DNA-mediated homogeneous binding assays for nucleic acids and proteins

Label-free chemiluminescent aptasensor for platelet-derived growth factor detection based on exonuclease-assisted cascade autocatalytic recycling amplification

Here an exonuclease III (Exo III)-assisted cascade autocatalytic recycling amplification (Exo-CARA) strategy is proposed for label-free chemiluminescent (CL) detection of platelet-derived growth factor BB (PDGF-BB) by taking advantage of both recognition property of aptamer and cleavage function of Exo III. Functionally, this system consists of a duplex DNA (aptamer-blocker hybrid), two kinds of hairpin structures (MB1 and MB2), and Exo III. Upon recognizing and binding with PDGF-BB, aptamer folds into a close configuration, which initiates the proposed Exo-CARA reaction (Recyclings I→II→III→II). Finally, numerous "caged" G-quadruplex sequences on DNAzyme1 and DNAzyme2 release that intercalate hemin to catalyze the oxidation of luminol by H2O2 to generate an amplified CL signal, achieving excellent specificity and high sensitivity with a detection limit of 6.8×10(-13) M PDGF-BB. The proposed strategy has the advantages of simple design, isothermal conditions, homogeneous reaction without separation and washing steps, effective-cost without the need of labeling, and high amplification efficiency, which might be a universal and promising protocol for the detection of a variety of biomolecules whose aptamers undergo similar conformational changes.

Assembly of multiple DNA components through target binding toward homogeneous, isothermally amplified, and specific detection of proteins

We describe a strategy of utilizing specific target binding to trigger assembly of three DNA components that are otherwise unable to spontaneously assemble with one another. This binding-induced DNA assembly forms a three-arm DNA junction, subsequently initiating nicking endonuclease-assisted isothermal fluorescence signal amplification. Real-time monitoring of fluorescence enables amplified detection of specific protein targets. The implementation of the strategy necessitates the simultaneous binding of a single target molecule with two affinity ligands each conjugated to a DNA motif. Simple alternation of affinity ligands enables different protein targets to induce the formation of the DNA junction and subsequent isothermal amplification. The use of the strategy allowed us to develop a sensitive assay for proteins with three appealing features: homogeneous analysis without the need for separation, isothermal amplification, and high specificity. Streptavidin was chosen as an initial target to establish and optimize the assay. Sensitivity of protein detection was improved by 1000-fold upon the application of isothermal amplification. A limit of detection of 10 pM was achieved for detection of prostate-specific antigen in buffer and diluted serum. The combination of its three appealing features makes the assay attractive for potential applications in molecular diagnosis, point-of-care testing, and on-site analysis.

A highly sensitive plasmonic DNA assay based on triangular silver nanoprism etching

Specific nucleic acid detection by using simple and low-cost assays is important in clinical diagnostics, mutation detection, and biodefense applications. Most current methods for the quantification of low concentrations of DNA require costly and sophisticated instruments. Here, we have developed a facile DNA detection platform based on a plasmonic triangular silver nanoprism etching process, in which the shape and size of the nanoprisms were altered accompanied by a substantial surface plasmon resonance shift. Through the combination of enzyme-linked hybridization chain reaction amplification and inherent sensitivity of plasmonic silver nanoprims, this assay could detect as low as 6.0 fM target DNA. Considering the high sensitivity and selectivity of this plasmonic DNA assay, it is expected to be of great interest in clinical diagnostics.

Simple and efficient method to purify DNA-protein conjugates and its sensing applications

DNA-protein conjugates are very useful in analytical chemistry for target recognition and signal amplification. While a number of methods for conjugating DNA with proteins are known, methods for purification of DNA-protein conjugates from reaction mixture containing unreacted proteins are much less investigated. In this work, a simple and efficient approach to purify DNA-invertase conjugates from reaction mixture via a biotin displacement strategy to release desthiobiotinylated DNA-invertase conjugates from streptavidin-coated magnetic beads was developed. The conjugates purified by this approach were utilized for quantitative detection of cocaine and DNA using a personal glucose meter through structure-switching DNA aptamer sensors and competitive DNA hybridization assays, respectively. In both cases, the purified DNA-invertase conjugates showed better performance compared to the same assays using unpurified conjugates. The approach demonstrated here can be further expanded to other DNA and proteins to generate purified DNA-protein conjugates for analytical and other applications.

Exonuclease III-aided autocatalytic DNA biosensing platform for immobilization-free and ultrasensitive electrochemical detection of nucleic acid and protein

Homogenous electrochemical biosensor has attracted substantial attention owing to its simplicity, rapid response, and improved recognition efficiency compared with heterogeneous biosensor, but the relatively low detection sensitivity and the limited detection analytes prohibit its potential applications. To address these issues, herein, a simple, rapid, isothermal, and ultrasensitive homogeneous electrochemical DNA biosensing platform for target DNA and protein detection has been developed on the basis of an exonuclease III (Exo III)-aided autocatalytic target recycling strategy. A ferrocene-labeled hairpin probe (HP1) is ingeniously designed, which contains a protruding DNA fragment at 3'-termini as the recognition unit for target DNA. Also, the DNA fragment that could be used as secondary target analogue was introduced, but it was caged in the stem region of HP1. In the presence of target DNA, its recognition with the protruding fragment of HP1 triggered the Exo III cleavage process, accompanied with the target recycling and autonomous generation of secondary target analogues. This accordingly resulted into the autonomous accumulation of ferrocene-labeled mononucleotide, inducing a distinct increase in the electrochemical signal owing to its elevated diffusivity toward indium tin oxide (ITO) electrode surface. The autocatalytic biosensing system was further extended for protein detection by advising an aptamer hairpin switch with the use of thrombin as a model analyte. The current developed autocatalytic and homogeneous strategy provided an ultrasensitive electrochemical detection of DNA and thrombin down to the 0.1 and 5 pM level, respectively, with a high selectivity. It should be further used as a general autocatalytic and homogeneous strategy toward the detection of a wide spectrum of analytes and may be associated with more analytical techniques. Thus, it holds great potential for the development of ultrasensitive biosensing platform for the applications in bioanalysis, disease diagnostics, and clinical biomedicine.

Terminal protection of small molecule-linked DNA for small molecule-protein interaction assays

Methods for the detection of specific interactions between diverse proteins and various small-molecule ligands are of significant importance in understanding the mechanisms of many critical physiological processes of organisms. The techniques also represent a major avenue to drug screening, molecular diagnostics, and public safety monitoring. Terminal protection assay of small molecule-linked DNA is a demonstrated novel methodology which has exhibited great potential for the development of simple, sensitive, specific and high-throughput methods for the detection of small molecule–protein interactions. Herein, we review the basic principle of terminal protection assay, the development of associated methods, and the signal amplification strategies adopted for performance improving in small molecule–protein interaction assay.

Optical aptasensors for quantitative detection of small biomolecules: a review

Aptasensors are aptamer-based biosensors with excellent recognition capability towards a wide range of targets. Specially, there have been ever-growing interests in the development of aptasensors for the detection of small molecules. This phenomenon is contributed to two reasons. On one hand, small biomolecules play an important role in living organisms with many kinds of biological function, such as antiarrhythmic effect and vasodilator activity of adenosine. On the other hand, the concentration of small molecules can be an indicator for disease diagnosis, for example, the concentration of ATP is closely associated with cell injury and cell viability. As a potential analysis tool in the construction of aptasensors, optical analysis has attracted much more interest of researchers due to its high sensitivity, quick response and simple operation. Besides, it promises the promotion of aptasensors in performance toward a new level. Review the development of optical aptasensors for small biomolecules will give readers an overall understanding of its progress and provide some theoretical guidelines for its future development. Hence, we give a mini-review on the advance of optical aptasensors for small biomolecules. This review focuses on recent achievements in the design of various optical aptasensors for small biomolecules, containing fluorescence aptasensors, colorimetric aptasensors, chemiluminescence aptasensors and other optical aptasensors.

(DNS)C: a fluorescent, environmentally sensitive cytidine derivative for the direct detection of GGG triad sequences

With the goal of developing a fluorescent nucleoside sensitive to its environment, in this study we synthesized (DNS)C, a novel modified 2'-deoxycytidine bearing a 5-(dimethylamino)naphthalene-1-sulfonyl (dansyl) moiety at the N4 position, and tested its properties in monomeric and oligomeric states. (DNS)C undergoes intramolecular photoinduced electron transfer between its dansyl and cytosine units, resulting in remarkable changes in fluorescence that depend on the choice of solvent. In addition, the fluorescence behavior and thermal stability of oligonucleotides containing (DNS)C are dependent on the nature of the flanking and neighboring bases. Notably, (DNS)C exhibits fluorescence enhancement only in fully matched duplex DNA containing a GGG triad sequence. The environmental sensitivity of (DNS)C can be exploited as a fluorescence tool for monitoring the interactions of DNA with other biomolecules, including DNA, RNA, and proteins.

Detection of single-nucleotide polymorphisms using an ON-OFF switching of regenerated biosensor based on a locked nucleic acid-integrated and toehold-mediated strand displacement reaction

Although various strategies have been reported for single-nucleotide polymorphisms (SNPs) detection, development of a time-saving, specific, and regenerated electrochemical sensing platform still remains a realistic goal. In this study, an ON-OFF switching of a regenerated biosensor based on a locked nucleic acid (LNA)-integrated and toehold-mediated strand displacement reaction technique is constructed for detection of SNPs. The LNA-integrated and methylene blue-labeled capture probe with an external toehold is designed to switch on the sensing system. The mutant-type DNA probe completes complementary with the capture probe to trigger the strand displacement reaction, which switches off the sensing system. However, when the single-base mismatched wild-type DNA probe is presented, the strand displacement reaction cannot be achieved; therefore, the sensing system still keeps the ON state. This DNA sensor is stable over five reuses. We further testify that the LNA-integrated sequence has better recognition ability for SNPs detection compared to the DNA-integrated sequence. Moreover, this DNA senor exhibits a remarkable discrimination capability of SNPs among abundant wild-type targets and 6000-fold (m/m) excess of genomic DNA. In addition, it is selective enough in complex and contaminant-ridden samples, such as human urine, soil, saliva, and beer. Overall, these results demonstrate that this reliable DNA sensor is easy to be fabricated, simple to operate, and stable enough to be readily regenerated.

Rational design of a redox-labeled chiral target for an enantioselective aptamer-based electrochemical binding assay

A series of redox-labeled L-tyrosinamide (L-Tym) derivatives was prepared and the nature of the functional group and the chain length of the spacer were systematically varied in a step-by-step affinity optimization process of the tracer for the L-Tym aptamer. The choice of the labeling position on L-Tym proved to be crucial for the molecular recognition event, which could be monitored by cyclic voltammetry and is based on the different diffusion rates of free and bound targets in solution. From this screening approach an efficient electroactive tracer emerged. Comparable dissociation constants Kd were obtained for the unlabeled and labeled targets in direct or competitive binding assays. The enantiomeric tracer was prepared and its enantioselective recognition by the corresponding anti-D-Tym aptamer was demonstrated. The access to both enantiomeric tracer molecules opens the door for the development of one-pot determination of the enantiomeric excess when using different labels with well-separated redox potentials for each enantiomer.

Enhanced colorimetric immunoassay accompanying with enzyme cascade amplification strategy for ultrasensitive detection of low-abundance protein

Methods based on enzyme labels have been developed for colorimetric immunoassays, but most involve poor sensitivity and are unsuitable for routine use. Herein, we design an enhanced colorimetric immunoassay for prostate-specific antigen (PSA) coupling with an enzyme-cascade-amplification strategy (ECAS-CIA). In the presence of target PSA, the labeled alkaline phosphatase on secondary antibody catalyzes the formation of palladium nanostructures, which catalyze 3,3′,5,5′-tetramethylbenzidine-H₂O₂ system to produce the colored products, thus resulting in the signal cascade amplification. Results indicated that the ECAS-CIA presents good responses toward PSA, and allows detection of PSA at a concentration as low as 0.05 ng mL⁻¹. Intra- and inter-assay coefficients of variation are below 9.5% and 10.7%, respectively. Additionally, the methodology is validated for analysis of clinical serum specimens with consistent results obtained by PSA ELISA kit. Importantly, the ECAS-CIA opens a new horizon for protein diagnostics and biosecurity.

Aptamer-based homogeneous protein detection using cucurbit[7]uril functionalized electrode

A new strategy for homogeneous protein detection is developed based on a cucurbit[7]uril (CB[7]) functionalized electrode. The analytical procedure consists of the binding of target protein to its aptamer in the test solution, followed by an exonuclease-catalyzed digestion of methylene blue (MB) tag labeled DNA oligonucleotides. Since CB[7] molecules immobilized on the electrode may efficiently capture the released MB-labeled nucleotides, the MB tags are concentrated to the electrode surface and subsequently yield highly sensitive electrochemical signal, which is related to the concentration of the target protein. The method combines the host-guest properties of CB[7] with the immobilization-free homogeneous assay, providing a powerful tool for protein detection. Taking the detection of osteopontin as an example, the proposed method can have a linear response to the target protein in a range from 50 to 500 ng mL(-1) with a detection limit of 10.7 ng mL(-1). It can also show high specificity and good reproducibility, and can be used directly for the assay of osteopontin in serum samples.

Mismatches improve the performance of strand-displacement nucleic Acid circuits

Catalytic hairpin assembly (CHA) has previously proven useful as a transduction and amplification method for nucleic acid detection. However, the two hairpin substrates in a CHA circuit can potentially react non-specifically even in the absence of a single-stranded catalyst, and this non-specific background degrades the signal-to-noise ratio. The introduction of mismatched base pairs that impede uncatalyzed strand exchange reactions led to a significant decrease of the background signal, while only partially damping the signal in the presence of a catalyst. Various types and lengths of mismatches were assayed by fluorimetry, and in many instances, our MismatCHA designs yielded 100-fold increased signal-to-background ratios compared to a ratio of 4:1 with the perfectly matched substrates. These observations could be of general utility for the design of non-enzymatic nucleic acid circuits.

Combining peptide and DNA for protein assay: CRIP1 detection for breast cancer staging

In this work, a novel method for a protein assay is proposed which uses the specific protein-binding peptide of the target protein and sequence-specific DNA to interact with the target as the capture and detection probe, respectively. Meanwhile, since the DNA sequence can be coupled with gold nanoparticles to amplify the signal readout, a sensitive and easily operated method for protein assay is developed. We have also employed a transcription factor named as cysteine-rich intestinal protein 1 (CRIP1), which has been identified as an ideal biomarker for staging of breast cancer, as the model protein for this study. With the proposed method, CRIP1 can be determined in a linear range from 1.25 to 10.13 ng/mL, with a detection limit of 1.25 ng/mL. Furthermore, the proposed method can be directly used to assay CRIP1 in tissue samples. Owing to its desirable sensitivity, excellent reproducibility, and high selectivity, the proposed method may hold great potential in clinical practice in the future.

Direct detection of circulating microRNAs in serum of cancer patients by coupling protein-facilitated specific enrichment and rolling circle amplification

A simple method for direct detection of circulating miRNAs in serum by coupling p19 protein-facilitated specific enrichment and RCA.

Chemical colorimetric square wave and its derived logic gates based on tunable growth of plasmonic gold nanoparticles

AuNP-based chemical colorimetric square wave (CCSW) and logic gates were constructed based on the colorimetric signal change via the controllable growth of AuNPs.

A label-free electrochemical biosensor for highly sensitive and selective detection of DNA via a dual-amplified strategy

In this work, by combining the enzymatic recycling reaction with the DNA functionalized gold nanoparticles (AuNPs)-based signal amplification, we have developed an electrochemical biosensor for label-free detection of DNA with high sensitivity and selectivity. In the new designed biosensor, a hairpin-structured probe HP was designed to hybridize with target DNA first, and an exonuclease ExoIII was chosen for the homogeneous enzymatic cleaving amplification. The hybridization of target DNA with the probe HP induced the partial cleavage of the probe HP by ExoIII to release the enzymatic products. The enzymatic products could then hybridize with the hairpin-structured capture probe CP modified on the electrode surface. Finally, DNA functionalized AuNPs was further employed to amplify the detection signal. Due to the capture of abundant methylene blue (MB) molecules by both the multiple DNAs modified on AuNPs surface and the hybridization product of capture DNA and enzymatic products, the designed biosensor achieved a high sensitivity for target DNA, and a detection limit of 0.6 pM was obtained. Due to the employment of two hairpin-structured probes, HP and CP, the proposed biosensor also exhibited high selectivity to target DNA. Moreover, since ExoIII does not require specific recognition sequences, the proposed biosensor might provide a universal design strategy to construct DNA biosensor which can be applied in various biological and medical samples.

Enzyme-free amplified detection of nucleic acids based on self-sustained replication of RNAzyme and its application in tumor cell detection

A system based on exponential amplification of self-sustained replication of RNAzyme was developed for quantitative detection of linker DNA that can be recognized by base complementarity. The hybridization of the linker DNA with two RNA ligase subunits formed an RNA enzyme that catalyzes the joining of two oligonucleotide substrates. The ligated product opens a hairpin molecular beacon, resulting in the generation of a higher fluorescence intensity. The product of this reaction depends on the concentration of the linker DNA, allowing one to determine the concentration of target DNA in a sample. Furthermore, based on the high specificity and affinity of cell aptamer with its target cells, this amplification strategy has been successfully applied in detection of cancer cells. The exceptional amplification power of the RNAzyme along with the simple assay protocol makes direct cell detection possible in real-world samples with minimal sample pretreatments. This process is analogous to quantitative PCR (qPCR) but can be applied to the detection of nucleic acid and cells, as well as proteins and small molecules that are relevant to medical diagnostics.

A label-free luminescent switch-on assay for ATP using a G-quadruplex-selective iridium(III) complex

We report herein the G-quadruplex-selective property of a luminescent cyclometallated iridium(III) complex for the detection of adenosine-5'-triphosphate (ATP) in aqueous solution. The ATP-binding aptamer was employed as the ATP recognition unit, while the iridium(III) complex was used to monitor the formation of the G-quadruplex structure induced by ATP. The sensitivity and fold enhancement of the assay were higher than those of the previously reported assay using the organic dye crystal violet as a fluorescent probe. This label-free luminescent switch-on assay exhibits high sensitivity and selectivity towards ATP with a limit of detection of 2.5 µM.

Target-induced self-assembly of DNA nanomachine on magnetic particle for multi-amplified biosensing of nucleic acid, protein, and cancer cell

A biosensing system is established for the multi-amplified detection of DNA or specific substrates of aptamers under isothermal conditions, which combines nicked rolling circle amplification (N-RCA) and beacon assisted amplification (BAA) with sensitive colorimetric technique by using DNAzymes as reporter units. According to the configuration, the analysis of DNA is accomplished by recognizing the target to capture nucleic acid-functionalized magnetic particles, followed by the self-assembly of the other two nucleic acids into multicomponent DNA supramolecular structure on magnetic particles. After magnetic separation, the circularization with ligase and the fragmentation with polymerase activate N-RCA and BAA in the presence of polymerase, dNTPs, and the nicking endonuclease, successively producing horseradish peroxidase (HRP)-mimicking DNAzymes that act as colorimetric reporter to catalyze the oxidation of ABTS(2-) by H2O2 in the presence of hemin. Under the optimized conditions, we obtain a wide dynamic range for DNA analysis over 6 orders of magnitude from 1.0 × 10(-14) to 1.0 × 10(-9)M with a low limit of detection of 6.8 × 10(-15)M. In the absence of a target, neither self-assembly of nucleic acids nor amplification process can be initiated, indicating an excellent selectivity of the proposed strategy. Similarly, an analogous system is activated by cancer cells or lysozyme through cooperative self-assembly of nucleic acids on magnetic particles in the presence of respective substrates of aptamers to synthesize HRP-mimicking DNAzymes that give the readout signal for the recognition events, achieving LODs of 81 Ramos cells and 7.2 × 10(-15)M lysozyme, respectively.

A polyvalent aptamer system for targeted drug delivery

Poor efficacy and off-target systemic toxicity are major problems associated with current chemotherapeutic approaches to treat cancer. We developed a new form of polyvalent therapeutics that is composed of multiple aptamer units synthesized by rolling circle amplification and physically intercalated chemotherapy agents (termed as "Poly-Aptamer-Drug"). Using a leukemia cell-binding aptamer and doxorubicin as a model system, we have successfully constructed Poly-Aptamer-Drug systems and demonstrated that the Poly-Aptamer-Drug is significantly more effective than its monovalent counterpart in targeting and killing leukemia cells due to enhanced binding affinity (≈ 40 fold greater) and cell internalization via multivalent effects. We anticipate that our Poly-Aptamer-Drug approach will yield new classes of tunable therapeutics that can be utilized to effectively target and treat cancers while minimizing the side effects of chemotherapy.

Assembling DNA through affinity binding to achieve ultrasensitive protein detection

Recent advances in DNA assembly and affinity binding have enabled exciting developments of nanosensors and ultrasensitive assays for specific proteins. These sensors and assays share three main attractive features: 1) the detection of proteins can be accomplished by the detection of amplifiable DNA, thereby dramatically enhancing the sensitivity; 2) assembly of DNA is triggered by affinity binding of two or more probes to a single target molecule, thereby resulting in increased specificity; and 3) the assay is conducted in solution with no need for separation, thus making the assay attractive for potential point-of-care applications. We illustrate here the principle of assembling DNA through affinity binding, and we highlight novel applications to the detection of proteins.

A label-free G-quadruplex-based luminescent switch-on assay for the selective detection of histidine

A label-free G-quadruplex-based luminescent switch-on assay has been developed for the selective detection of micromolar histidine in aqueous solution. In this study, an iridium(III) complex was employed as a G-quadruplex-specific luminescent probe while a guanine-rich oligonucleotide (Pu27, 5'-TG4AG3TG4AG3TG4A2G2-3')/cupric ion (Cu(2+)) ensemble was employed as a recognition unit for histidine. The initial luminescence of the iridium(III) complex in the presence of G-quadruplex DNA is effectively quenched by Cu(2+) ions due to the Cu(2+)-mediated unfolding of the G-quadruplex motif. The addition of histidine sequesters Cu(2+) ions from the ensemble, thereby restoring the luminescence of the system. The assay could detect down to 1 μM of histidine in aqueous media, and also exhibited good selectivity for histidine over other amino acids with the use of the cysteine, masking agent N-ethylmaleimide. Furthermore, the application of the assay for the detection of histidine in diluted urine samples was demonstrated.

Aptamer-based label-free detection of PDGF using ruthenium(II) complex as luminescent probe

We report a simple, cost-effective, and label-free detection method, consisting of a platelet-derived growth factor (PDGF) binding aptamer and hydrophobic Ru(II) complex as a sensor system for PDGF. The binding of PDGF with the aptamer results in the weakening of the aptamer-Ru(II) complex, monitored by luminescence signal. A substantial enhancement in the luminescence intensity of Ru(II) complex is observed in the presence of aptamer due to the hydrophobic interaction. Upon addition of PDGF, the luminescence intensity is decreased, due to the stronger interaction between the aptamer and PDGF resulting in the displacement of Ru(II) complex to the aqueous solution. Our assay can detect a target specifically in a complex medium such as the mixture of proteins, at a concentration of 0.8 pM.

A parallel G-quadruplex-selective luminescent probe for the detection of nanomolar calcium(II) ion

A parallel G-quadruplex-selective iridium(III) complex has been synthesized and employed as a luminescent probe in a label-free G-quadruplex-based detection assay for Ca(2+) ions in aqueous solution. In this assay, a guanine-rich oligonucleotide (G4, 5'-G4T4G4-3') initially exists in an antiparallel G-quadruplex conformation, resulting in a low luminescence signal. Upon incubation with Ca(2+) ions, the antiparallel G-quadruplex is induced into a parallel G-quadruplex conformation, which greatly enhances the luminescence emission of the iridium(III) probe. This method was highly sensitive for Ca(2+) ions with a limit of detection in the nanomolar range, and was selective for Ca(2+) over other metal ions.

Cyclic enzymatic amplification method (CEAM) based on exonuclease III for highly sensitive bioanalysis

Nucleic acid molecular probes (NAMPs) have been widely used in the sensing of various chemical and biological substances, as well as physical parameters. However, for traditional nucleic acid molecular probes, the stoichiometric 1:1 binding ratio limits the signal enhancement and thus the sensitivity of the assay. In order to overcome this problem, the cyclic enzymatic amplification method (CEAM) based on exonuclease III has been applied in optical and electrical detection of DNA, proteins and small molecules with excellent sensitivity, selectivity, versatility and simplicity. In this review, the working principle of CEAM is first introduced, followed by the applications of CEAM using different output signals for various analytes. Finally, experimental designs and procedures of CEAM are discussed in detail using displacing probes-based CEAM and linear molecular beacons (LMBs)-based CEAM as two examples.