Enzyme-free colorimetric detection of DNA by using gold nanoparticles and hybridization chain reaction amplification

Enzyme-Free Amplification by Nano Sticky Balls for Visual Detection of ssDNA/RNA Oligonucleotides

Visual detection of nucleic acids provides simple and rapid screening for infectious diseases or environmental pathogens. However, sensitivity is the current bottleneck, which may require enzymatic amplification for targets in low abundance and make them incompatible with detection at resource-limited sites. Here we report an enzyme-free amplification that provides a sensitive visual detection of ssDNA/RNA oligonucleotides on the basis of nano "sticky balls". When target oligonucleotides are present, magnetic microparticles (MMPs) and gold nanoparticles (AuNPs) were linked together, allowing the collection of AuNPs after magnetic attraction. Subsequently, the collected AuNPs, which carry many oligonucleotides, were used as the sticky balls to link a second pair of MMPs and polymer microparticles (PMPs). Thus, because the magnetic field can attract the MMPs as well as the linked PMPs to the sidewall, the reduction of suspended PMPs yields a change of light transmission visible by the naked eye. Our results demonstrate that the limit of detection is 10 amol for ssDNAs (228 fM in 45 μL) and 75 amol for ssRNAs (1.67 pM in 45 μL). This method is also compatible with the serum environment and detection of a microRNA, miR-155, derived from human breast cancer cells. With significantly improved sensitivity for visual detection, it provides great potential for point-of-care applications at resource-limited sites.

Enzyme-free fluorescent biosensor for the detection of DNA based on core-shell Fe3O4 polydopamine nanoparticles and hybridization chain reaction amplification

A novel, highly sensitive assay for quantitative determination of DNA is developed based on hybridization chain reaction (HCR) amplification and the separation via core-shell Fe3O4 polydopamine nanoparticles (Fe3O4@PDA NPs). In this assay, two hairpin probes are designed, one of which is labeled with a 6-carboxyfluorescein (FAM). Without target DNA, auxiliary hairpin probes are stable in solution. However, when target DNA is present, the HCR between the two hairpins is triggered. The HCR products have sticky ends of 24 nt, which are much longer than the length of sticky ends of auxiliary hairpins (6 nt) and make the adsorption much easier by Fe3O4@PDA NPs. With the addition of Fe3O4@PDA NPs, HCR products could be adsorbed because of the strong interaction between their sticky ends and Fe3O4@PDA NPs. As a result, supernatant of the solution with target DNA emits weak fluorescence after separation by magnet, which is much lower than that of the blank solution. The detection limit of the proposed method is as low as 0.05 nM. And the sensing method exhibits high selectivity for the determination between perfectly complementary sequence and target with single base-pair mismatch. Importantly, the application of the sensor for DNA detection in human serum shows that the proposed method works well for biological samples.

Cleavage-based hybridization chain reaction for electrochemical detection of thrombin

In the present work, we constructed a new label-free "inter-sandwich" electrochemical aptasensor for thrombin (TB) detection by employing a cleavage-based hybridization chain reaction (HCR). The designed single-stranded DNA (defined as binding DNA), which contained the thrombin aptamer binding sequence, a DNAzyme cleavage site and a signal reporter sequence, was first immobilized on the electrode. In the absence of a target TB, the designed DNAzymes could combine with the thrombin aptamer binding sequence via complementary base pairing, and then Cu(2+) could cleave the binding DNA. In the presence of a target TB, TB could combine with the thrombin aptamer binding sequence to predominantly form an aptamer-protein complex, which blocked the DNAzyme cleavage site and prevented the binding DNA from being cleaved by Cu(2+)-dependent DNAzyme. As a result, the signal reporter sequence could leave the electrode surface to trigger HCR with the help of two auxiliary DNA single-strands, A1 and A2. Then, the electron mediator hexaammineruthenium (III) chloride ([Ru(NH3)6](3+)) was embedded into the double-stranded DNA (dsDNA) to produce a strong electrochemical signal for the quantitative measurement of TB. For further amplification of the electrochemical signal, graphene reduced by dopamine (PDA-rGO) was introduced as a platform in this work. With this strategy, the aptasensor displayed a wide linearity in the range of 0.0001 nM to 50 nM with a low detection limit of 0.05 pM. Moreover, the resulting aptasensor exhibited good specificity and acceptable reproducibility and stability. Because of these factors, the fabrication protocol proposed in this work may be extended to clinical application.

An enzyme-free and amplified colorimetric detection strategy via target-aptamer binding triggered catalyzed hairpin assembly

Here we introduce an enzyme-free and colorimetric detection strategy for small molecule adenosine. The approach is based on the adenosine-aptamer binding triggered liberation of an initiator strand that consecutively catalyzes DNA hairpins hybridized from singles to couples. These couples induce gold nanoparticles assembled via crosslinking, which could be visualized by a color change.

Label-free colorimetric aptasensor for IgE using DNA pseudoknot probe

The development of simple and low-cost approaches to the detection of immunoglobulin E (IgE) would provide a method for the early diagnosis and prevention of atopic diseases. The current methods of detection are generally tedious, multi-step processes and are limited by the high cost of the labeled proteins. We describe here a label-free structure-switching colorimetric method for the simple measurement of IgE using DNA pseudoknot probes and gold nanoparticles. In the absence of a target the IgE aptamer probe adopts a pseudoknot conformation that dissociates a capture probe from the unmodified gold nanoparticles. However, when IgE binds to the aptamer probe, the pseudoknot is resolved, leading to a favorable hybridization between the 3' terminal loop of the aptamer probe and the capture probe; this induces the aggregation of the gold nanoparticles. As a result, the colorimetric IgE sensor using this structure-switching mechanism is sensitive, specific and convenient, and the assay works even when challenged with complicated biological matrixes such as vaginal fluids. The proposed method is expected to be of great clinical value for IgE detection and could be used, after appropriate design, for sensing applications of other structured aptamers.

High-sensitivity detection of ATP using a localized surface plasmon resonance (LSPR) sensor and split aptamers

A highly sensitive localized surface plasmon resonance (LSPR) aptasensor for detection of adenosine triphosphate (ATP) has been developed. The sensor utilizes two split ATP aptamers, one (receptor fragment) being covalently attached to the surface of a gold nanorod (GNR) and the other labeled with a random DNA sequence and TAMRA dye (probe fragment). In the presence of both ATP and the probe fragment, a significant shift takes place in the wavelength of the LSPR band. This phenomenon is a consequence of the fact that the split fragments assemble into an intact folded structure in the presence of ATP, which brings about a decrease in the distance between the GNR surface and TAMRA dye and an associated LSPR wavelength. By using this sensor system, concentrations of ATP in the range of 10 pM-10 μM can be determined. In addition, by taking advantage of its denaturation properties, the LSPR aptasensor can be reused by simply subjecting it to quadruple salt-addition/2M NaCl washing steps. That the new method is applicable to biological systems was demonstrated by its use to measure ATP concentrations in E. coli and, thus to determine cell concentrations as low as 1.0×10(3) CFU.

Highly sensitive colorimetric determination of amoxicillin in pharmaceutical formulations based on induced aggregation of gold nanoparticles

A novel, simple and highly sensitive colorimetric method is developed for determination of Amoxicillin (AMX). The system is based on aggregation of citrate-capped gold nanoparticles (AuNP) in acetate buffer (pH=4.5) in the presence of the degradation product of Amoxicillin (DPAMX). It was found that the color of gold nanoparticles changed from red to purple and the intensity of surface plasmon resonance (SPR) peak of AuNPs decreased. A new absorption band was appeared in the wavelength range of 600-700nm upon addition of DPAMX. The absorbance ratio at the wavelength of 660 and 525nm (A660/A525) was chosen as the analytical signal indirectly related to AMX concentration. The linearity of the calibration graph was found over the concentration range of 0.3-4.5μM AMX with a correlation coefficient of 0.9967. Under the optimum experimental conditions, the detection limit was found to be 0.15μM. The applicability of the method was successfully demonstrated by analysis of AMX in pharmaceutical formulations including capsules and oral suspensions.

Molecular beacon mediated circular strand displacement strategy for constructing a ratiometric electrochemical deoxyribonucleic acid sensor

A novel ratiometric electrochemical sensor for sensitive and selective determination of deoxyribonucleic acid (DNA) had been developed based on signal-on and signal-off strategy. The target DNA hybridized with the loop portion of ferrocene (Fc) labeled hairpin probe immobilized on the gold electrode (GE), the Fc away from the surface of GE and the methylene blue (MB) was attached to an electrode surface by hybridization between hairpin probe and MB labeled primer. Such conformational changes resulted in the oxidation peak current of Fc decreased and that of MB increased, and the changes of dual signals are linear with the concentration of DNA. Furthermore, with the help of strand-displacement polymerization, polymerase catalyzed the extension of the primer and the sequential displacement of the target DNA, which led to the release of target and another polymerization cycle. Thus the circular strand displacement produced the multiplication of the MB confined near the GE surface and Fc got away from the GE surface. Therefore, the recognition of target DNA resulted in both the "signal-off" of Fc and the "signal-on" of MB for dual-signal electrochemical ratiometric readout. The dual signal strategy offered a dramatic enhancement of the stripping response. The dynamic range of the target DNA detection was from 10(-13) to 10(-8) mol L(-1) with a detection limit down to 28 fM level. Compared with the single signaling electrochemical sensor, the dual-signaling electrochemical sensing strategy developed in this paper was more selective. It would have important applications in the sensitive and selective electrochemical determination of other small molecules and proteins.

An enzyme-free and label-free fluorescent biosensor for small molecules by G-quadruplex based hybridization chain reaction

An enzyme-free and label-free fluorescent biosensor is developed by G-quadruplex-based hybridization chain reaction (HCR) for small molecules, using adenosine triphosphate (ATP) as the model. Aptamer probes for the recognition of small molecules are hybridized with blocking probes. The G-quadruplex sequences are incorporated into one of the two HCR hairpin probes. In the presence of small molecules (ATP), the formation of aptamer-ATP bioaffinity complexes induces the release of blocking probes; the released blocking probes initiate HCR and numerous G-quadruplexes along DNA nanowires are self-assembled after the HCR process. Using N-methyl mesoporphyrin IX (NMM) as the fluorophore, a "turn-on" fluorescence response can be achieved and detected as low as 15 μmol L(-1) of ATP. This biosensor is applied to detect ATP in biologic samples with satisfactory results.

Carbon nanodots as ligand exchange probes in Au@C-dot nanobeacons for fluorescent turn-on detection of biothiols

Au nanoparticle-carbon dot core-shell (Au@C-dot) nanocomposite was synthesized in aqueous medium at room temperature using the carbon dots as reducing agents themselves. The carbon nanodots also function as an effective stabilizer by forming a thin layer surrounding Au nanoparticles (Au NPs) similar to self-assembled monolayers. Ligand exchange with thiol containing biomolecules resulted in the release of carbon dots from the Au NP surface leading to an enhancement of fluorescence. Simultaneously the agglomeration of Au NPs stimulated by the interaction of biothiols led to changes in the surface plasmon properties of Au NPs. A detailed spectroscopic investigation revealed a combination of static and dynamic quenching being involved in the process. Thus, the Au nanoparticle-carbon dot composite could be used as a dual colorimetric and fluorometric sensor for biothiols ranging from amino acids, peptides, proteins, enzymes etc. with a detection limit of 50 nM.

Colorimetric detection of mercury ion based on unmodified gold nanoparticles and target-triggered hybridization chain reaction amplification

A novel unmodified gold nanoparticles (AuNPs)-based colorimetric strategy for label-free, specific and sensitive mercury ion (Hg(2+)) detection was demonstrated by using thymine-Hg(2)(+)-thymine (T-Hg(2)(+)-T) recognition mechanism and hybridization chain reaction (HCR) amplification strategy. In this protocol, a structure-switching probe (H0) was designed to recognize Hg(2+) and then propagated a chain reaction of hybridization events between two other hairpin probes (H1 and H2). In the absence of Hg(2+), all hairpin probes could stably coexist in solution, the exposed sticky ends of hairpin probes were capable of stabilizing AuNPs. As a result, salt-induced AuNPs aggregation could be effectively prevented. In the presence of Hg(2+), thymine bases of H0 could specifically interact with Hg(2+) to form stable T-Hg(2)(+)-T complex. Consequently, the hairpin structure of H0 probe was changed. As H1/H2 probes were added, the HCR process could be triggered and nicked double-helixes were formed. Since it was difficult for the formed nicked double-helixes to inhibit salt-induced AuNPs aggregation, a red-to-blue color change was observed in the colloid solution as the salt concentration increased. With the elegant amplification effect of HCR, a detection limit of around 30 nM was achieved (S/N=3), which was about 1-2 orders of magnitudes lower than that of previous unmodified AuNPs-based colorimetric methods. By using the T-Hg(2)(+)-T recognition mechanism, high selectivity was also obtained. As an unmodified AuNPs-based colorimetric strategy, the system was simple in design, convenient in operation, and eliminated the requirements of separation processes, chemical modifications, and sophisticated instrumentations.

Label-free colorimetric detection of biothiols utilizing SAM and unmodified Au nanoparticles

Herein, a sensitive and selective sensor for biothiols based on colorimetric assay is reported. S-adenosyl-L-methionine (SAM) could induce the selective aggregation of unmodified gold nanoparticles (AuNPs) by electrostatic interaction. In the presence of biothiols, such as glutathione (GSH), homocysteine (Hcy), and cysteine (Cys), AuNPs prefer to react with thiols of biothiols rather than SAM due to the formation of Au-S bond. Thus, the AuNPs turn from the aggregation to the dispersion state, and the corresponding color variation in the process of anti-aggregation of AuNPs can be used for the quantitative screening of biothiols through UV-vis spectroscopy or by the naked eye. Under optimized conditions, a good linear relationship in the range of 0.4-1.2 µM is obtained for Cys, 0.2-0.9 µM for GSH, and 0.6-3.0 µM for Hcys. The detection limits of this assay for GSH, Cys and Hcys are 35.8 nM, 21.7 nM, and 62.4 nM, respectively. This colorimetric assay exhibits rapid operation (within 5 min), high selectivity and sensitivity towards biothiols with tunable dynamic ranges.

Graphene quantums dots combined with endonuclease cleavage and bidentate chelation for highly sensitive electrochemiluminescent DNA biosensing

A novel strategy for highly sensitive electrochemiluminescence (ECL) detection of DNA was proposed based on site-specific cleavage of BamHI endonuclease combined with the excellent ECL activity of graphene quantum dots (GQDs) and bidentate chelation of the dithiocarbamate DNA (DTC-DNA) probe assembly. The difference between photoluminescence and ECL spectral peaks suggested that a negligible defect existed on the GQDs surface for generation of an ECL signal. The formed DTC-DNA was directly attached to the gold surface by bidentate anchoring (S-Au-S bonds), which conferred a strong affinity between the ligands and the gold surface, increasing the robustness of DNA immobilization on the gold surface. BamHI endonuclease site-specifically recognized and cleaved the duplex symmetrical sequence, which made the double-stranded DNA fragments and GQDs break off from the electrode surface, inducing a decrease of the ECL signal. Using hepatitis C virus-1b genotype complementary DNA (HCV-1b cDNA) as a model, a novel signal-off ECL DNA biosensor was developed based on variation of the ECL intensity before and after digestion of the DNA hybrid. Electrochemical impedance spectroscopy confirmed the successful fabrication of the ECL DNA biosensor. This ECL biosensor for HCV-1b cDNA determination exhibited a linear range from 5 fM to 100 pM with a detection limit of 0.45 fM at a signal-to-noise ratio of 3 and showed satisfactory selectivity and good stability, which validated the feasibility of the designed strategy. The proposed strategy may be conveniently combined with other specific biological recognition events for expansion of the biosensing application, especially in clinical diagnoses.

Highly sensitive “signal-on” electrochemiluminescent biosensor for the detection of DNA based on dual quenching and strand displacement reaction

A “signal-on” electrochemiluminescent DNA biosensing platform was proposed based on dual quenching and the strand displacement reaction.

An enzyme-free and amplified colorimetric detection strategy: assembly of gold nanoparticles through target-catalytic circuits

Herein we introduce an enzyme-free and amplified colorimetric detection strategy, which is based on gold nanoparticle (AuNP) aggregation through target-catalytic DNA circuits (HCR and CHA).

A novel electrochemical biosensor for DNA detection based on exonuclease III-assisted target recycling and rolling circle amplification

A strategy for electrochemical detection of DNA by exonuclease III-assisted DNA recycling and the rolling circle amplification was developed.

Visual detection of nucleic acids based on Mie scattering and the magnetophoretic effect

Visual detection of nucleic acid biomarkers by magnetically attracted microparticles that change solution turbidity via Mia scattering.

Ultrasensitive electrochemical biosensing for DNA using quantum dots combined with restriction endonuclease

A sensitive platform using endonuclease and AuNPs as well as environmental Bi film for the detection of DNA has been developed.

Label-free colorimetric aptasensor for sensitive detection of ochratoxin A utilizing hybridization chain reaction

The combination of high selectivity of aptamer with the peroxidase-mimicking property of DNAzyme has presented considerable opportunities for designing colorimetric aptasensor for detection of ochratoxin A (OTA). The activities of both aptamer (as biorecognition element) and DNAzyme (as signal amplification element) are blocked via base pairing in the hairpin structure. Hybridization chain reaction (HCR) between two hairpin DNAs was employed to further improve the sensitivity of this method. The presence of OTA triggers the opening of the hairpin structure and the beginning of HCR, which results in the release of many DNAzyme, and generates enhanced colorimetric signals, which is correlated to the amounts of OTA with linear range between 0.01 to 0.32 nM, and the limit of detection is 0.01 nM under optimal conditions. OTA in yellow rice wine and wheat flour samples was also detected using this method. We demonstrate that a new colorimetric method for the detection of OTA has been established, which is simple, easy to conduct, label-free, sensitive, high throughput, and cost-saving.

Binding-induced collapse of DNA nano-assembly for naked-eye detection of ATP with plasmonic gold nanoparticles

The detection of small molecules depends heavily on complicated GC-MS (Gas chromatography-mass spectrometry), HPLC (High-performance liquid chromatography) and some other complicated instruments that are not suitable for point of care detection. Here, we have demonstrated a fast (in 10min), simple (instrument-free) and effective detection platform for small molecule-ATP. In our design, we engineered the hybridization region of aptamer and assembled it into a superstructure to avoid the exposed flexible ends. The binding of ATP triggered the collapse of the superstructures to produce single stranded DNA that can obviously tune the plasmonic coupling of unmodified gold nanoparticles (AuNPs). Compared to detection platforms based on fully hybridized aptamer double helix, the detection time was significantly decreased to 10min. The resulting color change can be recognized by naked eyes. Our detection is highly specific and selective. Furthermore, a logic gate with multiplexed detection capability for ATP and DNA were demonstrated.

Statistical analysis of gold nanoparticle-induced oxidative stress and apoptosis in myoblast (C2C12) cells

Nanoscale gold particles (Au-NPs) with a diameter below 20nm are notably important candidates for various important applications because of their extraordinary quantum size effects. Their high surface area-to-volume ratio facilitates their very high reactivities; therefore, they can be utilised in different ways in biomedical applications. For example, these nanoparticles can penetrate into cells and bind with proteins or DNA and are therefore potential nanostructures employed for sensing and detecting various biological identities. In the present work, we synthesised Au-NPs via a colloidal process using chloroauric acid (HAuCl4·4H2O) and trisodium citrate dihydrate (N3C6H5O7) as a reducing agent. The shape evolution and the structural properties of these NPs were investigated in detail using TEM and high resolution HR-TEM investigations. Different doses of Au NPs have been applied to treat C2C12 myoblast cells in a 24-h incubation period, and a dose-dependent study has also been performed. The cells were cultivated in DMEM with FBS and antibiotics (strepto-penicillin) at 37°C in a 5% humidified environment of CO2 and 95% air. Cell viability analysis using MTT assays revealed that increased concentration of Au NPs (100-1000 ng/mL) resulted in a decreased density of cells. The amount of reactive oxygen species (ROS) in C2C12 cells analysed with Au-NPs (in a dose-dependent manner), and the RT-PCR data demonstrated the up-regulation of caspase-3 and caspase-7 genes in C2C12 cells after treatment with Au-NPs. These results have been confirmed by detailed confocal microscopy (CLSM) studies. In addition, the quantitative analysis of the Au-NPs was also confirmed by statistical analytical parameters, such as precision, accuracy, linearity, limits of detection (LOD) and limit of quantitation (LOQ), quantitative recoveries and relative standard deviation (RSD), and the analyses again exhibited a significant and large effect of Au NPs on C2C12 cells.

Assistant deoxyribonucleic acid recycling with Zn(2+) and molecular beacon for electrochemical detection of deoxyribonucleic acid via target-triggered assembly of mutated DNAzyme

A novel enzyme-free amplification strategy was designed for sensitive electrochemical detection of deoxyribonucleic acid (DNA) based on Zn(2+) assistant DNA recycling via target-triggered assembly of mutated DNAzyme. A gold electrode was used to immobilize molecular beacon (MB) as the recognition probe and perform the amplification procedure. In the presence of target DNA, the hairpin probe 1 was opened, and the DNAzyme was liberated from the caged structure. The activated DNAzyme first hybridized and then cleaved the MB in the presence of cofactor Zn(2+). After cleavage, the MB was cleaved into two pieces and the ferrocene (Fc) labeled piece dissociated from the gold electrode, thus obviously decreasing the Fc signal and forming a free DNAzyme strand. Finally, each target-induced activated DNAzyme underwent many cycles to trigger the cleavage of many MB substrates. Therefore, the peak current of Fc dramatically decreased to approximately zero. The strategy showed a detection limit at 35 fM levels, which was about 2 orders of magnitude lower than that of the conventional hybridization without Zn(2+)-based amplification. The Zn(2+) assistant DNA recycling offers a versatile platform for DNA detection in a cost-effective manner, and has a promising application in clinical diagnosis.

Label-free and enzyme-free sensitive fluorescent detection of human immunodeficiency virus deoxyribonucleic acid based on hybridization chain reaction

A label-free and enzyme-free sensitive fluorescent detection of human immunodeficiency virus (HIV) deoxyribonucleic acid (DNA) based on isothermal hybridization chain reaction (HCR) was developed. A G-quadruplex sequence which was incorporated into one of the two hairpin probes was inactive in the absence of target DNA. However, at the presence of target DNA numerous G-quadruplexes along DNA nanowires were self-assembled through HCR. Using N-methyl mesoporphyrin IX (NMM) as the fluorophore, a "turn-on" fluorescent response would be achieved and detected as low as 0.5 nmol L(-1) of HIV DNA. This proposed method was applied to detect HIV DNA in biologic samples with satisfactory results.

Improved ligation-mediated PCR method coupled with T7 RNA polymerase for sensitive DNA detection

The ligation-mediated polymerase chain reaction (PCR) method is widely applied for detecting short-length DNA target. The primary principle of this method is based on the linkage of two separated DNA probes as PCR templates via simultaneous hybridization with DNA target by DNA ligase. Even before taking into account low ligation efficiency, a 1:1 stoichiometric ratio between DNA target and the produced PCR template would put an intrinsic limitation on the detection sensitivity. In order to solve this problem, we have developed an improved ligation-mediated PCR method. It is designed such that a transcription reaction by T7 RNA polymerase is integrated into the ligation reaction. In this way, the produced joint DNA strand composed by two DNA probes can be used as a template both in the transcription reaction and the following PCR process. Then a great number of RNA strands containing the same sequence as DNA target are transcribed to act as a target to initiate new cyclic reactions of ligation and transcription. The results indicate that our proposed method can improve the detection sensitivity by ~2 orders of magnitude compared with the conventional ligation-mediated PCR method.

Diagnostic applications of nucleic acid circuits

CONSPECTUS: While the field of DNA computing and molecular programming was engendered in large measure as a curiosity-driven exercise, it has taken on increasing importance for analytical applications. This is in large measure because of the modularity of DNA circuitry, which can serve as a programmable intermediate between inputs and outputs. These qualities may make nucleic acid circuits useful for making decisions relevant to diagnostic applications. This is especially true given that nucleic acid circuits can potentially directly interact with and be triggered by diagnostic nucleic acids and other analytes. Chemists are, by and large, unaware of many of these advances, and this Account provides a means of touching on what might seem to be an arcane field. We begin by explaining nucleic acid amplification reactions that can lead to signal amplification, such as catalytic hairpin assembly (CHA) and the hybridization chain reaction (HCR). In these circuits, a single-stranded input acts on kinetically trapped substrates via exposed toeholds and strand exchange reactions, refolding the substrates and allowing them to interact with one another. As multiple duplexes (CHA) or concatemers of increasing length (HCR) are generated, there are opportunities to couple these outputs to different analytical modalities, including transduction to fluorescent, electrochemical, and colorimetric signals. Because both amplification and transduction are at their root dependent on the programmability of Waston-Crick base pairing, nucleic acid circuits can be much more readily tuned and adapted to new applications than can many other biomolecular amplifiers. As an example, robust methods for real-time monitoring of isothermal amplification reactions have been developed recently. Beyond amplification, nucleic acid circuits can include logic gates and thresholding components that allow them to be used for analysis and decision making. Scalable and complex DNA circuits (seesaw gates) capable of carrying out operations such as taking square roots or implementing neural networks capable of learning have now been constructed. Into the future, we can expect that molecular circuitry will be designed to make decisions on the fly that reconfigure diagnostic devices or lead to new treatment options.

A sensitive and selective colorimetric method for detection of copper ions based on anti-aggregation of unmodified gold nanoparticles

A highly sensitive and selective colorimetric method for detection of copper ions, based on anti-aggregation of D-penicillamine (D-PC) induced aggregated gold nanoparticles (AuNPs) was developed. Copper ions can hinder the aggregation of AuNPs induced by D-PC, through formation of mixed-valence complex with D-PC that is a selective copper chelator. In the presence of a fixed amount of D-PC, the aggregation of AuNPs decreases with increasing concentrations of Cu(2+) along with a color change from blue to red in AuNPs solution and an increase in the absorption ratio (A520/A650). Under the optimum experimental conditions (pH 7, [AuNPs] =3.0 nmol L(-1) and [NaCl]=25 mmol L(-1)), a linear calibration curve for Cu(2+) was obtained within the range of 0.05-1.85 µmol L(-1) with a limit of detection (3Sb) of 30 nmol L(-1). Excellent selectivity toward Cu(2+) was observed among various metal ions due to a specific complex formation between Cu(2+) and D-PC. The proposed method has been successfully applied for the detection of Cu(2+) in various real samples.

Next-generation in situ hybridization chain reaction: higher gain, lower cost, greater durability

Hybridization chain reaction (HCR) provides multiplexed, isothermal, enzyme-free, molecular signal amplification in diverse settings. Within intact vertebrate embryos, where signal-to-background is at a premium, HCR in situ amplification enables simultaneous mapping of multiple target mRNAs, addressing a longstanding challenge in the biological sciences. With this approach, RNA probes complementary to mRNA targets trigger chain reactions in which metastable fluorophore-labeled RNA hairpins self-assemble into tethered fluorescent amplification polymers. The properties of HCR lead to straightforward multiplexing, deep sample penetration, high signal-to-background, and sharp subcellular signal localization within fixed whole-mount zebrafish embryos, a standard model system for the study of vertebrate development. However, RNA reagents are expensive and vulnerable to enzymatic degradation. Moreover, the stringent hybridization conditions used to destabilize nonspecific hairpin binding also reduce the energetic driving force for HCR polymerization, creating a trade-off between minimization of background and maximization of signal. Here, we eliminate this trade-off by demonstrating that low background levels can be achieved using permissive in situ amplification conditions (0% formamide, room temperature) and engineer next-generation DNA HCR amplifiers that maximize the free energy benefit per polymerization step while preserving the kinetic trapping property that underlies conditional polymerization, dramatically increasing signal gain, reducing reagent cost, and improving reagent durability.

A simple colorimetric DNA detection by target-induced hybridization chain reaction for isothermal signal amplification

A novel DNA detection method is presented based on a gold nanoparticle (AuNP) colorimetric assay and hybridization chain reaction (HCR). In this method, target DNA hybridized with probe DNA modified on AuNP, and triggered HCR. The resulting HCR products with a large number of negative charges significantly enhanced the stability of AuNPs, inhibiting aggregation of AuNPs at an elevated salt concentration. The approach was highly sensitive and selective. Using this enzyme-free and isothermal signal amplification method, we were able to detect target DNA at concentrations as low as 0.5 nM with the naked eye. Our method also has great potential for detecting other analytes, such as metal ions, proteins, and small molecules, if the target analytes could make HCR products attach to AuNPs.

Nucleic acid-regulated perylene probe-induced gold nanoparticle aggregation: a new strategy for colorimetric sensing of alkaline phosphatase activity and inhibitor screening

A positively charged perylene probe (probe 1) could induce aggregation of the gold nanoparticles (Au NPs). As a result, significant assay solution color changes were observed. A duplex DNA (DNA-1) could induce aggregation of the perylene probe. It was observed that DNA-1 could efficiently regulate the probe 1-induced Au NP aggregation. When probe 1 and DNA-1 were first mixed, DNA-1 induced aggregation of the perylene probe. Au NPs were subsequently added, and no induced aggregation of the Au NPs was observed. Thus the color of the assay solution remained to be red. The assay is quite sensitive; 200 pM DNA-1 could cause a clear solution color change. On the basis of this observation, a novel method for the detection of alkaline phosphatase (ALP) activity has been demonstrated. Our method does not require covalent immobilization of the nucleic acid, or the addition of an excess amount of salt. It is sensitive and convenient.

Enzyme-free and label-free ultrasensitive electrochemical detection of DNA and adenosine triphosphate by dendritic DNA concatamer-based signal amplification

Hybridization chain reaction (HCR) strategy has been well developed for the fabrication of various biosensing platforms for signal amplification. Herein, a novel enzyme-free and label-free ultrasensitive electrochemical DNA biosensing platform for the detection of target DNA and adenosine triphosphate (ATP) was firstly proposed, in which three auxiliary DNA probes were ingeniously designed to construct the dendritic DNA concatamer via HCR strategy and used as hexaammineruthenium(III) chloride (RuHex) carrier for signal amplification. With the developed dendritic DNA concatamer-based signal amplification strategy, the DNA biosensor could achieve an ultrasensitive electrochemical detection of DNA and ATP with a superior detection limit as low as 5 aM and 20 fM, respectively, and also demonstrate a high selectivity for DNA and ATP detection. The currently proposed dendritic DNA concatamer opens a promising direction to construct ultrasensitive DNA biosensing platform for biomolecular detection in bioanalysis and clinical biomedicine, which offers the distinct advantages of simplicity and cost efficiency owing to no need of any kind of enzyme, chemical modification or labeling.