THE ATTACHMENT AND CHARACTERIZATION OF DNA PROBES ON GaAs-BASED SEMICONDUCTOR SURFACES

Abstract

Immobilization of nucleic acid molecules on solid surfaces is the core of numerous important technologies in the genomics, disease diagnostics and biosensors applications. The architecture and density of immobilized probe molecules depend on the type of the solid surface on which they are anchored. Even though many different types of surfaces have been studied as substrates for deoxyribonucleic acid (DNA) attachment, the development of a new type of substrate, which is reproducible, stable, highly controlled and easily transferred to practical applications, is still needed. Recent studies have shown that As terminated GaAs-based semiconductors can be used as substrates for immobilized DNA layers.

In this study, I aim to understand the attachment of nucleic acid onto the surfaces of As-terminated GaAs- based semiconductors and focus on improving the "brush-structure", which is essential for high quality of biochip based on a DNA layer. Attachment of 8-base and 100-base thiolated ssDNA layers on arsenic terminated GaAs(001) was achieved and characterized. The covalent bonds between the thiolated oligonucleotides with As atoms on the GaAs surface were investigated using x-ray photoelectron spectroscopy (XPS), and the surface morphology was obtained using atomic force microscopy (AFM) and field emission scanning electron microscopy (FESEM). In addition, I studied the effect of DNA length and the presence of a good solvent, such as water, on the oligonucleotides on a GaAs surface. I also investigated the effects of the thiol-based spacer and electrolyte concentration to improve the brush-like structure of the DNA layer. Finally, irradiation effects and AlGaAs resonators have been studied for the applications of DNA brush layer on GaAs as biosensor during the change of attachment probe DNA and hybridization to target DNA.

For the 8-base thiolated ssDNA case, AFM results showed that the layer thickness was about ~2.2 nm in dry mode and increased in wet mode. Replacement reaction from N- , O- As bonds to S-As bonds was observed with addition of MCH as indicated by analysis of XPS spectra. The concentration of electrolyte affected the brush like layer structure. In the case of the longer, more flexible DNA with 100 bases, the DNA molecules strongly interacted with each other and formed big cluster, of 330~440nm in diameter on the surface. Finally, for the applications, a high level of radiation destroyed the brush layer. An AlGaAs resonator used as proof of concept a change in mass by a change in resonance frequency under hybridization reaction with complementary target DNA. This result shows that the design is viable and has a defection of ~25pg.