A cost-effective detection of low-abundance mutation with DNA three-way junction structure and lambda exonuclease

Gene point mutation information translation and detection: Leveraging single base extension and CRISPR/Cas12a

Gene point mutations play a significant role in the development of cancer. Therefore, developing a sensitive, specific, and universally applicable method for detecting gene point mutation is crucial for clinical diagnosis, prognosis, and cancer treatment. Recently, gene point mutation detection methods based on CRISPR/Cas12a detection have emerged. However, existing methods generally lack universality and specificity. In this study, we have developed a CRISPR/Cas12a-based method that combines improved allele-specific polymerase chain reaction and single base extension to translate the point mutation information in the target dsDNA into length information in ssDNA activators to overcome the limitations associated with PAM sequences in the CRISPR/Cas12a system. Our method achieved a detection limit of 0.002% for clinically significant EGFR T790M mutation. The CRISPR/Cas12a system we constructed demonstrates high sensitivity, specificity, and universality in detecting gene point mutations, making it a promising tool for clinical cancer screening.

Recognition of Oligonucleotide C by Polydopamine-Coated Solid-State Nanopores

Selective recognition of short oligonucleotides at the single-molecule level is particularly important for early disease detection and treatment. In this work, polydopamine (PDA)-coated nanopores were prepared via self-polymerization as a solid-state nanopore sensing platform for the recognition of oligonucleotide C (PolyC). The PDA coating possesses abundant active sites, such as indole, amino, carboxyl, catechol, and quinone structures, which had interactions with short oligonucleotides to slow down the translocation rate. PDA-coated nanopores selectively interact with PolyC20 by virtue of differences in hydrogen bonding forces, generating a larger blocking current, while polyA and polyT demonstrated very small blockings. At the same time, PDA-coated nanopores can sensitively distinguish PolyC with different lengths, such as 20, 14, and 10 nt. The functionalization of PDA on the solid-state nanopore provides an opportunity for the rational design of the recognition surface for biomolecules.

DNAzyme-templated exponential isothermal amplification for sensitive detection of lead pollution and high-throughput screening of microbial biosorbents

Very low concentrations of lead (Pb²⁺) pollution can have far-reaching adverse impacts on human health, due to the cumulative toxicity of Pb²⁺. Herein, we report a DNAzyme-templated exponential isothermal amplification strategy (termed DNAzymee) for the ultrasensitive detection of Pb²⁺ pollution and the high-throughput screening of microbial biosorbents to remove Pb²⁺ pollution. DNAzyme can specifically recognize Pb²⁺, and this recognition event can be amplified by the subsequent exponential isothermal amplification reaction (EXPAR) and monitored by a G-quadruplex specific dye. The proposed design showed a low limit of detection (95 pM) and could identify Pb²⁺ pollution in different real samples with high precision. In particular, the proposed assay was used to screen Pb²⁺ biosorbents, and the results showed that Leuconostoc mesenteroides is a promising microbial biosorbent for removing Pb²⁺ pollution. Thus, the DNAzymee assay can serve as a platform to monitor lead pollution in the environment and screen efficient biosorbents for the control of lead pollution.

Endonuclease IV-Regulated DNAzyme Motor for Universal Single-nucleotide Variation Discrimination

Single-nucleotide variation (SNV) detection plays significant roles in disease diagnosis and treatment. Generally, auxiliary probe, restricted design rules, complicated detection system, and repeated experimental parameter optimization are needed to obtain satisfactory tradeoff between sensitivity and selectivity for SNV discrimination, especially when different mutant sites need to be distinguished. To overcome these limitations, we developed a universal, straightforward, and relatively cheap SNV discrimination strategy, which simultaneously possessed high sensitivity and selectivity. The excellent performance of this strategy was ascribed to the SNV discrimination property of endonuclease IV (Endo IV) and the different hydrolysis behavior between free deoxyribozyme (DNAzyme) and the trapped DNAzyme to the substrates modified on gold nanoparticles (AuNPs). When Endo IV recognized the mutant-type target (MT), free DNAzyme was released from the probe, and the DNAzyme motor was activated with the help of cofactor Mn²⁺ to generate an amplified fluorescence signal. On the contrary, the wild-type target (WT) could not effectively trigger the DNAzyme motor. Moreover, for different SNV types, the corresponding probe could be designed by simply changing the sequence hybridized with the target and retaining the DNAzyme sequence. Thus, the fluorescence signal generation system does not need to change for different SNV targets. Five clinical-related SNVs were determined with the limit of detection (LOD) ranging from 0.01 to 0.05%, which exhibited competitive sensitivity over existing SNV detection methods. This strategy provided another insight into the properties of Endo IV and DNAzyme, expanded the applications of DNAzyme motor, and has great potential to be used for precision medicine.