Mismatch-Guided Deoxyribonucleic Acid Assembly Enables Ultrasensitive and Multiplex Detection of Low-Allele-Fraction Variants in Clinical Samples

A dual-trigger entropy driven circuit based on competitive hybridization for highly specific enzyme-free detection of single nucleotide polymorphisms

Single nucleotide polymorphisms (SNPs) play a pivotal role in the detection of major diseases and the breeding of molecular designs. However, current SNP detection methods often rely heavily on expensive proteases, or alternatively, enzyme-free detection methods grapple with limited specificity. Addressing this issue, our study presents an enzyme-free, highly specific, simple, and efficient detection platform. First, we introduced additional base mismatches into the traditional entropy-driven circuit (EDC) reaction to establish a foundational distinction between mutant (MT) and wild-type (WT) sequences. On this basis, we introduced the concept of competitive hybridization and developed a dual-trigger EDC (DEDC) reaction platform, which responded to both wild-type targets (WT) and mutant targets (MT). By strategically leveraging the signals from both WT and MT, we constructed a ratiometric signal output mode, substantially enhancing the discrimination factor between WT and MT and maximizing the specificity of the detection system. Within the DEDC reaction system, the sole driving force is the increase in the system's entropy, with no enzymes involved throughout the entire process, thereby achieving simple and efficient specific detection of SNPs. Notably, MT, previously considered an interference in assays, is repurposed as a trigger signal, making DEDC particularly suitable for the identification of heterozygous samples with low mutational abundances. By analyzing the performance of this platform and using it for genotyping detection of soybean real genome samples, the practical application potential of the CTMSD platform was verified. The CTMSD platform based on EDC reactions has the potential to become a universal biosensing paradigm for future biochemical applications.

Nonequilibrium hybridization-driven CRISPR/Cas adapter with extended energetic penalty for discrimination of single-nucleotide variants

Accurate identification of single-nucleotide variants (SNVs) is critical in clinical diagnostics but remains challenging due to subtle free energy variations, particularly for hard-to-detect SNVs such as wobble base pairs and those in high guanine-cytosine (GC) regions. Here we report a high-energetic-penalty SNV detection (HEPSD) platform that redesigns the hybridization regions of CRISPR RNA (crRNA) in the CRISPR/Cas12a system. This system employs a binary crRNA architecture design that enables the activation of the cleavage activity of Cas12a while amplifying the energetic penalty for single-nucleotide mismatches through nonequilibrium hybridization-driven regulation. Consequently, the entire targeting region of CRISPR/Cas exhibits a marked preference for mutations in genomic DNA, while preventing false activation induced by sequences containing a single mismatched nucleotide. Moreover, HEPSD exhibits exceptional differentiation performance for hard-to-detect SNVs including wobble mutations at extreme GC contents. As proof of principle, profiling of BRAF V600E and EGFR L858R tumor mutations down to a 0.01% variant allele frequency was achieved, enabling accurate discrimination of 132 clinical sample pairs, which showed high consistency with quantitative polymerase chain reaction-based techniques and next-generation sequencing. The proven effectiveness of this platform showcases its potential for clinical molecular diagnostics and expands the fundamental scope of hybridization-based protocols.

PAM-Independent CRISPR-Cas12a System for Specific Assays of Single Nucleotide Variants

The CRISPR-Cas12a system has been extensively utilized in nucleic acid detection owing to its remarkable sensitivity and specificity. Nonetheless, its strict dependency on the presence of a protospacer adjacent motif (PAM) within double-stranded DNA (dsDNA) introduces considerable limitations, thereby constraining its applicability, flexibility, and broader accessibility in molecular diagnostics. Here, we communicate a universal, robust, and high-fidelity method for a PAM-independent nucleic acid assay based on the CRISPR-Cas12a system, named TRACER (mutant target-recognized PAM-independent CRISPR-Cas12a enzyme reporting system). TRACER can effectively distinguish target nucleic acids at concentrations as low as 0.5 aM, thereby enabling it to identify the presence of a 0.1% single nucleotide variant (SNV)-included mutant-type gene in heterozygotes. Thus, TRACER exhibits comparable sensitivity, specificity, and accuracy to Sanger sequencing in analyzing the SNV-related clinical tumor samples. Overall, TRACER introduces a brand-new perspective for SNV assays by eliminating the dependency on PAM sites and significantly expands the application range of the CRISPR-Cas12a system, thus holding immense potential for clinical diagnostics, biomedical research, and drug discovery.

Ag+-Mediated DNA Nanomachine Cascade Nanomaterial Amplification Enable One-Pot Electrochemical Analysis of Circulating Tumor DNA

Circular tumor DNA (ctDNA) is a trace nucleic acid that functions as an essential tumor marker. In this context, the present study proposes a one-pot electrochemical analysis of ctDNA EGFR L858R in lung cancer leveraging a Ag+-mediated DNA nanosphere (I amplification) and cation exchange reaction (II amplification), and Cu2+ acts as a signal molecule. Once the target L858R exists, it specifically destroys the structure of DNA nanosphere@Ag+, and large amounts of Ag+ are released. After the addition of copper sulfide nanoparticles, Cu2+ can be replaced by a cation exchange reaction. Eventually, the electrochemical signal of Cu2+ is elevated. The analytical performance of the method is satisfactory, L858R can be detected in the linear range of 1 aM-1 fM with a detection limit of 0.3 aM. Furthermore, the system exhibits notable selectivity in differentiating base mismatch targets and other ctDNA sequences. The recovery rate of blood samples is between 95.5 and 105%. The electrochemical results from the analysis of 42 clinical blood samples are consistent with those of the quantitative real-time polymerase chain reaction, computed tomography, and pathology results. In summary, this novel strategy utilizes preprepared functional nucleic acid nanomaterials and cascade amplification, which is expected to contribute to the sensitive and expeditious detection of trace nucleic acids.

Reaction Pathway Differentiation Enabled Fingerprinting Signal for Single Nucleotide Variant Detection

Accurate identification of single-nucleotide variants (SNVs) is paramount for disease diagnosis. Despite the facile design of DNA hybridization probes, their limited specificity poses challenges in clinical applications. Here, a differential reaction pathway probe (DRPP) based on a dynamic DNA reaction network is presented. DRPP leverages differences in reaction intermediate concentrations between SNV and WT groups, directing them into distinct reaction pathways. This generates a strong pulse-like signal for SNV and a weak unidirectional increase signal for wild-type (WT). Through the application of machine learning to fluorescence kinetic data analysis, the classification of SNV and WT signals is automated with an accuracy of 99.6%, significantly exceeding the 80.7% accuracy of conventional methods. Additionally, sensitivity for variant allele frequency (VAF) is enhanced down to 0.1%, representing a ten-fold improvement over conventional approaches. DRPP accurately identified D614G and N501Y SNVs in the S gene of SARS-CoV-2 variants in patient swab samples with accuracy over 99% (n = 82). It determined the VAF of ovarian cancer-related mutations KRAS-G12R, NRAS-G12C, and BRAF-V600E in both tissue and blood samples (n = 77), discriminating cancer patients and healthy individuals with significant difference (p < 0.001). The potential integration of DRPP into clinical diagnostics, along with rapid amplification techniques, holds promise for early disease diagnostics and personalized diagnostics.

Tandem-Controlled Dynamic DNA Assembly Enables Temporally-Selective Orthogonal Regulation of cGAS-STING Stimulation

Despite advances in the controlled reconfiguration of DNA structures for biological applications, the dearth of strategies that allow for orthogonal regulation of immune pathways remains a challenge. Here, we report for the first time an endogenous and exogenous tandem-regulated DNA assembly strategy that enables orthogonally controlled stimulation of the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway. A DNA motif containing two palindromic sequences is engineered with an abasic site (AP)-connected blocking sequence to inhibit its self-assembly function, while apurinic/apyrimidinic endonuclease 1 (APE1)-triggered enzymatic cleavage of the AP site enables the reconfiguration and self-assembly of DNA motif into long double-stranded structures, thus realizing allosteric activation of the catalytic activity of cGAS to produce 2'3'-cyclic-GMP-AMP for STING stimulation. Importantly, we demonstrate that APE1-regulated DNA assembly allows for cell-selective activation of cGAS-STING signaling. Furthermore, by re-engineering the DNA motif with a photocleavable group, enzyme-triggered DNA assembly allows the cGAS-STING stimulation to operate (switched "ON"), whereas light-mediated fragmentation of the double-stranded DNA enables termination of such stimulation (switched "OFF"), thereby achieving orthogonal control over immune regulation. This work highlights an endogenous and exogenous tandem regulated strategy to modulate the cGAS-STING pathway in an orthogonally controlled manner.

Programming the Dynamic Range of Nanochannel Biosensors for MicroRNA Detection Through Allosteric DNA Probes

Solid-state nanochannel biosensors are extensively utilized for microRNA (miRNA) detection owing to their high sensitivity and rapid response. However, conventional nanochannel biosensors face limitations in their fixed dynamic range, restricting their versatility and efficacy. Herein, we introduce tunable triblock DNA probes with varying affinities for target miRNA to engineer solid-state nanochannel biosensors capable of customizable dynamic range adjustment. The triblock DNA architecture comprises a poly-adenine (polyA) block for adjustable surface density anchoring, alongside stem and loop blocks for modulating structural stability. Through systematic manipulation of these blocks, we demonstrate the ability to achieve diverse target binding affinities and detection limits, achieving an initial 81-fold dynamic range. By combining probes with various affinities, we extend this dynamic range significantly to 10,900-fold. Furthermore, by implementing a sequestration mechanism, the effective dynamic range of the nanochannel biosensor is narrowed to only a 3-fold span of target concentrations. The customizable dynamic range of these advanced nanochannel biosensors makes them highly promising for a broad spectrum of biomedical and clinical applications.

Development and validation of an ultrasensitive qPCR method to identify and quantify EGFR T790M in cell-free DNA

BACKGROUND

Circulating tumor DNA (ctDNA) is a promising biomarker for cancer prognosis and drug development. A major challenge in the ctDNA determination method is discriminating ctDNA from highly similar but significantly more abundant wild-type DNA sensitively and accurately.

METHOD

An ultrasensitive qPCR method termed Triple Enrichment Amplification of Mutation PCR (TEAM-PCR) was developed to detect EGFR T790M mutation.

RESULTS

EGFR T790M was quantified over the assay range of 25-106 copies/reaction in the presence of 106 wild-type copies. This method was fully validated following the essential bioanalysis guidance, with the limit of detection (LOD) being five copies/reaction.

CONCLUSION

This study established and validated a qPCR-based strategy to detect EGFR T790M mutation with ultra-high sensitivity and reliability.

Thermodynamics and Kinetics-Directed Regulation of Nucleic Acid-Based Molecular Recognition

Nucleic acid-based molecular recognition plays crucial roles in various fields like biosensing and disease diagnostics. To achieve optimal detection and analysis, it is essential to regulate the response performance of nucleic acid probes or switches to match specific application requirements by regulating thermodynamics and kinetics properties. However, the impacts of thermodynamics and kinetics theories on recognition performance are sometimes obscure and the relative conclusions are not intuitive. To promote the thorough understanding and rational utilization of thermodynamics and kinetics theories, this review focuses on the landmarks and recent advances of nucleic acid thermodynamics and kinetics and summarizes the nucleic acid thermodynamics and kinetics-based strategies for regulation of nucleic acid-based molecular recognition. This work hopes such a review can provide reference and guidance for the development and optimization of nucleic acid probes and switches in the future, as well as for advancements in other nucleic acid-related fields.

Modular CRISPR/Cas12a synergistic activation platform for detection and logic operations

The revolutionary technology of CRISPR/Cas has reshaped the landscape of molecular biology and molecular engineering. This tool is of interest to researchers in multiple fields, including molecular diagnostics, molecular biochemistry circuits, and information storage. As CRISPR/Cas spreads to more niche areas, new application scenarios and requirements emerge. Developing programmability and compatibility of CRISPR/Cas becomes a critical issue in the new phase. Here, we report a redundancy-based modular CRISPR/Cas12a synergistic activation platform (MCSAP). The position, length, and concentration of the redundancy in the split DNA activators can finely regulate the activity of Cas12a. With the redundant structure as an interface, MCSAP serves as a modular plug-in to seamlessly integrate with the upstream molecular network. MCSAP successfully performs three different tasks: nucleic acid detection, enzyme detection, and logic operation. MCSAP can work as an effector for different molecular networks because of its compatibility and programmability. Our platform provides powerful yet easy-to-use tools and strategies for the fields of DNA nanotechnology, molecular engineering, and molecular biology.

Custom-Designed Probes for the Accurate Determination of Epidermal Growth Factor Receptor Mutations and Their Allelic Configuration

The identification of single nucleotide polymorphisms (SNPs) is of paramount importance for disease diagnosis and clinical prognostication. In the context of nonsmall cell lung cancer (NSCLC), the emergence of resistance mutations, exemplified by the epidermal growth factor receptor (EGFR) T790 M and C797S, is intricately linked to the therapeutic efficacy of EGFR tyrosine kinase inhibitors (EGFR-TKIs). Herein, a highly efficient and specific SNP detection platform for T790 M and C797S mutations has been engineered through the integration of an asymmetric polymerase chain reaction (PCR) and an ingeniously tailored four-way junction (4WJ) probe. Notably, a molecular beacon (MB) probe was judiciously designed to discern the allelic configuration of these mutations. The administration of first- and third-generation EGFR-TKIs demonstrates therapeutic efficacy solely when the mutations are in the trans configuration, characterized by a low fluorescence signal. In contrast, significant fluorescence by the MB probe is indicative of the C797S mutation being in a cis arrangement with T790M, thereby rendering the cells refractory to the therapeutic interventions of both first- and third-generation EGFR-TKIs. The assay is capable of concurrently detecting two point-mutations and ascertaining their allelic positions in a single test within 1.5 h, enhancing both efficiency and simplicity. It also exhibits high accuracy in the identification of clinical samples, offering promising implications for therapeutic guidelines. By enabling tailored treatment plans based on specific genetic profiles, our approach not only advances the precision of NSCLC treatment strategies but also marks a significant contribution to personalized medicine.

Modified Unit-Mediated Strand Displacement Reactions for Direct Detection of Single Nucleotide Variants in Active Double-Stranded DNA

Accurate identification of single nucleotide variants (SNVs) in key driver genes holds a significant value for disease diagnosis and treatment. Fluorescent probes exhibit tremendous potential in specific, high-resolution, and rapid detection of SNVs. However, additional steps are required in most post-PCR assays to convert double-stranded DNA (dsDNA) products into single-stranded DNA (ssDNA), enabling them to possess hybridization activity to trigger subsequent reactions. This process not only prolongs the complexity of the experiment but also introduces the risk of losing target information. In this study, we proposed two strategies for enriching active double-stranded DNA, involving PCR based on obstructive groups and cleavable units. Building upon this, we explored the impact of modified units on the strand displacement reaction (SDR) and assessed their discriminatory efficacy for mutations. The results showed that detection of low variant allele frequencies (VAF) as low as 0.1% can be achieved. The proposed strategy allowed orthogonal identification of 45 clinical colorectal cancer tissue samples with 100% specificity, and the results were generally consistent with sequencing results. Compared to existing methods for enriching active targets, our approach offers a more diverse set of enrichment strategies, characterized by the advantage of being simple and fast and preserving original information to the maximum extent. The objective of this study is to offer an effective solution for the swift and facile acquisition of active double-stranded DNA. We anticipate that our work will facilitate the practical applications of SDR based on dsDNA.

Endonuclease IV and T4 ligase enhanced detection of mutations in low abundance

We propose a mutant detection approach based on endonuclease IV and DNA ligase in combination with qPCR. The enzymes functioned cooperatively to facilitate PCR for low abundance DNA detection. We demonstrate that our approach can distinguish mutations as low as 0.01%, indicating the potential application of this strategy in early cancer diagnosis.