Graphene based nanomaterials, such as graphene oxide (GO), reduced graphene oxide (rGO) and CVD graphene, with their unique physical and chemical properties, are emerging as extraordinary materials for use in biosensing applications. The aim of this PhD thesis is to study the interaction of biomolecules assembling (DNA and proteins) on these nanostructures. Our study incorporates experimental demonstrations and theoretical explanations for fundamental complications that emerged during the interaction of biomolecules with the two-dimensional materials. In this thesis, to examine these challenges, we designed a DNA-based biosensing platform that utilized a GO platform. We experimentally demonstrated the DNA sensing platform consisting of aggregation-induced emission (AIE) molecule...[ Read more ]

Graphene based nanomaterials, such as graphene oxide (GO), reduced graphene oxide (rGO) and CVD graphene, with their unique physical and chemical properties, are emerging as extraordinary materials for use in biosensing applications. The aim of this PhD thesis is to study the interaction of biomolecules assembling (DNA and proteins) on these nanostructures. Our study incorporates experimental demonstrations and theoretical explanations for fundamental complications that emerged during the interaction of biomolecules with the two-dimensional materials. In this thesis, to examine these challenges, we designed a DNA-based biosensing platform that utilized a GO platform. We experimentally demonstrated the DNA sensing platform consisting of aggregation-induced emission (AIE) molecules and complementary DNA (comDNA) adsorbed on GO. We experimentally turned the AIE molecule on and off by adjusting its distance from the GO sheet, which quenched depending on its distance from the graphene plane. The changes in florescence are reproducible, which demonstrates the probe’s ability to identify the binding state of the DNA. From a theoretical perspective, we performed a molecular dynamic simulation to study the strong π-π interactions between the single-strand DNA (ssDNA) and GO. Our simulation shows ssDNA binds strongly to graphene by reduced center of the mass and binding free energies. When ssDNA-GO introduced to comDNA, the complex hybridized and relieves GO, evidenced by increased distance and reduced interactions between dsDNA and graphene, eliminating quenching effect and turned on the AIE molecule. Our protocol uses AIE molecule as a probe thus avoided the complicated steps involved in covalent functionalization and allowed the rapid and label-free detection of DNA molecules. In the second study, we utilized a specific graphene binding peptide (GBP) that noncovalently binds to graphene. The GBP was incorporated with engineered proteins SpyTag and SpyCatcher. From a theoretical perspective, simple systems that self-assembles into complex structures through fundamental interactions and logical rules can result. Therefore, protein systems were adsorbed on graphene and a binding mechanism was explored, confirming its mode of interaction on the nanomaterials. As an experimental perspective, this provides a promising method to programmably assemble these bimolecular complexes onto graphene-based materials. We experimentally demonstrated a unique mechanism involving the interactions of biomolecules with graphene-based materials at a nanoscale resolution to design for pure biological applications.