Application of Nanomaterials to Enhance Polymerase Chain Reaction

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.

High-sensitivity qPCR detection method based on silver flower-like LSPR-active material

Quantitative polymerase chain reaction (qPCR) technology offers advantages such as easy operation and high specificity, but also faces issues like lengthy detection time and low sensitivity. This paper proposes a method by using novel SERS-active silver flower-like material to enhance the fluorescence signal generated by qPCR instrument, so as to shorten the detection time and improve the detection sensitivity. In this method, silver flower-like material is first prepared on substrates using a lyotropic liquid crystal soft template combined with electrodeposition growth. Then, an ultrasonic device is used to peel the active material into aqueous solution, and the peeling efficiency reaches 90%. Using rhodamine 6G (R6G) as the qPCR amplification detection molecule, the fluorescence signal generated from the flower-like material-containing sample is increased by 20%. Finally, the qPCR amplification effect is detected with the commercially available new coronavirus nucleic acid detection kit. The results showed that the CT value decreased from 35 to 31 after adding the silver flower-like material, and the detection efficiency increased by 20%. Meanwhile, no non-specific amplification is observed. For COVID-19 samples at S7 concentration, the positive detection rate rises from 1/200 to 2/3 by our method.

Research Progress Towards and Prospects of Carbon Dots Derived from Tea and Chinese Medicinal Materials

This review focuses on the research progress related to carbon dots (CDs) derived from Chinese herbal medicines and tea, covering preparation methods, physicochemical properties, and application fields. It elaborates on preparation approaches like hydrothermal, solvothermal, microwave-assisted, and ultrasonic-assisted methods, and their influence on CDs' structure and properties. It also explores CDs' structural and optical properties. The application fields include antibacterial, sensing, bioimaging, photocatalysis, hemostasis, and energy. Carbon dots show antibacterial activity by destroying bacterial cell membranes, they can detect various substances in sensing, are important for bioimaging, degrade organic pollutants in photocatalysis, have hemostatic and anti-inflammatory effects, and can be used as battery anode materials. Despite progress, challenges remain in improving yield, quantum yield, property control, and understanding their mechanism of action. This review provides a reference for related research and looks ahead to future directions.

Rapid Real-Time PCR Based on Core-Shell Tecto-Dendrimer-Entrapped Au Nanoparticles

Rapid real-time PCR (generally <1 h) has broad prospects. In this study, we synthesized a new type of nanomaterial core-shell tecto-dendrimer coated with Au nanoparticles (Au CSTDs) for research in this field. The experimental results showed that Au CSTDs could significantly shorten the time of real-time PCR (from 72 to 28 min) with different templates, while the detection limit reached 10 copies and the nonspecific amplification was significantly reduced. Furthermore, experimental analyses and theoretical studies using the finite element simulation method confirmed that Au CSTDs function by synergistically enhancing electrostatic adsorption and thermal conductivity. These properties play a key role in improving real-time PCR, especially in particle-particle interactions. This study contributes an advanced method to rapid real-time PCR, which is expected to remarkably improve the efficiency, lower the detection limit, and enhance the specificity of molecular detection.

Capped Plasmonic Gold and Silver Nanoparticles with Porphyrins for Potential Use as Anticancer Agents-A Review

Photothermal therapy (PTT) and photodynamic therapy (PDT) are potential cancer treatment methods that are minimally invasive with high specificity for malignant cells. Emerging research has concentrated on the application of metal nanoparticles encapsulated in porphyrin and their derivatives to improve the efficacy of these treatments. Gold and silver nanoparticles have distinct optical properties and biocompatibility, which makes them efficient materials for PDT and PTT. Conjugation of these nanoparticles with porphyrin derivatives increases their light absorption and singlet oxygen generation that create a synergistic effect that increases phototoxicity against cancer cells. Porphyrin encapsulation with gold or silver nanoparticles improves their solubility, stability, and targeted tumor delivery. This paper provides comprehensive review on the design, functionalization, and uses of plasmonic silver and gold nanoparticles in biomedicine and how they can be conjugated with porphyrins for synergistic therapeutic effects. Furthermore, it investigates this dual-modal therapy's potential advantages and disadvantages and offers perspectives for future prospects. The possibility of developing gold, silver, and porphyrin nanotechnology-enabled biomedicine for combination therapy is also examined.

Nanotechnology-Enabled PCR with Tunable Energy Dynamics

This Perspective elucidates the transformative impacts of advanced nanotechnology and dynamic energy systems on the polymer chain reaction (PCR), a cornerstone technique in biomedical research and diagnostic applications. Since its invention, the optimization of PCR-specifically its efficiency, specificity, cycling rate, and detection sensitivity-has been a focal point of scientific exploration. Our analysis spans the modulation of PCR from both material and energetic perspectives, emphasizing the intricate interplay between PCR components and externally added entities such as molecules, nanoparticles (NPs), and optical microcavities. We begin with a foundational overview of PCR, detailing the basic principles of PCR modulation through molecular additives to highlight material-level interactions. Then, we delve into how NPs, with their diverse material and surface properties, influence PCR through interface interactions and hydrothermal conduction, drawing parallels to molecular behaviors. Additionally, this Perspective ventures into the energetic regulation of PCR, examining the roles of electromagnetic radiation and optical resonators. We underscore the advanced capabilities of optical technologies in PCR regulation, characterized by their ultrafast, residue-free, and noninvasive nature, alongside label-free detection methods. Notably, optical resonators present a pioneering approach to control PCR processes even in the absence of light, targeting the often-overlooked water component in PCR. By integrating discussions on photocaging and vibrational strong coupling, this review presents innovative methods for the precise regulation of PCR processes, envisioning a new era of PCR technology that enhances both research and clinical diagnostics. The synergy between nanotechnological enhancements and energy dynamics not only enriches our understanding of PCR but also opens new avenues for developing rapid, accurate, and efficient PCR systems. We hope that this Perspective will inspire further innovations in PCR technology and guide the development of next-generation clinical detection instruments.

Classification and applications of nanomaterials in vitro diagnosis

With the rapid development of clinical diagnosis and treatment, many traditional and conventional in vitro diagnosis technologies are unable to meet the demands of clinical medicine development. In this situation, nanomaterials are rapidly developing and widely used in the field of in vitro diagnosis. Nanomaterials have distinct size-dependent physical or chemical properties, and their optical, magnetic, electrical, thermal, and biological properties can be modulated at the nanoscale by changing their size, shape, chemical composition, and surface functional groups, particularly because they have a larger specific surface area than macromaterials. They provide an amount of space to modify different molecules on their surface, allowing them to detect small substances, nucleic acids, proteins, and microorganisms. Combining nanomaterials with in vitro diagnosis is expected to result in lower detection limits, higher sensitivity, and stronger selectivity. In this review, we will discuss the classfication and properties of some common nanomaterials, as well as their applications in protein, nucleic acids, and other aspect detection and analysis for in vitro diagnosis, especially on aging-related nanodiagnostics. Finally, it is summarized with guidelines for in vitro diagnosis.

Review of Detection Limits for Various Techniques for Bacterial Detection in Food Samples

Foodborne illnesses can be infectious and dangerous, and most of them are caused by bacteria. Some common food-related bacteria species exist widely in nature and pose a serious threat to both humans and animals; they can cause poisoning, diseases, disabilities and even death. Rapid, reliable and cost-effective methods for bacterial detection are of paramount importance in food safety and environmental monitoring. Polymerase chain reaction (PCR), lateral flow immunochromatographic assay (LFIA) and electrochemical methods have been widely used in food safety and environmental monitoring. In this paper, the recent developments (2013-2023) covering PCR, LFIA and electrochemical methods for various bacterial species (Salmonella, Listeria, Campylobacter, Staphylococcus aureus (S. aureus) and Escherichia coli (E. coli)), considering different food sample types, analytical performances and the reported limit of detection (LOD), are discussed. It was found that the bacteria species and food sample type contributed significantly to the analytical performance and LOD. Detection via LFIA has a higher average LOD (24 CFU/mL) than detection via electrochemical methods (12 CFU/mL) and PCR (6 CFU/mL). Salmonella and E. coli in the Pseudomonadota domain usually have low LODs. LODs are usually lower for detection in fish and eggs. Gold and iron nanoparticles were the most studied in the reported articles for LFIA, and average LODs were 26 CFU/mL and 12 CFU/mL, respectively. The electrochemical method revealed that the average LOD was highest for cyclic voltammetry (CV) at 18 CFU/mL, followed by electrochemical impedance spectroscopy (EIS) at 12 CFU/mL and differential pulse voltammetry (DPV) at 8 CFU/mL. LOD usually decreases when the sample number increases until it remains unchanged. Exponential relations (R2 > 0.95) between LODs of Listeria in milk via LFIA and via the electrochemical method with sample numbers have been obtained. Finally, the review discusses challenges and future perspectives (including the role of nanomaterials/advanced materials) to improve analytical performance for bacterial detection.

The 60 nm gold nanoparticles improve qPCR amplification efficiency through specific palindromic sequences (GGATCC or ACCGGT) in primers

BACKGROUND

Polymerase chain reaction (PCR) technology and quantitative real-time PCR (qPCR) technology are widely used in clinical diagnosis and research, but amplification efficiency and sensitivity are still key problems for researchers. An increasing number of reports show that gold nanoparticles (AuNPs) can be used to improve the sensitivity and amplification efficiency of PCR. Here, we found that 60 nm gold nanoparticles with a positive charge (60 nm- Au+) can enhance the amplification efficiency of qPCR.

METHODS

Mouse DNA was extracted by the alkaline lysis method. Primer 5.0 software was used to design primers and mutation primers, and the DNA fragments were obtained by the method of synthesizing plasmids. The qPCR was applied to amplify target gene fragments.

RESULTS

The amplification efficiency of qPCR was improved by about 1.828 times in the experimental group with 60 nm- Au+ compared with the control group without 60 nm- Au+. The primer pair contains a specific palindromic sequence (GGATCC or ACCGGT). And 60 nm Au+ did not enhance the amplification efficiency of qPCR when the above primer was mutated.

CONCLUSIONS

The primers contain special palindrome sequences (GGATCC or ACCGGT) with 60 nm- Au+ can enhance the amplification efficiency of qPCR. Therefore, it suggests a more in-depth understanding of the mechanism and function of gold nanoparticles and primer sequences. This study has presented some implications for gold nanoparticles application in the development of qPCR technology.

Development of multiplex gold nanoparticles biosensors for ultrasensitive detection and genotyping of equine herpes viruses

Gold nanoparticles (GNPs) biosensors can detect low viral loads and differentiate between viruses types, enabling early diagnosis and effective disease management. In the present study, we developed GNPs biosensors with two different capping agent, citrate-GNPs biosensors and polyvinylpyrrolidone (PVP)-GNPs biosensors for detection of EHV-1 and EHV-4 in multiplex real time PCR (rPCR). Citrate-GNPs and PVP-GNPs biosensors can detect dilution 1010 of EHV-1 with mean Cycle threshold (Ct) 11.7 and 9.6, respectively and one copy as limit of detection, while citrate-GNPs and PVP-GNPs biosensors can detect dilution 1010 of EHV-4 with mean Ct 10.5 and 9.2, respectively and one copy as limit of detection. These findings were confirmed by testing 87 different clinical samples, 4 more samples were positive with multiplex GNPs biosensors rPCR than multiplex rPCR. Multiplex citrate-GNPs and PVP-GNPs biosensors for EHV-1 and EHV-4 are a significant breakthrough in the diagnosis of these virus types. These biosensors offer high sensitivity and specificity, allowing for the accurate detection of the target viruses at very low concentrations and improve the early detection of EHV-1 and EHV-4, leading to faster control of infected animals to prevent the spread of these viruses.

PCR inhibitors and facilitators - Their role in forensic DNA analysis

Since its inception, DNA typing technology has been practiced as a robust tool in criminal investigations. Experts usually utilize STR profiles to identify and individualize the suspect. However, mtDNA and Y STR analyses are also considered in some sample-limiting conditions. Based on DNA profiles thus generated, forensic scientists often opine the results as Inclusion, exclusion, and inconclusive. Inclusion and exclusion were defined as concordant results; the inconclusive opinions create problems in conferring justice in a trial- since nothing concrete can be interpreted from the profile generated. The presence of inhibitor molecules in the sample is the primary factor behind these indefinite results. Recently, researchers have been emphasizing studying the sources of PCR inhibitors and their mechanism of inhibition. Furthermore, several mitigation strategies- to facilitate the DNA amplification reaction -have now found their place in the routine DNA typing assays with compromised biological samples. The present review paper attempts to provide a comprehensive review of PCR inhibitors, their source, mechanism of inhibition, and ways to mitigate their effect using PCR facilitators.

Enhancement Effects and Mechanism Studies of Two Bismuth-Based Materials Assisted by DMSO and Glycerol in GC-Rich PCR

Polymerase chain reaction (PCR) has extensive bioanalytical applications in molecular diagnostics and genomic research studies for rapid detection and precise genomic amplification. Routine integrations for analytical workflow indicate certain limitations, including low specificity, efficiency, and sensitivity in conventional PCR, particularly towards amplifying high guanine-cytosine (GC) content. Further, there are many ways to enhance the reaction, for example, using different PCR strategies such as hot-start/touchdown PCR or adding some special modifications or additives such as organic solvents or compatible solutes, which can improve PCR yield. Due to the widespread use of bismuth-based materials in biomedicine, which have not yet been used for PCR optimization, this attracts our attention. In this study, two bismuth-based materials that are inexpensive and readily available were used to optimize GC-rich PCR. The results demonstrated that ammonium bismuth citrate and bismuth subcarbonate effectively enhanced PCR amplification of the GNAS1 promoter region (∼84% GC) and APOE (75.5% GC) gene of Homo sapiens mediated by Ex Taq DNA polymerase within the appropriate concentration range. Combining DMSO and glycerol additives was critical in obtaining the target amplicons. Thus, the solvents mixed with 3% DMSO and 5% glycerol were used in bismuth-based materials. That allowed for better dispersion of bismuth subcarbonate. As for the enhanced mechanisms, the surface interaction of PCR components, including Taq polymerase, primer, and products with bismuth-based materials, was maybe the main reason. The addition of materials can reduce the melting temperature (T_m), adsorb polymerase and modulate the amount of active polymerase in PCR, facilize the dissociation of DNA products, and enhance the specificity and efficiency of PCR. This work provided a class of candidate enhancers for PCR, deepened our understanding of the enhancement mechanisms of PCR, and also explored a new application field for bismuth-based materials.