Nanoscale structures play a fundamental role in diverse scientific areas, including biology and information technology. It is necessary to develop methods that can observe nanoscale structures and dynamic processes that involve them. Colloidal plasmonic nanoparticles (plasmonic “atoms”) and their clusters (plasmonic “molecules”) are nanoscale objects with remarkable optical properties that provide new opportunities for sensing and imaging on the relevant length and time scales. Many biology questions require optically monitoring of the dynamic behavior of biological systems on single molecule level. In contrast to the commonly used fluorescent probes which have the problem of bleaching, blinking and relatively weak signals, plasmonic probes display superb brightness, persistency and photostability, thus enable long observation time and high temporal and spacial resolutions. When plasmonic atoms are clustered together, their resonances redshift while the intensities increase as a result of plasmon coupling. These optical responses are dependent on the interparticle gaps and the overall geometry, which makes plasmonic molecules capable of detecting biomolecule clustering and measuring nanometer scale distance fluctuations. In this dissertation, individual plasmonic atoms are firstly evaluated as imaging probe and their interactions with lipid membrane are tested on a newly developed on-chip black lipid membrane system. Subsequently, plasmonic dimers (plasmon rulers) prepared through DNA-programmed self-assembly are monitored to detect the mechanical properties of single biopolymers. Measurement of the spring constant of short (tens of nucleotides or base pairs) DNAs is demonstrated through plasmon coupling microscopy. Colloidal plasmonic atoms of various materials, sizes and shapes scatter vivid colors in the full-visible range. Assembling them into plasmonic molecules provides additional degrees of freedom for color manipulation. More importantly, the electric field in the gaps of plasmonic molecules can be enhanced by several orders of magnitude, which is highly desirable in single molecule sensing applications. In this dissertation, the fundamentals of plasmonic coupling are investigated through one-dimensional gold nanosphere chains. Using the directed self-assembly approach, multichromatic color-switchable plasmonic nanopixels composed of plasmonic atoms and molecules of various materials, sizes, shapes and geometries are integrated in one image with nanometer precision, which facilitates the encoding of complex spectral features with high relevance in security tagging and high density optical data storage. / 2017-01-01T00:00:00Z