Effects of Superparamagnetic Nanoparticle Clusters on the Polymerase Chain Reaction

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.

Dynamic behavior of floating magnetic liquid marbles under steady and pulse-width-modulated magnetic fields

Liquid marbles show promising potential for digital microfluidic devices due to their lower friction with the platform surface than non-covered droplets. In this study, the manipulation of a biocompatible magnetic liquid marble with a magnetic shell (LMMS) is experimentally studied. The movement of the floating LMMS on the water surface, which is actuated by DC and pulse width modulation (PWM) magnetic fields, is investigated under the influence of various parameters, including the LMMS volume, the initial distance of the LMMS from the magnetic coil tip, the magnetic coil current, the PWM frequency and its duty cycle. The LMMS has a shorter travel time to the magnetic coil tip under a DC magnetic field by increasing the magnetic coil current, decreasing the initial distance and its volume. In the PWM mode, these parameters show similar behavior; moreover, increasing the PWM duty cycle and decreasing the PWM frequency shorten the travel time. It is demonstrated that actuation by a PWM magnetic field with step-by-step movement provides better control over manipulation of the floating magnetic marble. The dynamic behavior of an LMMS is compared to a ferrofluid marble (FM), which is formed using a ferrofluid instead of water as its core. It is observed that the LMMS has a lower velocity than the FM.

Multifunctional Nanoparticle Platform for Surface Accumulative Nucleic Acid Amplification and Rapid Electrochemical Detection: An Application to Pathogenic Coronavirus

Of various molecular diagnostic assays, the real-time reverse transcription polymerase chain reaction is considered the gold standard for infection diagnosis, despite critical drawbacks that limit rapid detection and accessibility. To confront these issues, several nanoparticle-based molecular detection methods have been developed to a great extent, but still possess several challenges. In this study, a novel nucleic acid amplification method termed nanoparticle-based surface localized amplification (nSLAM) is paired with electrochemical detection (ECD) to develop a nucleic acid biosensor platform that overcomes these limitations. The system uses primer-functionalized Fe3O4-Au core-shell nanoparticles for nucleic acid amplification, which promotes the production of amplicons that accumulate on the nanoparticle surfaces, inducing significantly amplified currents during ECD that identify the presence of target genetic material. The platform, applying to the COVID-19 model, demonstrates an exceptional sensitivity of ∼1 copy/μL for 35 cycles of amplification, enabling the reduction of amplification cycles to 4 cycles (∼7 min runtime) using 1 fM complementary DNA. The nSLAM acts as an accelerator that actively promotes and participates in the nucleic acid amplification process through direct polymerization and binding of amplicons on the nanoparticle surfaces. This ultrasensitive fast-response system is a promising method for detecting emerging pathogens like the coronavirus and can be extended to detect a wider variety of biomolecules.

Magnetically Driven Manipulation of Nonmagnetic Liquid Marbles: Billiards with Liquid Marbles

Liquid marbles are droplets encapsulated by a layer of hydrophobic nanoparticles and have been extensively employed in digital microfluidics and lab-on-a-chip systems in recent years. In this study, magnetic liquid marbles were used to manipulate nonmagnetic liquid marbles. To achieve this purpose, a ferrofluid liquid marble (FLM) was employed and attracted toward an electromagnet, resulting in an impulse to a water liquid marble (WLM) on its way to the electromagnet. It was observed that the manipulation of the WLM by the FLM was similar to the collision of billiard balls except that the liquid marbles exhibited an inelastic collision. Taking the FLM as the projectile ball and the WLM as the other target balls, one can adjust the displacement and direction of the WLM precisely, similar to an expert billiard player. Firstly, the WLM displacement can be adjusted by altering the liquid marble volumes, the initial distances from the electromagnet, and the coil current. Secondly, the WLM direction can be adjusted by changing the position of the WLM relative to the connecting line between the FLM center and the electromagnet. Results show that when the FLM or WLM volume increases by five times, the WLM shooting distance approximately increases by 200% and decreases by 75%, respectively.

Enhanced Diamagnetic Repulsion of Blood Cells Enables Versatile Plasma Separation for Biomarker Analysis in Blood

A hemolysis-free and highly efficient plasma separation platform enabled by enhanced diamagnetic repulsion of blood cells in undiluted whole blood is reported. Complete removal of blood cells from blood plasma is achieved by supplementing blood with superparamagnetic iron oxide nanoparticles (SPIONs), which turns the blood plasma into a paramagnetic condition, and thus, all blood cells are repelled by magnets. The blood plasma is successfully collected from 4 mL of blood at flow rates up to 100 µL min^-1 without losing plasma proteins, platelets, or exosomes with 83.3±1.64% of plasma volume recovery, which is superior over the conventional microfluidic methods. The theoretical model elucidates the diamagnetic repulsion of blood cells considering hematocrit-dependent viscosity, which allows to determine a range of optimal flow rates to harvest platelet-rich plasma and platelet-free plasma. For clinical validations, it is demonstrated that the method enables the greater recovery of bacterial DNA from the infected blood than centrifugation and the immunoassay in whole blood without prior plasma separation.

A lab-on-a-chip for free-flow electrophoretic preconcentration of viruses and gel electrophoretic DNA extraction

A lab-on-a-chip for FFE preconcentration of viruses and gel electrophoretic DNA extraction: complete preparation of amplifiable DNA from dilute specimens.

A 3D-Printed Millifluidic Platform Enabling Bacterial Preconcentration and DNA Purification for Molecular Detection of Pathogens in Blood

Molecular detection of pathogens in clinical samples often requires pretreatment techniques, including immunomagnetic separation and magnetic silica-bead-based DNA purification to obtain the purified DNA of pathogens. These two techniques usually rely on handling small tubes containing a few millilitres of the sample and manual operation, implying that an automated system encompassing both techniques is needed for larger quantities of the samples. Here, we report a three-dimensional (3D)-printed millifluidic platform that enables bacterial preconcentration and genomic DNA (gDNA) purification for improving the molecular detection of target pathogens in blood samples. The device consists of two millichannels and one chamber, which can be used to preconcentrate pathogens bound to antibody-conjugated magnetic nanoparticles (Ab-MNPs) and subsequently extract gDNA using magnetic silica beads (MSBs) in a sequential manner. The platform was able to preconcentrate very low concentrations (1–1000 colony forming units (CFU)) of Escherichia coli O157:H7 and extract their genomic DNA in 10 mL of buffer and 10% blood within 30 min. The performance of the platform was verified by detecting as low as 1 CFU of E. coli O157:H7 in 10% blood using either polymerase chain reaction (PCR) with post gel electrophoresis or quantitative PCR. The results suggest that the 3D-printed millifluidic platform is highly useful for lowering the limitations on molecular detection in blood by preconcentrating the target pathogen and isolating its DNA in a large volume of the sample.

Metal nanoparticle assisted polymerase chain reaction for strain typing of Salmonella Typhi

Salmonella enterica serotype Typhi (S. Typhi) is the causative agent of typhoid fever and remains a major health threat in most of the developing countries. The prompt diagnosis of typhoid directly from the patient's blood requires high level of sensitivity and specificity. Some of us were the first to report PCR based diagnosis of typhoid. This approach has since then been reported by many scientists using different genomic targets. Since the number of bacteria circulating in the blood of a patient can be as low as 0.3 cfu ml(-1), there is always a room for improvement in diagnostic PCR. In the present study, the role of different types of nanoparticles was investigated to improve the existing PCR based methods for diagnosis and strain typing of S. Typhi (targeting Variable Number of Tandem Repeats [VNTR]) by using optimized PCR systems. Three different types of nanoparticles were used i.e., citrate stabilized gold nanoparticles, rhamnolipid stabilized gold and silver nanoparticles, and magnetic iron oxide nanoparticles. The non-specific amplification was significantly reduced in VNTR typing when gold and silver nanoparticles were used in an appropriate concentration. More importantly, the addition of nanoparticles decreased the non-specificity to a significant level in the case of multiplex PCR thus further validating the reliability of PCR for the diagnosis of typhoid.

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.

Magnetic silica nanoparticle–Taq polymerase hybrids for multiple uses in polymerase chain reaction

Magnetic-silica core–shell nanoparticles were proposed as a fast purification strategy for recombinant enzymes and their subsequent usability in catalysis reactions. A proof-of-concept study with Taq polymerase hybrids was demonstrated.