The folded structure of a protein is stabilized by many, but relatively weak, interactions and is consequently subjected to conformational fluctuations that occur either locally or globally and at various timescales. There are ample examples in the literature, showing how such fluctuations are important for proteins to perform physiological functions. However, experimentally capturing conformational transitions that take place at a specific region of the protein, and are relevant to function, is challenging. This is especially true for experiments using spectroscopy based techniques, since intrinsic spectroscopic signals arising from natural amino acids often lack site specificity, due to spectral overlapping, degeneracy, and coupling, or insensitivity to environmental changes. To overcome this limitation, a common practice is to introduce one or multiple external spectroscopic probes into the protein systems of interest. However, the introduction of any foreign moiety, except an isotopic label, into a protein, will unavoidably perturb its native structure and dynamics. To minimize such perturbations, it is imperative to use probes that are structurally similar to the existing scaffold, such as unnatural amino acids (UAAs). Therefore, in this thesis we describe the utility of several UAAs as site-specific spectroscopic probes as well as their applications in the study of various chemical and biophysical problems. Specifically, we demonstrate that - 1) several nitrile containing aromatic moieties can serve as site-specific infrared and circular dichroism probes, useful to interrogate the hydration status, stability and structure of proteins, among other applications; 2) the fluorescence property of the fluorophores in both 5-cyanotryptophan and 7-cyanotryptophan is sensitive to hydration, making them useful as protein local fluorescence reporters; 3) the carbonyl stretching vibration of 4-oxoproline exhibits a sensitive dependence on its local electrostatic environment, hence can be used to study the structure and dynamics of individual proline residues in proteins; and 4) the UAA, methyl ester of Aspartic Acid, not only has unique infrared utilities but also facilitates the formation of α-sheet in amyloid fibrils.