Addition of gold nanoparticles to real-time PCR: effect on PCR profile and SYBR Green I fluorescence

Nano-PCR for the early detection of tomato leaf curl virus

Nano-PCR is a potential tool for the early detection of plant viruses. In the current study, different concentrations of silver nanoparticles (20 nm) and magnesium oxide nanoparticles (50 nm) were included in the PCR mixture to improve the sensitivity of PCR for the detection of tomato leaf curl virus. The inclusion of nanoparticles in single or combination in PCR mixture has resulted in improvement of PCR sensitivity. Four-fold improvement was exhibited by the inclusion of 3 ng/µL silver nanoparticles, whereas the combination of silver and magnesium oxide nanoparticles (3 ng/µL and 200 ng/µL, respectively), resulted in a 4.5-fold improvement. The inclusion of 200 ng/µL of magnesium oxide nanoparticles in the PCR mixture exhibited a 7.6-fold increase in PCR sensitivity. Replacement of magnesium chloride with a combination of silver and magnesium oxide nanoparticles (3 ng/µL and 275 ng/µL, respectively) resulted in a 12-fold increase. A 13-fold improvement in PCR sensitivity was observed by the replacement of magnesium chloride in PCR buffer with 275 ng/µL of magnesium oxide nanoparticles. This could also produce detectable amplicon in PCR with a minimum of 25 cycles, resulting in a 26.5% reduction in the duration of PCR. This is the first report on the use of magnesium oxide nanoparticles in PCR for the early detection and better management of tomato leaf curl virus.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13205-023-03842-2.

The use of HRM shifts in qPCR to investigate a much neglected aspect of interference by intracellular nanoparticles

Genetic molecular studies used to understand potential risks of engineered nanomaterials (ENMs) are incomplete. Intracellular residual ENMs present in biological samples may cause assay interference. This report applies the high-resolution melt (HRM) feature of RT-qPCR to detect shifts caused by the presence of gold nanoparticles (AuNPs). A universal RNA standard (untreated control) sample was spiked with known amounts of AuNPs and reverse transcribed, where 10 reference genes were amplified. The amplification plots, dissociation assay (melt) profiles, electrophoretic profiles and HRM difference curves were analysed and detected interference caused by AuNPs, which differed according to the amount of AuNP present (i.e. semi-quantitative). Whether or not the assay interference was specific to the reverse transcription or the PCR amplification step was tested. The study was extended to a target gene-of-interest (GOI), Caspase 7. Also, the effect on in vitro cellular samples was assessed (for reference genes and Caspase 7). This method can screen for the presence of AuNPs in RNA samples, which were isolated from biological material in contact with the nanomaterials, i.e., during exposure and risk assessment studies. This is an important quality control procedure to be implemented when quantifying the expression of a GOI from samples that have been in contact with various ENMs. It is recommended to further examine 18S, PPIA and TBP since these were the most reliable for detecting shifts in the difference curves, irrespective of the source of the RNA, or, the point at which the different AuNPs interacted with the assay.

Applications of gold nanoparticles in ELISA, PCR, and immuno-PCR assays: A review

Development of state-of-the-art assays for sensitive and specific detection of disease biomarkers has received significant interest for early detection and prevention of various diseases. Enzyme Linked Immunosorbent assays (ELISA) and Polymerase Chain Reaction (PCR) are two examples of proteins and nucleic acid detection assays respectively, which have been widely used for the sensitive detection of target analytes in biological fluids. Recently, immuno-PCR has emerged as a sensitive detection method, where high specificity of sandwich ELISA assays is combined with high sensitivity of PCR for trace detection of biomarkers. However, inherent disadvantages of immuno-PCR assays limit their application as rapid and sensitive detection method in clinical settings. With advances in nanomaterials, nanoparticles-based immunoassays have been widely used to improve the sensitivity and simplicity of traditional immunoassays. Owing to facile synthesis, surface functionalization, and superior optical and electronic properties, gold nanoparticles have been at the forefront of sensing and detection technologies and have been extensively studied to improve the efficacies of immunoassays. This review provides a brief history of immuno-PCR assays and specifically focuses on the role of gold nanoparticles to improve the sensitivity and specificity of ELISA, PCR and immuno-PCR assays.

ZnO Nanolower-Based NanoPCR as an Efficient Diagnostic Tool for Quick Diagnosis of Canine Vector-Borne Pathogens

Polymerase chain reaction (PCR) is a unique technique in molecular biology and biotechnology for amplifying target DNA strands, and is also considered as a gold standard for the diagnosis of many canine diseases as well as many other infectious diseases. However, PCR still faces many challenges and issues related to its sensitivity, specificity, efficiency, and turnaround time. To address these issues, we described the use of unique ZnO nanoflowers in PCR reaction and an efficient ZnO nanoflower-based PCR (nanoPCR) for the molecular diagnosis of canine vector-borne diseases (CVBDs). A total of 1 mM of an aqueous solution of ZnO nanoflowers incorporated in PCR showed a significant enhancement of the PCR assay with respect to its sensitivity and specificity for the diagnosis of two important CVBDs, Babesia canis vogeli and Hepatozoon canis. Interestingly, it drastically reduced the turnaround time of the PCR assay without compromising the yield of the amplified DNA, which can be of benefit for veterinary practitioners for the improved management of diseases. This can be attributed to the favorable adsorption of ZnO nanoflowers to the DNA and thermal conductivity of ZnO nanoflowers. The unique ZnO nanoflower-assisted nanoPCR greatly improved the yield, purity, and quality of the amplified products, but the mechanism behind these properties and the effects and changes due to the different concentrations of ZnO nanoflowers in the PCR system needs to be further studied.

Nanoporous anodic aluminum oxide internalized with gold nanoparticles for on-chip PCR and direct detection by surface-enhanced Raman scattering

Nanoporous anodic aluminum oxide (AAO) internalized with gold nanoparticles was utilized as an integrated platform miniaturized for consecutively performing on-chip PCR and downstream detection of the target DNA amplicons using surface-enhanced Raman scattering (SERS).

The presence of residual gold nanoparticles in samples interferes with the RT-qPCR assay used for gene expression profiling

BACKGROUND

RT-qPCR is routinely used in expression profiling of toxicity pathway genes. However, genetic and molecular level studies used to determine, understand and clarify potential risks of engineered nanomaterials (ENMs) are still incomplete. Concerns regarding possible interference caused by intracellular ENMs during analyses have been raised. The aim of this study was to verify a qPCR procedure for gene expression assays, which can be used in toxicity and exposure assessments.

RESULTS

Amplification of ten reference genes was performed to test the expression stability. A preliminary study was performed on RNA from BEAS-2B cells that had been treated with AuNPs. Also, a reference total RNA standard from ten cell lines was spiked with various amounts of the same AuNP. This treatment mimics exposure assessment studies, where assay-interference may be caused by intracellular residual ENMs still being present in the biological samples (during and after isolation/purification procedures). Both types of RNA samples were reverse transcribed and then amplified by qPCR. The qPCR-related software and statistical programs used included BestKeeper, NormFinder, REST and qBase+. These results proved that using standard qPCR analysis and statistical programs should not be the only procedure applied to verify the assay for gene expression assessment related to ENMs. A comparison of SYBR Green to EVA Green was discussed, in addition to a comparison to the latest reports regarding the influence of ENM thermal conductivity, surface interactions with ENMs, effects of ENM size and charge, as well as, the limit of detection in a qPCR assay.

CONCLUSIONS

AuNPs have the potential to interfere with the assay mechanism of RT-qPCR, thus, assay verification is required for AuNP-related gene expression studies used to evaluate toxicity. It is recommended to use HSP90 and YWHAZ as reference genes, i.e. these were the most stable in our study, irrespective of the source of the RNA, or, the point at which the AuNPs interacted with the assay. This report describes steps that can be utilised to generate a suitable method for gene expression studies associated with toxicity testing of various ENMs. For example, RNA standards that have been spiked with known amounts of ENMs should be run in conjunction with the unknown samples, in order to verify any RT-qPCR assay and determine the degree of error.

The presence of residual gold nanoparticles in samples interferes with the RT-qPCR assay used for gene expression profiling

Background

RT-qPCR is routinely used in expression profiling of toxicity pathway genes. However, genetic and molecular level studies used to determine, understand and clarify potential risks of engineered nanomaterials (ENMs) are still incomplete. Concerns regarding possible interference caused by intracellular ENMs during analyses have been raised. The aim of this study was to verify a qPCR procedure for gene expression assays, which can be used in toxicity and exposure assessments.

Results

Amplification of ten reference genes was performed to test the expression stability. A preliminary study was performed on RNA from BEAS-2B cells that had been treated with AuNPs. Also, a reference total RNA standard from ten cell lines was spiked with various amounts of the same AuNP. This treatment mimics exposure assessment studies, where assay-interference may be caused by intracellular residual ENMs still being present in the biological samples (during and after isolation/purification procedures). Both types of RNA samples were reverse transcribed and then amplified by qPCR. The qPCR-related software and statistical programs used included BestKeeper, NormFinder, REST and qBase+. These results proved that using standard qPCR analysis and statistical programs should not be the only procedure applied to verify the assay for gene expression assessment related to ENMs. A comparison of SYBR Green to EVA Green was discussed, in addition to a comparison to the latest reports regarding the influence of ENM thermal conductivity, surface interactions with ENMs, effects of ENM size and charge, as well as, the limit of detection in a qPCR assay.

Conclusions

AuNPs have the potential to interfere with the assay mechanism of RT-qPCR, thus, assay verification is required for AuNP-related gene expression studies used to evaluate toxicity. It is recommended to use HSP90 and YWHAZ as reference genes, i.e. these were the most stable in our study, irrespective of the source of the RNA, or, the point at which the AuNPs interacted with the assay. This report describes steps that can be utilised to generate a suitable method for gene expression studies associated with toxicity testing of various ENMs. For example, RNA standards that have been spiked with known amounts of ENMs should be run in conjunction with the unknown samples, in order to verify any RT-qPCR assay and determine the degree of error.

Electronic supplementary material

The online version of this article (doi:10.1186/s12951-017-0299-9) contains supplementary material, which is available to authorized users.

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.

Modified gold nanoparticles for intracellular delivery of anti-liver cancer siRNA

To overcome the rapid enzymatic degradation and low transfection efficiency of siRNA, the delivery carriers for siRNA is a therapeutic demand to increase its stability. Gold nanoparticles (AuNPs) modified by branched polyethyleneimine (bPEI) were developed as an efficient and safe intracellular delivery carriers for siRNA. The current study implied that siRNA designed against an oncogene c-Myc could be delivered by a modified AuNPs complex without significant cytotoxicity. The comparative semi-quantitative and quantitative real time PCR were used to measure the c-Myc gene expression after transfection with naked siRNA and siRNA/bPEI/AuNPs, but AuNPs interfered with PCR. However, the c-Myc protein translation was successfully detected in the transfected HuH7 cells with naked siRNA and siRNA/bPEI/AuNPs and it was found to be inhibited by siRNA/bPEI/AuNPs more than naked siRNA. The results validate the successful silencing of c-Myc gene. Accordingly, it may confirm the promising and effective delivery of siRNA by bPEI/AuNPs. The complex enhances the cellular uptake of siRNA without significant cytotoxicity and confirms that bPEI modified AuNPs could be used as a good candidate for safe cellular delivery of siRNA.

Nanosized Fe3O4 an efficient PCR yield enhancer-Comparative study with Au, Ag nanoparticles

Nanomaterials-assisted PCR is a promising field of nanobiotechnology that amalgamates nanomaterials into the conventional PCR system to achieve better amplification of desired product. With literature documenting the variable effects of these nanomaterials on the PCR yield and amplification; it was thought worthwhile to compare the PCR enhancing efficiency of three transition metal nanoparticles in form of stable colloidal suspensions at varying concentrations.The nanoparticles(NPs) of silver, gold and magnetite were chemically synthesized by reducing their respective salts and characterized using UV-vis spectroscopy. Their morphology was assessed using nanoparticle tracking system and AFM. The effect of these nanofluids on amplification of 800 bp prokaryotic DNA template with 30% GC content was studied using conventional thermal cycler. The reaction kinetics for all the three nanofluids yielded a Gaussian curve of amplification with varying concentrations. The ammonium salt of oleic acid coated magnetite (Fe3O4) nanoparticles at a concentration of 0.72 × 10(-2)nM and average size of 33 nm demonstrated highest amplification efficiency of 190% as compared to the citrate stabilized AgNP-25 nm (45%) and AuNP-15.19 nm (134%) using a conventional PCR system. The major reasons that allow Fe3O4 NPs outperform the other 2 transition metal NP's seem to be attributed to its heat conduction property as well as effective adsorption of PCR components onto the ammonium salt of oleic acid coated magnetite nanofluids. The data from our study offers valuable information for the application of ferrofluids as economically, efficient and effective alternative for nanomaterial-assisted PCR yield enhancers.

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.

Development of a high-throughput real time PCR based on a hot-start alternative for Pfu mediated by quantum dots

Hot start (HS) PCR is an excellent alternative for high-throughput real time PCR due to its ability to prevent nonspecific amplification at low temperature. Development of a cost-effective and simple HS PCR technique to guarantee high-throughput PCR specificity and consistency still remains a great challenge. In this study, we systematically investigated the HS characteristics of QDs triggered in real time PCR with EvaGreen and SYBR Green I dyes by the analysis of amplification curves, standard curves and melting curves. Two different kinds of DNA polymerases, Pfu and Taq, were employed. Here we showed that high specificity and efficiency of real time PCR were obtained in a plasmid DNA and an error-prone two-round PCR assay using QD-based HS PCR, even after an hour preincubation at 50 °C before real time PCR. Moreover, the results obtained by QD-based HS PCR were comparable to a commercial Taq antibody DNA polymerase. However, no obvious HS effect of QDs was found in real time PCR using Taq DNA polymerase. The findings of this study demonstrated that a cost-effective high-throughput real time PCR based on QD triggered HS PCR could be established with high consistency, sensitivity and accuracy.

Employment of nanomaterials in polymerase chain reaction: insight into the impacts and putative operating mechanisms of nano-additives in PCR

The latest developments in the field of nanomaterial-assisted PCR are evaluated with a focus on putative operating mechanisms.

Enhanced PCR amplification of GC-rich DNA templates by gold nanoparticles

Gold nanoparticles (AuNPs) have been reported to facilitate double-stranded DNA dissociation and improve performance of several PCR systems. Here we investigated AuNPs' effect on GC-rich DNA amplification. We found that AuNPs could enhance PCR amplification of the GNAS1 promoter region (∼84% GC) mediated by Pfu or Taq DNA polymerase. However, under optimal concentrations of AuNPs, higher amounts of Taq were required. Furthermore, the GC-rich FMR1 (80.4% GC) gene of Homo sapiens as well as exoT (67.3% GC), exsE (71% GC) and pqqF genes (74% GC) of Pseudomonas aeruginosa were also efficiently amplified. AuNPs can become an effective additive in GC-rich PCR and facilitate analysis of challenging genomic sequence in basic and clinical research.

NanoPCR observation: different levels of DNA replication fidelity in nanoparticle-enhanced polymerase chain reactions

Nanoparticle-assisted PCR (polymerase chain reaction) technology is getting more and more attention recently. It is believed that some of the DNA recombinant technologies will be upgraded by nanotechnology in the near future, among which DNA replication is one of the core manipulation techniques. So whether or not the DNA replication fidelity is compromised in nanoparticle-assisted PCR is a question. In this study, a total of 16 different metallic and non-metallic nanoparticles (NPs) were tested for their effects on DNA replication fidelity in vitro and in vivo. Sixteen types of nanomaterials were distinctly different in enhancing the PCR efficiency, and their relative capacity to retain DNA replication fidelity was largely different from each other based on rpsL gene mutation assay. Generally speaking, metallic nanoparticles induced larger error rates in DNA replication fidelity than non-metallic nanoparticles, and non-metallic nanomaterials such as carbon nanopowder or nanotubes were still safe as PCR enhancers because they did not compromise the DNA replication fidelity in the Taq DNA polymerase-based PCR system.