A major goal in advancing modern bio-sensing and bio-microelectronic applications is to thoroughly understand the surface binding of biomolecules on solid substrate. Developing next generation biosensors and microelectronic devices involves addressing the following issues: improving the non-specific or non-covalent binding between biomolecules and substrate; enhancing the chemical and physical stabilities of the bio-interface, and understanding and exploiting the electronic properties of the solid substrates. The ultimate goal of this project is to design and develop a sharp, well-defined and stable interface between biomolecules and semiconductor substrate, which in this case is the silicon surface. A well-characterized interface based upon covalent binding between biomolecules and semiconductor surfaces was designed using the functionalized self-assembled monolayers (SAM) on Si(111) surface and specific shaped-restricted DNA molecules. This type of interface can serve as a prototype for the future devices in biosensing and single molecule detection. The spectroscopic and microscopic benchmarks were initially established using fullerene C60 as a model to understand the attachment chemistry of large molecules with amine-terminated SAM on Si(111) surface. X-ray photoelectron spectroscopy (XPS) and Infrared spectroscopic (IR) studies, supported by computational investigations, verified the covalent attachment of C60 to the amine-terminated SAM on Si(111) surface. XPS revealed that secondary amine group is formed between the C60 and the 11-amino-1-undecene SAM on the surface. The appearance of the pi-pi* C 1s shake-up peak confirmed the presence of C60 on the surface. IR studies verified several characteristic features of C60 skeleton vibration and the 11-amino-1-undecene vibrational signature. Atomic force microscopy (AFM) revealed the topography of the C60-modied surface with molecular resolution. This C60 attachment confirmed the configuration, stability and reactivity of the interface system. In addition, the model system set reliable references for the surface analysis methods. A parallel study was performed on Au(111) surface for comparison with the results obtained on the silicon substrate. The reaction between fullerene molecules and ∼1% 11-amino-1-undecene diluted in decene SAM on Si(111) surface yielded accordingly diluted and uniformly distributed C60 molecules on the surface, which indicated that the amine groups were the reactive sites. The biomolecule/semiconductor interface was tailored with the same amine-terminated SAM on Si(111) surface and thiol-DNA molecules, which is achieved by using a sulfo-succinimidyl 4-(N-maleimidomethyl)-cyclohexane-1-carboxylate (SSMCC) crosslinker molecule. The shape-restricted thiol-DNA was anchored to the surface through the formation of covalent bonds as confirmed by XPS and time-of-flight secondary ion mass spectroscopy (TOF-SIMS). The AFM was used to visualize the well-defined and selective covalent binding of thiol-DNA molecules on SAM-covered Si(111). In addition, AFM and contact angle measurements were employed to study the change of the surface topography and the change of the surface hydrophilicity following each step of the DNA attachment chemistry on silicon. After the observation, the DNA-modified surface was washed with the DNA-digesting enzyme DNaseI to remove the nucleic acids leaving the thio-group covalently bonded to the surface, as confirmed by TOF-SIMS. The fact that the sulfur atoms remain on the surface after the thiol-DNA-covered silicon substrate is treated with the DNA digestion enzyme is a direct proof that the thiol groups play the main role in a specific...