Taqman-MGB nanoPCR for Highly Specific Detection of Single-Base Mutations

Nanoparticle-assisted PCR: fundamentals, mechanisms, and forensic implications

Polymerase Chain Reaction (PCR) has transformed forensic DNA analysis but is still limited when dealing with compromised trace or inhibitor-containing samples. Nanotechnology has been integrated into nanoPCR (nanoparticle-assisted PCR) to overcome these obstacles. Nanomaterials improve PCR sensitivity, selectivity, and efficiency. Examples of these materials are semiconductor quantum dots and metal nanoparticles. They enhance DNA binding to primers, stabilize enzymes, and function as effective heat conductors, making accurate amplification possible even with tainted samples. The developments in nanoPCR have potential uses in forensics, as they allow for the more sensitive analysis of smaller, polluted, or deteriorated samples. Nevertheless, there are methodological and ethical issues. To provide credible and legitimate forensic evidence, rigorous validation and standardization of NanoPCR techniques are vital. The article addresses the relevant ethical and methodological aspects in forensic casework while examining the integration of nanotechnology into PCR.

The nucleic acid reactions on the nanomaterials surface for biomedicine

Integrating nucleic acids (NAs) with nanomaterials has substantially advanced biomedical research, enabling critical applications in biosensing, drug delivery, therapeutics, and the synthesis of nanomaterials. At the core of these advances are the reactions of NAs on nanomaterial surfaces, encompassing conjugation (covalent and non-covalent), detachment (physical and chemical), and signal amplification (enzyme-mediated signal amplification, enzyme-free signal amplification, and DNA Walker). Here, we review the fundamental mechanisms and recent progress in nucleic acid reactions on nanomaterial surfaces, discuss emerging applications for diagnostics, nanomedicine, and gene therapy, and explore persistent challenges in the field. We offer a forward-looking perspective on how future developments could better control, optimize, and harness these reactions for transformative advances in nanomedicine and biomedical engineering.

Establishment and application of a qPCR method for differential detection of Brucella S2 vaccine strain

BACKGROUND

Brucellosis is one of the most serious zoonotic bacterial diseases in the world. The disease has caused serious harm to people and livestock, hindered the healthy development of the breeding industry, and led to serious economic losses.At present, the prevention and control of this kind of disease is still based on vaccine immunization. However, after the widely used vaccine is inoculated to livestock, there is no widely used differential diagnosis method to distinguish vaccine immune antibodies from natural infection antibodies. Quarantine and purification work is difficult to carry out. In addition, there are few studies using real-time PCR(qPCR) methods in the differential diagnosis of natural virulent strains and vaccine strains of brucellosis.The purpose of this study is to establish a rapid, sensitive and accurate differential diagnosis method for Brucella S2 vaccine strain, and to solve the problem of lack of identification of Brucella S2 vaccine strain and natural virulent strain in clinical detection.It avoids the killing of some livestock due to the positive antibody of the Brucella S2 vaccine strain, and can also identify sick animals from immune herds, reducing the economic losses of farms, and providing certain technical support for the quarantine and purification of epidemic diseases.

RESULTS

In this study, combined with TaqMan probe-based qPCR technology, specific primers and probes were designed according to the specific deletion genes of the Brucella S2 vaccine strain,which could be used as marker genes.The qPCR and duplex qPCR detection methods of Brucella were successfully established.The method has good specificity, sensitivity and repeatability, the lowest limit of detection can reach 1 × 101 copies/μL, the sensitivity is about 100 times higher than that of conventional PCR, and there is no cross-reaction with Escherichia coli,Salmonella,streptococcus and other common strains.The coefficient of variation between groups was less than 0.6%, and the coefficient of variation within groups was less than 0.55%.Subsequently, this method was used to monitor the antibody levels in goat inoculated with different doses of Brucella S2 vaccine strain, and the method could also detect the corresponding nucleic acid signals in goat milk samples, and the clinical samples were detected. In summary, this method has good specificity, sensitivity and repeatability, and can be used for the differential diagnosis of clinical brucellosis.

CONCLUSIONS

This study successfully established a duplex qPCR detection method for the differential diagnosis of the Brucella S2 vaccine strain. From the establishment of the method to the clinical application of the method, it shows that the method can be used for the differential diagnosis of clinical brucellosis.

Dual-signal, one-step simultaneous monitoring of genetic mutation in multiple gene regions using Fe3O4@Au and MOF

Genetic testing plays a crucial role in guiding individualized medication, however, detecting fine structural mutations in genes continues to present significant challenges. This study introduces a dual-signal fluorescence system, termed Fe3O4@Au@PEG@P1+MOF@P2, that integrates magnetic separation of Fe3O4@Au with NH2-MIL-88 (MOF) catalysis. Initially, the specimen (T1/T2) facilitated the formation of a specific complex (Fe3O4@Au@PEG@P1+T1/T2) with Fe3O4@Au@PEG@P1. The subsequent addition of Hoechst-33258 produced a robust fluorescence signal at 460 nm, enabling the identification of mutations in the first gene regions. Following this, MOF@P2 was introduced to activate the catalyst through P2 pairing with T2. The complex Fe3O4@Au@PEG@P1+T1/T2+P2+Hoechst-33258 was subsequently isolated using an external magnetic field. Upon adding OPD, fluorescent DAP was detected at 560 nm, allowing for the identification of mutations in the second gene regions. The research demonstrated that the variation in fluorescence signals increased with a higher number of base substitutions and deletion mutations, with deletion mutations resulting in a notably greater alteration rate compared to substitution mutations. Interestingly, triple base substitution mutations, characterized by lower clustering of non-continuous mutations, produced a more pronounced change in fluorescence signal than did a higher clustering of continuous mutations (codon mutations). This single-step methodology effectively differentiates among the number and types of mutations across multiple gene regions while assessing the degree of mutation clustering. Overall, this technology significantly enhances the current capabilities for detecting fine structural mutations in genes. Furthermore, the approach exhibits high sensitivity in detecting concentrations of T1 and T2 ranging from 10-15 M to 10-9 M, with detection limits of 0.19 fM and 0.24 fM, even in 5 % serum samples.

Association of Sheep Tail Type with the T Gene Single Nucleotide Polymorphisms Loci

This study aimed to develop an effective tail typing detection technology based on the TaqMan probe technology for genotyping different sheep tail types. A total of 122 Hulun Buir short-tailed sheep and 50 Hu sheep were enrolled in the study to compare their tail morphologies, lengths, and widths. Through the Sanger sequencing of loci 333 and 334 in the second exon of the T gene, distinct genotypes of various types of Hulun Buir short-tailed sheep and Hu sheep were identified. In addition, the TaqMan probe technology was employed to genotype the two SNP loci of the T gene in the two types of sheep. It was observed that the second exon of the T gene in Hulun Buir short-tailed sheep at loci 333 and 334 exhibited two genotypes, CT/CT and CT/GG, but this feature was not detected for the T gene in Hu sheep. The detection accuracy of the TaqMan probe technology for sheep tail types exceeded 70%, suggesting that it is an effective tail-typing detection technology. This study provides a solid economic foundation and theoretical ideas that will improve the breeding of short-tailed sheep.

Mutation-Selected Amplification droplet digital PCR: A new single nucleotide variant detection assay for TP53R249S mutant in tumor and plasma samples

The early detection of gene mutations in physiological and pathological processes is a powerful approach to guide decisions in precision medicine. However, detecting low-copy mutant DNA from clinical samples poses a challenge due to the enrichment of wild-type DNA backgrounds. In this study, we devised a novel strategy, named Mutation-Selected Amplification droplet digital PCR (MSA-ddPCR), to quantitatively analyze single nucleotide variants (SNVs) at low variant allele frequencies (VAFs). Using TP53R249S (a hotspot mutation associated with hepatocellular carcinoma) as a model, we optimized the concentration ratio of primers, the annealing temperature and nucleic acid amplification modifiers. Subsequently, we evaluated the linear range and precision of MSA-ddPCR by detecting TP53R249S and TP53wild-type (TP53WT) plasmid DNA, respectively. MSA-ddPCR demonstrated superior ability to discriminate between mutant DNA and wild-type DNA compared to traditional TaqMan-MGB PCR. We further applied MSA-ddPCR to analyze the TP53R249S mutation in 20 plasma samples and 15 formalin-fixed paraffin-embedded (FFPE) tissue samples, and assessed the agreement rates between MSA-ddPCR and amplicon high-throughput sequencing. The results showed that the limit of blanks of MSA-ddPCR are 0.449 copies μL-1 in the FAM channel and 0.452 copies μL-1 in the VIC channel. MSA-ddPCR could accurately quantify VAFs as low as 0.01 %, surpassing existing PCR and next-generation sequencing (NGS) methods. In the detection of clinical samples, a high correlation was found between MSA-ddPCR and amplicon high-throughput sequencing. Additionally, MSA-ddPCR outperformed sequencing methods in terms of detection time and simplicity of data analysis. MSA-ddPCR can be easily implemented into clinical practice and serve as a robust tool for detecting mutant genes due to its high sensitivity and accuracy.

Detection of Single Nucleotide Polymorphisms of Circulating Tumor DNA by Strand Displacement Amplification Coupled with Liquid Chromatography

The detection of multiple single nucleotide polymorphisms (SNPs) of circulating tumor DNA (ctDNA) is still a great challenge. In this study, we designed enzyme-assisted nucleic acid strand displacement amplification combined with high-performance liquid chromatography (HPLC) for the simultaneous detection of three ctDNA SNPs. First, the trace ctDNA could be hybridized to the specially designed template strand, which initiated the strand displacement nucleic acid amplification process under the synergistic action of DNA polymerase and restriction endonuclease. Then, the targets would be replaced with G-quadruplex fluorescent probes with different tail lengths. Finally, the HPLC-fluorescence assay enabled the separation and quantification of multiple signals. Notably, this method can simultaneously detect both the wild type (WT) and mutant type (MT) of multiple ctDNA SNPs. Within a linear range of 0.1 fM-0.1 nM, the detection limits of BRAF V600E-WT, EGFR T790M-WT, and KRAS 134A-WT and BRAF V600E-MT, EGFR T790M-MT, and KRAS 134A-MT were 29, 31, and 11 aM and 22, 29, and 33 aM, respectively. By using this method, the mutation rates of multiple ctDNA SNPs in blood samples from patients with lung or breast cancer can be obtained in a simple way, providing a convenient and highly sensitive analytical assay for the early screening and monitoring of lung cancer.

Enzyme-Assisted Nucleic Acid Amplification in Molecular Diagnosis: A Review

Infectious diseases and tumors have become the biggest medical challenges in the 21st century. They are driven by multiple factors such as population growth, aging, climate change, genetic predispositions and more. Nucleic acid amplification technologies (NAATs) are used for rapid and accurate diagnostic testing, providing critical information in order to facilitate better follow-up treatment and prognosis. NAATs are widely used due their high sensitivity, specificity, rapid amplification and detection. It should be noted that different NAATs can be selected according to different environments and research fields; for example, isothermal amplification with a simple operation can be preferred in developing countries or resource-poor areas. In the field of translational medicine, CRISPR has shown great prospects. The core component of NAAT lies in the activity of different enzymes. As the most critical material of nucleic acid amplification, the key role of the enzyme is self-evident, playing the upmost important role in molecular diagnosis. In this review, several common enzymes used in NAATs are compared and described in detail. Furthermore, we summarize both the advances and common issues of NAATs in clinical application.

Application of Nanomaterials to Enhance Polymerase Chain Reaction

Polymerase Chain Reaction (PCR) is one of the most common technologies used to produce millions of copies of targeted nucleic acid in vitro and has become an indispensable technique in molecular biology. However, it suffers from low efficiency and specificity problems, false positive results, and so on. Although many conditions can be optimized to increase PCR yield, such as the magnesium ion concentration, the DNA polymerases, the number of cycles, and so on, they are not all-purpose and the optimization can be case dependent. Nano-sized materials offer a possible solution to improve both the quality and productivity of PCR. In the last two decades, nanoparticles (NPs) have attracted significant attention and gradually penetrated the field of life sciences because of their unique chemical and physical properties, such as their large surface area and small size effect, which have greatly promoted developments in life science and technology. Additionally, PCR technology assisted by NPs (NanoPCR) such as gold NPs (Au NPs), quantum dots (QDs), and carbon nanotubes (CNTs), etc., have been developed to significantly improve the specificity, efficiency, and sensitivity of PCR and to accelerate the PCR reaction process. This review discusses the roles of different types of NPs used to enhance PCR and summarizes their possible mechanisms.

Adaptive therapy to circumvent drug resistance to tyrosine kinase inhibitors in cancer: is it clinically relevant?

INTRODUCTION

Cancer is highly adaptable and is constantly evolving against current targeted therapies such as tyrosine kinase inhibitors. Despite advances in recent decades, the emergence of drug resistance to tyrosine kinase inhibitors constantly hampers therapeutic efficacy of cancer treatment. Continuous therapy versus intermittent clinical regimen has been a debate in drug administration of cancer patients. An ecologically-inspired shift in cancer treatment known as 'adaptive therapy' intends to improve the drug administration of drugs to cancer patients that can delay emergence of drug resistance.

AREAS COVERED

We discuss improved understanding of the concept of drug resistance, the basis of continuous therapy, intermittent clinical regimens, and adaptive therapy will be reviewed. In addition, we discuss how adaptive therapy provides guidance for future cancer treatment.

EXPERT OPINION

The current understanding of drug resistance in cancer leads to poor prognosis and limited treatment options in patients. Fighting drug resistance mutants is constantly followed by new forms of resistance. In most reported cases, continuous therapy leads to drug resistance and an intermittent clinical regimen vaguely delays it. However, adaptive therapy, conceptually, exploits multiple parameters that can suppress the growth of drug resistance and provides safe treatment for cancer patients in the future.

Tetra-primer ARMS-PCR combined with dual-color fluorescent lateral flow assay for the discrimination of SARS-CoV-2 and its mutations with a handheld wireless reader

Several virulent variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have emerged along with the spread of this virus throughout the population. Some variants can exhibit increased transmissibility and reduced immune neutralization reactivity. These changes are deeply concerning issues that may hinder the ongoing effort of epidemic control measures, especially mass vaccination campaigns. The accurate discrimination of SARS-CoV-2 and its emerging variants is essential to contain the coronavirus disease 2019 pandemic. Herein, we report a low-cost, facile, and highly sensitive diagnostic platform that can simultaneously distinguish wild-type (WT) SARS-CoV-2 and its two mutations, namely, D614G and N501Y, within 2 h. WT or mutant (M) nucleic acid fragments at each allelic locus were selectively amplified by the tetra-primer amplification refractory mutation system (ARMS)-PCR assay. Allele-specific amplicons were simultaneously detected by two test lines on a quantum dot nanobead (QB)-based dual-color fluorescent test strip, which could be interpreted by the naked eye or by a home-made fluorescent strip readout device that was wirelessly connected to a smartphone for quantitative data analysis and result presentation. The WT and M viruses were indicated and were strictly discriminated by the presence of a green or red band on test line 1 for the D614G site and test line 2 for the N501Y site. The limits of detection (LODs) for the WT and M D614G were estimated as 78.91 and 33.53 copies per μL, respectively. This assay was also modified for the simultaneous detection of the N and ORF1ab genes of SARS-CoV-2 with LODs of 1.90 and 6.07 copies per μL, respectively. The proposed platform can provide a simple, accurate, and affordable diagnostic approach for the screening of SARS-CoV-2 and its variants of concern even in resource-limited settings.

Establishment of a Rapid Typing Method for Coronavirus Disease 2019 Mutant Strains Based on PARMS Technology

Purpose: This study aims to establish a competitive allele-specific PCR based on penta-primer amplification refractory mutation system (PARMS) technology to detect the key mutation sites of variant of concern (VOC) of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus for rapid typing. Methods: Competitive allele-specific primers and universal primers were designed for the key gene mutation sites N501Y, E484K, L452R, and K417N of SARS-CoV-2 VOCs, respectively.Using the principle of allele-specific polymerase chain reaction and fluorescence energy resonance transfer, different VOCs can be differentiated. Results: Using reverse transcribed cDNA of different VOCs as specimens, through double-blind detection, different VOC types can be effectively identified, with an accuracy rate of 100%. Through the identification and detection of different VOCs, effective differentiation can be achieved. Conclusions: The system has high specificity and sensitivity, with a detection limit of 1.28 copies/reaction.PARMS technology is fast, efficient, and low-cost. It is used for the identification and detection of the popular SARS-CoV-2 VOCs, which is helpful for the rapid and accurate prevention and control of COVID-19 epidemic.

A tailored LNA clamping design principle: Efficient, economized, specific and ultrasensitive for the detection of point mutations

In the development of personalized medicine, the ultrasensitive detection of point mutations that correlate with diseases is important to improve the efficacy of treatment and guide clinical medication. In this study, locked nucleic acid (LNA) was introduced as an amplification suppressor of a massive number of wild-type alleles in an amplification refractory mutation system (ARMS) to achieve the detection of low-abundance mutations with high specificity and sensitivity of at least 0.1%. By integrating the length of clamp, base type, number and position of LNA modifications, we have established a "shortest length with the fewest LNA bases" principle from which each LNA base would play a key role in the affinity and the ability of single base discrimination could be improve. Finally, based on this LNA design guideline, a series of the most important single point mutation sites of epidermal growth factor receptor (EGFR) was verified to achieve the optimal amplification state which as low as 0.1% mutation gene amplification was not affected under the wild gene amplification was completely inhibited, demonstrating that the proposed design principle has good applicability and versatility and is of great significance for the detection of circulating tumor DNA.