Plasmonic Optical Wells-Based Enhanced Rate PCR.

Rapid, sensitive, inexpensive point-of-care molecular diagnostics are crucial for the efficient control of spreading viral diseases and biosecurity of global health. However, the gold standard, polymerase chain reaction (PCR) is time-consuming and expensive and needs specialized testing laboratories. Here, we report a low-cost yet fast, selective, and sensitive Plasmonic Optical Wells-Based Enhanced Rate PCR: POWER-PCR. We optimized the efficient optofluidic design of 3D plasmonic optical wells via the computational simulation of light-to-heat conversion and thermophoretic convection in a self-created plasmonic cavity. The POWER-PCR chamber with a self-passivation layer can concentrate incident light to accumulate molecules, generate rapid heat transfer and thermophoretic flow, and minimize the quenching effect on the naked Au surface. Notably, we achieved swift photothermal cycling of nucleic acid amplification in POWER-PCR on-a-chip in 4 min 24 s. The POWER-PCR will provide an excellent solution for affordable and sensitive molecular diagnostics for precision medicine and preventive global healthcare.

Bubble-free diatoms polymerase chain reaction.

Polymerase chain reaction (PCR) in small fluidic systems not only improves speed and sensitivity of deoxyribonucleic acid (DNA) amplification but also achieves high-throughput quantitative analyses. However, air bubble trapping and growth during PCR has been considered as a critical problem since it causes the failure of DNA amplification. Here we report bubble-free diatom PCR by exploiting a hierarchically porous silica structure of single-celled algae. We show that femtoliters of PCR solution can be spontaneously loaded into the diatom interior without air bubble trapping due to the surface hydrophilicity and pore structure of the diatom. We discover that a large pressure gradient between air bubbles and nanopores rapidly removes residual air bubbles through the periodically arrayed nanopores during thermal cycling. We demonstrate the DNA amplification by diatom PCR without air bubble trapping and growth. Finally, we successfully detect DNA fragments of SARS-CoV-2 with as low as 10 copies/µl by devising a microfluidic device integrated with diatoms assembly. We believe that our work can be applied to many PCR applications for innovative molecular diagnostics and provides new opportunities for naturally abundant diatoms to create innovative biomaterials in real-world applications.

Quantum Electrodynamic Behavior of Chlorophyll in a Plasmonic Nanocavity.

Plasmonic nanocavities have been used as a novel platform for studying strong light-matter coupling, opening access to quantum chemistry, material science, and enhanced sensing. However, the biomolecular study of cavity quantum electrodynamics (QED) is lacking. Here, we report the quantum electrodynamic behavior of chlorophyll-a in a plasmonic nanocavity. We construct an extreme plasmonic nanocavity using Au nanocages with various linker molecules and Au mirrors to obtain a strong coupling regime. Plasmon resonance energy transfer (PRET)-based hyperspectral imaging is applied to study the electrodynamic behaviors of chlorophyll-a in the nanocavity. Furthermore, we observe the energy level splitting of chlorophyll-a, similar to the cavity QED effects due to the light-matter interactions in the cavity. Our study will provide insight for further studies in quantum biological electron or energy transfer, electrodynamics, the electron transport chain of mitochondria, and energy harvesting, sensing, and conversion in both biological and biophysical systems.

Ultrasensitive and real-time optical detection of cellular oxidative stress using graphene-covered tunable plasmonic interfaces.

Reactive oxygen species (ROS) regulate various physiological and pathological conditions in cells by interacting with signaling molecules and inducing oxidative stress. Therefore, sensitive monitoring of ROS levels in living cells is important to track cellular state and study the complex role of ROS in the development of various pathologies. Herein, we present an optically tunable plasmonic interface covered with graphene to monitor cellular ROS levels with superior sensitivity and cellular comfortability. As a sensing principle, we employed plasmon resonance energy transfer (PRET)-based spectral quenching dips modulated by redox-active cytochrome c for real-time monitoring. By transferring graphene layers to plasmonic nanoparticles immobilized on a glass substrate, the scattering profiles of the nanoprobes were adjusted in terms of the position, width, and intensity of the peaks to determine the optimal conditions for measuring the PRET signal. Using the optimized graphene-covered plasmonic nanoprobe, we obtained calibration curves over a wide concentration range from femtomoles to millimoles for hydrogen peroxide based on the change in the PRET signal. Before monitoring cellular ROS, we confirmed that a high density of cells adhered well to the graphene-covered plasmonic interface by observing immunofluorescence images of the cytoskeleton of the immobilized cells. Finally, we monitored the real-time ROS generated by the cells under oxidative stress conditions by directly measuring the spectral changes of the probes around the cells. We believe that the proposed graphene-covered tunable plasmonic interface has versatile applicability for investigating cellular stress and disease progression by monitoring ROS levels under various cellular conditions.

High-spatial and colourimetric imaging of histone modifications in single senescent cells using plasmonic nanoprobes.

Histones are closely related to the state of chromatin, and epigenetic modification of their tail results in regulation in cells. Therefore, developing various analytical tools to map the changes in position and distribution of histone modifications is helpful in studying underlying mechanisms. Herein, we propose a high-spatial and colourimetric imaging method using plasmonic nanoparticles as probes to visualize heterochromatin histone markers in a single nucleus. We visualized the reorganization between repressive histone markers, H3K9me3 and H3K27me3, caused by oncogene-induced senescence based on the scattering colours and spectral shift of plasmonic nanoprobes to longer wavelengths using their distance-dependent coupling effect. The measured scattering profiles were correlated with the computation results simulating the scattering spectra according to the arrangements and distances among the plasmonic nanoprobes. The plasmonic nanoprobe-based high-spatial hyperspectral imaging provides an advanced way to study the dynamics of histone modifications for predicting the progression of diseases or senescence.

Adjustable and Versatile 3D Tumor Spheroid Culture Platform with Interfacial Elastomeric Wells.

Three-dimensional (3D) cell culture platforms have recently received a great deal of attention, as these systems are able to recapitulate the in vivo microenvironment of tissues or tumors. Herein, we describe adjustable and versatile elastomeric well structures for spheroid formation and their use for in situ analyses as a tunable 3D cell culture platform. Elastomeric spherical wells are fabricated using a one-step interfacial reaction between aqueous droplets on immiscible liquid polydimethylsiloxane (PDMS) without any template or expensive equipment. Because of their differing surface tensions, spherical wells are spontaneously formed on liquid PDMS with various sizes and curvatures that are easily controlled. Using arrays of these optimized wells, single tumor spheroids within each well were successfully formed at high efficiency (up to 97%) by coculturing tumor cells and fibroblasts to reflect the complex microenvironment of cancer tissue. Moreover, the tumor spheroids formed within the interfacial wells were directly applied for observing drug responses and monitoring reactive oxygen species (ROS) to investigate tumor cell responses to drugs or their 3D microenvironment. We believe that our proposed platform provides a significant contribution to the multimodal analyses of anticancer therapeutics and the tumor microenvironment.