Ultrasensitive Electrochemiluminescence Biosensor for mRNA Based on Polymerase Assisted Signal Amplification

What DNA Polymerase Is Preferable in miRNA Assay Coupled with Isothermal Circular Strand Displacement Polymerization Reaction (ICSDPR)?

The products generated in the isothermal circular strand displacement polymerization reaction (ICSDPR) initiated with miRNA-141 were studied. The obtained results demonstrated that if ICSDPR was catalyzed with Large Klenow Fragment (lKF), the canonical duplex and some byproducts, which were not described previously, were observed. The HMW byproducts were shown to be produced as a result of lKF-insisted polymerization of capture hairpin (HP) used in ICSDPR. Contrary to original HP, HMW byproducts are not capture probes because upon polymerization they lack the ability to bind the target. Interestingly, the replacement of lKF with Klenow Fragment (3'-5' exo-) (KFexo-) prevented the generation of HMW byproducts but did not affect the synthesis of other ICSDPR products. In the presence of both DNA polymerases, the second byproduct, named target-dependent byproduct (TD byproduct), was formed when the capture HP and target sequence formed a perfect duplex. Using an imperfect complex with unpaired nucleotides at the 3'-end of the target sequence prevented the formation of TD byproduct in ICSDPR. The knowledge of mechanisms of the formation of the byproducts and use of KFexo- in catalysis of ICSDPR allowed to develop a highly sensitive plate-based assay of miRNA-141 with the detection limit and sensitivity coefficient of 1.7 fM and 1,400,000 RLU/M, respectively. The amplification index characteristic of KFexo- catalyzed ICSDPR was 22,000. The proposed assay of miRNA-141 showed high specificity toward the target.

Hairpin DNA-Mediated isothermal amplification (HDMIA) techniques for nucleic acid testing

Nucleic acid detection is of great importance in a variety of areas, from life science and clinical diagnosis to environmental monitoring and food safety. Unfortunately, nucleic acid targets are always found in trace amounts and their response signals are difficult to be detected. Amplification mechanisms are then practically needed to either duplicate nucleic acid targets or enhance the detection signals. Polymerase chain reaction (PCR) is one of the most popular and powerful techniques for nucleic acid analysis. But the requirement of costly devices for precise thermo-cycling procedures in PCR has severely hampered the wide applications of PCR. Fortunately, isothermal molecular reactions have emerged as promising alternatives. The past decade has witnessed significant progress in the research of isothermal molecular reactions utilizing hairpin DNA probes (HDPs). Based on the nucleic acid strand interaction mechanisms, the hairpin DNA-mediated isothermal amplification (HDMIA) techniques can be mainly divided into three categories: strand assembly reactions, strand decomposition reactions, and strand creation reactions. In this review, we introduce the basics of HDMIA methods, including the sensing principles, the basic and advanced designs, and their wide applications, especially those benefiting from the utilization of G-quadruplexes and nanomaterials during the past decade. We also discuss the current challenges encountered, highlight the potential solutions, and point out the possible future directions in this prosperous research area.

A novel electrochemical DNA biosensor for transgenic soybean detection based on triple signal amplification

A novel electrochemical DNA biosensor was developed and MON89788 of soybean transgenic gene sequence was detected based on a strategy of rolling circle amplification (RCA) and gold nanoparticle cube (AuNPC)-labeled multiple probes. First, the mercapto-modified capture DNA was immobilized on the surface of the Fe3O4@Au magnetic nanoparticles via an Au-S bond, and the capture DNA was opened and complementarily hybridized with the target DNA to form a double-stranded DNA. In the 10 × reaction buffer, Exonuclease III (ExoIII) specifically recognized and sheared the double-stranded DNA to release the target DNA, which led to the next round of reaction. Afterward, AuNP cube-loaded ssDNA (AuNPC/DNA) was added with the rolling circle reaction with the help of Phi29 DNA polymerase and T4 ligase. Finally, [Ru(NH3)6]3+ was attracted directly by the anionic phosphate of ssDNA via electrostatic interaction. The determination was carried out by using chronocoulometry (CC), and the CC signal was recorded. The mass amount of DNA strands extended infinitely on the AuNPs cube and numerous [Ru(NH3)6]3+ were absorbed, thus the detected signal was highly amplified. The corresponding CC signal showed a good linear relationship with the logarithm of the target DNA concentration in the range of 1 × 10-16 to 1 × 10-7 mol L-1, with a detection limit of 4.5 × 10-17 mol L-1. Specific gene sequence of MON89788 in soybean samples was determined, and the recoveries ranged from 97.3% to 102.0%. This sensor is one of the most sensitive sensors for genetic sequence assessment at present. Moreover, it demonstrates good selectivity, stability, and reproducibility.

Ultrasensitive electroluminescence biosensor for a breast cancer marker microRNA based on target cyclic regeneration and multi-labeled magnetized nanoparticles

An electrochemiluminescent (ECL) biosensor is described for the determination of the breast cancer biomarker microRNA. The method is based on the amplification via target cyclic regeneration through a system of hairpin DNA probes, primers, and Klenow fragment of DNA polymerases combined with CdTe quantum dots (QDs) and gold nanoparticles. The assay is performed by exploiting the luminescence properties of CdTe-QDs and K₂S₂O₈ as a co-reactive agent to increase the ECL signal. It was successfully applied to ECL-based detection of a 20-mer microRNA. The sensor has a linear response in the 0.1 fM to 0.2 pM microRNA concentration range and a detection limit as low as 33 aM. The assay has been applied to the determination of microRNA spiked in serum samples, and recoveries ranged from 94.4 to 100.5%. Graphical abstract A novel electroluminescence biosensor based on the amplification of target cyclic regeneration is described. It is achieved by using a system of hairpin DNA probes, primers, and Klenow fragment of DNA polymerases combined with CdTe QDs and Au NPs, and was successfully applied to microRNA detection.

An aptamer biosensor for leukemia marker mRNA detection based on polymerase-assisted signal amplification and aggregation of illuminator

A novel electrochemical luminescence (ECL) aptamer biosensor via polymerase amplification is constructed for label-free detection of leukemia marker mRNA (miR-16). In order to achieve the ultrasensitive detection of the target mRNA, the cyclic target chain displacement polymerization of leukemia marker mRNA assisted with Klenow fragment of DNA polymerase is employed. The determination is carried out by recording the ECL emission of pyridine ruthenium (Ru(bpy)₃²⁺) complexes embedded into the assistance DNA (ADNA) loaded on the nanogold surface, after the hybridization reaction between the probe DNA (PDNA) and the remaining sequence of the CP's stem part, and the formation of a core-shell sun-like structure. The mercapto-modified capture DNA (CP) is immobilized on the surface of a magneto-controlled glassy carbon electrode by Au-S bond. The CP is opened and hybridized with the target mRNA to form double-stranded DNA. In the presence of polymerase, primer DNA, and bases (dNTPs), the primer chain gets access to its complementary sequence of the stem part and then triggers a polymerization of the DNA strand, leading to the release of mRNA and starting the next polymerization cycle. Finally, the composite of PDNA-covered and ADNA-covered (embedded with Ru(bpy)₃²⁺) gold nanoparticles (hereafter called AuNPs@(PDNA+ADNA-Ru(bpy)₃²⁺) is added, and the ECL intensity is recorded. Because of the polymerization cycle and the aggregation of the illuminator of Ru(bpy)₃²⁺, the detected signal is amplified significantly. The results showed that the corresponding ECL signal has a good linear relationship with a logarithm of target mRNA concentration in the range of 1 × 10^-16 to 1 × 10^-7 mol/L, with a detection limit of 4.3 × 10^-17 mol/L. The mRNA spiked in the human serum sample is determined, and the recoveries are from 97.2 to 102.0%. This sensor demonstrates good selectivity, stability, and reproducibility. Graphical abstract ᅟ.