Endonuclease IV based competitive DNA probe assay for differentiation of low-abundance point mutations by discriminating stable single-base mismatches

Effective delivery of CRISPR/dCas9-SAM for multiplex gene activation based on mesoporous silica nanoparticles for bladder cancer therapy

The molecular complexity of bladder cancer restricts reliance on single-feature or single-gene targeted therapies, necessitating integrated individualized treatments and multi-gene interventions. In this study, we introduced the CRISPR/dCas9-SAM system to BCa treatment, known for its high specificity, low off-target effects, and reduced genetic toxicity, making it ideal for multiplexed gene activation at minimal cost-just 20 nucleotides per target. However, despite its potential in complex gene therapy and cellular engineering, challenges persist due to safety concerns associated with viral vectors and the risk of off-target effects during in vivo delivery, necessitating the development of new vectors. Herein, we reported pH-sensitive hollow mesoporous silica nanoparticles modified with PLZ4 ligands (PLZ4-Lip@AMSN/CRISPR/dCas9-SAM, PLACS NPs) for precise targeting of bladder tumors and co-delivery of CRISPR/dCas9-SAM system. With good stability and high plasmid loading capacity, they efficiently co-delivered dCas9-VP64, MS2-P65-HSF1, and sgRNA. Compared to Lipofectamine 3000, these nanoparticles exhibited superior lysosomal escape capability, significantly enhancing transfection efficiency in bladder cancer cells. Moreover, PLACS NPs simultaneously activated the expression of four target genes, inhibiting proliferation and migration, and promoting apoptosis in bladder cancer cells. In vivo, they achieved efficient gene editing at tumor sites, significantly inhibiting bladder tumor growth. Real-time imaging revealed their substantial accumulation and prolonged retention at bladder tumor sites without significant liver targeting and major organ damage, showcasing good specificity and biosafety. This study overcomes in vivo delivery challenges of multi-component CRISPR/dCas9 systems, enabling precise gene editing and anti-tumor effects, presenting an innovative strategy for targeted therapy in bladder cancer treatment. STATEMENT OF SIGNIFICANCE: This study introduces a newly-developed approach to address key challenges in bladder cancer gene therapy, namely low gene upregulation efficiency, limited targeting specificity, and inefficient nucleic acid delivery. By integrating the CRISPR/dCas9-SAM system, we achieve highly specific gene activation with minimal off-target effects, enabling the addition of treatment targets with just 20 nucleotides per target. To improve bladder cancer targeting, we developed PLACS NPs, a mesoporous silica nanoparticle system that enhances plasmid delivery, transfection efficiency, and endosomal escape. This system shows good tumor targeting and significant anti-tumor effects in bladder cancer, without significant liver targeting and major organ toxicity, offering promising therapeutic potential and broad clinical applications.

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.

An Auto-Reading probe system for detecting deletion mutations In liquid biopsy with direct quantification of mutation abundance

Background

Deletion mutations have been confirmed to be closely related to the occurrence and progression of different hereditary diseases and tumors. Specifically, the deletion of a small number of bases is more challenging to be captured and differentiated. In non-invasive prenatal testing (NIPT) and liquid biopsy targeting circulating tumor DNA, obtaining accurate mutation abundance in targeted DNA is a crucial step in the detection process. However, the quantification of mutation abundance with existing methods is not accurate enough.

Results

Herein, we developed the " Auto-Reading" probe detection system based on our previous work. Through theoretical modeling and experimental calculations, we verified the successful application of our system in NIPT and early cancer diagnosis, enabling effective discrimination of different mutant abundances.

Significance

Our method overcomes the interference of reaction concentrations on signal detection, allowing direct quantification of mutation abundance without the need for purification of PCR products. The detection system is cost-effective and feasible for laboratory use. We believe the system will facilitate broad applications in mutation detection.

Identification of DNA variants at ultra-low variant allele frequencies via Taq polymerase cleavage of wild-specific blockers

Detecting mutations related to tumors holds immense clinical significance for cancer diagnosis and treatment. However, the presence of highly redundant wild DNA poses a challenge for the advancement of low-copy mutant ctDNA genotyping in cancer cases. To address this, a Taqman qPCR strategy to identify rare mutations at low variant allele fractions (VAFs) has been developed. This strategy combines mutant-specific primers with wild-specific blockers. Diverging from other blocker-mediated PCRs, which rely on primer-induced strand displacement or the use of modified oligos resistant to Taq polymerase, our innovation is built upon the cleavage of specific blockers by Taq polymerase. Given its unique design, which does not hinge on strand displacement or base modification, we refer to this novel method as unmodified-blocker cleavage PCR (UBC-PCR). Multiple experiments consistently confirmed that variant distinction was improved significantly by introduction of 5' unmatched blockers into the reaction. Moreover, UBC-PCR successfully detected mutant DNA at VAFs as low as 0.01% across six different variant contexts. Multiplex UBC-PCR was also performed to identify a reference target and three mutations with a sensitivity of 0.01% VAFs in one single tube. In profiling the gene status from 12 lung cancer ctDNA samples and 22 thyroid cancer FNA DNA samples, UBC-PCR exhibited a 100% concordance rate with ddPCR and a commercial ARMS kit, respectively. Our work demonstrates that UBC-PCR can identify low-abundance variants with high sensitivity in multiplex reactions, independent of strand displacement and base modification. This strategy holds the potential to significantly impact clinical practice and precision medicine.

Recent Progress in Single-Nucleotide Polymorphism Biosensors

Single-nucleotide polymorphisms (SNPs), the most common form of genetic variation in the human genome, are the main cause of individual differences. Furthermore, such attractive genetic markers are emerging as important hallmarks in clinical diagnosis and treatment. A variety of destructive abnormalities, such as malignancy, cardiovascular disease, inherited metabolic disease, and autoimmune disease, are associated with single-nucleotide variants. Therefore, identification of SNPs is necessary for better understanding of the gene function and health of an individual. SNP detection with simple preparation and operational procedures, high affinity and specificity, and cost-effectiveness have been the key challenge for years. Although biosensing methods offer high specificity and sensitivity, as well, they suffer drawbacks, such as complicated designs, complicated optimization procedures, and the use of complicated chemistry designs and expensive reagents, as well as toxic chemical compounds, for signal detection and amplifications. This review aims to provide an overview on improvements for SNP biosensing based on fluorescent and electrochemical methods. Very recently, novel designs in each category have been presented in detail. Furthermore, detection limitations, advantages and disadvantages, and challenges have also been presented for each type.

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.

Guiding-Strand-Controlled DNA Nucleases with Enhanced Specificity and Tunable Kinetics for DNA Mutation Detection

Nucleases are powerful tools in various biomedical applications, such as genetic engineering, biosensing, and molecular diagnosis. However, the commonly used nucleases (endonuclease IV, apurinic/apyrimidinic endonuclease-1, and λ exonuclease) are prone to the nonspecific cleavage of single-stranded DNA, making the desired reactions extremely low-yield and unpredictable. Herein, we have developed guiding-strand-controlled nuclease systems and constructed theoretical kinetic models to explain their mechanisms of action. The models displayed excellent agreement with the experimental results, making the kinetics highly predictable and tunable. Our method inhibited the nonspecific cleavage of single-stranded probes while maintaining highly efficient cleavage of double-stranded DNA. We also demonstrated the clinical practicability of the method by detecting a low-frequency mutation in a genomic DNA sample extracted from the blood of a patient with cancer. The limit of detection could be 0.01% for PTEN rs121909219. We believe that our findings provide a powerful tool for the field and the established model provides us a deeper understanding of the enzymatic activities of DNA nucleases.

Thermodynamics and kinetics guided probe design for uniformly sensitive and specific DNA hybridization without optimization

Sensitive and specific DNA hybridization is essential for nucleic acid chemistry. Competitive composition of probe and blocker has been the most adopted probe design for its relatively high sensitivity and specificity. However, the sensitivity and specificity were inversely correlated over the length and concentration of the blocker strand, making the optimization process cumbersome. Herein, we construct a theoretical model for competitive DNA hybridization, which disclose that both the thermodynamics and kinetics contribute to the inverse correlation. Guided by this, we invent the 4-way Strand Exchange LEd Competitive DNA Testing (SELECT) system, which breaks up the inverse correlation. Using SELECT, we identified 16 hot-pot mutations in human genome under uniform conditions, without optimization at all. The specificities were all above 140. As a demonstration of the clinical practicability, we develop probe systems that detect mutations in human genomic DNA extracted from ovarian cancer patients with a detection limit of 0.1%.

Optimisation of nucleic acid probes and blocker strands can be laborious. Here the authors construct a theoretical model of competitive DNA hybridisation to design DNA probes for optimisation-free mutation detection.

Eliminating the secondary structure of targeting strands for enhancement of DNA probe based low-abundance point mutation detection

Nucleic acid probes are very useful tools in biological and medical science. However, the essential sensing mechanism of nucleic acid probes was prone to the interference of surrounding sequences. Especially when the target sequences formed secondary structures such as hairpin or quadruplex, the nucleic acid probes were hindered from hybridizing with target strands, greatly disabled the function of probes. Herein, we have established an Open strand based strategy for eliminating the influence of secondary structures on the performance of nucleic acid probes. The strategy was general toward different lengths, secondary structures and sequences of the targeting strand, and we found that the improvement was higher when the secondary structure of the targeting strand was more complicated. Experiments on synthetic single stranded DNA and real clinical genomic DNA samples were conducted for low abundance mutation detection, and the limit of detection for TERT-C228T and BRCA2 rs80359065 mutations could be 0.02% and 0.05% respectively, demonstrating the clinical practicability of our proposed strategy in low abundance mutation detection.

Endonuclease IV recognizes single base mismatch on the eighth base 3' to the abasic site in DNA strands for ultra-selective and sensitive mutant-type DNA detection

Since single nucleotide polymorphism (SNP) is related with many diseases and drug metabolic polymorphous and SNP genotyping is rising rapidly in many biological and medical areas, various methods of discriminating SNPs have been developed, one of which is an enzyme-based method. We uncovered a unique property of endonuclease IV due to which it can discriminate single base mismatches in different positions of DNA strands containing an abasic site, and we also discovered a new property: a mismatch in the +8 position could inhibit the cleavage of endonuclease IV. Then, we coupled +8 mismatch with other mismatches along with the discrimination effect of melting temperature to develop a new ultra-selective and sensitive genotyping system, which showed high discrimination factors. The detection limit was as low as 0.05-0.01%. Our new discovery improves the understanding of endonuclease IV. Also, the method could be applied to clinical real samples; thus, it merits further investigation and improvement for application in clinical utilization for early screening of specific diseases.

Combining cooperativity with sequestration: a novel strategy for discrimination of single nucleotide variants

We present a novel strategy for the discrimination of single nucleotide variants (SNVs) by combining cooperativity with sequestration, which displays remarkably high specificity (discrimination factors ranging from 67 to 618 with a median of 194) against 12 model SNVs and can be easily integrated with PCR amplification to detect KRAS G12D mutation.

Ultraspecific Multiplexed Detection of Low-Abundance Single-Nucleotide Variants by Combining a Masking Tactic with Fluorescent Nanoparticle Counting

To be able to detect simultaneously multiple single-nucleotide variants (SNVs) with both ultrahigh specificity and low-abundance sensitivity is of pivotal importance for molecular diagnostics and biological research. In this contribution, we for the first time developed a multiplex SNV detection method that combines the masking tactic with fluorescent nanoparticle (FNP) counting based on the sandwich design. The method presents a rivaling performance due to its advantageous features: the masking reagent was designed to hybridize with an extremely large amount of the wild-type sequence to render the assay with high specificity; FNP counting provides a sensitive multiplexed SNV detection; the sandwich design facilitates an easy separation to make the detection free of interferences from the matrix. For single SNV target discrimination, including the 6 most frequently occurring DNA KRAS gene mutations and 2 possible RNA KRAS gene mutations as well as 11 artificial mutations, the discrimination factor ranged from 204 to 1177 with the median being 545. Among the tested 19 SNVs, abundances as low as 0.05% were successfully identified in 14 cases, and an abundance as low as 0.1% was identified for the remaining 5 cases. For multiplexed detection of SNVs in the KRAS gene, abundances as low as 0.05-0.1% were achieved for multiple SNVs occurring at the same and different codons. As low as 0.05% low-abundance detection sensitivity was also achieved for PCR amplicons of human genomic DNA extracted from cell samples. This proposed method presents the potential for ultrahigh specific multiplexed detection of SNVs with low-abundance detection capability, which may be applied to practical applications.

Detection of low-abundance point mutations by competitive strand assisted endonuclease IV signal amplification system

Genetic mutations are important molecular biomarkers for cancer diagnosis and surveillance. Therefore, the development of methods for mutation detection characterized with straightforward, highly specific and sensitive to low-level mutations within various sequence contexts is extremely needed. Although some of the currently available methods have shown very encouraging results, their discrimination efficiency is still very low. Herein, we demonstrate a fluorescent probe coupled with blocker and property of melting temperature discrimination, which is able to identify the presence of known or unknown single-base variations at abundances down to 0.1% within 20 min. The discrimination factors between the perfect-match target and single-base mismatched target are determined to be 10.15-38.48. The method is sequence independent, which assures a wide range of application. The new method would be an ideal choice for high-throughput in vitro diagnosis and precise clinical treatment.