Full liberation of 2-Aminopurine with nucleases digestion for highly sensitive biosensing

2-Aminopurine (2-AP), a fluorescent isomer of adenine, is a popular fluorescent tag for DNA-based biosensors. The fluorescence of 2-AP is highly dependent on its microenvironment, i.e., almost non-fluorescent and merely fluorescent in dsDNA and ssDNA, respectively, but can be greatly brightened as mononucleotide. In most 2-AP-based biosensors, DNA transformation from dsDNA to ssDNA was employed, while selective digestion of 2-AP-labeled DNA with nucleases represents an appealing approach for improving the biosensor sensitivity. However, some detailed fundamental information, such as the reason for nuclease digestion, the influence of the labeling site, neighboring bases, or the label number of 2-AP for final signal output, are still largely unknown, which greatly limits the utility of 2-AP-based biosensors. In this work, using both steady- and excited-state fluorescence (lifetime), we demonstrated that nuclease digestion resulted in almost full liberation of 2-AP mononucleotides, and was free from labeling site and neighboring bases. Furthermore, we also found that nuclease digestion could lead to multiplexed sensitivity from increasing number of 2-AP labelling, but was not achievable for the conventional biosensors without full liberation of 2-AP. Considering the popularity of 2-AP in biosensing and other related applications, the above obtained information in sensitivity boosting is fundamentally important for future design of 2-AP-based biosensors.

Recombinase Polymerase Amplification Coupled with a Photosensitization Colorimetric Assay for Fast Salmonella spp. Testing

Salmonella spp. is one of the most serious foodborne pathogens causing millions of infection cases annually, especially in resource-limited areas. The standard culture method (2-3 days) and current nucleic acid amplification-based testing are not suitable for on-site testing in rural areas with heavy Salmonella spp. burden. Here, we developed a colorimetric recombinase polymerase amplification (RPA) method for fast and sensitive Salmonella spp. testing in 1 h. Specifically, the invA gene from the genomic DNA of Salmonella spp. was amplified isothermally to produce double-stranded DNA (dsDNA) amplicons, which were directly quantified by a photosensitization colorimetric assay. The proposed method offered the lowest detectable concentration of 5 × 10³ colony-forming units/mL (cfu/mL), which is much lower than that of ELISA (10⁵-10⁷ cfu/mL). The detectable limit could be further pushed down to 3 cfu/mL upon coupling with bacteria pre-enrichment for 6 h. Analysis of synthetic milk samples confirmed the high precision (90%) and specificity (95%) of the method for Salmonella spp. testing. Moreover, use of a DNA releaser could further simplify the whole testing operation. Because RPA features low-temperature amplification (25-42 °C) without the need for specific instruments and the dsDNA-based photosensitization colorimetric assay served as a simple and facile readout for RPA, our method thus allows fast and low-cost Salmonella spp. testing in food samples.

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.

Colorimetric Polymerase Chain Reaction Enabled by a Fast Light-Activated Substrate Chromogenic Detection Platform

Miniaturization of nucleic acid tests (NATs) into portable, inexpensive detection platforms may aid disease diagnosis in point-of-care (POC) settings. Colorimetric signals are ideal readouts for portable NATs, and it remains of high demand to develop color readouts that are simple, quantitative, and versatile. Thus motivated, we report a fast light-activated substrate chromogenic polymerase chain reaction (FLASH PCR) that uses DNA intercalating dyes (DIDs) to enable colorimetric nucleic acid detection and quantification. The FLASH system is established on our finding that DID-DNA intercalation can promote the rapid photooxidation of chromogenic substrates through light-induced production of singlet oxygen. Using this principle, we have successfully converted DID-based fluorescent PCR assays into colorimetric FLASH PCR. To demonstrate the practical applicability of FLASH PCR to POC diagnosis, we also fabricated two readout platforms, including a portable electronic FLASH reader and a paper-based FLASH strip. Using the FLASH reader, we were able to detect as low as 60 copies of DNA standards, a limit of detection (LOD) comparable with commercial quantitative PCR. The FLASH strip further enables the reader-free detection of PCR amplicons by converting the colorimetric signal into the visual measurement of distance as a readout. Finally, the practical applicability of the FLASH PCR was demonstrated by the detection and/or quantification of nucleic acid markers in diverse clinical and biological samples.

Sensitive and enzyme-free fluorescence polarization detection for miRNA-21 based on decahedral sliver nanoparticles and strand displacement reaction

A highly sensitive method for miRNA-21 detection has been developed, which relied on the principle of strand displacement reaction to achieve asymmetric signal amplification and combined with the enhanced effect of Ag₁₀NPs.