The authors describe an electrochemical method for the determination of the single-stranded DNA (ssDNA) oligonucleotide with a sequence derived from the genom of hepatitis B virus (HBV). It is making use of circular strand displacement (CSD) and rolling circle amplification (RCA) strategies mediated by a molecular beacon (MB). This ssDNA hybridizes with the loop portion of the MB immobilized on the surface of a gold electrode, while primer DNA also hybridizes with the rest of partial DNA sequences of MB. This triggers the MB-mediated CSD. The RCA is then initiated to produce a long DNA strand with multiple tandem-repeat sequences, and this results in a significant increase of the differential pulse voltammetric response of the electrochemical probe Methylene Blue at a rather low working potential of ?0.24 V (vs. Ag/AgCl). Under optimal experimental conditions, the assay displays an ultrahigh sensitivity (with a 2.6 aM detection limit) and excellent selectivity. Response is linear in the 10 to 700 aM DNA concentration range.
Graphical abstract Schematic of a voltammetric method for the determination of attomolar levels of target DNA. It is based on molecular beacon mediated circular strand displacement and rolling circle amplification strategies. Under optimal experimental conditions, the assay displays an ultrahigh sensitivity with a 2.6 aM detection limit and excellent selectivity.
MicroRNAs are endogenous noncoding RNAs that play critical roles in biological processes and can be considered as molecular markers for early diagnosis and pathogenesis of diseases. The authors describe a highly sensitive electrochemical biosensor for microRNA that is based on the use of tetrahedral DNA nanostructure probes and guanine nanowire amplification. The DNA tetrahedral probe is self-assembled on a gold electrode and enhances reactivity, accessibility, and molecular recognition efficiency. Combined with the tetrahedral probe, the guanine nanowire amplifies the signal and improves the analytical performance of the biosensor. Operated best at a voltage of typically 150 mV (vs. Ag/AgCl), the sensor has a linear response to the logarithmic microRNA concentration in the 500 f. to 10 nM range, with a 176 f. detection limit. It is highly selective and can be applied to real samples. It is concluded that this strategy has a good potential with respect to the determination of microRNA in clinical diagnosis and in biological research.
Graphical abstract Schematic of a tetrahedral DNA nanostructure-based amperometric biosensor coupled to guanine nanowire amplification for analysis of microRNA-21. This strategy is highly selective and also performs well for the detection of microRNA levels of breast cancer patients.
This paper describes a CdTe quantum dot-based fluorescence resonance energy transfer (FRET) based assay for the detection of the breast cancer biomarker microRNA. The method relies on energy transfer between DNA-templated silver nanoclusters (AgNCs) and CdTe QDs. Interaction between double strand oligonucleotide and QDs can be detected qualitatively through gel analysis and quantitatively by the signal amplification from AgNCs to QDs via FRET, best measured at an excitation wavelength of 350 nm and at emission wavelengths of 550 and 590 nm. Three microRNAs (microRNA-21, microRNA-155 and Let-7a) were quantified to verify the feasibility of the method, and a high sensitivity for microRNAs was achieved. Fluorescence intensity increases linearly with the log of the concentration of microRNA 155 in the 5.0 pM to 50 nM range, with a 1.2 pM detection limit.
Graphical abstract Schematic presentation of a quantum dot-based (QD-based) fluorescence resonance energy transfer technique for the detection of microRNA (miRNA). The method relies on energy transfer between DNA-templated silver nanoclusters (AgNCs) and QDs.
The authors describe a method for DNA target recognition and signal amplification that is based on the target-induced formation of a three way junction. The subsequent assembly of two DNA probes releases the inhibitory strand and triggers a downstream strand displacement amplification. This causes the formation of a G-rich single sequence that binds to a hemin monomer with its peroxidase-mimicking properties. The resulting peroxidase (POx) activity is quantified by using H2O2 and TMB as the substrate. In the presence of an inhibitor, in contrast, the POx-like activity is strongly reduced. This forms the basis for a highly sensitive DNA assay. It has a 0.8 pM detection limit when operated at a wavelength of 450 nm and was applied to the isothermal determination of target DNA with high selectivity.
Graphical abstract Schematic of the assay: Introduction of target results in the formation of a three way junction. The subsequent assembly of two probes releases the inhibitory strand and triggers a downstream strand displacement amplification, generating amount of G-rich single sequence which causes peroxidase-mimicking activity on binding to a hemin monomer.
The authors describe a fluorometric switch assay for microRNA (miRNA). It is based on nonenzymatic ligation-rolling circle amplification (NELRCA). A click chemistry-mediated functionalized linear template was prepared by self-cycling. It is capable of forming a modified circular template (MLT) with a triazole linkage for amplified agent. MiRNA can recognize a binding region of the MLT, activates the NELRCA, and converts into rolling circle amplification products (RCPs). Subsequently, the added FAM-labeled signal probes (FAM-SPs) can hybridize to the RCPs. This RCPs/FAM-SPs duplex is less adsorbed onto the graphene oxide (GO) so that fluorescence (best measured at excitation/emission wavelengths of 490/520 nm) increases. In contrast to classical GO-based adsorption and displacement sensing system, the designed hybridization and adsorption fluorescent switch-on platform can reduce the assay time, and improve the detection efficiency of target. Under optimal conditions, the sensing platform has a detection limit as low as 0.75 fM. It can well discriminate target miRNA from other kinds of miRNA. Conceivably, this method can be extended to the trace detection of other nucleic acid biomarkers, and simultaneous recognition of multiple targets, thereby improving the early clinical diagnostic accuracy of cancer.
Graphical abstract A hybridization and adsorption switch-on sensing system was fabricated on nonenzymatic ligation-rolling circle amplification. Modified circular template with 1,4-connect triazole linkage was adopted as an identified and amplified agent for high sensitive detection of microRNA.
MicroRNAs (miRNAs) are considered as being promising biomarkers for hematological malignancies, their aging, progression and prognosis. The authors have developed a method for the detection of miRNA-155 by using surface plasmon resonance (SPR) imaging coupled to a nucleic acid-based amplification strategy using gold nanoparticles (AuNPs). The target miRNA-155 is captured by surface-bound DNA probes. After hybridization, DNA-AuNP are employed for signal amplification via DNA sandwich assembly, resulting in a large increase in the SPR signal. This method can detect miRNA-155 in concentrations down to 45 pM and over dynamic that extends from 50 pM to 5 nM. The assay is highly specific and can discriminate even a single base mismatch. It also is reproducible, precise, and was successfully applied to the determination of miRNA-155 in spiked real samples where it gave recoveries in the range between 86% and 98%. This biosensor provides an alternative approach for miRNA detection in biomedical research and clinical diagnosis, which is highly effective and efficient.
Graphical abstract Schematic of a surface plasmon resonance imaging biosensor for detection of miRNA-155 using strand displacement amplification and gold nanoparticle.
A fluorometric ATP assay is described that makes use of carbon dots and graphene oxide along with toehold-mediated strand displacement reaction. In the absence of target, the fluorescence of carbon dots (with excitation/emission maxima at 360/447 nm) is strong and in the “on” state, because the signal probe hybridizes with the aptamer strand and cannot combine with graphene oxide. In the presence of ATP, it will bind to the aptamer and induce a strand displacement reaction. Consequently, the signal probe is released, the sensing strategy will change into the “off” state with the addition of graphene oxide. This aptasensor exhibits selective and sensitive response to ATP and has a 3.3 nM detection limit.
Graphical abstract Schematic of signal amplification by strand displacement in a carbon dot based fluorometric assay for ATP. This strategy exhibits high sensitivity and selectivity with a detection limit as low as 3.3 nM.
The authors describe a colorimetric method for the determination of Hg(II) ion. It is based on the color change from red to colorless as displayed by gold nanoparticle (AuNP) modified with thymine - rich DNA. Signal amplification is accomplished by free strand displacement recycling. In this strategy, Hg(II) unfolds the arch-trigger duplex due to the high affinity between Hg(II) and the thymines to form T-Hg(II)-T structures, thereby causing the release of trigger. The liberated trigger unfolds the hairpin structure of H1, and unfolded H1 further unfolds with H2. As a result, the H2 hairpin displaces trigger, and the released trigger unfolds another H1. This results in strong and enzyme-free strand displacement recycling amplification. The aggregation of DNA-AuNPs occurs in the presence of the duplex formed by hairpins H2 and H1. This results in a color change from red to colorless that can be visually observed. Under optimal conditions, the assay has a detection range over 4 orders of magnitude and a 3.4 nM detection limit. The assay is selective, sensitive, rapid and cost-effective. In our perception, it represents a useful platform for determination of Hg(II).
Graphical abstract Schematic presentation of the simple, rapid, low cost colorimetric detection of mercury(II) based on enzyme-free strand displacement amplification along with DNA-labeled AuNP.
An aptamer based assay is described for the colorimetric detection of adenosine. The presence of adenosine triggers the deformation of hairpin DNA oligonucleotide (HP1) containing adenosine aptamer and then hybridizes another unlabeled hairpin DNA oligonucleotide (HP2). This leads to the formation of a double strand with a blunt 3′ terminal. After exonuclease III (Exo III)-assisted degradation, the guanine-rich strand (GRS) is released from HP2. Hence, the adenosine-HP1 complex is released to the solution where it can hybridize another HP2 and initiate many cycles of the digestion reaction with the assistance of Exo III. This leads to the generation of a large number of GRS strands after multiple cycles. The GRS stabilize the red AuNPs against aggregation in the presence of potassium ions. If, however, GRS forms a G-quadruplex, it loses its ability to protect gold nanoparticles (AuNPs) from salt-induced AuNP aggregation. Therefore, the color of the solution changes from red to blue which can be visually observed. This colorimetric assay has a 0.13 nM detection limit and a wide linear range that extends from 5 nM to 1 μM.
Graphical abstract Schematic presentation of a colorimetric aptamer biosensor for adenosine detection based on DNA cycling amplification and salt-induced aggregation of gold nanoparticles.
A battery of logic gates, “YES”, “AND” and “OR”, are constructed using magnetic beads (MBs) modified by DNA which consists of a substrate strand (S) and a signal strand on which the logic operates. Inputs stemming from micro-RNA (which represent three cancer biomarkers) take the place of signal DNA. The released signal strand self-assembles into the hemin-G-quadruplex complex (DNAzyme) that catalyzes a blue-green dye (ABTS+) from the precursor ABTS. This dye (quantified at a wavelength of 414 nm) represents the output signal for the various logic gates. The method allows quantitative detection of microRNA of three kinds of logic gates in the range of 5 nM–500 nM with detection limits of 3.8 nM, 4.9 nM, 5.4 nM. Boolean logic circuitry is also achieved following the principles of multilevel strand displacement. Based on strand displacement and magnetic separation, this work demonstrates the possibility of designing a logic system using micro-RNA in live cell lysate as inputs, and its potential application in DNA computation and cancer diagnosis.
Graphical abstract Schematic representation of a battery of logic gates and the Boolean logic circuitry based on strand displacement and magnetic separation responding to multiple microRNA in cancer cell lysate.
MicroRNAs (miRNAs) play a considerable role in cancer occurrence and development, and have been identified as promising noninvasive biomarkers. The authors describe a voltammetric method for the determination of the cancer biomarker microRNA-21 (miRNA). It is based on a combination of a universal DNA signal transducer and isothermal target recycling amplification. A hairpin capture probe is bound to the target miRNA to form a duplex structure and to create a toehold in the transducer for initiating the target recycling amplification reaction. In contrast to traditional capture probes, a mismatched site is introduced to improve its ability to capture the target. In order to reduce the complex design procedures of the sequence and widen the applicability of this method, a signal transducer is introduced. Under optimal conditions, response to target miRNA is linear in the 0.5 to 2000 pM concentration range, with a 56 fM. detection limit (at an S/N ratio of 3). In order to characterize the process of target recycling and the stepwise modification of the electrode, real-time fluorescence, agarose gel electrophoresis, cyclic voltammetry, electrochemical impedance spectroscopy and chronocoulometry were used. The results indicate that this isothermal target recycling amplification results in an electrochemical biosensing scheme with wide potential for sensing other bioanalytes.
Graphical abstract Schematic illustration of the electrochemical biosensing platform for miRNA-21 detection based on isothermal target recycling amplification and DNA signal transducer triggered strategy.
The authors describe a fluorometric method for improving the determination of the cancer biomarker 8-hydroxy-2′-deoxyguanosine (8-OHdG). A nicking endonuclease (NEase)-powered 3-D DNA nanomachine was constructed by assembling hundreds of carboxyfluorescein-labeled single strand oligonucleotides (acting as signal reporter) and tens of swing arms (acting as single-foot DNA walkers) on a gold nanoparticle (AuNP). The activity of this DNA nanomachine was controlled by introducing the protecting oligonucleotides. In the presence of aptamer against 8-OHdG, the protecting oligonucleotides are removed from the swing arms by toehold-mediated strand displacement reaction. In the next step, detached DNA walker hybridizes to the labelled DNA so that the DNA nanomachine becomes activated. Special sequences of signal reporter in the formed duplex can be recognized and cleaved by NEase. As a result, the DNA walker autonomously and progressively moves along the surface of the AuNP, thereby releasing hundreds of signal reporters and causing a rapid increase in green fluorescence. This 3-D nanomachine is highly efficient because one aptamer can release hundreds of signal reporters. These unique properties allowed for the construction of a DNA nanomachine-based method for sensitively detecting 8-OHdG in concentrations as low as 4 pM. This is three orders of magnitude lower compared to previously reported methods.
Graphical abstract Schematic of a fluorometric method for determination of the cancer biomarker 8-hydroxy-2′-deoxyguanosine. A nicking endonuclease powered 3D-DNA nanomachine was used to improve the sensitivity. Limit of detection is three orders of magnitude lower than reported methods.
The authors describe a method for the colorimetric determination of unamplified microRNA. It is based on the use of citrate-capped gold nanoparticles (AuNPs) and, alternatively, a microRNA-probe hybrid or a magnetically extracted microRNA that serve as stabilizers against the salt-induced aggregation of AuNPs. The absorbance ratios A525/A625 of the reacted AuNP solutions were used to quantify the amount of microRNA. The assay works in the range of 5–25 pmol microRNA. The lower limit of detection (LOD) is 10 pmol. The performance of the method was tested by detection of microRNA-210-3p in totally extracted urinary microRNA from normal, benign, and bladder cancer subjects. The sensitivity and specificity for qualitative detection of urinary microRNA-210-3p using the assay are 74% and 88% respectively, which is consistent with real time PCR based assays. The assay was applied to the determination of specific microRNA by using its specific oligo targeter or following magnetic isolation of the desired microRNA. The method is simple, cost-efficient, has a short turn-around time and requires minimal equipment and personnel.
Graphical abstract Schematic of the two detection schemes: In the first approach, matched microRNA hybridizes with its specific probe to stabilize gold nanoparticles (AuNPs) against salt induced aggregation and to leave the red color of the AuNPs unchanged. In the second one, microRNA extracted via magnetic nanoparticles (MNP) stabilizes AuNPs against aggregation.
The authors describe an electrochemical sensing strategy for highly sensitive and specific detection of target (analyte) DNA based on an amplification scheme mediated by a multicomponent nucleic acid enzyme (MNAzyme). MNAzymes were formed by multicomponent complexes which produce amplified “output” signals in response to specific “input” signal. In the presence of target nucleic acid, multiple partial enzymes (partzymes) oligonucleotides are assembled to form active MNAzymes. These can cleave H0 substrate into two pieces, thereby releasing the activated MNAzyme to undergo an additional cycle of amplification. Here, the two pieces contain a biotin-tagged sequence and a byproduct. The biotin-tagged sequences are specifically captured by the detection probes immobilized on the gold electrode. By employing streptavidinylated alkaline phosphatase as an enzyme label, an electrochemical signal is obtained. The electrode, if operated at a working potential of 0.25 V (vs. Ag/AgCl) in solution of pH 7.5, covers the 100 pM to 0.25 μM DNA concentration range, with a 79 pM detection limit. In our perception, the strategy introduced here has a wider potential in that it may be applied to molecular diagnostics and pathogen detection.
Graphical abstract An electrochemical strategy for sequence-specific DNA detection based on multicomponent nucleic acid enzyme (MNAzyme) -mediated signal amplification.
The authors describe a novel assay for the detection of methylated DNA site. Rolling circle amplification and CdSe/ZnS quantum dots with high fluorescence efficiency are applied in this method. The CdSe/ZnS quantum dots act as electron donors, and hemin and oxygen (derived from hydrogen peroxide act as acceptors in photoinduced electron transfer. The assay, best performed at excitation/emission peaks of 450/620 nm, is sensitive and specific. Fluorometric response is linear in the 1 pM to 100 nM DNA concentration range, and the lowest detectable concentration of methylated DNA is 142 fM (S/N =?3). The method is capable of recognizing 0.01% methylated DNA in a mixture of methylated/unmethylated DNA.
Graphical abstract A novel method for methylated sites detection in DNA is established. Rolling circle amplification and photoinduced electron transfer. CdSe/ZnS quantum dots with high fluorescence efficiency act as the electron donor, while G-quadruplex/hemin and hydrogen peroxide derived oxygen act as electron acceptor. It presents a linear response towards 1 pM to 100 nM methylated DNA with a correlation coefficient of 0.9968, and the lowest detectable concentration of methylated DNA was 142 fM, with selectivity significantly superior to other methods.
Cardiac troponin (cTn) is a specific and sensitive biomarker for diagnosis of myocardial injury. Hence, numerous kinds of biosensors for cTn have been reported. Electrochemical methods possess inherent advantages over other kinds of sensors because they are specific, sensitive, and simple. By combining the advantages of electrochemical biosensors with those of nanomaterials, some interesting electrochemical biosensor for cTn can be obtained where the nanomaterials trigger substantial signal amplification. This review (with 101 refs.) summarizes the state of the art in electrochemical biosensing of cTn based on the use of nanomaterials. Following an introduction into the field, the use of nanomaterials in electrochemical sensing is briefly discussed. A next section covers strategies for signal amplification by using nanomaterials, with subsections on the use of nanowires, nanotubes, graphenes, and various other nanoparticles. The article concludes with a discussion of the prospects of nanomaterial-based signal amplification and on future research directions.
Graphical abstract Illustration of electrochemical biosensing of cardiac troponin (cTn) with various kinds of nanomaterials, including nanowires, nanotubes, graphene and nanoparticles, as the signal amplification modules.
An amperometric aptasensor is reported for the electrochemical determination of the epithelial cell adhesion molecule (EpCAM). It is based on a combination of EpCAM-driven toehold-mediated DNA recycling amplification, the specific recognition of EpCAM aptamer, and its binding to EpCAM. Hairpin probe 1 (Hp1) with a toehold region was modified with a 5′-thiol group (5’-SH) and self-assembled onto the surface of a gold electrode. Upon addition of EpCAM, the probe A (a 15-mer) is liberated from the aptamer/probe A complex and then hybridizes with the toehold domain of Hp1. This results in the exposure of another toehold for further hybridizing with hairpin probe 2 (Hp2) to displace probe A in the presence of Hp2 that was labeled with the electrochemical probe Methylene Blue (MB). Subsequently, liberated probe A is hybridized again with another Hp1 to start the next round of DNA recycling amplification by reusing probe A. This leads to the formation of plenty of MB-labeled DNA strands on the electrode surface and generates an amplified current. This 1:N probe-response amplification results in ultrasensitive and specific detection of EpCAM, with a 20 pg·mL?1 detection limit. The electrode is highly stable and regenerable. It was successfully applied to the determination of EpCAM in spiked human serum, urine and saliva, and thus provides a promising tool for early clinical diagnosis.
Graphical abstract Schematic illustration of the electrochemical detection for EpCAM. The method is based on aptamer-based recognition and EpCAM-driven toehold-mediated DNA recycling amplification. Hp1: Hairpin probe 1; Hp2: Hairpin probe 2; MB: Methylene blue; MCH: 6-Mercapto-1-hexanol; EpCAM: Epithelial cell adhesion molecule.
A toehold-aided DNA recycling amplification technology was developed based on the combination of toehold-aided DNA recycling and the hemin/G-quadruplex label. The dsDNA formed between aptamer and DNA1 was first immobilized on magnetic beads. On addition of target analyte (exemplified here for riboflavin), the aptamer-riboflavin complex is formed and DNA1 is released by the beads. After magnetic separation, the supernatant containing the released DNA1 is added to a solution containing the hairpin capture DNA on magnetic beads. DNA1 will hybridize with the hairpin capture DNA via toehold binding and branch migration. This process will open the hairpin structure, and an external toehold is formed in the newly formed dsDNA. On addition of reporter DNA containing the G-quadruplex, it will interact with the formed dsDNA via toehold binding and branch migration, resulting in the releasing of DNA1 and capturing of reporter DNA on the magnetic beads. The released DNA1 will bind to another hairpin capture DNA which can start another round of DNA1 recycling. Chemiluminescence (CL) is generated by the G-quadruplex-hemin-luminol CL reaction system. Under optimal conditions, the calibration plot is linear in the 0.1 to 700 nM riboflavin concentration range, with a 30 pM detection limit (at a signal-to-noise ratio of 3). The method was successfully applied to the quantitation of riboflavin in spiked urine samples.
The authors describe a fluorometric assay for ochratoxin A (OTA) that is based on the use of graphene oxide and RNase H-aided amplification. On addition of OTA, cAPT is replaced from the APT/cAPT hybridization complex and then hybridizes with RNA labeled with a fluorophore at the 5′-end. Eventually, the fluorophore is released by RNase H cleavage. As the concentration of OTA increases, more cAPTs are displaced, this leading to fluorescence enhancement (best measured at excitation/emission wavelengths of 495/515 nm). This RNase H-assisted cycle response results in strong signal amplification. The limit of detection, calculated on the basis of a signal to noise ratio of 3, is 0.08 ng·mL?1. Response is linear in the 0.08–200 ng·mL?1 OTA concentration range. The method is highly selective for OTA over ochratoxin B and aflatoxin B1. It was applied to the determination of OTA in red wine samples spiked at levels of 1, 7, and 50 ng·mL?1, and the recoveries ranged from 90.9 to 112%.
The authors describe an electrochemical sensor for the neonicotinoid insecticide imidacloprid (IMI) based on Pt-In catalytic nanocomposite film and Bromophenol blue amplification. The Pt-In nanocomposite film was deposited on the surface of a modified glassy carbon electrode. The composite molecularly imprinted polymer (MIP) was prepared by electro-polymerization using bromophenol blue doped o-aminophenol as functional monomer and 4-tert-butylcalix[6]arene-IMI supramolecular inclusion complex as template molecule. The experimental results showed that the current intensity of IMI was clearly amplified in the potential range from ?0.3 to ?1.8 V, because of the double amplification, based on the Pt-In film and Bromophenol blue catalysis. Moreover, the double recognition ability of the sensor, which relied on the MIP and the vacuum structure of 4-tert-butylcalix[6]arene, effectively increased the specific recognition performance. The feasibility of its practical applications has been demonstrated by the analysis of vegetable samples.
Graphical abstract A supramolecular imprinted electrochemical sensor for imidacloprid determination was prepared based on Pt-In nanocomposite film and bromophenol blue amplification. Because of the advantages of the specific recognition sites in MIPs and supramolecular chemistry, the sensor showed good selectivity for imidacloprid.
