Dopamine-assisted synthesis of carbon-coated silica for PCR enhancement

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.

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.

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.

Graphene oxide nanosheet-mediated fluorescent RPA "turn-on" biosensor for rapid RNAi transgenic plant detection

In this paper preliminarily verified that graphene oxide (GO) nanomaterials enhanced the recombinase polymerase amplification (RPA). GO nanosheets improved the efficiency of RPA amplification by absorbing ingredients to induce local aggregation. The recombinase initially aggregated with the primers to form nucleoprotein filaments, absorbed on the GO nanosheets, changing the structure. Therefore, an isothermal fluorescence biosensor was developed based on GO nanosheets enhanced the RPA to detect RNA interference (RNAi) transgenic plants. FAM-labeled primers were absorbed and quenched by the GO nanosheets. After amplification, the primers were extended into double-stranded DNA, detaching from the GO surface to recover the fluorescent signal. The biosensor displayed high sensitivity and selectivity and showed an excellent relationship ranging from 1.5 to 100 ng of genome DNA, with a detection limit (LOD) of 1.5 ng. Consequently, the biosensor provides an enhanced isothermal method for detecting genetically modified (GM) products and exhibits significant potential for molecular detection.

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

PURPOSE

Detection of single-base mutations is important for real-time monitoring of tumor progression, therapeutic effects, and drug resistance. However, the specific detection of single-base mutations from excessive wild-type background sequences with routine PCR technology remains challenging. Our objective is to develop a simple and highly specific qPCR-based single-base mutation detection method.

METHODS

Using EGRF T790M as a model, gold nanoparticles at different concentrations were separately added into the Taqman-MGB qPCR system to test specificity improvement, leading to the development of the optimal Taqman-MGB nanoPCR system. Then, these optimal conditions were used to test the range of improvement in the specificity of mutant-type and wild-type templates and the detection limit of mutation abundances in a spiked sample.

RESULTS

The Taqman-MGB nanoPCR was established based on the traditional qPCR, with significantly suppressed background noise and improved specificity for single-base mutation detection. With EGFR T790M as a template, we demonstrated that our Taqman-MGB nanoPCR system could improve specificity across a wide concentration range from 10-9 μM to 10 μM and detect as low as 0.95% mutation abundance in spiked samples, which is lower than what the traditional Taqman-MGB qPCR and existing PCR methods can detect. Moreover, we also proposed an experimentally validated barrier hypothesis for the mechanism of improved specificity.

CONCLUSION

The developed Taqman-MGB nanoPCR system could be a powerful tool for clinical single-base mutation detection.

Polyacrylamide/Phytic Acid/Polydopamine Hydrogel as an Efficient Substrate for Electrochemical Enrichment of Circulating Cell-Free DNA from Blood Plasma

A facile method has been developed for the rapid and efficient enrichment of DNAs from different media including synthetic single-strand DNAs (ssDNAs) from buffer solutions and cell-free DNAs (cfDNAs) from blood plasma through electric field-driven adsorption and desorption of DNAs by a polyacrylamide/phytic acid/polydopamine (PAAM/PA/PDA) hydrogel. The as-prepared PAAM/PA/PDA hydrogel possesses regular porosity with a large surface area, strong electric field responsiveness/good conductivity, and a rich aromatic structure, which can be used as an ideal adsorbent for DNA enrichment under a positive electric field. The enriched DNAs can be released efficiently when the positive electric field is converted to a negative electric field. The PAAM/PA/PDA hydrogel-based electrochemical method enables the completion of the process of DNA adsorption and release within 5 min and exhibits reasonable enrichment efficiencies and recovery rates of various DNAs. For instance, the high enrichment sensitivity (0.1 pmol L-1) together with the excellent recovery (>75%) of an ssDNA with 78 nucleotides is obtained. Combined with the PCR amplification technique, the practicability of the as-proposed method is demonstrated by the screening of circulating tumor DNAs (ctDNAs) with a BRAFV600E mutation in cfDNAs from the blood plasma samples of patients with papillary thyroid cancer or thyroid nodule and random patients from a clinical laboratory.

Effects of Surface Functional Groups on the Adhesion of SiO2 Nanospheres to Bio-Based Materials

The interactions between nanoparticles and materials must be considered when preparing functional materials. Although researchers have studied the interactions between nanoparticles and inorganic materials, little attention has been paid to those between nanoparticles and bio-based protein materials, like leather. In this study, organically modified silica nanospheres (SiO₂ nanospheres) loaded with rose fragrance were prepared using (3-aminopropyl) triethoxysilane (APTES), (3-mercaptopropyl) triethoxysilane (MPTES), or 3-(2, 3-epoxypropyloxy) propyl triethoxysilane (GPTES) using the sol-gel method. To study the interactions between the modified SiO₂ nanospheres and leather, a non-cross-linking adsorption experiment was conducted. According to the Dubinin–Radushkevich isotherm calculation, we found that the adsorption process of leather fiber and organically modified silica nanospheres is physical. The average adhesion energies of APTES-, MPTES-, and GPTES-modified SiO₂ nanospheres on the leather are 1.34016, 0.97289, and 2.09326 kJ/mol, respectively. The weight gain, adsorption capacity, and average adhesion energy show that the modified SiO₂ nanospheres can be adsorbed on leather in large quantities. The sensory evaluation confirmed that GPTES-modified SiO₂ nanospheres endowed the leather with an obvious rose aroma.

Enhancement of the polymerase chain reaction by tungsten disulfide

In this paper, we demonstrated that the polymerase chain reaction (PCR) could be dramatically enhanced by tungsten disulfide (WS₂). The results showed that the PCR efficiency could be increased with the addition of WS₂ and at a lower annealing temperature, which simplified the design and operation of PCR. Moreover, PCR with WS₂ showed better specificity and efficiency as compared with graphene oxide (GO) for a human genome DNA sample. The mechanism of enhancement of PCR by WS₂ was discussed according to the typical structure and the characteristics of selective adsorption of single-stranded DNA by WS₂. The results suggested that WS₂ as a PCR enhancer can promote the PCR performance and extend the PCR application in biomedical research, clinical diagnostic, and bioanalysis.

WS₂ as a PCR enhancer can promote the PCR performance and extend PCR bioapplication.

Bioinspired Photonic Barcodes with Graphene Oxide Encapsulation for Multiplexed MicroRNA Quantification

Multiplexed microRNA (miRNA) quantification has a demonstrated value in clinical diagnosis. In this paper, novel mussel-inspired photonic crystal (PhC) barcodes with graphene oxide (GO) encapsulation for multiplexed miRNA detection are presented. Using the excellent adhesion capability of polydopamine, the dispersed GO particles can be immobilized on the surfaces of the PhC barcodes to form an additional functional layer. The GO-decorated PhC barcodes have constant characteristic reflection peaks because the GO immobilization process not only maintains their periodic microstructure but also enhances their stability and anti-incoherent light-scattering capability. The immobilized GO particles are shown to enable high-sensitivity miRNA screening on the surface of the PhC barcodes by integration with a hybridization chain reaction amplification strategy. Because the PhC barcodes have stable encoding reflection peaks, multiplexed low-abundance miRNA quantification can also be achieved rapidly, accurately, and reproducibly by employing different GO-decorated PhC barcodes. These features should make GO-encapsulated PhC barcodes ideal for many practical applications.

Enhancement of PCR Sensitivity and Yield Using Thiol-modified Primers

Various additives can enhance the quality of PCR amplification, but these generally require considerable optimization to achieve peak performance. Here, we demonstrate that the use of thiol-modified primers can enhance both PCR sensitivity and yield. In experiments with V. parahaemolyticus genomic DNA, this primer modification enhances PCR sensitivity by more than 100-fold, with accompanying improvements in amplicon yield. Then, an artificial plasmid with the same primer binding regions and different internal amplification sequence was designed. The result showed that the amplification also be improved by using the same thiol-modified primers. It indicated the enhancement was not caused by the effect of the thiol-modified primers on the second structure of amplification sequence. Subsequent experiments demonstrate that the effects of this modification are potentially due to altered interaction between the primers and proteins in the reaction mixture. Amplification with thiol-modified primers was strongly inhibited by the presence of extraneous proteins relative to standard DNA primers, which indicates that thiol-modified primers may be inhibited due to interaction with these proteins. In contaminant-free reactions, however, the thiol-modified primers might interact more strongly with DNA polymerase, which could in turn improve PCR amplification.

Transition Metal Dichalcogenide Nanosheets for Visual Monitoring PCR Rivaling a Real-Time PCR Instrument

Monitoring the progress of polymerase chain reactions (PCRs) is of critical importance in bioanalytical chemistry and molecular biology. Although real-time PCR thermocyclers are ideal for this purpose, their high cost has limited their applications in resource-poor areas. Direct visual detection would be a more attractive alternative. To monitor the PCR amplification, DNA-staining dyes, such as SYBR Green I (SG), are often used. Although these dyes give higher fluorescence when binding to double-stranded DNA products, they also yield strong background fluorescence in the presence of a high concentration of single-stranded (ss) DNA primers. In this work, we screened various nanomaterials and found that graphene oxide (GO), reduced GO, molybdenum disulfide (MoS₂), and tungsten disulfide (WS₂) can quench the fluorescence of nonamplified negative samples while still retaining strong fluorescence of positive ones. The signal ratio of positive-over-negative samples was enhanced by around 50-fold in the presence of these materials. In particular, MoS₂ and WS₂ nearly fully retained the fluorescence of the positive samples. The mechanism for MoS₂ and WS₂ to enhance PCR signaling is attributed to the adsorption of both the ssDNA PCR primers and SG with an appropriate strength. MoS₂ can also suppress nonspecific amplification caused by excess polymerase. Finally, this method was used to detect extracted transgenic soya GTS 40-3-2 DNA after PCR amplification. Compared with the samples without nanomaterials, the addition of MoS₂ could better distinguish the concentration difference of the template DNA, and the sensitivity of visual detection rivaled that from a real-time PCR instrument.

Closer to the polydopamine structure: new insights from a combined 13C/1H/2H solid-state NMR study on deuterated samples

¹³C/¹H/²H ss-NMR on deuterated samples provide strong experimental evidence for the most probable monomer connectivity, π–π stacking, and the water dynamics in polydopamine.

A novel high drug loading mussel-inspired polydopamine hybrid nanoparticle as a pH-sensitive vehicle for drug delivery

A novel high drug loading pH-cleavable polymer hybrid nanoparticle was prepared via doxorubicin (DOX) grafted onto PEGylated, mussel-inspired polydopamine (PDA) and then coated onto hollow silica nanoparticles for drug delivery. A series of characterization shed light on the formation mechanisms of PDA coatings on hollow silica. We hypothesized that dopamine was first absorbed onto the surface of hollow silica and then began self-polymerization. A Dox-containing thiol moiety was fabricated with conjugation between doxorubicin hydrochloride and Mercaptopropionyalkali with a pH-cleavable hydrozone bond. Using a Michael addition reaction, several Dox-containing thiol moieties were grafted onto the surface of the PDA. The drug loading capacity can reach 35.43%. It can minimize the metabolic problem of silica. The released behavior of Dox can be significantly enhanced at endosomal pH compared to physiological pH. After folate modification, nanoparticles can lead to more cellular endocytosis. Meanwhile animal assays showed that more Dox accumulated in tumor tissue, which can enhanced the cytotoxicity to 4T1 cancer cells with a targeting group compared to free DOX and untargeted groups. Meanwhile, the tumor growth was significantly inhibited. This promising material shows a promising future as a drug delivery system.

Visible-Light-Driven Photocatalysts of Perfluorinated Silica-Based Fluorescent Carbon Dot/TiO2 for Tunable Hydrophilic-Hydrophobic Surfaces

In this study, a new hydrophilic-hydrophobic transition surface was designed via visible-light-induced photocatalytic perfluorinated silica-based fluorescent carbon nanoparticles (FNPs)/TiO₂. Perfluorinated silica-polydopamine hybrid FNPs (f-FNPs) were easily fabricated by carbonization in an emulsion system consisting of tetraethyl orthosilicate and dopamine, followed by the deposition of TiO₂ on f-FNPs, which demonstrated the reversal from hydrophobic to hydrophilic nature during successful photocatalysis. The synergistic effect of silica-carbon and the deposited TiO₂ NPs led to the decomposition of methylene blue under UV and visible light irradiation, demonstrating that FNPs/TiO₂ sustains photocatalytic activity. The profound contact angle with the catalytic kinetics curve and precise morphology and extension of cells detach antifouling exceptionally unrestricted the synergistic effect of silica-carbon on TiO₂ NPs on a coated paper substrate. Given the interest in the manipulation of hydrophobicity and hydrophilicity, this study can serve as a guideline for the fabrication of photocatalytic surfaces where water spreads completely.

Mechanistic Studies of Enhanced PCR Using PEGylated PEI-Entrapped Gold Nanoparticles

The polymerase chain reaction (PCR) is considered an excellent technique and is widely used in both molecular biology research and various clinical applications. However, the presence of byproducts and low output are limitations generally associated with this technique. Recently, the use of nanoparticles (NPs) has been shown to be very effective at enhancing PCR. Although mechanisms underlying this process have been suggested, most of them are mainly based on PCR results under certain situations without abundant systematic experimental strategy. In order to overcome these challenges, we synthesized a series of polyethylene glycol (PEG)-modified polyethylenimine (PEI)-entrapped gold nanoparticles (PEG-Au PENPs), each having different gold contents. The role of the synthesized NPs in improving the PCR technique was then systematically evaluated using the error-prone two-round PCR and GC-rich PCR (74% GC content). Our results suggest a possible mechanism of PCR enhancement. In the error-prone two-round PCR system, the improvement of the specificity and efficiency of the technique using the PEG-Au PENPs mainly depends on surface-charge-mediated electrostatic interactions. In the GC-rich PCR system, thermal conduction may be the dominant factor. These important findings offer a breakthrough in understanding the mechanisms involved in improving PCR amplification, as well as in the application of nanomaterials in different fields, particularly in biology and medicine.

One-Pot Synthesis of Fe(III)-Polydopamine Complex Nanospheres: Morphological Evolution, Mechanism, and Application of the Carbonized Hybrid Nanospheres in Catalysis and Zn-Air Battery

We report one-pot synthesis of Fe(III)-polydopamine (PDA) complex nanospheres, their structures, morphology evolution, and underlying mechanism. The complex nanospheres were synthesized by introducing ferric ions into the reaction mixture used for polymerization of dopamine. It is verified that both the oxidative polymerization of dopamine and Fe(III)-PDA complexation contribute to the "polymerization" process, in which the ferric ions form coordination bonds with both oxygen and nitrogen, as indicated by X-ray absorption fine-structure spectroscopy. In the "polymerization" process, the morphology of the complex nanostructures is gradually transformed from sheetlike to spherical at the feed Fe(III)/dopamine molar ratio of 1/3. The final size of the complex spheres is much smaller than its neat PDA counterpart. At higher feed Fe(III)/dopamine molar ratios, the final morphology of the "polymerization" products is sheetlike. The results suggest that the formation of spherical morphology is likely to be driven by covalent polymerization-induced decrease of hydrophilic functional groups, which causes reself-assembly of the PDA oligomers to reduce surface area. We also demonstrate that this one-pot synthesis route for hybrid nanospheres enables the facile construction of carbonized PDA (C-PDA) nanospheres uniformly embedded with Fe3O4 nanoparticles of only 3-5 nm in size. The C-PDA/Fe3O4 nanospheres exhibit catalytic activity toward oxygen reduction reaction and deliver a stable discharge voltage for over 200 h when utilized as the cathode in a primary Zn-air battery and are also good recyclable catalyst supports.

A hybrid composite of gold and graphene oxide as a PCR enhancer

A hybrid composite of Au/GO was synthesized and its capability as a PCR enhancer was demonstrated.