Molecular beacon structure mediated rolling circle amplification for ultrasensitive electrochemical detection of microRNA based on quantum dots tagging

Electrochemical biosensors for analysis of DNA point mutations in cancer research

Cancer is a genetic disease induced by mutations in DNA, in particular point mutations in important driver genes that lead to protein malfunctioning and ultimately to tumorigenesis. Screening for the most common DNA point mutations, especially in such genes as TP53, BRCA1 and BRCA2, EGFR, KRAS, or BRAF, is crucial to determine predisposition risk for cancer or to predict response to therapy. In this review, we briefly depict how these genes are involved in cancer, followed by a description of the most common techniques routinely applied for their analysis, including high-throughput next-generation sequencing technology and less expensive low-throughput options, such as real-time PCR, restriction fragment length polymorphism, or high resolution melting analysis. We then introduce benefits of electrochemical biosensors as interesting alternatives to the standard methods in terms of cost, speed, and simplicity. We describe most common strategies involved in electrochemical biosensing of point mutations, relying mostly on PCR or isothermal amplification techniques, and critically discuss major challenges and obstacles that, until now, prevented their more widespread application in clinical settings.

Rolling Circle Amplification-based Copper Nanoparticle Synthesis on Cyclic Olefin Copolymer Substrate and Its Application in Aptasensor

This study aimed to develop a label-free fluorescent aptasensor for the detection of diazinon (DZN) on a cyclic olefin copolymer (COC) substrate. The aptasensor design was based on rolling circle amplification (RCA) technology and the use of self-assembled copper nanoparticles (CuNPs). A dual-function (DF) probe, capable of binding to circular DNA and an aptamer, was designed and immobilized on a COC-bottom 96-well plate. An aptamer was used for selective recognition of DZN, and the specific site of the aptamer that strongly reacted with DZN was successfully identified using circular dichroism (CD) analysis. In presence of DZN, the aptamer and DZN formed a strong complex, thus providing an opportunity for hybridization of the DF probe and circular DNA, thereby initiating an RCA reaction. Repetitive poly thymine (T) sequence with a length of 30-mer, generated in the RCA reaction, served as a template for the synthesis of fluorescent copper nanoparticles, emitting an orange fluorescence signal (at approximately 620 nm) proportional to the amount of RCA product, within 10 min under UV irradiation. The CuNP fluorescence was imaged and quantified using an image analysis software. A linear correlation of the fluorescence signal was confirmed in the DZN concentration range of 0.1–3 ppm, with a detection limit of 0.15 ppm. Adoption of a label-free detection method, utilizing RCA and fluorescent CuNPs on COC substrates, reduced the need for complex equipment and requirements for DZN analysis, thereby representing a simple and rapid sensing method circumventing the limitations of current complex and labor-intensive methods.

Nucleic acid-based electrochemical biosensor: Recent advances in probe immobilization and signal amplification strategies

With the increasing importance of accurate and early disease diagnosis and the development of personalized medicine, DNA-based electrochemical biosensor has attracted broad scientific and clinical interests in the past decades due to its unique hybridization specificity, fast response time, and potential for miniaturization. In order to achieve high detection sensitivity, the design of DNA electrochemical biosensors depends critically on the improvement of the accessibility of target molecules and the enhancement of signal readout. Here, we summarize the recent advances in DNA probe immobilization and signal amplification strategies with a special focus on DNA nanostructure-supported DNA probe immobilization method, which provides the opportunity to rationally control the distance between probes and keep them in upright confirmation, as well as the contribution of functional nanomaterials in enhancing the signal amplification. The next challenge of biosensors will be the fabrication of point-of-care devices for clinical testing. The advancement of multidisciplinary areas, including nanofabrication, material science, and biochemistry, has exhibited profound promise in achieving such portable sensing devices. This article is categorized under: Diagnostic Tools > Biosensing Diagnostic Tools > Diagnostic Nanodevices Biology-Inspired Nanomaterials > Nucleic Acid-Based Structures.

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.

Physical and chemical template-blocking strategies in the exponential amplification reaction of circulating microRNAs

The detection of circulating miRNA through isothermal amplification wields many attractive advantages over traditional methods, such as reverse transcription RT-qPCR. However, it is challenging to control the background signal produced in the absence of target, which severely hampers applications of such methods for detecting low abundance targets in complex biological samples. In the present work, we employed both the cobalt oxyhydroxide (CoOOH) nanoflakes and the chemical modification of hexanediol to block non-specific template elongation in exponential amplification reaction (EXPAR). Adsorption by the CoOOH nanoflakes and the hexanediol modification at the 3' end effectively prevented no-target polymerization on the template itself and thus greatly improved the performance of EXPAR, detecting as low as 10 aM of several miRNA targets, including miR-16, miR-21, and miR-122, with the fluorescent DNA staining dye of SYBR Gold™. Little to no cross-reactivity was observed from the interfering strands present in 10-fold excess. Besides contributing to background reduction, the CoOOH nanoflakes strongly adsorbed nucleic acids and isolated them from a complex sample matrix, thus permitting successful detection of the target miRNA in the serum. We expect that simple but sensitive template-blocking EXPAR could be a valuable tool to help with the discovery and validation of miRNA markers in biospecimens. Graphical abstract.

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.

A carbon dot and molecular beacon based fluorometric sensor for the cancer marker microRNA-21

A carbon quantum dot (CQD) labeled molecular beacon was synthesized and applied to the detection of microRNA-21. The CQDs possess low cytotoxicity, excellent water solubility, and photostability. The CQDs were characterized by transmission electron microscopy, dynamic light scattering, Fourier-transform infrared spectroscopy, and fluorescence spectroscopy. The molecular beacon (MB) was labeled with the CQDs at the 5' end, and with Black Hole Quencher 1 (BHQ1) at the 3' end. The two labels act as the donor and acceptor parts of a FRET system, respectively. Only weak fluorescence is observed in the absence of microRNA-21, and in the presence of scrambled or mismatched sequences. However, in the presence of microRNA-21, fluorescence intensity of the CQDs at 460 nm (excitation at 360 nm) recovers. The hybridization of the hairpin structure of the MB with microRNA-21 opens the loop of MB. Consequently, the distance between the BHQ1 quencher and the CQDs is increased and fluorescence changes. The probe has high sensitivity (with a 0.3 nM limit of detection) and specificity. It can distinguish between microRNA-21 and its single mismatch mutant and hence represents a valuable tool for the early cancer diagnosis. Graphical abstract Schematic presentation of a fluorometric microR-21 assay using carbon dots carrying a molecular beacon (MB) labeled with a black hole quencher. Quenching is suppressed once the MB binds to microRNA-21.

Duplex-Specific Nuclease-Amplified Detection of MicroRNA Using Compact Quantum Dot-DNA Conjugates

Advances in nanotechnology have provided new opportunities for the design of next-generation nucleic acid biosensors and diagnostics. Indeed, combining advances in functional nanoparticles, DNA nanotechnology, and nuclease-enzyme-based amplification can give rise to new assays with advantageous properties. In this work, we developed a microRNA (miRNA) assay using bright fluorescent quantum dots (QDs), simple DNA probes, and the enzyme duplex-specific nuclease. We employed an isothermal target-recycling mechanism, where a single miRNA target triggers the cleavage of many DNA signal probes. The incorporation of DNA-functionalized QDs enabled a quantitative fluorescent readout, mediated by Förster resonance energy transfer (FRET)-based interaction with the DNA signal probes. Our approach splits the reaction in two, performing the enzyme-mediated amplification and QD-based detection steps separately such that each reaction could be optimized for performance of the active components. Target recycling gave ca. 3 orders of magnitude amplification, yielding highly sensitive detection with a limit of 42 fM (or 1.2 amol) of miR-148, with excellent selectivity versus mismatched sequences and other miRNAs. Furthermore, we used an alternative target (miR-21) and FRET pair for direct and absolute quantification of miR-21 in RNA extracts from human cancer and normal cell lines.

Luminescent quantum dots for miRNA detection

MicroRNAs (miRNAs) are a class of small non-coding RNAs that are involved in nearly all developmental processes and human pathologies. MiRNAs are considered to be promising biomarkers, since their dysregulation correlates with the development and progress of many diseases. Short length, sequence homology among family members, susceptibility to degradation, and low abundance in total RNA samples make miRNA analysis a challenging task. Photoluminescent semiconductor nanoparticles (quantum dots, QDs) possess unique properties such as bright photoluminescence, photostability and narrow emission peaks, wide possibilities for surface modification and bioconjugation, which serve as the basis for the development of different analytical methods for variety of analytes. Relatively small size of QDs' and their narrow distribution are especially important for miRNA assay. The combination of QD-based biosensors with amplification techniques makes it possible to identify the target miRNA at a single-particle level with the detection limit at the attomolar scale. This review describes the principles of signal generation: direct intensity measurements, different "signal on" and "signal off" mechanisms as well as electro-chemiluminescence. Special attention is paid to the FRET-based techniques. According to our knowledge this is the first review related to QDs application for miRNA detection.

Detection of nucleic acids with a novel stem-loop primer rolling circle amplification technique

This paper presents a new rolling circle amplification (RCA) technique using stem-loop primers (SLP). The technique enables detection of target DNA by either linear or exponential amplification (SLP-lRCA and SLP-eRCA) in both liquid and solid phases. For solid-phase detection, SLP-eRCA detects nucleic acids in four steps: (1) covalently immobilize an array of capture probes (CP) on a solid support; (2) hybridize the CP array with the DNA sample; (3) incubate the CP array with an RCA reaction containing two SLPs; (4) image the CP array. SLP-eRCA detects nucleic acids in liquid phase in one step: a real-time RCA reaction containing the DNA sample and two SLPs. Both liquid- and solid-phase detection methods employ a general rolling circle and an SLP. The other SLP is specific to the target. The technique was verified by detecting synthesized oligonucleotides and six different human papillomaviruses (HPVs), both in liquid phase and on a solid surface. The technique also detected two high-risk HPVs (HPV16 and HPV18) in cervical carcinoma cells (HeLa and SiHa) and clinical samples. This study provides proof-of-concept for the new RCA technique for nucleic acid detection, which overcomes major limitations of current RCA approaches.

The use of nanocrystal quantum dot as fluorophore reporters in molecular beacon-based assays

The utilization of molecular beacon (MB) biosensor probes to detect nucleic acid targets has received enormous interest within the scientific community. This interest has been stimulated by the operational qualities of MB-based probes with respect to their unique sensitivity and specificity. The design of MB biosensors entails not only optimizing the sequence of the loop to hybridize with the nucleic acid target or optimization of the length of the stem to tune the sensitivity but also the selection of the appropriate fluorophore reporter to generate the signal transduction read-out upon hybridization of the probe with the target sequence. Traditional organic fluorescent dyes are mostly used for signal reporting in MB assays but their optical properties in comparison to semiconductor fluorescent quantum dot (Qdot) nanocrystals are at a disadvantage. This review highlights the progress made in exploiting Qdot as fluorophore reporters in MB-based assays with the aim of instigating further development in the field of Qdot-MB technology. The development reported to date indicates that unparalleled fluorescence signal reporting in MB-based assays can be achieved using well-constructed Qdot fluorophores.

Rapid and Multiplexed MicroRNA Diagnostic Assay Using Quantum Dot-Based Förster Resonance Energy Transfer

The detection of next generation microRNA (miRNA) biomarkers has become a highly important aspect for clinical diagnostics. We use multiplexed Förster resonance energy transfer (FRET) between a luminescent Tb complex and three different semiconductor quantum dots (QDs) to sensitively detect three different miRNAs from a single 150 μL sample with ca. 1 nM (subpicomol) detection limits. The rapid and amplification-free mix-and-measure assay format is based on careful design of miRNA base pairing and stacking to selectively detect different miRNAs with very strong sequence homologies. Clinical applicability is demonstrated by sensitive multiplexed quantification of three miRNAs at low (2 to 10 nM) and varying concentrations in samples that contained up to 10% serum.

"Signal-on" photoelectrochemical biosensor for sensitive detection of human T-Cell lymphotropic virus type II DNA: dual signal amplification strategy integrating enzymatic amplification with terminal deoxynucleotidyl transferase-mediated extension

A novel "signal-on" photoelectrochemical (PEC) biosensor for sensitive detection of human T-cell lymphotropic virus type II (HTLV-II) DNA was developed on the basis of enzymatic amplification coupled with terminal deoxynucleotidyl transferase (TdT)-mediated extension strategy. The intensity of the photocurrent signal was proportional to the concentration of the HTLV-II DNA-target DNA (tDNA) by dual signal amplification. In this protocol, GR-CdS:Mn/ZnS nanocomposites were used as photoelectric conversion material, while pDNA was used as the tDNA recognizing unit. Moreover, the TdT-mediated extension and the enzymatic signal amplification technique were used to enhance the sensitivity of detection. Using this novel dual signal amplification strategy, the prototype of PEC DNA sensor can detect as low as ∼0.033 fM of HTLV-II DNA with a linear range of 0.1-5000 fM, with excellent differentiation ability even for single-base mismatches. This PEC DNA assay opens a promising platform to detect various DNA targets at ultralow levels for early diagnoses of different diseases.

Electrical and electrochemical monitoring of nucleic Acid amplification

Nucleic acid amplification is a gold standard technique for analyzing a tiny amount of nucleotides in molecular biology, clinical diagnostics, food safety, and environmental testing. Electrical and electrochemical monitoring of the amplification process draws attention over conventional optical methods because of the amenability toward point-of-care applications as there is a growing demand for nucleic acid sensing in situations outside the laboratory. A number of electrical and electrochemical techniques coupled with various amplification methods including isothermal amplification have been reported in the last 10 years. In this review, we highlight recent developments in the electrical and electrochemical monitoring of nucleic acid amplification.

Electron transfer mediated electrochemical biosensor for microRNAs detection based on metal ion functionalized titanium phosphate nanospheres at attomole level

MicroRNAs (miRNAs) have emerged as new candidates as diagnostic and prognostic biomarkers for the detection of a wide variety of cancers; thus, sensitive and selective detection of microRNAs is significant for early-phase cancer diagnosis and disease prevention. A novel and simple electrochemical miRNA biosensor was developed using Cd(2+)-modified titanium phosphate nanoparticles as signal unit, two DNA as capture probes, and Ru(NH3)6(3+) as electron transfer mediator. Large quantities of cadmium ions were mounted in titanium phosphate spheres to output the electrochemical signal. Because of the presence of Ru(NH3)6(3+) molecules that interacted with DNA base-pairs as electron wire, the electrochemical signal significantly increased more than 5 times. This approach achieved a wide dynamic linear range from 1.0 aM to 10.0 pM with an ultralow limit detection of 0.76 aM, exerting a substantial enhancement in sensitivity. Moreover, the proposed biosensor was sufficiently selective to discriminate the target miRNAs from homologous miRNAs and could be used for rapid and direct analysis of miRNAs in human serum. Therefore, this strategy provides a new and ultrasensitive platform for miRNA expression profiling in biomedical research and clinical diagnosis.

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.

A linear DNA probe as an alternative to a molecular beacon for improving the sensitivity of a homogenous fluorescence biosensing platform for DNA detection using target-primed rolling circle amplification

Linear single-labeled DNA probes are used in this RCA-based fluorescence strategy for DNA detection, which could effectively avoid the fluorescence quenching between neighboring signal probes using hairpin probe as signal probe.

Nanomaterials-Based Sensing Strategies for Electrochemical Detection of MicroRNAs

MicroRNAs (miRNAs) play important functions in post-transcriptional regulation of gene expression. They have been regarded as reliable molecular biomarkers for many diseases including cancer. However, the content of miRNAs in cells can be low down to a few molecules per cell. Thus, highly sensitive analytical methods for miRNAs detection are desired. Recently, electrochemical biosensors have held great promise as devices suitable for point-of-care diagnostics and multiplexed platforms for fast, simple and low-cost nucleic acid analysis. Signal amplification by nanomaterials is one of the most popular strategies for developing ultrasensitive assay methods. This review surveys the latest achievements in the use of nanomaterials to detect miRNAs with a focus on electrochemical techniques.

Rapid and reliable microRNA detection by stacking hybridization on electrochemiluminescent chip system

MicroRNAs play pivotal roles in many fundamental aspects of life. Because microRNAs have the characteristics of small size, similar sequence, and low abundance, it is challenging to identify microRNAs rapidly and specifically with high sensitivity. Herein, we developed an electrochemiluminescent (ECL) chip system for microRNA detection based on base-stacking hybridization and magnetic microparticle enrichment technology. In the designed system, the integration of the microfluidic system with ECL detection made it easy to assemble the multiple assay steps and allowed the construction of a device that is convenient to carry. A limit of detection of 1fmol was achieved with this assay. The proposed direct optical microRNA detection technique demonstrated an acceptable sensitivity combined with the advantages of reliability and rapidity.