An ultrasensitive colorimeter assay strategy for p53 mutation assisted by nicking endonuclease signal amplification

A novel catalytic colorimetric assay assisted by nicking endonuclease signal amplification (NESA) was developed. With the signal amplification, the detection limit of the p53 target gene can be as low as 1 pM, which is nearly 5 orders of magnitude lower than that of other previously reported colorimetric DNA detection strategies based on catalytic DNAzyme.     

Enzyme-regulated activation of DNAzyme: a novel strategy for a label-free colorimetric DNA ligase assay and ligase-based biosensing

The DNA nick repair catalyzed by DNA ligase is significant for fundamental life processes, such as the replication, repair, and recombination of nucleic acids. Here, we have employed ligase to regulate DNAzyme activity and developed a homogeneous, colorimetric, label-free and DNAzyme-based strategy to detect DNA ligase activity. This novel strategy relies on the ligation-trigged activation or production of horseradish peroxidase mimicking DNAzyme that catalyzes the generation of a color change signal; this results in a colorimetric assay of DNA ligase activity. Using T4 DNA ligase as a model, we have proposed two approaches to demonstrate the validity of the DNAzyme strategy. The first approach utilizes an allosteric hairpin-DNAzyme probe specifically responsive to DNA ligation; this approach has a wide detection range from 0.2 to 40?U?mL(-1) and a detection limit of 0.2?U?mL(-1). Furthermore, the approach was adapted to probe nucleic acid phosphorylation and single nucleotide mismatch. The second approach employs a "split DNA machine" to produce numerous DNAzymes after being reassembled by DNA ligase; this greatly enhances the detection sensitivity by a signal amplification cascade to achieve a detection limit of 0.01?U?mL(-1).     

A new colorimetric platform for ultrasensitive detection of protein and cancer cells based on the assembly of nucleic acids and proteins

An amplified colorimetric method has been developed for the detection of protein and cancer cells based on the assembly of nucleic acids and proteins for the first time. In this process, the assembly of nucleic acids was triggered by a biotinylated DNA strand after a sandwich immunoreaction. The biotinylated DNA strand and sandwich immunocomplex were connected by streptavidin. Then, the assembly of biotinylated bovine serum albumin (Biotin-BSA) and streptavidin-horseradish peroxidase (SA-HRP) occurred at a node of the assembled products of nucleic acids through the biotin-streptavidin reaction. Under the catalysis of horseradish peroxidase, 3,3′,5,5′-tetramethylbenzidine (TMB) was oxidized by H₂O₂ and the oxidized product was analyzed by its UV–vis absorbance signal and sensitive colorimetric detection. This colorimetric sensor could not only achieve the quantitative determination of protein by UV–vis absorbance but could also be applied for semiquantitative determination by digital visualization. Using alpha-fetoprotein (AFP) as the model target, this proposed colorimetric method showed a wide linear range from 5 pg/mL to 1 ng/mL with a detection limit of 1.95 pg/mL by the instrument, and even 5 pg/mL target protein could be distinguished simply by the naked eye. This approach was then expanded to detect cancer cells based on the recognition of folic acid receptors that were over-expressed on the cancer cells by folic acid-tethered DNA. More importantly, this strategy can be further used as a universal colorimetric method for the determination of viruses or other proteins by changing the corresponding antibodies.     

Enzyme‐Regulated Activation of DNAzyme: A Novel Strategy for a Label‐Free Colorimetric DNA Ligase Assay and Ligase‐Based Biosensing

The DNA nick repair catalyzed by DNA ligase is significant for fundamental life processes, such as the replication, repair, and recombination of nucleic acids. Here, we have employed ligase to regulate DNAzyme activity and developed a homogeneous, colorimetric, label‐free and DNAzyme‐based strategy to detect DNA ligase activity. This novel strategy relies on the ligation‐trigged activation or production of horseradish peroxidase mimicking DNAzyme that catalyzes the generation of a color change signal; this results in a colorimetric assay of DNA ligase activity. Using T4 DNA ligase as a model, we have proposed two approaches to demonstrate the validity of the DNAzyme strategy. The first approach utilizes an allosteric hairpin‐DNAzyme probe specifically responsive to DNA ligation; this approach has a wide detection range from 0.2 to 40 U mL^?1 and a detection limit of 0.2 U mL^?1. Furthermore, the approach was adapted to probe nucleic acid phosphorylation and single nucleotide mismatch. The second approach employs a “split DNA machine” to produce numerous DNAzymes after being reassembled by DNA ligase; this greatly enhances the detection sensitivity by a signal amplification cascade to achieve a detection limit of 0.01 U mL^?1.     

Colorimetric detection of immobilized horseradish peroxidase based on the co-oxidation of benzidine derivatives and 4-chloro-1-naphthol

Enzymatic co-oxidation of benzidine derivatives and 4-chloro-1-naphthol with hydrogen peroxide was studied for the colorimetric detection of horseradish peroxidase using the DNA microarray on glass surface technology. The co-oxidation of o-dianisidine and 4-chloro-1-naphthol affords a new product with the intense violet color characterized by a high rate of accumulation, good adsorbability on the glass surface, and stability. This reaction can be used as a detection system for the identification of β-lactamase genes on DNA microarrays. The DNA microarray technique using horseradish peroxidase and colorimetric detection is characterized by high sensitivity and reproducibility comparable to the characteristics of the microarrays with fluorescence detection.     

Optimization of DNA hybridization analysis on microarrays with colorimetric detection

A method of hybridization analysis on a DNA microarray using colorimetric detection on the basis of horseradish peroxidase has been developed. The effectiveness of the incorporation of biotin as a label in the DNA molecule in the PCR process is estimated and the conditions of hybridization of the biotin-labeled DNA with oligonucleotides immobilized on the surface of the array are optimized. The possibility of using the developed method is shown by the example of genotyping of CTX-M β-lactamases.     

Colorimetric detection of PCR products of DNA from pathogenic bacterial targets based on a simultaneously amplified DNAzyme

A novel strategy was devised for colorimetric analysis of the products of the polymerase chain reaction (PCR). The method takes advantage of simultaneous amplification of a horseradish peroxidase-mimicking DNAzyme (HRPzyme) during the PCR process. It is performed using a DNA specific forward primer and a universal reverse primer containing a complementary HRPzyme sequence. The double-strand PCR products, which include the HRPzyme sequence, are treated with a mixture of hemin and TMB (3,3′,5,5′–tetramethylbenzidine) in the presence of hydrogen peroxide. The resulting HRPzyme/hemin complex then promotes a peroxidase mimicking reaction, which produces the blue colored oxidized TMB. This colorimetric method can be more easily performed than previously developed gel based detection procedures and, as a result, can be conveniently applied to the specific and sensitive colorimetric analysis of DNA sequences arising from pathogenic bacteria. The potentially broad applicability of the new method has been demonstrated by its use in the identification of the 16s rDNA of Salmonella Typhimurium. Figure

A novel strategy was devised for simple colorimetric analysis of PCR products with amplification of a horseradish peroxidase-mimicking DNAzyme(HRPzyme). This colorimetric method can be much more easily performed than previously developed gel based detection procedures and potentially broad applicability for other DNA analysis.     

Colorimetric detection of hepatitis B virus (HBV) DNA based on DNA-templated copper nanoclusters

DNA detection plays an important role in early diagnosis of genetic disease. The conventional detection methods of DNA are based on expensive equipment, which do not meet the demands of developing countries. Thus, we developed a colorimetric method, which could be observed with naked eye and used copper nanoclusters for cost-effective. Moreover, the target of this method is the DNA in Hepatitis B virus that is one of the most popular chronic viral infections in developing countries over the past years. Our method was sensitive and the limit of detection was 12 × 10⁹ molecules. Three-base-pair mismatches target DNA was detected easily. These results revealed the favorable sensitivity and selectivity of this approach. Most importantly, our method may have potential applications in correct diagnosis of genetic disease and monitoring of gene therapy in the poverty-stricken areas.     

DNA detection method based on the two-dimensional aggregation and selective desorption of nanoparticle probes

A label-free two-dimensional colorimetric DNA sensor is reported. This sensor is based on the 2D aggregation of oligonucleotide-modified gold nanoparticle probes induced by the molecular hybridization of single-stranded oligonucleotide probes and their complementary single-stranded DNA targets. To detect the aggregation, we have developed a new detection method based on the selective desorption of nonaggregated nanoparticles. We will show here that this detection method is highly specific and allows the quantification of the DNA targets.     

Label-free detection of specific DNA sequence-telomere using unmodified gold nanoparticles as colorimetric probes

A simple and sensitive label-free colorimetric detection of telomere DNA has been developed. It was based on the color change of gold nanoparticles (AuNPs) due to DNA hybridization. UV–vis spectra and transmission electron microscopy (TEM) were used to investigate the change of AuNPs. Under the optimized conditions, the linear range for determination of telomere DNA was 5.7 × 10⁻¹³ to 4.5 × 10⁻⁶ mol/L. The detection limit (3σ) of this method has decreased to pico-molar level.     

A structure-switchable aptasensor for aflatoxin B1 detection based on assembly of an aptamer/split DNAzyme

An ultrasensitive, colorimetric and homogeneous strategy for aflatoxin B1 (AFB1) detection, which uses a DNA aptamer and two split DNAzyme halves, has been developed. Split halves of a hemin-binding DNAzymes is combined with an AFB1 aptamer to generate a homogeneous colorimetric sensor that undergoes an AFB1 induced DNA structural change. In the absence of AFB1, the split probes have peroxidase mimicking DNAzyme activity associated with catalysis of a color change reaction. Specific recognition of AFB1 by the aptamer component leads to structural deformation of the aptamer-DNAzyme complex, which causes splitting of the DNAzyme halves and a reduction in peroxidase mimicking activity. Therefore, a decrease of colorimetric signal arising from the catalytic process takes place upon in the presence of AFB1 in a concentration dependent manner in the 0.1–1.0 × 10⁴ ng/mL range and with a colorimetric detection limit of 0.1 ng/mL. The new assay system exhibits high selectivity for AFB1 over other mycotoxins and can be employed detect the presence of AFB1 in ground corn samples. Overall, the strategy should serve as the basis for the development of rapid, simple and low-cost methods for detection of mycotoxins.     

Colorimetric detection of PCR products of DNA from pathogenic bacterial targets based on a simultaneously amplified DNAzyme

A novel strategy was devised for colorimetric analysis of the products of the polymerase chain reaction (PCR). The method takes advantage of simultaneous amplification of a horseradish peroxidase-mimicking DNAzyme (HRPzyme) during the PCR process. It is performed using a DNA specific forward primer and a universal reverse primer containing a complementary HRPzyme sequence. The double-strand PCR products, which include the HRPzyme sequence, are treated with a mixture of hemin and TMB (3,3′,5,5′–tetramethylbenzidine) in the presence of hydrogen peroxide. The resulting HRPzyme/hemin complex then promotes a peroxidase mimicking reaction, which produces the blue colored oxidized TMB. This colorimetric method can be more easily performed than previously developed gel based detection procedures and, as a result, can be conveniently applied to the specific and sensitive colorimetric analysis of DNA sequences arising from pathogenic bacteria. The potentially broad applicability of the new method has been demonstrated by its use in the identification of the 16s rDNA of Salmonella Typhimurium.

A novel strategy was devised for simple colorimetric analysis of PCR products with amplification of a horseradish peroxidase-mimicking DNAzyme(HRPzyme). This colorimetric method can be much more easily performed than previously developed gel based detection procedures and potentially broad applicability for other DNA analysis.

     

Droplet-based microscale colorimetric biosensor for multiplexed DNA analysis via a graphene nanoprobe

The development of simple and inexpensive DNA detection strategy is very significant for droplet-based microfluidic system. Here, a droplet-based biosensor for multiplexed DNA analysis is developed with a common imaging device by using fluorescence-based colorimetric method and a graphene nanoprobe. With the aid of droplet manipulation technique, droplet size adjustment, droplet fusion and droplet trap are realized accurately and precisely. Due to the high quenching efficiency of graphene oxide (GO), in the absence of target DNAs, the droplet containing two single-stranded DNA probes and GO shows dark color, in which the DNA probes are labeled carboxy fluorescein (FAM) and 6-carboxy-X-rhodamine (ROX), respectively. The droplet changes from dark to bright color when the DNA probes form double helix with the specific target DNAs leading to the dyes far away from GO. This colorimetric droplet biosensor exhibits a quantitative capability for simultaneous detection of two different target DNAs with the detection limits of 9.46 and 9.67 × 10⁻⁸ M, respectively. It is also demonstrated that this biosensor platform can become a promising detection tool in high throughput applications with low consumption of reagents. Moreover, the incorporation of graphene nanoprobe and droplet technique can drive the biosensor field one more step to some extent.     

A facile and sensitive colorimetric detection for RNase A activity based on target regulated protection effect on plasmonic gold nanoparticles aggregation

In this work, a facile and sensitive colorimetric detection method was firstly reported for RNase A activity detection based on target regulated protection effect of chimeric DNA probe on the salt-induced aggregation of plasmonic gold nanoparticles.Compared with previous works of RNase A activity detection, this colorimetric assay integrated the advantages of sensitive, low cost, facile operation, rapid response and low biological toxicity.     

Tree-shaped paper strip for semiquantitative colorimetric detection of protein with self-calibration

This paper described a convenient semiquantitative method for colorimetric detection of protein with self-calibration integrated on the test strip. Hydrophilic paper was employed as microfluidic device for running colorimetric assay, tree-shaped design was developed to ensure uniform microfluidic flow for multiple branches. The approach was validated with bovine serum albumin (BSA) colorimetric detection, and colorimetric results observed by naked eyes were consistent with that from apparatus. The device could be coupled with digital transmission of images for remote monitoring system for diagnosis, food control, and environmental analysis.     

Gold nanoparticles immobilized on metal–organic frameworks with enhanced catalytic performance for DNA detection

In this work, gold nanoparticles (AuNPs) assembled on the surface of iron based metal–organic frameworks (MOFs), Fe-MIL-88, are facilely prepared through electrostatic interactions using polyethyleneimine (PEI) molecules as linker. The resulting hybrid materials possess synergetic peroxidase-like activity. Because iron based metal–organic frameworks, Fe-MIL-88, exhibits highly peroxidase-like activity, and AuNPs has the distinct adsorption property to single-stranded DNA (ssDNA) and double-stranded DNA (dsDNA). The peroxidase-like activity of Au@Fe-MIL-88 exhibit excellent switchable in response to specific DNA, ssDNA is easily adsorbed on the surface of the Au@Fe-MIL-88 hybrids, resulting in the reduce of the peroxidase-like activity of the hybrids. While it is recovered by the addition of target DNA, and the recovery degree is proportional to the target DNA concentration over the range of 30–150 nM with a detection limit of 11.4 nM. Based on these unique properties, we develop a label-free colorimetric method for DNA hybridization detection. In control experiment, base-mismatched DNA cannot induce recovery of the peroxidase-like activity. This detection method is simple, cheap, rapid and colorimetric.     

High sensitive and label-free colorimetric DNA detection based on nicking endonuclease-assisted activation of DNAzymes

Horseradish peroxidase mimicking DNAzyme (HRP-DNAzyme) attracts growing interest as an amplifying label for biorecognition and biosensing events, especially for DNA detection. However, in the traditional designs, one target molecule can only generate one HRP-DNAzyme, which limits the signal enhancement and thus its sensitivity. In this article, we propose an amplified and label-free colorimetric DNA detection strategy based on nicking endonuclease (NEase)-assisted activation of HRP-DNAzymes (NEAA-DNAzymes). This new strategy relies on the hairpin-DNAzyme probe and NEase-assisted target recycling. In the hairpin-DNAzyme probe, the HRP-DNAzyme sequence is protected in a “caged” inactive structure, whereas the loop region includes the target complementary sequence. Upon hybridization with target, the beacon is opened, resulting in the activation of the HRP-DNAzyme. Meanwhile, upon formation of the duplex, the NEase recognizes a specific nucleotide sequence and cleaves the hairpin-DNAzyme probe into two fragments. After nicking, the fragments of the hairpin-DNAzyme probe spontaneously dissociate from the target DNA. Amplification is accomplished by another hairpin-DNAzyme probe hybridizing to the released intact target to continue the strand-scission cycle, which results in activation of numerous DNAzymes. The activated HRP-DNAzymes generate colorimetric or chemiluminescence readout signals, thus providing the amplified detection of DNA. The detection limit of the colorimetric method is 10 pmol/L, which are three orders of magnitude lower than that without NEase. In addition, the detection limit of the chemiluminescence method is 0.2 pmol/L. Meanwhile, this strategy also exhibits high discrimination ability even against single-base mismatch.     

Gold nanoparticle-enabled real-time ligation chain reaction for ultrasensitive detection of DNA

A simple and ultrasensitive colorimetric DNA assay based on the detection of the product of a ligation chain reaction (LCR) and the use of gold nanoparticles (AuNPs) as signal generators has been developed. During LCR, the AuNPs were ligated together, resulting in a distinct color change in real time after a sufficient number of thermal cycles. The cumulative nature of the protocol produced a detection limit of 20 aM with a selectivity factor of 10(3).     

A Highly-Sensitive Colorimetric Assay Method for Antibody Array Based on an Tyramide Signal Amplification System

In this work, a highly-sensitive and cost-effective detection approach based on the integration of tyramide signal amplification with a silver enhancement method (SEM-TSA) has been developed successfully. To demonstrate the feasibility of this approach, human IgG as a model target protein was employed and its concentration was assayed based on colorimetric detection. The analytical parameters including the concentrations of detection antibody, streptavidin-horseradish peroxidase, biotinyl tyramide, and streptavidin-nanogold were systematically optimized. The quantitative analysis was performed and a dynamic range was obtained from 0.18 ng/mL to 39.1 ng/mL, while no detectable images could be observed when the silver enhancement method (SEM) without TSA was used. The detection limits were 0.18 ng/mL and 21 ng/mL for SEM-TSA and SEM, respectively. The results showed that sensitivity of the presented colorimetric assay significantly increased by two-orders of magnitude. In addition, this method has been successfully applied in analyzing normal human serum samples. The results suggested the colorimetric detection method based on TSA-SEM has promising potential applications in biomedical analysis and clinical diagnosis.     

基于银/铂纳米模拟酶表面修饰的铜离子比色检测方法研究

通过对银/铂纳米簇(Ag/Pt NCs)的表面修饰调控其催化活性,建立了一种高灵敏的比色法检测Cu2+.巯基丙酸能够抑制Ag/Pt NCs的催化活性,而巯基丙酸与Cu2+作用后,将导致上述抑制作用减弱.基于上述原理,通过测量Ag/Pt NCs 催化TMB-H2O2反应产生的显色信号,可以实现Cu2+的比色检测.本方法检测Cu2+的线性范围为10～100 nmol/L,检出限(3σ)为5.0 nmol/L.将本方法应用于实际水样中Cu2+的检测,结果表明,本方法具有操作简单、成本低、灵敏度高、特异性好等优点.