs, termed "miRNA fingerprints", is more specific and informative than an individual miRNA as biomarker. Thus, multiplex assays for simultaneous quantification of multiple miRNAs could be more potent in clinical practice. However, current available assays normally require pre-enrichment, amplification and labeling steps, and most of them are semi-quantitative or lack of multiplexing capability. In this study, we developed a quasi-targeted proteomics assay for multiplexed miRNA quantification by a combination of DNA-peptide probes and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Specifically, the signal of target miRNAs (i.e., miR-21, miR-let7a, miR-200c, miR-125a and miR-15b) was converted into the mass response of reporter peptides by hybridization of miRNAs with DNA-peptide probes and subsequent tryptic digestion to release the peptides. After a careful optimization of conditions related to binding, conjugation, hybridization and multiple reaction monitoring (MRM) detection, the assay was validated for each miRNA and the limit of quantification (LOQ) for all the miRNAs can achieve 1 pM. Moreover, crosstalk between DNA-peptide probes in multiplex assay was sophisticatedly evaluated. Using this quasi-targeted proteomics assay, the level of target miRNAs was determined in 3 human breast cell lines and 36 matched pairs of breast tissue samples. Finally, simplex assay and qRT-PCR were also performed for a comparison. This approach grafts the strategy of targeted proteomics into miRNA quantification and may offer a new way for multiplexed miRNA profiling.

Serum miRNA signature diagnoses and discriminates murine colitis subtypes and predicts ulcerative colitis in humans

Inflammatory bowel disease (IBD) is difficult to diagnose due to nonspecific and variable symptoms, and lack of reliable diagnostic tests. Current methods are invasive, non-sensitive, non-predictive, and do not easily discriminate between its two main forms. Consequently, there remains a great need for reliable serum markers for IBD. Here, using a longitudinal study of various mouse models of colitis, we identified a serum miRNA signature that indicated the development of colitis and discriminated between inflammations of various origins (colitis from arthritis). Unlike the existing biomarkers, the newly identified signature also serves to distinguish individuals at risk, predict the type of inflammation, and evaluate the response to therapeutics. Moreover, the miRNA signature identified in mice predicted ulcerative colitis with 83.3% accuracy. In future, the signature identified herein could play a central role in monitoring inflammatory disorders and therapeutic responses in patients, thereby paving the way for personalized medicine.

miRNA assays in the clinical laboratory: workflow, detection technologies and automation aspects

microRNAs (miRNAs) are short non-coding RNA molecules that regulate gene expression in eukaryotes. Their differential abundance is indicative or even causative for a variety of pathological processes including cancer or cardiovascular disorders. Due to their important biological function, miRNAs represent a promising class of novel biomarkers that may be used to diagnose life-threatening diseases, and to monitor disease progression. Further, they may guide treatment selection or dosage of drugs. miRNAs from blood or derived fractions are particularly interesting candidates for routine laboratory applications, as they can be measured in most clinical laboratories already today. This assures a good accessibility of respective tests. Albeit their great potential, miRNA-based diagnostic tests have not made their way yet into the clinical routine, and hence no standardized workflows have been established to measure miRNAs for patients' benefit. In this review we summarize the detection technologies and workflow options that exist to measure miRNAs, and we describe the advantages and disadvantages of each of these options. Moreover, we also provide a perspective on data analysis aspects that are vital for translation of raw data into actionable diagnostic test results.

Integrating optical tweezers with up-converting luminescence: a non-amplification analytical platform for quantitative detection of microRNA-21 sequences

We report a single-microsphere based imaging assay for detecting microRNA-21 sequences with a detection limit of 12 fM.

MiRNA Quantitation with Microelectrode Sensors Enabled by Enzymeless Electrochemical Signal Amplification

Quantification of circulating microRNAs (miRNAs) is of great interest because of their potentials as disease biomarkers. Currently, quantitative reverse transcription polymerase chain reaction (qRT-PCR) and microarray are considered mainstream techniques for miRNA identification and quantitation. However, these 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 a triple-stem DNA-redox probe structure on a gold microelectrode and introducing a reductant, tris(2-carboxyethyl) phosphine hydrochloride (TCEP) in the detection buffer solution to achieve ultrasensitive miRNAs detection with a detection limit of 0.1 fM.