DNA nanotechnology is a rapidly evolving field that exploits the remarkable properties of DNA molecules to create complex and functional nanostructures. One of the key techniques in DNA nanotechnology is self-assembly, wherein DNA molecules are designed to interact and assemble into specific structures with precise control over their size, shape, and composition. This dissertation focuses on the self-assembly of plasmonic, fluorescent, and magnetic nanoparticles in both 2D and 3D using DNA as a programmable scaffold, and explores their applications in various areas, including biosensing and magnetic metamaterials.Chapter 1 provides a comprehensive overview of DNA nanotechnology, self-assembly techniques, and DNA origami. The principles of DNA self-assembly are discussed, including the design rules for creating DNA nanostructures with precise control over their shape and size. The versatility of DNA as a programmable scaffold is highlighted, allowing for the assembly of diverse nanoparticles with unique functionalities. The chapter also discusses the fundamentals of DNA origami, a powerful technique that utilizes the folding of a long single-stranded DNA template to create complex nanostructures with high precision. In Chapter 2, a novel ligand exchange method is presented, which allows for the functionalization of quantum dots (QDs) with DNA to form self-assembled heterodimers. The heterodimers serve as probes for detection, with one QD acting as a reporter and the other AuNP (gold nanoparticle) as a quencher. The chapter elaborates on the design and fabrication of the QD-AuNP heterodimer. The changes in photoluminescence (PL) signals upon binding of the heterodimers to target DNA molecules are investigated. Chapter 3 focuses on the application of the heterodimer probes in the development of a biosensor for nucleic acid detection. The biosensor is designed based on the change in PL signal upon target DNA binding, allowing for sensitive and selective detection. The chapter provides details on the fabrication and characterization of the biosensor, including the optimization of xvi experimental parameters such as probe design and concentration, and target DNA concentration. The performance of the biosensor is also evaluated using different target DNA concentrations. The kinetics of the DNA displacement process in the biosensor are also investigated, shedding light on the dynamics of target DNA binding and release from the heterodimers. In Chapter 4, a novel method for the self-assembly of gold-coated magnetic nanoparticles in 3D using DNA as a scaffold is presented. The chapter discusses the fabrication of DNA-modified magnetic nanoparticles and their subsequent self-assembly into 3D structures by exploiting the programmable base-pairing interactions of DNA molecules. The chapter highlights the unique capabilities of this 3D self-assembly approach and discusses the future prospects and potential directions for further research in this area. In conclusion, this dissertation presents a comprehensive investigation into the use of DNA nanotechnology for the self-assembly of plasmonic, fluorescent, and magnetic nanoparticles in 2D and 3D. The methods and findings presented in this dissertation contribute to the advancement of DNA nanotechnology and demonstrate the potential of self-assembled nanostructures for various applications, including biosensing, nucleic acid detection, DNA data storage and magneto-plasmonic measurements.