The authors describe a colorimetric method for the determination of the staphylococcal enterotoxin B (SEB) that also allows for visual readout. The assay is based on the growth of gold nanoparticles (AuNPs) mediated by a hemin/G-quadruplex DNAzyme which generates a color change from red to blue in the presence of SEB. The method is enzyme-free and does not require a label. The kinetics of the formation of the AuNPs is controlled by the hemin/G-quadruplex DNAzyme and this is key to the signal generation mechanism. In the presence of SEB, the reactions between aptamer and target modulated the amount of single probe G strands that form DNAzyme capable of consuming hydrogen peroxide. The growth process of AuNPs is influenced by the resulting concentration of H2O2 and leads to the color change. Under optimal conditions, a linear relationship exists between absorbance and SEB concentration in the range from 0.1 to 500 pg·mL￣1 which covers the clinically relevant range. In case of visual detection, the lower limit of detection is 1 pg·mL?1. The assay described here is sensitive, comparably inexpensive and can detect SEB rapidly without the need for sophisticated equipment. In our perception, the method has a wide scope in that it may be adapted to various nucleic acids, proteins and other biomolecules if respective aptamers are available.
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) 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 colorimetric assay is described for the detection of BCR/ABL fusion genes. Polyamidoamine (PAMAM) dendrimers were placed on peroxidase (POx) mimicking Au@Pt nanoparticles to form a nanocomposite of type Au@Pt-PAMAM. Capture DNA probe is a designed nucleic acid strand that specifically binds target DNA to the surface of the electrode. The capture probe was attached to magnetic beads via biotin and avidin interaction. The hairpin structure of the capture probe can only be opened by the complementary BCR/ABL DNA. This results in a highly specific assay. The POx-mimicking property of the Au@Pt-PAMAM causes the formation of a blue dye by reaction of H2O2 and 3,3,3′,3′-tetramethylbenzidine (TMB) which is measured by a microplate reader. Under optimum conditions, the absorbance increases linearly the 1 pM to 100 nM BCR/ABL concentration range, and the detection limit is as low as 190 fM. The method is highly selective and was successfully applied to the determination of fusion genes in spiked real samples. Conceivably, it possesses a large potential in clinical testing of patients suffering from chronic myeloid leukemia.
Graphical abstract Au@PtNP, an efficient catalyst, is bound with polyamidoamine (PAMAM) dendrimer to amplify the colorimetric signal. With the introduction of streptavidin-magnetic beads to remove non-specific signals, a novel colorimetric sensor is constructed to detect BCR/ABL fusion genes.
The authors describe an array for chemiluminescence (CL) based determination of cardiac troponin T (cTnT), an important cardiovascular disease marker. The tracing tag consists of silver nanoparticles (AgNPs) loaded with guanine-rich DNA sequences and detection antibody in a high numerical ratio. The loaded AgNPs were then reacted with hemin to form a hemin/G-quadruplex DNAzyme. A disposable immunosensor array was fabricated by immobilizing capture antibody on corresponding sensing sites on a glass chip. Once a sandwich immunocomplex is formed on the array, the tracing tag catalyzes the CL reaction of the luminol-p-iodophenol and H2O2 system to produce a CL signal, which is collected by a CCD camera. An intuitive CL image is obtained containing all of the spots on the array. Under optimal conditions, the method shows a wide linear range over 4 orders of magnitude (from 0.003 to 270 ng·L?1), a detection limit down to 84 fg·L?1, and a throughput as high as 44 tests·h?1. The results obtained with serum samples are in acceptable agreement with reference values. The AgNP-based tracing tag as well as the immunoassay method shows a promising potential for point-of-care testing for the early clinical diagnosis of cardiovascular disease.
Graphical abstract Schematic presentation of silver nanoparticles (AgNPs) functionalized with hemin/G-quadruplex DNAzyme for highly sensitive chemiluminescence (CL) immunoassay of cardiac troponin T (cTnT) on a glass chip array.
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.
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.
5-Hydroxymethylcytosine in DNA (5hmC-DNA) plays an important biological role in sculpting the epigenetic landscape. Its presence is linked to diseases, especially cancers. The authors describe an amperometric biosensor for the determination of 5hmC. It is based on a chemical modification of the hydroxy group of 5hmC in the DNA sequence. Enzymatic signal amplification is accomplished by using DNA methyltransferase (M.HhaI-DNA-cytosine-5-methyltransferase) to achieve chemical modification. A graphene-perylenetetracarboxylic acid nanocomposite was used to modify a glassy carbon electrode (GCE) that acts as a substrate electrode. A composite consisting of horseradish peroxidase on silica/poly(acrylic acid) brushes is employed as the signal amplification unit. Under the optimized conditions, there is a linear response to the logarithm of the 5hmC-DNA concentration in the range from 0.5 to 30 nM, with a 0.23 nM detection limit (at an S/N ratio of 3) in the potential range from ?0.3 V to -0.8 V at 100 mV/s. The bioassay has excellent specificity and can even discriminate the similar base 5mC.
Graphical abstract An amperometric biosensor is fabricated for 5-hydroxymethylcytosine (5hmC) determination, where DNA methyltransferase was used to achieve chemical modification of 5hmC, and spherical poly(acrylic acid) brushes conjugated horseradish peroxidase was used as the signal amplification unit. The biosensor showed high sensitivity and specificity.
Electrochemical DNA sensors represent a simple, accurate and economical platform for DNA detection. Gold nanoparticles are known to be efficient labels in electrochemical sensors and to be viable materials to modify the surface of electrodes thereby to enhance the detection limit of the sensor. For surface modification, gold nanoparticles are used in combination with nanomaterials like graphene, graphene oxide, or carbon nanotubes to improve electrochemical performance in general. This review (with 116 refs.) mainly covers the advances made in recent years in the use of gold nanoparticles in DNA sensing. It is divided into the following main sections: (a) An introduction covers aspects of electrochemical sensing of DNA and of appropriate nanomaterials in general. (b) The use of gold nanoparticles in DNA is specifically addressed next, with subsections on AuNPs acting as electrochemical labels, electron transfer mediators, signal amplifiers, carriers of electroactive molecules, catalysts, immobilization platforms, on silver enhancement strategies, on AuNPs modified with carbonaceous materials (such as graphenes and nanotubes), and on multiple amplification schemes. The review concludes with a discussion of current challenges and trends in terms of highly sensitive DNA based sensing using AuNPs.
Graphical abstract The review describes the state of the art in the use of gold nanoparticles in the electrochemical DNA sensors and contains sections on the use of AuNPs as labels, signal amplifiers, carriers of electroactive molecules, catalyst, immobilization platform, and on silver enhancement and multiple amplification strategies.
The authors introduce a method for spatially arranged DNA immobilization on 10-nm gold nanoparticles (GNP) deposited on a silicon substrate carrying nanogapped interdigitated electrodes. The GNPs are covalently bound to the surface via silane chemistry, and the single steps of fabrication are monitored by FTIR spectroscopy and atomic force microscopy. This GNP deposition technique is shown to reduce the size of the nanogaps to 130 nm. FTIR also was used to monitor the immobilization of DNA on the surface of the interdigitated electrodes. This method allows DNA to be immobilized in a uniform and homogenous way. The utility of the method is demonstrated by immobilizing probe DNA on the surface and detecting target DNA specific for the human papilloma virus via fluorescence with a detection limit as low as 1 pM. In our perception, this method for GNP-mediated DNA immobilization enables high-performance sensing of a wide range of target (analyte) DNA.
Graphical abstract Schematic presentation of gold nanoparticle-mediated and spatially resolved deposition of DNA on nano-gapped interdigitated electrodes. The method was applied to the chemiluminescent determination of the human papillomavirus
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.
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 have investigated (a) the self-assembly of single-stranded DNA (ssDNA) on glass surfaces, and (b) the interaction of DNA with liquid crystals (LCs) on solid surfaces. The results suggest that ssDNA (compared to dsDNA) on the solid interface causes particularly different orientations in LCs. The LC molecules assume a uniform homeotropic orientation on the surface with a typical surface ssDNA coverage of ~2.4 × 1012 molecules per square cm. Once complementary DNA is hybridized on the surface, the homotropic orientation of the LCs becomes disrupted. This orientation transition can be visually observed by using a crossed polarizer. The findings were exploiting to design an assay for target DNA (= analyte DNA) that has an ~0.1 nM detection limit. The assay is highly selective and can easily differentiate target DNA from single-base mismatch and non-complementary DNA. In our perception, it represents a powerful, label-free and portable DNA detection scheme.
Graphical abstract Schematic illustration of the mechanism for orientation behavior of a liquid crystal film supported on different surfaces. The homeotropic orientation of LC molecules was induced by ssDNA with appropriate surface coverage and was disrupted by ssDNA with lower or higher surface coverage or P1/T1 complex. 5CB: 4-Cyano-4′-pentylbiphenyl. TEA: Triethoxysilylbutyraldehyde.
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 an SPR sensor chip coated with gold nanoparticles (AuNPs) that enables highly sensitive determination of genetically modified (GM) crops. Detection is based on localized surface plasmon resonance (LSPR) with its known sensitivity to even minute changes in refractive index. The device consists of a halogen light source, a light detector, and a cuvette cell that contains a sensor chip coated with AuNPs. It is operated in the transmission mode of the optical path to enhance the plasmonic signal. The sample solution containing target DNA (e.g. from the GM crop) is introduced into the cuvette with the sensor chip whose surface was functionalized with a capture DNA. Following a 30-min hybridization, the changes of the signal are recorded at 540 nm. The chip responds to target DNA in the 1 to 100 nM concentration range and has a 1 nM detection limit. Features of this sensor chip include a short reaction time, ease of handling, and portability, and this enables on-site detection and in-situ testing.
Graphical abstract A localized surface plasmon resonance (LSPR)-based nanoplasmonic spectroscopic device enabling a highly sensitive biosensor is developed for the detection of genetically modified (GM) DNA founded in Roundup Ready (RR) soybean.
An aptamer based method is described for the electrochemical determination of ampicillin. It is based on the use of DNA aptamer, DNA functionalized gold nanoparticles (DNA-AuNPs), and single-stranded DNA binding protein (ssDNA-BP). When the aptamer hybridizes with the target DNA on the AuNPs, the ssDNA-BP is captured on the electrode surface via its specific interaction with ss-DNA. This results in a decreased electrochemical signal of the redox probe Fe(CN)63? which is measured best at a voltage of 0.188 mV (vs. reference electrode). In the presence of ampicillin, the formation of aptamer-ampicillin conjugate blocks the further immobilization of DNA-AuNPs and ssDNA-BP, and this leads to an increased response. The method has a linear reposne that convers the 1 pM to 5 nM ampicillin concentration range, with a 0.38 pM detection limit (at an S/N ratio of 3). The assay is selective, stable and reproducible. It was applied to the determination of ampicillin in spiked milk samples where it gave recoveries ranging from 95.5 to 105.5%.
Graphical abstract Schematic of a simple and sensitive electrochemical apta-biosensor for ampicillin detection. It is based on the use of gold nanoparticles (AuNPs), DNA aptamer, DNA functionalized AuNPs (DNA-AuNPs), and single-strand DNA binding protein (SSBP).
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 an electrochemical DNA nanosensor based on the use of single gold nanowire electrodes (AuNWEs). The probe DNA is immobilized on the AuNWE via Au-S bonds that are formed between thiol-terminated DNA and the gold surface. Single AuNWEs were prepared by an improved laser-assisted pulling method and hydrofluoric acid etching. The nanoelectrodes were characterized by cyclic voltammetry and COMSOL simulation. Square wave voltammetry was used to monitor the DNA hybridization event between probe DNA and target DNA by using Methylene Blue (MB) as an intercalator of dsDNA. Under optimal conditions, the peak current for MB (best measured at a potential of ?0.2 V vs. Ag/AgCl) increases linearly with the logarithm of the analyte concentration in the 1.0 f. to 10 nM range, with a 0.48 fmM detection limit at an S/N ratio of 3. The assay is highly selective, reproducible and stable. Considering the small overall dimensions and high sensitivity, this nanoelectrode potentially can be applied to in-vivo sensing of DNA inside living cells
Graphical abstract Schematic presentation of an electrochemical DNA nanosensor using single gold nanowire electrodes and based on the interaction of thiol-terminated DNA and gold surface. It was used to detect complementary DNA with high selectivity and sensitivity.
A method is described for the determination of the polarity of mixed organic solvents by using the fluorescent probe Hostasol Red (HR) desposited on the outer surface of nanosized zeolite L. Organic solvents and their mixtures can be roughly classified according to their polarity with bare eyes and fluorometrically. Emission peaks range from 520 to 640 nm. Some solvents act as quenchers. The method is studied with series of protic and nonprotic solvents, and with selected mixtures of organic solvents.
Graphical abstract The dye Hostalene Red adsorbed on nanosized zeolite shows strong fluorescence solvatochromism. This can be exploited to quickly assess the polarity of solvents and solvent mixtures.
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.
