Biophotonics denotes the utilization of light to study biology and has provided many new tools and insights for life science. For example, molecular imaging by light microscopes with fluorescent probes has gained considerable attention owing to its high sensitivity and multiplexing capabilities. Optical tweezers employing focused laser beams can individually trap micrometer-sized objects and measure biomolecular interactions. Optogenetics has demonstrated photonic control of genetically modified cells and opened up new avenues for manipulating biological events in live cells and animals. Although conventional biophotonic techniques often satisfy the requirements of cell biologists, the diffraction of light inevitably restricts their applicability to single biomolecules (e.g. proteins, DNA, and RNA) with characteristic sizes on the nanometer scale. Based on the localized surface plasmon resonance, plasmonic nanoantennae-mediated molecular sensing, manipulation and fabrication offer a promising way to overcome the diffraction limit of light by leveraging highly confined and strong electromagnetic hot-spots. Creatively utilizing interactions between hot-spots, biomolecules, cells and materials generates novel biological applications both in vitro and in vivo.

Here, I first present a method, named nanoplasmonic optoporation, for precise gene regulation by the creation of transient nanopores in cell membranes. Induced by the irradiation of near-infrared light, the enhanced surface plasmon resonance of gold particles allows us to photothermally create ~40 nm nanopores with a ~30 min lifetime. Sequential molecular delivery into somatic cells is demonstrated with single-cell precision, as well as at the larger centimeter-scale of conventional cell culture. Nanoplasmonic-mediated gene regulation in stem cells is demonstrated with higher efficiency than conventional transfection methods.

Second, graphene nanopores are created and integrated with an optical antenna with a single fabrication step, light-induced gold nanorods melting. Nanometer-sized heating source created by photothermal effect of gold nanorods resting on a graphene membrane created nanoscale pores with hemispherically shaped nanoantennas. The approach yields the significant advantage of parallel nanopore fabrication compared to the conventional sequential process using an electron beam. The atomically-thin nature of graphene, together with nanoplasmonic properties of integrated antennas, makes this unique nanopore a potential platform for high resolution and high throughput nucleic acid analysis in single-molecular level. The optical function of an integrated plasmonic nanoantenna is demonstrated by multifold fluorescent signal enhancement during the translocation of single DNA molecules through a graphene nanopore. Graphene nanopores integrated with optical antennae could offer a new avenue for simultaneous electrical and optical enhanced DNA sequencing in the future.

Third, a simple, high-sensitive, and robust method for the detection of microRNA cancer markers has been demonstrated by oligonucleotide-conjugated plasmonic nanoparticles. Due to surface plasmon resonance effects, single metallic nanoparticles provide an extremely strong light scattering signal that lowered the detection threshold and improved sensitivity for the detection of single microRNAs. In addition, dimer-type probes were designed to induce red-shift in their scattering when hybridized with target microRNAs. It is possible to achieve single-molecular detection by simply counting red-shifted nanoparticles. To further apply this method for point-of-care diagnosis, a portable total internal reflection illumination system was designed and integrated with nanoplasmonic-based sensors.

In the end of this thesis, I conclude with the outlook of nanoplasmonic integrated nanofluidics for medical diagnostics and in vivo nanoplasmonic manipulation of genetic circuits. Nanoplasmonic integrated nanopores are promising for the precise control of nano-scaled environments for DNA or RNA analysis. On the other hand, another source of excitement comes from applications of multiple plasmonic nanomaterial-controlled gene circuit engineering. Nanoplasmonic gene regulation mediated by photothermal effects might provide multiple manipulations with high spatial and temporal resolution. Studying nanoplasmonic-mediated sensing and delivery could provide new avenues for understanding how biological systems function at the molecular level.