Determination of RNase H activity via real-time monitoring of target-triggered rolling circle amplification

A novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension reaction

We herein present a novel ultrasensitive RNase H assay based on phosphorothioated-terminal hairpin formation and self-priming extension (PS-THSP) reaction. The detection probe employed as a key component in this technique serves as a substrate for RNase H and triggers the PS-THSP reaction upon the RNase H-mediated degradation of the probe. As a consequence, a large number of long concatemeric amplification products could be produced and used to identify the RNase H activity through the fluorescence signals produced by the nucleic acid-specific fluorescent dye, SYTO 9. Importantly, the use of the gp32 protein allowed the PS-THSP reaction to be performed at 37 °C, ultimately enabling an isothermal one-step RNase H assay. Based on this sophisticated design principle, the RNase H activity was very sensitively detected, down to 0.000237 U mL-1 with high specificity. We further verified its practical applicability through its successful application to the screening of RNase H inhibitors. With its operational convenience and excellent analytical performance, this technique could serve as a new platform for RNase H assay in a wide range of biological applications.

Electrogenerated chemiluminescence resonance energy transfer between luminol and MnO2 nanosheets decorated with Cu2O nanoparticles for sensitive detection of RNase H

In the present work, a novel approach was developed for the preparation of Cu₂O nanoparticle decorated MnO₂ nanosheets (Cu₂O@MnO₂). Uniformly dispersed Cu₂O nanocrystals were produced on the surface of MnO₂ nanosheets by in situ reduction under refluxing conditions. The unique structure of the used MnO₂ nanosheet support played a vital role in the preparation of such Cu₂O@MnO₂ nanocomposites. The electrogenerated chemiluminescence (ECL) resonance energy transfer can occur between the luminol/H₂O₂ system and Cu₂O@MnO₂ nanocomposites, resulting in a decrease of the ECL intensity, which can be used to fabricate an ECL sensor. Cu₂O@MnO₂ nanocomposite modified heterologous DNA/RNA duplexes were modified on the GCE to construct an ECL-RET system, leading to the decrease of ECL intensity. As a highly conserved damage repair protein, RNase H can specifically hydrolyze RNA in DNA/RNA strands to release Cu₂O@MnO₂ nanocomposites and recover the ECL signal. As a result, an "off-on" mode ECL sensor for sensitive RNase H assay was fabricated. Under the optimal conditions, the detection limit of RNase H is 0.0005 U mL^-1, which is superior to other approaches. The proposed method provides a universal platform for monitoring RNase H, and exhibits great potential in bioanalysis.

CRISPR/Cas12a collateral cleavage activity for an ultrasensitive assay of RNase H

We herein describe an ultrasensitive RNase H assay by utilizing CRISPR/Cas12a collateral cleavage activity. Based on this unique design principle, the RNase H activity was successfully determined down to 0.00024 U mL^-1, which is quite superior to those of alternative approaches.

DNA-based ribonuclease detection assays

Ribonucleases are useful as biomarkers and can be the source of contamination in laboratory samples, making ribonuclease detection assays important in life sciences research. With recent developments in DNA-based biosensing, several new techniques are being developed to detect ribonucleases. This review discusses some of these methods, specifically those that utilize G-quadruplex DNA structures, DNA-nanoparticle conjugates and DNA nanostructures, and the advantages and challenges associated with them.

AuNanostar@4-MBA@Au Core-Shell Nanostructure Coupled with Exonuclease III-Assisted Cycling Amplification for Ultrasensitive SERS Detection of Ochratoxin A

The "turn-on" mode surface-enhanced Raman scattering (SERS) aptasensor for ultrasensitive ochratoxin A (OTA) detection was developed based on the SERS "hot spots" of AuNanostar@4-MBA@Au core-shell nanostructures (AuNS@4-MBA@Au) and exonuclease III (Exo III)-assisted target cycle amplification strategy. Compared with conventional gold nanoparticles, AuNS@4-MBA@Au provides a much higher SERS enhancement factor because AuNS exhibits a larger surface roughness and the lightning rod effect, as well as an excellent electromagnetic field between the AuNS core and the Au shell, which contribute to the superstrong SERS signal. Meanwhile, Exo III-assisted target cycle amplification can be used as an effective method for the further amplified detection of OTA. Additionally, the utilization of streptavidin magnesphere paramagnetic particles offers a green, economical, and facile technology for the accumulation and separation of the signal probe AuNS@4-MBA@Au from solution. All these factors lead to a significant enhancement of detectable signals and superhigh sensitivity. As a result, the limit of detection as low as 0.25 fg mL^-1 could be achieved, which was lower than that in the other reported literatures on SERS methods for OTA detection as we know. The developed SERS aptasensor also provides a promising tool for foodstuff detection.

An RNase H-powered DNA walking machine for sensitive detection of RNase H and the screening of related inhibitors

Ribonuclease H (RNase H), an intracellular ribonuclease, plays a crucial role in cellular processes and especially relates to many disease processes. Here, we report a novel signal amplification strategy based on an RNase H-powered DNA walking machine for specific and sensitive RNase H activity detection. The DNA walking machine is composed of a small quantity of DNA walker strands and abundant FAM-labeled DNA-RNA chimeric strands on a single gold nanoparticle (AuNP). RNase H can specifically degrade the RNA fragment in a DNA-RNA hybrid duplex and trigger the autonomous movement of a DNA walker strand on the AuNP surface. During this process, each step of the walking can release the FAM-labeled RNA from the surface of the AuNP, realizing the signal amplification for RNase H sensing. This method has been successfully utilized for RNase H activity detection in a complex system and applied for screening of related inhibitors. Therefore, our RNase H-powered DNA walking machine gives a novel platform for RNase H activity detection and RNase H-associated drug discovery.

An enzyme-initiated DNAzyme motor for RNase H activity imaging in living cell

A signal amplification strategy based on an enzyme-initiated DNAzyme motor for sensitive imaging of RNase H activity in living cell.

An allosteric switch-based hairpin for label-free chemiluminescence detection of ribonuclease H activity and inhibitors

To assay enzyme activities and screen its inhibitors, we demonstrated a novel label-free chemiluminescent (CL) aptasensor for the sensitive detection of RNase H activity based on hairpin technology. The specific hairpin structure was a DNA-RNA chimeric strand, which contained a streptavidin aptamer sequence and a blocked RNA sequence. RNase H could specifically recognize and cleave the RNA sequence of the DNA-RNA hybrid stem, liberating the streptavidin aptamer which could be accumulated by streptavidin-coated magnetic microspheres (SA-MP). Then the CL signal was generated due to an instantaneous derivatization reaction between the specific CL reagent 3,4,5-trimethoxyphenyl-glyoxal (TMPG) and the guanine (G) nucleotides in the SA aptamer. This novel assay method exhibited a good linear relationship in the range of 0.1-10 U mL-1 under the optimized conditions. Our results suggested that the developed system was a promising platform for monitoring the RNase H activity and showed great potential in biomedical studies and drug screening.

Target-Activated DNA Polymerase Activity for Sensitive RNase H Activity Assay

Herein, the ribonuclease H (RNase H) activity assay based on the target-activated DNA polymerase activity is described. In this method, a detection probe composed of two functional sequences, a binding site for DNA polymerase and a catalytic substrate for RNase H, serves as a key component. The detection probe, at its initial state, suppresses the DNA polymerase activity, but it becomes destabilized by RNase H, which specifically hydrolyzes RNA in RNA/DNA hybrid duplexes. As a result, DNA polymerase recovers its activity and initiates multiple primer extension reactions in a separate TaqMan probe-based signal transduction module, leading to a significantly enhanced fluorescence "turn-on" signal. This assay can detect RNase H activity as low as 0.016 U mL^-1 under optimized conditions. Furthermore, its potential use for evaluating RNase H inhibitors, which have been considered potential therapeutic agents against acquired immune deficiency syndrome (AIDS), is successfully explored. In summary, this approach is quite promising for the sensitive and accurate determination of enzyme activity and inhibitor screening.

The staining efficiency of cyanine dyes for single-stranded DNA is enormously dependent on nucleotide composition

The staining of nucleic acids with fluorescent dyes is one of the most fundamental technologies in relevant areas of science. For reliable and quantitative analysis, the staining efficiency of the dyes should not be very dependent on the sequences of the specimens. However, this assumption has not necessarily been confirmed by experimental results, especially in the staining of ssDNA (and RNA). In this study, we found that both SYBR Green II and SYBR Gold did not stain either homopyrimidines or ssDNA composed of only adenine (A) and cytosine (C). However, these two dyes emit strong fluorescence when the ssDNA contains both guanine (G) and C (and/or both A and thymine (T)) and form potential Watson-Crick base pairs. Interestingly, SYBR Gold, but not SYBR Green II, strongly stains ssDNA consisting of G and A (or G and T). Additionally, we found that the secondary structure of ssDNA may play an important role in DNA staining. To obtain reliable results for practical applications, sufficient care must be paid to the composition and sequence of ssDNA.

Ultrasensitive fluorescent aptasensor for CRP detection based on the RNase H assisted DNA recycling signal amplification strategy

An aptamer-based method for the ultrasensitive fluorescence detection of C-reactive protein (CRP) was developed using the ribonuclease H (RNase H) assisted DNA recycling signal amplification strategy. In this assay, CRP can specifically bind to the aptamer of CRP and the DNA chain of P1 is released from the aptamer/P1 (Ap/P1) complexes. After the addition of the fluorescence labeled (5-FAM) RNA, P1 hybridizes with fluorescence labeled RNA to form a P1/RNA double strand. When RNase H is added, the RNA with fluorescence labeling in the double strand is specifically cut into nucleotide fragments, which cannot be adsorbed on the surface of the GO, so as to generate a fluorescence signal. In the absence of CRP, fluorescence labeled RNA cannot hybridize with P1 to form double strands, which is able to directly adsorb on the surface of GO, resulting in no fluorescence signal. The detection limit is as low as 0.01 ng mL-1, with a linear dynamic range from 50 pg mL-1 to 100 ng mL-1. This sensor is able to detect CRP in spiked human serum, urine and saliva. Thus, it shows a great application prospect in disease diagnosis and prognosis.

Flap endonuclease-initiated enzymatic repairing amplification for ultrasensitive detection of target nucleic acids

A new isothermal nucleic acid amplification method termed FERA (Flap endonuclease-initiated Enzymatic Repairing Amplification) is developed for the ultrasensitive detection of target nucleic acids. In the FERA method, flap endonuclease (FEN) catalyzes the hydrolytic cleavage at the junction of single- and double-stranded DNAs which is formed only in the presence of target nucleic acids, and releases short oligonucleotides to promote the cyclic enzymatic repairing amplification (ERA) combined with FEN-based amplification. As a result, a large amount of single- and double-stranded DNAs are generated under the isothermal conditions, leading to the high fluorescence intensity from the SYBR I green dye. Relying on the powerful amplification method, we successfully determined the target nucleic acids with a limit of detection as low as 15.16 aM, which corresponds to approximately 180 molecules in 20 μL reaction volume, and verified the practical applicability by detecting long target nucleic acids derived from Chlamydia trachomatis.