Exonuclease III-assisted multiple cycle amplification for the sensitive detection of DNA with zero background signal

Detection of low-abundant DNA is essential for disease diagnosis and treatment. DNA polymerase-based amplification is frequently used due to its excellent sensitivity, but it suffers from time-consuming and labour-intensive procedures, complex template/primer design, and inherent nonspecific amplification. Alternatively, Exonuclease III (Exo III)-assisted target recycling provides a new approach for DNA assay because of its simplicity and general applicability, but it suffers from high background signal due to the nonspecific Exo III digestion and poor sensitivity due to single cycle signal amplification. Herein, we demonstrate the development of Exo III-assisted multiple cycle amplification (exonuclease chain reaction) for the sensitive detection of DNA with zero background signal. The binding of single-stranded DNA binding protein (SSB) to the hairpin probes can protect them from nonspecific digestion by Exo III, resulting in near zero background signal. The presence of the target DNA initiates the Exo III-triggered multiple cycle amplification, enabling the achievement of high sensitivity with a detection limit of 3 fM and excellent selectivity with single base mismatch discrimination capability, holding great potential in disease diagnosis and biomedical research.

Recent trends in electrochemiluminescence aptasensors and their applications

Aptamers are single stranded DNA or RNA ligands which can be selected for different targets from proteins to small organic dyes. In the past few years great progress has been accomplished in the development of aptamer based bioanalytical assays with different detection techniques. Among them, electrochemiluminescence (ECL) aptasensors are very promising because they have the advantages of both electrochemical and chemiluminescence biosensors, such as high sensitivity, low background, cost effectiveness, and ease of control. In this review, we summarize the recent efforts to construct novel and improved ECL aptasensors and their application.

Strand Displacement-Induced Enzyme-Free Amplification for Label-Free and Separation-Free Ultrasensitive Atomic Fluorescence Spectrometric Detection of Nucleic Acids and Proteins

In previous work, we have developed a simple strategy for a label-free and separation-free bioassay for target DNA and protein, with the limit of detection at the nM level only. Herein, taking advantage of atomic fluorescence spectrometric detection of metal ions and amplification of DNA, a label-free and separation-free ultrasensitive homogeneous DNA analytical platform for target DNA and protein detection was developed on the basis of an enzyme-free strand displacement signal amplification strategy for dramatically improved detectability. Using the T-Hg²⁺-T hairpin structure as the probe, the target DNA binds with HP (T-Hg²⁺-T hairpin structure) and released the Hg²⁺ first; then, the P4 (help DNA) hybridizes with target-P3 complex and free the target DNA, which is used to trigger another reaction cycle. The cycling use of the target amplifies the mercury atomic fluorescence intensity for ultrasensitive DNA detection. Moreover, the enzyme-free strand displacement signal amplification analytical system was further extended for protein detection by introducing an aptamer-P2 arched structure with thrombin as a model analyte. The current homogeneous strategy provides an ultrasensitive AFS detection of DNA and thrombin down to the 0.3 aM and 0.1 aM level, respectively, with a high selectivity. This strategy could be a promising unique alternative for nucleic acid and protein assay.

A upconversion luminescene biosensor based on dual-signal amplification for the detection of short DNA species of c-erbB-2 oncogene

High-sensitivity detection of trace amounts of c-erbB-2 oncogene was reported to be equal to or surpass the ability of CA 15-3 for early diagnosis and/or follow-up recurrent screening of breast cancer. Therefore, in the current study, by using upconversion nanoparticles (UCNPs), rare earth-doped NaYF4:Yb(3+)/Er(3+) as the luminescent labels, a upconversion luminescent (UCL) biosensor based on dual-signal amplification of exonuclease III (ExoIII)-assisted target cycles and long-range self-assembly DNA concatamers was developed for the detection of c-erbB-2 oncogene. The proposed biosensor exhibited ultrasensitive detection with limit as low as 40 aM, which may express the potential of being used in trace analysis of c-erbB-2 oncogene and early diagnosis of breast cancer.

Label-free, homogeneous, and ultrasensitive detection of pathogenic bacteria based on target-triggered isothermally exponential amplification

A novel colorimetric biosensing strategy for highly selective and ultrasensitive detection of pathogenic bacteria based on target-triggered EXPAR by the property of polymerase and nicking activity of restriction endonuclease has been reported.

A label-free biosensor for selective detection of DNA and Pb2+ based on a G-quadruplex

Schematic representation of the DNA and Pb²⁺ detection method.

Application of Europium Multiwalled Carbon Nanotubes as Novel Luminophores in an Electrochemiluminescent Aptasensor for Thrombin Using Multiple Amplification Strategies

A novel electrochemiluminescent (ECL) aptasensor was proposed for the determination of thrombin (TB) using exonuclease-catalyzed target recycling and hybridization chain reaction (HCR) to amplify the signal. The capture probe was immobilized on an Au-GS-modified electrode through a Au-S bond. Subsequently, the hybrid between the capture probe and the complementary thrombin binding aptamer (TBA) was aimed at obtaining double-stranded DNA (dsDNA). The interaction between TB and its aptamer led to the dissociation of dsDNA because TB has a higher affinity to TBA than the complementary strands. In the presence of exonuclease, aptamer was selectively digested and TB could be released for target recycling. Extended dsDNA was formed through HCR of the capture probe and two hairpin DNA strands (NH2-DNA1 and NH2-DNA1). Then, numerous europium multiwalled carbon nanotubes (Eu-MWCNTs) could be introduced through amidation reaction between NH2-terminated DNA strands and carboxyl groups on the Eu-MWCNTs, resulting in an increased ECL signal. The multiple amplification strategies, including the amplification of analyte recycling and HCR, and high ECL efficiency of Eu-MWCNTs lead to a wide linear range (1.0×10(-12)-5.0×10(-9) mol/L) and a low detection limit (0.23 pmol/L). The method was applied to serum sample analysis with satisfactory results.

Carbon nanoparticle-protected aptamers for highly sensitive and selective detection of biomolecules based on nuclease-assisted target recycling signal amplification

Based on the protective properties of carbon nanoparticles for aptamers against the digestion of nuclease, we have developed a nuclease-assisted target recycling signal amplification method for highly sensitive detection of biomolecules, such as ATP and kanamycin. The high binding specificity between aptamers and targets leads to excellent selectivity of the assay.

Scaling up an electrochemical signal with a catalytic hairpin assembly coupling nanocatalyst label for DNA detection

A new strategy for the electrochemical detection of DNA based on catalytic hairpin assembly combined with nanocatalyst label-based redox cycling reaction signal amplification. A superior detection limit of 0.3 aM toward DNA was achieved.

Label-free, isothermal and ultrasensitive electrochemical detection of DNA and DNA 3′-phosphatase using a cascade enzymatic cleavage strategy

A label-free, isothermal and cascade enzymatic cleavage strategy was developed for the ultrasensitive electrochemical detection of DNA and DNA 3′-phosphatase.

Programmable Mg2+-dependent DNAzyme switch by the catalytic hairpin DNA assembly for dual-signal amplification toward homogeneous analysis of protein and DNA

The catalytic hairpin DNA assembly-programmed Mg²⁺-dependent DNAzyme switch was proposed for dual-signal amplified detection of protein and DNA.

Highly sensitive fluorescence detection of target DNA by coupling exonuclease-assisted cascade target recycling and DNAzyme amplification

Because of the intrinsic importance of nucleic acid as bio-targets, the simple and sensitive detection of nucleic acid is very essential for biological studies and medical diagnostics. Herein, a simple, isothermal and highly sensitive fluorescence detection of target DNA was developed with the combination of exonuclease III (Exo III)-assisted cascade target recycling and DNAzyme amplification. A hairpin DNA probe was designed, which contained the 3'-protruding DNA fragment as target recognition unit, the caged DNA fragment in the stem region as target analogue, and the caged 8-17 DNAzyme sequence in the loop region as signal response unit. Upon sensing of target DNA, the 3'-strand of hairpin DNA probe could be stepwise removed by Exo III, accompanied by the releasing of target DNA and autonomous generation of new target analogues for the successive hybridization and cleavage process. Simultaneously, the 8-17 DNAzyme unit could be exponentially released from this hairpin DNA probe and activated for the cyclic cleavage toward the ribonucleotide-containing molecular beacon substrate, inducing a remarkable fluorescence signal amplification for target detection. A low detection limit of 20 fM with an excellent selectivity toward target DNA could be achieved. The developed cascade amplification strategy may be further extended for the detection of a wide spectrum of analytes including protein and biological small molecules by combining DNA aptamer technology.

Dual hairpin-like molecular beacon based on coralyne-adenosine interaction for sensing melamine in dairy products

This study presents a novel dual hairpin-like molecular beacon (MB) for the selective and sensitive detection of melamine (MA) based on the conjugation of MA and thymine. In this protocol, the coordination between coralyne and adenosine (A) leaded a dual hairpin-like MB and the fluorophore-quencher pair is close proximity resulting in the fluorescence quenching. With the addition of MA, it conjugated with thymine in the loop part of dual hairpin-like MB by triple H-bonds, triggering the dissociation of the dual hairpin-like MB. The resulting spatial separation of the fluorophore from quencher induced the enhancement in fluorescence emission. Under the optimized conditions, the sensor exhibited a wide linear range of 8×10(-9)-1.6×10(-5) M (R(2)=0.9969) towards MA, with a low detection limit of 5 nM, approximately 4000 times lower than the Drug Administration and the US Food estimated MA safety limit. The real milk samples were also investigated with a satisfying result.

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.