Targeted detection of bio-molecules in vivo and in the environment is a key area of research. Surface enhanced Raman spectroscopy (SERS) is emerging as a noninvasive platform for detection of a large variety of biomolecules. Here, bionanotechnology was investigated to further enhance the capabilities of SERS as a biosensor platform. Specifically, a system was developed using oligonucleotide labeled nanoparticles for multiplex detection of small nucleotide polymorphisms in the K-Ras oncogene at a 10 pM detection limit. The binding kinetics and fluorescence quenching of CTAB coated gold nanorods were also investigated for use in detection of hydrophobic biomolecules. Fluorescence quenching of Nile Red and IR-786 was found to be independent of binding affinity, as determined by surface plasmon resonance. A novel method of functionalizing proteins to nanoparticles was developed for use in SERS and other nanoparticles based platforms. The system uses selenocysteine mediated cleavage of a protein splicing element known as an intein. The selenocysteine activated protein can then be functionalized to any selenocysteine reactive surface or functional group in a pH dependent manner. After development using a maltose binding protein model, fluorescein labeling of an intein tagged single chain antibody against the A33 cancer antigen was confirmed by florescence activated cell sorting.