Rapid DNA detection by interface PCR on nanoparticles

A roadmap to high-speed polymerase chain reaction (PCR): COVID-19 as a technology accelerator

The limit of detection (LOD), speed, and cost of crucial COVID-19 diagnostic tools, including lateral flow assays (LFA), enzyme-linked immunosorbent assays (ELISA), and polymerase chain reactions (PCR), have all improved because of the financial and governmental support for the epidemic. The most notable improvement in overall efficiency among them has been seen with PCR. Its significance for human health increased during the COVID-19 pandemic, when it emerged as the commonly used approach for identifying the virus. However, because of problems with speed, complexity, and expense, PCR deployment in point-of-care settings continues to be difficult. Microfluidic platforms offer a promising solution by enabling the development of smaller, more affordable, and faster PCR systems. In this review, we delve into the engineering challenges associated with the advancement of high-speed microfluidic PCR equipment. We introduce criteria that facilitate the evaluation and comparison of factors such as speed, LOD, cycling efficiency, and multiplexing capacity, considering sample volume, fluidics, PCR reactor geometry and materials, as well as heating/cooling methods. We also provide a comprehensive list of commercially available PCR devices and conclude with projections and a discussion regarding the current obstacles that need to be addressed in order to progress further in this field.

Amine-Functionalized Quantum Dots as a Universal Fluorescent Nanoprobe for a One-Step Loop-Mediated Isothermal Amplification Assay with Single-Copy Sensitivity

Loop-mediated isothermal amplification (LAMP) has received considerable attention for decentralized (point-of-care and on-site) nucleic acid testing in view of its simple temperature control (60-65 °C) and short assay time (15-60 min). There remains a challenge in its wide adoption and acceptance due to the limitations of the existing amplification result reporter probes, e.g., photobleaching of organic fluorophore and reduced sensitivity of the pH-sensitive colorimetric dye. Herein, we demonstrate CdSeS/ZnS quantum dots (semiconductor fluorescent nanocrystals with superior photostability than organic fluorophore) with surface modification of cysteamine (amine-QDs) as a new reporter probe for LAMP that enabled single-copy sensitivity (limit of detection of 83 zM; 20 μL reaction volume). For a negative LAMP sample (absence of target sequence), positively charged amine-QDs remained dispersed due to interparticle electrostatic repulsion. While for a positive LAMP sample (presence of target sequence), amine-QDs became precipitated. The characterization data showed that amine-QDs were embedded in magnesium pyrophosphate crystals (generated during positive LAMP), thus leading to their coprecipitation. This amine-QD-based one-step LAMP assay advances the field of QD-based nucleic acid amplification assays in two aspects: (1) compatibility─one-step amplification and detection (versus separation of amplification and detection steps); and (2) universality─the same amine-QDs for different target sequences (versus different oligonucleotide-modified QDs for different target sequences).

Biological Molecules-Governed Plasmonic Nanoparticle Dimers with Tailored Optical Behaviors

Self-assembly opens new avenues to direct the organization of nanoparticles (NPs) into discrete structures with predefined configuration and association numbers. Plasmonic NP dimers provide a well-defined system for investigating the plasmonic coupling and electromagnetic (EM) interaction in arrays of NPs. The programmability and structural plasticity of biomolecules offers a convenient platform for constructing of NP dimers in a controllable way. Plasmonic coupling of NPs enables dimers to exhibit tunable optical properties, such as surface-enhanced Raman scattering (SERS), chirality, photoluminescence, and electrochemiluminescence (ECL) properties, which can be tailored by altering the biomolecules, the building blocks with distinct compositions, sizes and morphology, the interparticle distances, as well as the geometric configuration of the constituent NPs. An overview of recent developments in biological molecules-governed NP dimers, the tailored optical behaviors, and challenges in enhancing optical signals and proposing plasmonic biosensors are discussed in this Perspective.

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.

Orientational nanoparticle assemblies and biosensors

Assemblies of nanoparticles (NPs) have regional correlated properties with new features compared to individual NPs or random aggregates. The orientational NP assembly contributes greatly to the collective interaction of individual NPs with geometrical dependence. Therefore, orientational NPs assembly techniques have emerged as promising tools for controlling inorganic NPs spatial structures with enhanced interesting properties. The research fields of orientational NP assembly have developed rapidly with characteristics related to the different methods used, including chemical, physical and biological techniques. The current and potential applications, important challenges remain to be investigated. An overview of recent developments in orientational NPs assemblies, the multiple strategies, biosensors and challenges will be discussed in this review.

A PCR based magnetic assembled sensor for ultrasensitive DNA detection

An ultrasensitive method for DNA detection based on magnetic assembly induced by polymerase chain reaction (PCR) was developed. The sensor showed a low limit of detection (LOD) of 4.26 aM with a wide range of target DNA from 0.01 fM to 10,000 fM.

Nanoscale superstructures assembled by polymerase chain reaction (PCR): programmable construction, structural diversity, and emerging applications

Polymerase chain reaction (PCR) is an essential tool in biotechnology laboratories and is becoming increasingly important in other areas of research. Extensive data obtained over the last 12 years has shown that the combination of PCR with nanoscale dispersions can resolve issues in the preparation DNA-based materials that include both inorganic and organic nanoscale components. Unlike conventional DNA hybridization and antibody-antigen complexes, PCR provides a new, effective assembly platform that both increases the yield of DNA-based nanomaterials and allows researchers to program and control assembly with predesigned parameters including those assisted and automated by computers. As a result, this method allows researchers to optimize to the combinatorial selection of the DNA strands for their nanoparticle conjugates. We have developed a PCR approach for producing various nanoscale assemblies including organic motifs such as small molecules, macromolecules, and inorganic building blocks, such as nanorods (NRs), metal, semiconductor, and magnetic nanoparticles (NPs). We start with a nanoscale primer and then modify that building block using the automated steps of PCR-based assembly including initialization, denaturation, annealing, extension, final elongation, and final hold. The intermediate steps of denaturation, annealing, and extension are cyclic, and we use computer control so that the assembled superstructures reach their predetermined complexity. The structures assembled using a small number of PCR cycles show a lower polydispersity than similar discrete structures obtained by direct hybridization between the nanoscale building blocks. Using different building blocks, we assembled the following structural motifs by PCR: (1) discrete nanostructures (NP dimers, NP multimers including trimers, pyramids, tetramers or hexamers, etc.), (2) branched NP superstructures and heterochains, (3) NP satellite-like superstructures, (4) Y-shaped nanostructures and DNA networks, (5) protein-DNA co-assembly structures, and (6) DNA block copolymers including trimers and pentamers. These results affirm that this method can produce a variety of chemical structures and in yields that are tunable. Using PCR-based preparation of DNA-bridged nanostructures, we can program the assembly of the nanoscale blocks through the adjustment of the primer intensity on the assembled units, the number of PCR cycles, or both. The resulting structures are highly complex and diverse and have interesting dynamics and collective properties. Potential applications of these materials include chirooptical materials, probe fabrication, and environmental and biomedical sensors.

Upconversion nanoparticle-based Förster resonance energy transfer for detecting the IS6110 sequence of Mycobacterium tuberculosis complex in sputum

Upconversion nanoparticles (UCNPs), which are excited at near-infrared wavelength (980 nm), emit high-energy photons. Since UCNPs display a high signal-to-noise ratio and no photobleaching, they are extremely useful for diagnostic application. In this study, we applied UCNPs for detecting the IS6110 sequence of the Mycobacterium tuberculosis complex (MTBC) and evaluated the feasibility of the system for use in molecular diagnostics. Using biotinylated primers, IS6110 DNA PCR was performed and the PCR amplicon was then mixed with streptavidin-conjugated UCNPs, followed by intercalation with SYTOX Orange dye. Fluorescence detection for the Förster resonance energy transfer (FRET) of the UCNPs (UCNP-FRET) was then performed. The estimated lowest detection by UCNP-FRET was 10(2) copies/μL of IS6110 DNA (157 bp). The kappa agreement of the UCNP-FRET assay with conventional PCR was 0.8464 (95% confidence interval, 0.7442-0.9486) and false-negative results were reduced. Our results demonstrated the successful implementation of the UCNP-FRET system in detecting the IS6110 sequence of the MTBC and its potential application for molecular diagnostics.

Effects of upconversion nanoparticles on polymerase chain reaction

Nanoparticles (NPs) are attractive materials owing to their physical and electrochemical properties, which make them extremely useful in diagnostic applications. Photon upconversion is the phenomenon where high-energy photons are emitted upon excitation of low-energy photons. Nucleic acids detection based on upconversion nanoparticles (UCNPs), which display a high signal-to-noise ratio and no photobleaching, has been widely applied. We evaluated whether UCNPs can improve polymerase chain reaction (PCR) specificity and affect PCR amplification. The effects of UCNPs with a diameter size of 40, 70, and 250 nm were evaluated using 3 PCR kits (AccuPower PCR PreMix, AmpliTaq Gold 360 Master Mix, and HotStarTaq Plus Master Mix) and 3 real-time PCR kits (AccuPower GreenStar qPCR PreMix, SYBR Green PCR Master Mix, and QuantiTect SYBR Green PCR Kit). Quantum dots were used for comparison with the UCNPs. In the presence of an appropriate concentration of UCNPs, PCR specificity was optimized. UCNPs of 40-nm size improved PCR specificity more effectively than did UCNPs sized 70 or 250 nm. As the size and concentrations of the UCNPs were increased, PCR amplification was more severely inhibited. At lower annealing temperatures (25°C–45°C), addition of the 40 nm UCNP (1 µg/µL) to the PCR reagent produced specific PCR products without nonspecific sequence amplification. Therefore, UCNPs of different sizes, with different DNA polymerases used in the commercial kits, showed different inhibitory effects on PCR amplification. These results demonstrate that optimization of UCNPs, added to reaction mixtures at appropriate concentrations, can improve PCR specificity. However, the mechanism underlining UCNPs effect on PCR remains unclear and will require further investigation.

Alternating Plasmonic Nanoparticle Heterochains Made by Polymerase Chain Reaction and Their Optical Properties

Organization of nanoparticles (NPs) of different materials into superstructures of higher complexity represents a key challenge in nanotechnology. Polymerase chain reaction (PCR) was used in this study to fabricate chains consisting of plasmonic NPs of different sizes, thus denoted heterochains. The NPs in such chains are connected by DNA oligomers, alternating in a sequence big-small-big-small-... and spanning lengths in the range of 40-300 nm by varying the number of PCR cycles. They display strong plasmonic chirality at 500-600 nm, the chiral activity revealing nonmonotonous dependence on the length of heterochains. We find the strength of surface-enhanced Raman scattering (SERS) to increase with chain length, while the chiral response initially increased and then decreased with the number of PCR cycles. The relationship between the optical properties of the heterochains and their structure/length is discussed. The length-dependent intense optical response of the plasmonic NP heterochains holds great potential for biosensing applications.

Regiospecific plasmonic assemblies for in situ Raman spectroscopy in live cells

Multiple properties of plasmonic assemblies are determined by their geometrical organization. While high degree of complexity was achieved for plasmonic superstructures based on nanoparticles (NPs), little is known about the stable and structurally reproducible plasmonic assemblies made up from geometrically diverse plasmonic building blocks. Among other possibilities, they open the door for the preparation of regiospecific isomers of nanoscale assemblies significant both from a fundamental point of view and optical applications. Here, we present a synthetic method for complex assemblies from NPs and nanorods (NRs) based on selective modification of NRs with DNA oligomers. Three types of assemblies denoted as End, Side, and Satellite isomers that display distinct elements of regiospecificity were prepared with the yield exceeding 85%. Multiple experimental methods independently verify various structural features, uniformity, and stability of the prepared assemblies. The presence of interparticle gaps with finely controlled geometrical parameters and inherently small size comparable with those of cellular organelles fomented their study as intracellular probes. Against initial expectations, SERS intensity for End, Side, and Satellite isomers was found to be dependent primarily on the number of the NPs in the superstructures rationalized with the help of electrical field simulations. Incubation of the label-free NP-NR assemblies with HeLa cells indicated sufficient field enhancement to detect structural lipids of mitochondria and potentially small metabolites. This provided the first proof-of-concept data for the possibility of real-time probing of the local organelle environment in live cells. Further studies should include structural optimization of the assemblies for multitarget monitoring of metabolic activity and further increase in complexity for applications in transformative optics.

Nanoparticles in molecular diagnostics

The aim of this chapter is to provide an overview of the available and emerging molecular diagnostic methods that take advantage of the unique nanoscale properties of nanoparticles (NPs) to increase the sensitivity, detection capabilities, ease of operation, and portability of the biodetection assemblies. The focus will be on noble metal NPs, especially gold NPs, fluorescent NPs, especially quantum dots, and magnetic NPs, the three main players in the development of probes for biological sensing. The chapter is divided into four sections: a first section covering the unique physicochemical properties of NPs of relevance for their utilization in molecular diagnostics; the second section dedicated to applications of NPs in molecular diagnostics by nucleic acid detection; and the third section with major applications of NPs in the area of immunoassays. Finally, a concluding section highlights the most promising advances in the area and presents future perspectives.