Genetic analysis with nanoPCR

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.

Development and Evaluation of NanoPCR for the Detection of Goose Parvovirus

Simple Summary

Gosling plague (GP), an acute, virulent infectious disease caused by goose parvovirus (GPV), is a serious problem for livestock and poultry breeding. At present, there is no effective treatment available. The disease is vertically transmitted in geese, and some infected pregnant females are often recessive carriers of the virus, making it very difficult for farmers to detect GPV in the clinical setting. Although there are many clinical testing methods for GPV, some of them still suffered from shortcomings such as being time-consuming and labor-intensive. In this study, gold nanoparticles were put into a conventional PCR reaction system, and the first nanoPCR reaction was successfully established to detect infected GPV in the clinic, thus providing a practical method for the detection of GPV clinical infection.

Abstract

Gosling plague (GP) is an acute and hemorrhagic infectious disease caused by goose parvovirus (GPV). The goose industry suffers significant economic losses as a result of GP, which is found to be widespread worldwide, with high rates of morbidity and mortality. Our group developed a novel technique for detecting GPV nanoparticle-assisted polymerase chain reaction (nanoPCR) and the characterization of its specificity and sensitivity. It was developed by using the traditional polymerase chain reaction (PCR) and nanoparticles. The findings of this study revealed that GPV nanoPCR products were 389 bp in length, and the lower limit of the nanoPCR assay was 4.68 × 10² copies/μL, whereas that of the conventional PCR assay was 4.68 × 10⁴ copies/μL. A total of 230 geese suspected of GPV were detected using nanoPCR, with a positive rate of 83.0% and a specificity of 73%, respectively. Overall, we present a hitherto undocumented method for identifying GPV by using nanoPCR to aid in the evaluation of subclinical illness.

Tooth as a Source of DNA in Forensic or Investigative Genetics: An Overview

Deoxyribonucleic acid (DNA) is the genetic code of most organisms including humans. In the last few years, DNA analysis methods are applied to forensic cases for human identification which is termed forensic or investigative genetics. It is often challenging to obtain and interpret DNA from routine samples like blood in severely decomposed or disfigured bodies recovered from incineration, immersion, trauma, mutilation, and decomposition as in incidents of fire, explosion, or murder. The tooth can survive any extreme environment with minimum risk of contamination making it a valuable alternative source of DNA in such cases. Tooth structures like the enamel (amelogenin protein), dentin, cementum, pulp, and adherent tissues like bone and periodontal fibers are sources from which DNA can be obtained. Various methods have been described for DNA extraction. There are numerous applications of DNA analysis like identification of the deceased or missing victim or the unknown culprit from a crime scene, solving paternity issues, determining the occurrence of any genetic disease, and determining the ancestry. This article briefly summarizes an overview of the tooth as a valuable DNA source and various methods and challenges related to DNA analysis.

Capping Gold Nanoparticles to Achieve a Protein-like Surface for Loop-Mediated Isothermal Amplification Acceleration and Ultrasensitive DNA Detection

Loop-mediated isothermal amplification (LAMP) is a popular DNA amplification method. Gold nanoparticles (AuNPs) were reported to enhance the efficiency of LAMP, although the underlying mechanism remained elusive. Since AuNPs strongly adsorb a range of ligands, preadsorbed ligands cannot be easily displaced. In this work, we systematically investigated the effect of surface-modified AuNPs on LAMP by varying the order of mixing of AuNPs with each reagent in the LAMP system (Mg²⁺, template DNA, dNTPs, primers, and polymerase). Mixing the AuNPs with the primers delayed the LAMP based on SYBR green I fluorescence. While other orders of mixing had little effect, all accelerated the reaction. We then tested other common ligands including polymers (polyethylene glycol and polyvinylpyrrolidone), inorganic ions (Br^-), proteins, glutathione (GSH), and DNA (A₁₅) on AuNP-LAMP. The boosted AuNP performance on LAMP was most obvious when the AuNPs formed a protein-like surface. Finally, using GSH-capped AuNPs, a detection limit of around 100 copies/μL^-1 of target DNA was achieved. This work has identified a ligand-capped AuNP strategy to boost LAMP and yielded a higher sensitivity in DNA sensing, which also deepens our understanding of AuNP-assisted LAMP.

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.

Effect of green GO/Au nanocomposite on in-vitro amplification of human DNA

Recently nanomaterials have attracted interest for increasing efficiency of polymerase chain reaction (PCR) systems. Here, the authors report on the usefulness of green graphene oxide/gold (GO/Au) nanocomposites for enhancement of PCR reactions. In this study, green GO/Au nanocomposite was prepared with Matricaria chamomilla extract as reducing/capping agent for site-directed nucleation of Au^o atoms on surface of GO sheets. The as-prepared green GO/Au nanocomposites were then characterised with UV-VIS spectrophotometer and scanning electron microscopy. Later, the effect of these nanocomposites was studied on end-point and real-time PCR employed for amplification of human glyceraldehyde-3-phosphate dehydrogenase gene. The results indicated that GO/Au nanocomposite can improve both end-point and real-time PCR methods at the optimum concentrations, possibly through interaction between GO/Au nanocomposite and the materials in PCR reaction, and through providing increased thermal convection by the GO surface as well as the Au nanostructures. In conclusion, it can be suggested that green GO/Au nanocomposite is a biocompatible and eco-friendly candidate as enhancer of in-vitro molecular amplification strategies.

Highly sensitive detection of prostate cancer specific PCA3 mimic DNA using SERS-based competitive lateral flow assay

Accurate analysis of prostate cancer specific biomarkers plays an important role in the early diagnosis of prostate cancer. Traditional colorimetric lateral flow assay (LFA) has the limitations of low detection sensitivity and qualitative or semiquantitative detection. In this study, we developed a novel surface-enhanced Raman scattering (SERS)-based competitive LFA for the rapid and highly sensitive quantitative evaluation of prostate cancer antigen 3 (PCA3) mimic DNA. Herein, the competitive hybridization interaction with capture DNA between target PCA3 mimic DNA and reporter DNA-labeled SERS nanotags results in a change in the amount of SERS nanotags on the test line. The quantitative analysis of target PCA3 mimic DNA was realized by monitoring the Raman peak intensity of SERS nanotags on the test line. The limit of detection of PCA3 mimic DNA was estimated to be 3 fM, which is about three orders of magnitude more sensitive than that of a commercially available kit. By combining the outstanding characteristics of the well-established SERS-based competitive strategy and LFA platform, our design has strong potential for the early diagnosis of prostate cancer and other diseases.

Development of gold nanoparticles biosensor for ultrasensitive diagnosis of foot and mouth disease virus

Background

Nano-PCR is a recent tool that is used in viral diseases diagnosis. The technique depends on the fundamental effects of gold nanoparticles (AuNPs) and is considered a very effective and sensitive tool in the diagnosis of different diseases including viral diseases. Although several techniques are currently available to diagnose foot and mouth disease virus (FMDV), a highly sensitive, highly specific technique is needed for specific diagnosis of the disease. In the present work, a novel AuNPs biosensor has been designed using thiol-linked oligonucleotides that recognize the conserved 3D gene of FMDV.

Results

The AuNPs-FMDV biosensor specifically recognizes RNA standards of FMDV, but not that of swine vesicular disease virus (SVDV) isolates. The analytical sensitivity of the AuNPs-FMDV biosensor was 10 copy number RNA standards in RT-PCR and 1 copy number RNA standard in real-time rRT-PCR with a 94.5% efficiency, 0.989 R², a − 3.544 slope and 100% specificity (no cross-reactivity with SVDV). These findings were confirmed by the specific and sensitive recognition of 31 Egyptian FMDV clinical isolates that represents the three FMDV serotypes (O, A, and SAT2).

Conclusions

The AuNPs-FMDV biosensor presents in this study demonstrates a superior analytical and clinical performance for FMDV diagnosis. In addition, this biosensor has a simple workflow and accelerates epidemiological surveillance, hence, it is qualified as an efficient FMDV diagnosis tool for quarantine stations and farms particularly in FMDV endemic areas.

Electronic supplementary material

The online version of this article (10.1186/s12951-018-0374-x) contains supplementary material, which is available to authorized users.

Development of nanoparticle-assisted PCR assay in the rapid detection of brain-eating amoebae

Brain-eating amoebae (Acanthamoeba spp., Balamuthia mandrillaris, Naegleria fowleri) have gained increasing attention owing to their capacity to produce severe human and animal infections involving the brain. Early detection is a pre-requisite in successful prognosis. Here, we developed a nanoPCR assay for the rapid detection of brain-eating amoebae using various nanoparticles. Graphene oxide, copper and alumina nanoparticles used in this study were characterized using Raman spectroscopy measurements through excitation with a He-Ne laser, while powder X-ray diffraction patterns were taken on a PANanalytical, X'Pert HighScore diffractometer and the morphology of the materials was confirmed using high-resolution transmission electron microscopy (HRTEM). Using nanoparticle-assisted PCR, the results revealed that graphene oxide, copper oxide and alumina nanoparticles significantly enhanced PCR efficiency in the detection of pathogenic free-living amoebae using genus-specific probes. The optimal concentration of graphene oxide, copper oxide and alumina nanoparticles for Acanthamoeba spp. was determined at 0.4, 0.04 and 0.4 μg per mL respectively. For B. mandrillaris, the optimal concentration was determined at 0.4 μg per mL for graphene oxide, copper oxide and alumina nanoparticles, and for Naegleria, the optimal concentration was 0.04, 4.0 and 0.04 μg per mL respectively. Moreover, combinations of these nanoparticles proved to further enhance PCR efficiency. The addition of metal oxide nanoparticles leads to excellent surface effect, while thermal conductivity property of the nanoparticles enhances PCR productivity. These findings suggest that nanoPCR assay has tremendous potential in the clinical diagnosis of parasitic infections as well as for studying epidemiology and pathology and environmental monitoring of other microbes.

Enhancing the specificity of polymerase chain reaction by graphene oxide through surface modification: zwitterionic polymer is superior to other polymers with different charges

Graphene oxides (GOs) with different surface characteristics, such as size, reduction degree and charge, are prepared, and their effects on the specificity of polymerase chain reaction (PCR) are investigated. In this study, we demonstrate that GO with a large size and high reduction degree is superior to small and nonreduced GO in enhancing the specificity of PCR. Negatively charged polyacrylic acid (PAA), positively charged polyacrylamide (PAM), neutral polyethylene glycol (PEG) and zwitterionic polymer poly(sulfobetaine) (pSB) are used to modify GO. The PCR specificity-enhancing ability increases in the following order: GO-PAA < GO-PAM < GO-PEG < GO-pSB. Thus, zwitterionic polymer-modified GO is superior to other GO derivatives with different charges in enhancing the specificity of PCR. GO derivatives are also successfully used to enhance the specificity of PCR for the amplification of human mitochondrial DNA using blood genomic DNA as template. Molecular dynamics simulations and molecular docking are performed to elucidate the interaction between the polymers and Pfu DNA polymerase. Our data demonstrate that the size, reduction degree and surface charge of GO affect the specificity of PCR. Based on our results, zwitterionic polymer-modified GO may be used as an efficient additive for enhancing the specificity of PCR.

Magnetic Bead/Gold Nanoparticle Double-Labeled Primers for Electrochemical Detection of Isothermal Amplified Leishmania DNA

A novel methodology for the isothermal amplification of Leishmania DNA using labeled primers combined with the advantages of magnetic purification/preconcentration and the use of gold nanoparticle (AuNP) tags for the sensitive electrochemical detection of such amplified DNA is developed. Primers labeled with AuNPs and magnetic beads (MBs) are used for the first time for the isothermal amplification reaction, being the amplified product ready for the electrochemical detection. The electrocatalytic activity of the AuNP tags toward the hydrogen evolution reaction allows the rapid quantification of the DNA on screen-printed carbon electrodes. Amplified products from the blood of dogs with Leishmania (positive samples) are discriminated from those of healthy dogs (blank samples). Quantitative studies demonstrate that the optimized method allows us to detect less than one parasite per microliter of blood (8 × 10(-3) parasites in the isothermal amplification reaction). This pioneering approach is much more sensitive than traditional methods based on real-time polymerase chain reaction (PCR), and is also more rapid, cheap, and user-friendly.

Facile solvothermal preparation of monodisperse gold nanoparticles and their engineered assembly of ferritin-gold nanoclusters

Herein, we report a quick and simple synthesis of water-soluble gold nanoparticles using a HAuCl4 and oleylamine mixture. Oleylamine serves as a reduction agent as well as a stabilizer for nanoparticle surfaces. The particle sizes can be adjusted by modulating reaction temperature and time. Solvothermal reduction of HAuCl4 with oleylamine can be confirmed by measuring the product in Fourier transform infrared (FTIR) spectroscopy. The plasmon band shifting from yellow to red confirms a nanosized particle formation. Amide bonds on the surface of the nanoparticles formed hydrogen bonds with one another, resulting in a hydrophobic monolayer. Particles dispersed well in nonpolar organic solvents, such as in hexane or toluene, by brief sonication. Next, we demonstrated the transfer of gold nanoparticles into water by lipid capsulation using 1-myristoyl-2-hydroxy-sn-glycero-3-phosphocholine (MHPC), 1,2-distearoyl-sn-glycero-3-phosphoethanolamine-N-(methoxy polyethylene glycol)-2000 (DPPE-PEG2k), and 1,2-dioleoyl-sn-glycero-3-N-{5-amino-1-carboxypentyl}iminodiacetic acid succinyl nickel salt [DGS-NTA(Ni)]. The particle concentration can be obtained using an absorbance in ultraviolet-visible (UV-vis) spectra (at 420 nm). Instrumental analyses using transmission electron microscopy (TEM), energy-dispersive X-ray (EDX) analysis, dynamic light scattering (DLS), and FTIR confirmed successful production of gold nanoparticles and fair solubility in water. Prepared gold particles were selectively clustered via engineered ferritin nanocages that provide multiple conjugation moieties. A total of 5-6 gold nanoparticles were clustered on a single ferritin nanocage confirmed in TEM. Reported solvothermal synthesis and preparation of gold nanoclusters may serve as an efficient, alternate way of preparing water-soluble gold nanoparticles, which can be used in a wide variety of biomedical applications.

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.

Mechanism studies on nanoPCR and applications of gold nanoparticles in genetic analysis

Recently, the applications of nanomaterial-assisted polymerase chain reaction (nanoPCR) have received considerable attention. Several potential mechanisms have been proposed, but mainly according to the results of PCR assays under specific conditions and lacking direct and general evidence. The mechanism of nanoPCR has not been elucidated yet. Here, taking gold nanoparticles (AuNPs) as an example, we report the three general effects of AuNPs: (1) AuNPs adsorb polymerase and modulate the amount of active polymerase in PCR, which was directly demonstrated by a simple and straightforward colorimetric assay and the dynamic light scattering measurements. (2) AuNPs adsorb primers and decrease the melting temperatures (Tm) of the duplexes formed with perfectly matched and mismatched primers and increase the Tm difference between them. (3) AuNPs adsorb PCR products and facilitate the dissociation of them in the denaturing step. All these effects were confirmed by addition of a rationally selected surface adsorbent, bovine thrombin, to highly efficiently modulate the surface adsorption of PCR components. These findings suggested that AuNPs should have multiple effects on PCR: (1) to regulate PCR in a case-by-case way via modulating the amount of active polymerase in PCR; (2) to improve PCR specificity in the annealing step via increasing the Tm difference between the perfectly matched and mismatched primers; (3) to improve PCR efficiency via speeding up the dissociation of the PCR products in the denaturing step. Taken together, we proposed the mechanism of nanoPCR is that the surface interaction of PCR components (polymerase, primers, and products) with AuNPs regulates nanoPCR. We further demonstrated that the applications of these findings improve the PCR of the amelogenin genes and Hepatitis B virus gene for genetic analysis. These findings could also provide helpful insight for the applications of other nanomaterials in nanoPCR.