The authors describe a fluorometric assay for microRNA. It is based on two-step amplification involving (a) strand displacement replication and (b) rolling circle amplification. The strand displacement amplification system is making use of template DNA (containing a sequence that is complementary to microRNA-21) and nicking enzyme sites. After hybridization, the microRNA strand becomes extended by DNA polymerase chain reaction and then cleaved by the nicking enzyme. The DNA thus produced acts as a primer in rolling circle amplification. Then, the DNA probe SYBR Green II is added to bind to ssDNA to generate a fluorescent signal which increases with increasing concentration of microRNA. The method has a wide detection range that covers the10 f. to 0.1 nM microRNA concentration range and has a detection limit as low as 1.0 fM. The method was successfully applied to the determination of microRNA-21 in the serum of healthy and breast cancer patients.
Graphical abstract Schematic of a fluorometric microRNA assay based on two-step amplification involving strand displacement replication and rolling circle amplification. DNA probe SYBR Green II is then bound to ssDNA to generate a fluorescent signal which increases with increasing concentration of microRNA.
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.
A DNAzyme-embedded hyperbranched DNA dendrimer is used as a colorimetric signal amplifier in an ultrasensitive detection scheme for nucleic acids. The hyperbranched DNA dendrimers were constructed by single-step autonomous self-assembly of three structure-free DNA monomers. A cascade of self-assembly reactions between the first and second strands leads to the formation of linear DNA concatemers containing overhang flank fragments. The third strand, which bears a peroxidase-mimicking DNAzyme domain, serves as a bridge to trigger self-assembly between the first and second strands across the side chain direction. This results in a chain branching growth of the DNAzyme-embedded DNA dendrimer. This signal amplifier was incorporated into the streptavidin-biotin detection system which comprises an adaptor oligonucleotide and a biotinylated capture probe. The resulting platform is capable of detecting a nucleic acid target with an LOD as low as 0.8 fM. Such sensitivity is comparable if not superior to most of the reported enzyme-free (and even enzyme-assisted) signal amplification strategies. The DNA dendrimer based method is expected to provide a universal platform for extraordinary signal enhancement in detecting other nucleic acid biomarkers by altering the respective sequences of adaptor and capture probe.
Graphical abstract Schematic of an assembly of a DNAzyme-embedded hyperbranched DNA dendrimer which operates as a signal amplifier for nucleic acids detection. The nanostructure is constructed by autonomous self-assembly of three DNA monomers. Colored letters represent each domain, and complementary domains are marked by asterisk. Domain d represents the DNAzyme sequence.
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 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.
An isothermal colorimetric method is described for amplified detection of the CaMV 35S promoter sequence in genetically modified organism (GMO). It is based on (a) target DNA-triggered unlabeled molecular beacon (UMB) termini binding, and (b) exonuclease III (Exo III)-assisted target recycling, and (c) hemin/G-quadruplex (DNAzyme) based signal amplification. The specific binding of target to the G-quadruplex sequence-locked UMB triggers the digestion of Exo III. This, in turn, releases an active G-quadruplex segment and target DNA for successive hybridization and cleavage. The Exo III impellent recycling of targets produces numerous G-quadruplex sequences. These further associate with hemin to form DNAzymes and hence will catalyze H2O2-mediated oxidation of the chromogenic enzyme substrate ABTS2? causing the formation of a green colored product. This finding enables a sensitive colorimetric determination of GMO DNA (at an analytical wavelength of 420 nm) at concentrations as low as 0.23 nM. By taking advantage of isothermal incubation, this method does not require sophisticated equipment or complicated syntheses. Analyses can be performed within 90 min. The method also discriminates single base mismatches. In our perception, it has a wide scope in that it may be applied to the detection of many other GMOs.
Graphical abstract An isothermal and sensitive colorimetric method is described for amplified detection of CaMV 35S promoter sequence in genetically modified organism (GMO). It is based on target DNA-triggered molecular beacon (UMB) termini-binding and exonuclease III assisted target recycling, and on hemin/G-quadruplex (DNAzyme) signal amplification.
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.
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.
The authors describe a colorimetric method for the determination of DNA based on the deaggregation of gold nanoparticles (AuNPs) induced by exonuclease III (Exo III). DNA amplification is accomplished by Exo III to generate large quantities of the residual DNA. Residual DNA tethers onto the surfaces of AuNPs which prevents their aggregation. Hence, the color of the solution is red. However, in the absence of DNA, salt-induced aggregation is not prevented, and the bluish-purple color of the aggregated AuNPs is observed. The ratio of absorbances at 525 and 625 nm increases up to 150 nM DNA concentrations, and the LOD is as low as 3.0 nM. It is shown that the presence of 300 nM concentrations of random DNA (with a mass up to 10-fold that of target DNA) does not interfere. The method was successfully applied to the analysis of DNA in spiked serum samples. The method is simple, reliable, and does not require complicated amplification steps and expensive instrumentation.
Graphical abstract Schematic of a sensing strategy for DNA detection by exonuclease III-induced deaggregation of gold nanoparticles. DNA concentrations as low as 3 nM can be detected via colorimetric monitoring of the color change from red to purple-blue.
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.
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.
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.
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.
An electrochemical biosensor for determination of DNA is described that is based on the reaction of regulated DNA (reg-DNA) first with substrated DNA (subs-DNA) to form a reaction intermediate. The intermediate binds target DNA (T) by hybridization and initiates a branch migration leading to the production of complex of substrated DNA and target DNA (TC). Once TC is produced, it reacts with assisted DNA (ass-DNA) through a toehold exchange mechanism, yielding the product complex of substrated DNA and assisted DNA (CS). The target is then released back into the solution and and catalyzes the next cycle of toehold-exchange with the reaction intermediate of substrated DNA and regulated DNA (CPR). Unlike in a conventional DNA toehold that is hardwired with the branch migration domain, the allosteric DNA toehold is designed into a reg-DNA which is independent of the branch migration domain. Under the optimal experimental conditions and at a working potential as low as 0.18 V, response to DNA is linear in the 1 fM to 1000 pM concentration range, and the detection limit is 0.83 fM. The assay is highly specific and can discriminate target DNA even from a single-base mismatch. It was applied to the analysis of DNA spiked plasma samples.
Graphical abstract Schematic illustration of the electrochemical strategy for target DNA detection based on regulation of DNA strand displacement using an allosteric DNA toehold strategy. It can be used to analyze DNA-spiked plasma samples and has a low detection limit of 0.83 fM.
This review (with (318) refs) describes progress made in the design and synthesis of morphologically different metal oxide nanoparticles made from iron, manganese, titanium, copper, zinc, zirconium, cobalt, nickel, tungsten, silver, and vanadium. It also covers respective composites and their function and application in the field of electrochemical and photoelectrochemical sensing of chemical and biochemical species. The proper incorporation of chemical functionalities into these nanomaterials warrants effective detection of target molecules including DNA hybridization and sensing of DNA or the formation of antigen/antibody complexes. Significant data are summarized in tables. The review concludes with a discussion or current challenge and future perspectives.
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.
A nanocomposite composed of graphene oxide and magnetite (Fe3O4) was coated with the ionic liquid (IL) 1,3-didecyl-2-methylimidazolium chloride and used to capture and separate hemin from serum samples. The critical parameters affecting the extraction of analyte, such as pH, surfactant and adsorbent amounts, and desorption conditions were studied and optimized. Following magnetic separation and desorption with a 5:1 mixture of acetic acid and acetone, hemin (an iron porphyrin complex) was quantified by FAAS of iron. Under optimum conditions, the enrichment factor was 96. The calibration curve was linear in the 4.8 to 730 μg L?1 concentration range, the limit of detection was 3.0 μg L?1, and the relative standard deviations (RSDs) for single-sorbent repeatability and sorbent-to-sorbent reproducibility were less than 3.9 % and 10.2 % (n = 5), respectively. The adsorbent displayed adsorption capacity as high as 200 mg g?1, indicating IL-coated Fe3O4/GO to be a good sorbent for the adsorption of hemin. The method was validated by determining serum hemin in the presence of a large excess (480-fold) of Fe3+ without considerable interference. The results compare well to those obtained with a commercial hemin assay kit. The results show that this method can be successfully applied to the enrichment and determination of hemin in acid digested serum samples of breast cancer patients.
Graphical abstract Fe3O4/GO nanocomposites were coated with the ionic liquid 1,3-didecyl-2-methylimidazolium chloride and used as the sorbent for the separation and preconcentration of hemin from blood serum samples prior to determination using by flame AAS.
A sensing device was constructed for the amperometric determination of nitrite. It is based on the use of titanium dioxide (TiO2) nanotubes template with natural fibers and carrying hemin acting as the electron mediator. A glassy carbon electrode (GCE) was modified with the hemin/TNT nanocomposite. The electrochemical response to nitrite was characterized by impedance spectroscopy and cyclic voltammetry. An amperometric study, performed at a working potential of + 0.75 V (vs. Ag/AgCl), showed the sensor to enable determination of nitrite with a linear response in the 0.6 to 130 μM concentration range and with a 59 nM limit of detection. Corresponding studies by differential study voltammetry (Ep?=?0.75 V) exhibited a linear range from 0.6?×?10?6 to 7.3?×?10?5 M with a limit of detection of 84 nM. The sensing device was applied to the determination of nitrite in spiked tap and lake water samples.
Graphical abstract Natural fibers templated synthesis of TNT immobilized hemin as electron transfer mediator for quantitative detection of nitrite with detection limit of 59 nM and good electrochemical sensitivity and the method can be used for quantitative determination of nitrite in water samples.
The authors report on a new approach for the determination of the breast cancer biomarker microRNA-155 (miRNA-155). It is based on the measurement of the fluorescence shift of oligonucleotide-templated copper nanoclusters (DNA-CuNC). A probe DNA was designed that acts as a template for the preparation of CuNC which, under 400 nm excitation, exhibit strong fluorescence enhancement at 490 nm and a 90 nm Stokes shift after binding to target miRNA-155 and formation of a DNA-RNA heteroduplex. Under the optimal conditions, the fluorescence of the DNA-CuNC increases with increasing concentration of miRNA-155 in the range from 50 pM to 10 nM, with a 11 pM detection limit. The assay has excellent selectivity over noncomplementary RNA. The method was applied to the determination of miRNA-155 in the presence of human plasma and saliva.
Graphical abstract Schematic of the detection strategy that relies on the fluorescence shift of DNA-CuNCs resulting from the specific binding of DNA-CuNCs with target miRNA-155. Fluorescence intensities are linearly proportional to the concentrations of target RNA from 50 pM to 10 nM.
