Terminal deoxynucleotidyl transferase associated with split G-quadruplex/hemin deoxyribozyme amplification detection for various contaminants in milk based on pregnancy test strip platform

An efficient signal amplification strategy with low background based on a G-quadruplex-enriched DNA nanonetwork for ultrasensitive electrochemical detection of mucin 1

Herein, a G-quadruplex-enriched DNA nanonetwork (GDN) self-assembled via Y-modules was designed to construct an ultrasensitive electrochemical biosensing platform with low background for the detection of mucin 1 related to cancers. The single-stranded DNA (ssDNA) S1 converted from target mucin 1 could hybridize with ssDNA S2 and ssDNA S3 with split G-quadruplex fragments at ends to form Y-modules and self-assemble into a GDN, which can capture abundant electroactive substance hemin for a significant electrochemical signal. Impressively, compared with conventional G-quadruplex nanowires with low loading capacity and poor structural stability, the GDN assembled by Y-modules was able to load more signaling probes and obtain a more stable structure for the support of G-quadruplexes, thereby outputting a stronger and more stable electrochemical signal. Moreover, a complete G-quadruplex assembled from two split G-quadruplex effectively reduced the background signal and thus improved the signal-to-noise ratio for the sensitive detection of mucin 1. As a result, the constructed electrochemical biosensor based on GDN achieved ultrasensitive detection of target mucin 1 with a detection limit down to 0.15 fg mL-1 and was successfully applied to analyze mucin 1 in human serum samples, exhibiting great potential for protein biomarker analysis and clinical diagnosis of diseases.

Quantitative immunosensor for dibenz[a,h]anthracene on-site detection in oilfield chemicals based on computer-aided antibody

A paper sensor, a gold nanoparticles-based lateral flow immunochromatographic assay (GNPs-LFIA), was successfully established for the rapid quantitative detection of dibenz[a,h]anthracene (DBA) in drilling fluids (DFs). Computational analysis was employed to rationally design a novel hapten to effectively expose the active site of DBA, resulting in the successful development of a monoclonal antibody with high sensitivity and specificity. The half-maximum inhibitory concentration was 5.814 ng/mL. Then, the GNPs-LFIA was established following the optimization of the extraction agent and method. The limit of detection for DF samples was 0.273 mg/kg. Recovery experiments showed a high level of consistency with the results obtained by high-performance liquid chromatography-fluorescence detection, which indicated that the established GNPs-LFIA offered exceptional accuracy and reliability. Consequently, this method is well-suited for the rapid screening and determination of DBA in oilfield chemicals and presents a technical solution to identify polycyclic aromatic hydrocarbons.

Commercial Strip-Inspired One-Pot CRISPR-Based Chip for Multiplexed Detection of Respiratory Viruses

The absence of sensitive, multiplexed, and point-of-care assays poses a critical obstacle in promptly responding to emerging human respiratory virus (HRV) pandemics. Herein, RECOGNIZER (re-building commercial pregnancy strips via large-size nanoflowers), an innovative one-pot CRISPR assay, is presented that employs commercially available strips to identify several types of HRVs. The superiority of the RECOGNIZER assay mainly relies on two aspects: (i) DNA nanoflowers possessing a high surface-to-volume ratio and well-defined surface allow for a considerable probe loading density and minimized non-specific interaction, achieving an impressive signal-to-noise proportion exceeding tenfold at 1 nM target. (ii) The design of the one-pot reaction, multi-channel chip, and custom-made app enables the rapid, sample-to-answer, and multiplexed analysis of four HRVs in 25 min. This assay demonstrates a sensitivity of 5.42 pM for synthetic SARS-CoV-2 RNA and 10 copies µL-1 for SARS-CoV-2 plasmids after pre-amplification. Finally, the proposed approach indicated 100% accuracy in 50 clinical swab samples, demonstrating the robust performance in distinguishing SARS-CoV-2 from other HRVs. The versatility and scalability of RECOGNIZER renders it a user-friendly platform for virus infection monitoring, offering significant potential for improving pandemic response efforts.

New sensing methods using commercially available products: Based on PGM and PTS

In recent years, detection technology has made remarkable progress in the field of food safety, in vitro diagnosis, and environment monitoring under the impetus of trace substances detection requirements. However, in sharp contrast to the rapid development of detection technology, its marketization process is relatively lagging behind. One possible approach is to integrate novel sensing strategies with mature commercial devices, such as personal glucose meters (PGMs) and pregnancy test strips (PTS) to speed up their marketization process. In this review, we systematically summarized design principle, evolution, and application progress for the integration of novel sensing strategies with commercial devices PGMs and PTS. Meanwhile, key factors and difficulties for the integration novel sensing strategies with commercial devices were emphasized. More importantly, the future of prospects and remaining challenges were discussed.

A Massively Parallel In Vivo Assay of TdT Mutants Yields Variants with Altered Nucleotide Insertion Biases

Terminal deoxynucleotidyl transferase (TdT) is a unique DNA polymerase capable of template-independent extension of DNA. TdT's de novo DNA synthesis ability has found utility in DNA recording, DNA data storage, oligonucleotide synthesis, and nucleic acid labeling, but TdT's intrinsic nucleotide biases limit its versatility in such applications. Here, we describe a multiplexed assay for profiling and engineering the bias and overall activity of TdT variants with high throughput. In our assay, a library of TdTs is encoded next to a CRISPR-Cas9 target site in HEK293T cells. Upon transfection of Cas9 and sgRNA, the target site is cut, allowing TdT to intercept the double-strand break and add nucleotides. Each resulting insertion is sequenced alongside the identity of the TdT variant that generated it. Using this assay, 25,623 unique TdT variants, constructed by site-saturation mutagenesis at strategic positions, were profiled. This resulted in the isolation of several altered-bias TdTs that expanded the capabilities of our TdT-based DNA recording system, Cell HistorY Recording by Ordered InsertioN (CHYRON), by increasing the information density of recording through an unbiased TdT and achieving dual-channel recording of two distinct inducers (hypoxia and Wnt) through two differently biased TdTs. Select TdT variants were also tested in vitro, revealing concordance between each variant's in vitro bias and the in vivo bias determined from the multiplexed high throughput assay. Overall, our work and the multiplex assay it features should support the continued development of TdT-based DNA recorders, in vitro applications of TdT, and further study of the biology of TdT.

A massively parallel in vivo assay of TdT mutants yields variants with altered nucleotide insertion biases

Terminal deoxynucleotidyl transferase (TdT) is a unique DNA polymerase capable of template-independent extension of DNA with random nucleotides. TdT's de novo DNA synthesis ability has found utility in DNA recording, DNA data storage, oligonucleotide synthesis, and nucleic acid labeling, but TdT's intrinsic nucleotide biases limit its versatility in such applications. Here, we describe a multiplexed assay for profiling and engineering the bias and overall activity of TdT variants in high throughput. In our assay, a library of TdTs is encoded next to a CRISPR-Cas9 target site in HEK293T cells. Upon transfection of Cas9 and sgRNA, the target site is cut, allowing TdT to intercept the double strand break and add nucleotides. Each resulting insertion is sequenced alongside the identity of the TdT variant that generated it. Using this assay, 25,623 unique TdT variants, constructed by site-saturation mutagenesis at strategic positions, were profiled. This resulted in the isolation of several altered-bias TdTs that expanded the capabilities of our TdT-based DNA recording system, Cell History Recording by Ordered Insertion (CHYRON), by increasing the information density of recording through an unbiased TdT and achieving dual-channel recording of two distinct inducers (hypoxia and Wnt) through two differently biased TdTs. Select TdT variants were also tested in vitro , revealing concordance between each variant's in vitro bias and the in vivo bias determined from the multiplexed high throughput assay. Overall, our work, and the multiplex assay it features, should support the continued development of TdT-based DNA recorders, in vitro applications of TdT, and further study of the biology of TdT.

One-pot isothermal amplification permits recycled activation of CRISPR/Cas12a for sensing terminal deoxynucleotidyl transferase activity

This study introduces a one-pot isothermal amplification assay for ultrasensitive analysis of terminal deoxynucleotidyl transferase (TdT) activity. The system realizes recycled activation of CRISPR/Cas12a, enabling exceptional signal amplification. This approach maximizes the simplicity of the detection method, offering a promising avenue for molecular disease diagnosis.