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

Rapid and highly sensitive colorimetric LAMP assay and integrated device for visual detection of monkeypox virus

BACKGROUND

The monkeypox virus (MPXV) is a linear double-stranded DNA virus with a large genome that causes tens of thousands of infections and hundreds of deaths in at least 40 countries and regions worldwide. Therefore, timely and accurate diagnostic testing could be an important measure to prevent the ongoing spread of MPXV and widespread epidemics.

RESULTS

Here, we designed multiple sets of primers for the target region of MPXV for loop-mediated isothermal amplification (LAMP) detection and identified the optimal primer set. Then, the specificity in fluorescent LAMP detection was verified using the plasmids containing the target gene, pseudovirus and other DNA/RNA viruses. We also evaluated the sensitivity of the colorimetric LAMP detection system using the plasmid and pseudovirus samples, respectively. Besides, we used monkeypox pseudovirus to simulate real samples for detection. Subsequent to the establishment and introduction of a magnetic beads (MBs)-based nucleic acid extraction technique, an integrated device was developed, characterized by rapidity, high sensitivity, and remarkable specificity. This portable system demonstrated a visual detection limit of 137 copies/mL, achieving sample-to-answer detection within 1 h.

SIGNIFICANCE

The device has the advantages of integration, simplicity, miniaturization, and visualization, which help promote the realization of accurate, rapid, portable, and low-cost testing. Meanwhile, this platform could facilitate efficient, cost-effective and easy-operable point-of-care testing (POCT) in diverse resource-limited settings in addition to the laboratory.

Advances in superparamagnetic iron oxide nanoparticles modified with branched polyethyleneimine for multimodal imaging

Multimodal imaging are approaches which combines multiple imaging techniques to obtain multi-aspect information of a target through different imaging modalities, thereby greatly improve the accuracy and comprehensiveness of imaging. Superparamagnetic iron oxide nanoparticles (SPIONs) modified with branched polyethyleneimine have revealed good biocompatibility and stability, high drug loading capacity and nucleic acid transfection efficiency. SPIONs have been developed as functionalized platforms which can be further modified to enhance their functionalities. Those further modifications facilitate the application of SPIONs in multimodal imaging. In this review, we discuss the methods, advantages, applications, and prospects of BPEI-modified SPIONs in multimodal imaging.

A pendulum-type electrochemical aptamer-based sensor for continuous, real-time and stable detection of proteins

Continuous detection of proteins is crucial for health management and biomedical research. Electrochemical aptamer-based (E-AB) sensor that relies on binding affinity between a recognition oligonucleotide and its specific target is a versatile platform to fulfill this purpose. Yet, the vast majority of E-AB sensors are characterized by voltammetric methods, which suffer from signal drifts and low-frequency data acquisition during continuous operations. To overcome these limitations, we developed a novel E-AB sensor empowered by Gold nanoparticle-DNA Pendulum (GDP). Using chronoamperometric interrogation, the developed sensor enabled drift-resistant, high-frequency, and real-time monitoring of vascular endothelial growth factor (VEGF), a vital signaling protein that regulates angiogenesis, endothelial cell proliferation and vasculogenesis. We assembled VEGF aptamer-anchored GDP probes to a reduced graphene modified electrode, where a fast chronoamperometric current transient occurs as the GDP rapidly transport to the electrode surface. In the presence of target molecules, longer and concentration-dependent time decays were observed because of slower motion of the GDP in its bound state. After optimizing several decisive parameters, including composition ratios of GDP, probe density, and incubation time, the GDP empowered E-AB sensor achieves continuous, selective, and reversible monitoring of VEGF in both phosphate buffered saline (PBS) solutions and artificial urine with a wide detection range from 13 fM to 130 nM. Moreover, the developed sensor acquires signals on a millisecond timescale, and remains resistant to signal degradation during operation. This study offers a new approach to designing E-AB architectures for continuous biomolecular monitoring.

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.

Polyethyleneimine-Based Drug Delivery Systems for Cancer Theranostics

With the development of nanotechnology, various types of polymer-based drug delivery systems have been designed for biomedical applications. Polymer-based drug delivery systems with desirable biocompatibility can be efficiently delivered to tumor sites with passive or targeted effects and combined with other therapeutic and imaging agents for cancer theranostics. As an effective vehicle for drug and gene delivery, polyethyleneimine (PEI) has been extensively studied due to its rich surface amines and excellent water solubility. In this work, we summarize the surface modifications of PEI to enhance biocompatibility and functionalization. Additionally, the synthesis of PEI-based nanoparticles is discussed. We further review the applications of PEI-based drug delivery systems in cancer treatment, cancer imaging, and cancer theranostics. Finally, we thoroughly consider the outlook and challenges relating to PEI-based drug delivery systems.

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.

Spatiotemporal Regulation of Metal Ions in the Polymerase Chain Reaction

The polymerase chain reaction (PCR) has been widely used in medical diagnosis and forensic identification due to its ultrahigh sensitivity and signal amplification. Metal ions (i.e., Cu²⁺, Zn²⁺) have been considered PCR inhibitors and rarely shown their positive roles in PCR amplification until our report, in which we discovered that metal ions can significantly improve the PCR specificity and the yield of target DNA sequences. For an in-depth investigation with taking copper ions as a typical model, here we found an interesting spatiotemporal regulation mechanism of metal ions in PCR. The ionic concentration window for improving PCR specificity not only was independent of annealing temperature but also can be well regulated by both the annealing time and extension time. Using the ionic concentration window as a measure, the time affects either the amount or the sequence length of nonspecific amplicons in the space. The mechanism proposed in this work will deepen our understanding of the unneglectable roles of metal ions in DNA replication and meanwhile provide a new strategy for designing regulation kits for PCR-based biomedical applications.

Fos-Related Antigen 1 May Cause Wnt-Fzd Signaling Pathway-Related Nephroblastoma in Children

This study aimed to investigate the role of the primary Fos-related antigen 1 (Fosl-1) oncogene in nephroblastoma by studying 60 childhood nephroblastoma and 58 paraneoplastic carcinoma cases. The Fosl-1 expression was detected using immunohistochemistry. In vitro culture of nephroblastoma cells was performed by viral transfection to establish Fosl-1 overexpression and gene knockout models. Flow cytometry and nano-PCR were used to detect apoptosis and mRNA expression in related pathway genes. Immunohistochemical results showed that the positive expression of Fosl-1 in the nuclei of nephroblastoma tissue was 78%, among which metastasis rate was 61.7%; correspondingly, it was 8%, and 100% in adjacent tissues. The qPCR results indicated that MMP9, Wnt1, and Fzd1 were significantly upregulated after Fosl-1 overexpression compared with the normal embryonic tissue cells, control, and gene knockout groups (P <0.05). Fosl-1 could cause the occurrence, development, and metastasis of childhood nephroblastoma through wingless/int1/Frizzled-related signaling pathways.

Effective CpG Delivery Using Zwitterion-Functionalized Dendrimer-Entrapped Gold Nanoparticles to Promote T Cell-Mediated Immunotherapy of Cancer Cells

Recently, cell-based immunotherapy has become one of the most promising ways to completely eliminate cancer. The major challenge is to effectively promote a proper immune response to kill the cancer cells by activated T cells. This study investigated the effect of T cell-mediated immunotherapy trigged by Au DENPs-MPC (zwitterion 2-methacryloyloxyethyl phosphorylcholine (MPC)-functionalized dendrimer-entrapped gold nanoparticles) loading oli-godeoxynucleotides (ODN) of unmethylated cytosine guanine dinucleotide (CPG). Here, we first synthesized Au DENPs-MPC, evaluated their capability to compress and transfect CpG-ODN to bone marrow dendritic cells (BMDCs), and investigated the potential to use T cells stimulated by matured BMDCs to inhibit the growth of tumor cells. The developed Au DENPs-MPC could apparently reduce the toxicity of Au DENPs, and enhanced transfer CpG-ODN to the BMDCs for the maturation as demonstrated by the 44.41–48.53% increase in different surface maturation markers. The transwell experiments certificated that ex vivo activated T cells display excellent anti-tumor ability, which could effectively inhibit the growth of tumor cells. These results suggest that Au DENPs-MPC can deliver CpG-ODN efficiently to enhance the antigen presentation ability of BMDCs to activate T cells, indicating that T cells-based immunotherapy mediated by Au DENPs-MPC loaded with CpG-ODN may become the most promising treatment of cancer.

Rapid and highly sensitive one-tube colorimetric RT-LAMP assay for visual detection of SARS-CoV-2 RNA

Coronavirus disease 2019 (COVID-19), caused by SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) is a highly contagious disease. To tame the continuously raging outbreak of COVID-19, developing a cheap, rapid and sensitive testing assay is absolutely imperative. Herein, we developed a one-tube colorimetric RT-LAMP assay for the visual detection of SARS-CoV-2 RNA. The assay integrates Si-OH magnetic beads (MBs)-based fast RNA extraction and rapid isothermal amplification in a single tube, thus bypassing the RNA elution step and directly amplifying on-beads RNA molecules with the visualized results. This one-tube assay has a limit of detection (LOD) as low as 200 copies/mL for sample input volumes of up to 600 μL, and can be performed in less than 1 h from sample collection to result readout. This assay demonstrated a 100% concordance with the gold standard test RT-qPCR test by using 29 clinical specimens and showed high specificity. This one-tube colorimetric RT-LAMP assay can serve as an alternative platform for a rapid and sensitive diagnostic test for COVID-19 and is particularly suitable for use at community clinics or township hospitals.

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.

Adoptive cellular immunotherapy of tumors via effective CpG delivery to dendritic cells using dendrimer-entrapped gold nanoparticles as a gene vector

PEGylated Au DENPs ({(Au⁰)₂₅-G5·NH₂-mPEG₂₀}) are synthesized and used as a novel nonviral vector to deliver CpG to mature BMDCs for the subsequent activation of T cells for adoptive tumor immunotherapy.

Efficient polymerase chain reaction assisted by metal-organic frameworks

As a powerful tool for obtaining sufficient DNA from rare DNA resources, polymerase chain reaction (PCR) has been widely used in various fields, and the optimization of PCR is still in progress due to the dissatisfactory specificity, sensitivity and efficiency. Although many nanomaterials have been proven to be capable of optimizing PCR, their underlying mechanisms are still unclear. So far, the scientifically compelling and functionally evolving metal–organic framework (MOF) materials with high specific surface area, tunable pore sizes, alterable surface charges and favourable thermal conductivity have not been used for PCR optimization. In this study, UiO-66 and ZIF-8 were used to optimize error-prone two round PCR. The results demonstrated that UiO-66 and ZIF-8 not only enhanced the sensitivity and efficiency of the first round PCR, but also increased the specificity and efficiency of the second round PCR. Moreover, they could widen the annealing temperature range of the second round PCR. The interaction of DNA and Taq polymerase with MOFs may be the main reason. This work provided a candidate enhancer for PCR, deepened our understanding on the enhancement mechanisms of nano-PCR, and explored a new application field for MOFs.

Many new materials have the ability to optimize polymerase chain reaction (PCR). Metal-organic frame materials UiO-66 and ZIF-8 can enhance sensitivity, specificity and efficiency of PCR, indicating their potential as PCR enhancers.

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.

Ultrasensitive Detection of HIV DNA with Polymerase Chain Reaction-Dynamic Light Scattering

Early diagnosis of HIV biomarkers or genes is the key to reducing acquired immunodeficiency syndrome (AIDS) mortality. In our work, we developed a novel polymerase chain reaction-dynamic light scattering (PCR-DLS) assay for one-step sensitive detection of HIV DNA based on the average-diameter change of gold nanoparticles (AuNPs). This is the first PCR assay that makes use of the DLS technique as a signal read-out, with the particle size measured by DLS increasing with the concentration of target DNA. With the help of the AuNP probes, this PCR-DLS assay can effectively improve the specificity of PCR reactions, which can greatly increase the detection sensitivity, with a detection limit of 1.8 aM (S/N = 3). In addition, the proposed strategy was successfully used to analyze target DNA in human serum samples, indicating that the PCR-DLS assay has a promising potential application for rapid and early clinical diagnosis of HIV infection.

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.

Preparation of Gold Nanocomposites with Tunable Charge and Hydrophobicity via the Application of Polymer/Surfactant Complexation

During the synthesis of gold nanoparticle (NP) assemblies, the interfacial charge and hydrophobicity of the primary particles play a distinguished role. In the present article, we demonstrate that the association of poly(ethyleneimine) (PEI) capped gold NPs with sodium alkyl sulfates provide a powerful route for the manipulation of these interfacial properties. Dynamic light-scattering, electrophoretic mobility, UV-vis-near-infrared spectroscopy, nanoparticle tracking analysis, and transmission electron microscopy measurements were used to characterize the PEI/surfactant/gold nanoassemblies. The results indicate the formation of gold NPs surrounded by a PEI/surfactant shell with composition-dependent charge and hydrophobicity. The mean size and the aggregation of the nanoassemblies can be fine tuned by the amount of surfactant bound to the primary gold NPs as well as by the application of controlled mixing methods. The specific features of the prepared nanocomposites may be further exploited in next-generation applications.

Graphene oxide enhances the specificity of the polymerase chain reaction by modifying primer-template matching

Aiming at improved specificity, nanoparticle assisted polymerase chain reaction (PCR) has been widely studied and shown to improve PCR. However, the reliability and mechanism of this method are still controversial. Here, we demonstrated that 1 μg/mL of graphene oxide (GO) effectively enhances the specificity of the error-prone multi-round PCR. Mismatched primers were designed as interference to produce nonspecific products when the same amounts of matched and mismatched primers were added into semi-multiplex PCR. It was found that GO can enhance specificity by suppressing the amplification of mismatched primers. We monitored the primer-template-polymerase-GO interactions involved in the PCR using a capillary electrophoresis/laser-induced fluorescence polarization (CE-LIFP) assay. The results showed that the addition of GO promoted the formation of a matched primer-template complex, but suppressed the formation of a mismatched primer-template complex during PCR, suggesting that interactions between the primers and GO play an essential role. Furthermore, we successfully amplified the FOXL2 gene from PEGFP-N1 vectors using GO to eliminate the nonspecific products in PCR. Taken together, these results suggest that the GO can be used as an efficient additive for improving the conventional PCR system.

Effect of antifouling dendrimers and Au DENPs on the enhancement of PCR amplification

The polymerase chain reaction (PCR) has been considered as one of the most fundamental techniques to amplify and analyze specific DNA fragments in the field of molecular biology and clinical medicine. Recently, a variety of nanoparticles (NPs) have been regarded as a novel method to enhance both the quality and yield of PCR technique. Herein, we report the use of generation 5 (G5) poly(amidoamine) (PAMAM) dendrimers and dendrimer-entrapped gold nanoparticles (Au DENPs) modified with polyethylene glycol (PEG) moieties and (or) acetyl groups as a novel class of enhancers to improve the PCR amplification. We set up the nonspecific PCR and two-round PCR as model systems to investigate mechanisms of enhanced PCR. Our results show that dendrimer-based derivatives seem to enhance the PCR specificity. It is worth noting that the modification of antifouling PEG significantly lowered the optimization capability of the corresponding dendrimers, although this inhibition effect can be remarkably compromised by the entrapment of Au NPs. Furthermore, we found that in the presence of Au NPs, the thermal conductivity induced by Au NPs could play the dominant role in the PCR optimization, whereas in the absence of Au NPs, the electrostatic interaction of the dendrimers with PCR components may be the major factor affecting the PCR system. Our results also showed that the optimal concentrations of the materials in the two test systems were very close, which indicates that the developed dendrimer derivatives with good thermal stability may be the efficient PCR additives for enhancing different PCR systems.

Gold nanoparticle-assisted polymerase chain reaction: effects of surface ligands, nanoparticle shape and material

The concentration, shape, material, and surface functionalization effects of gold nanoparticles on PCR outcome have been studied with two PCR gene diagnostic models.