UC San Diego

Traditionally known as the genetic code, in recent years DNA has been engineered in new ways and applied toward novel applications in materials science and bio- nanotechnology. The nanometer features and highly specific base-pairing of DNA has enabled its use to build complex 2 - and 3D nano-architectures and nano-structures. Specific DNA scaffolds include branched DNA junctions, 2D and 3D DNA "tiles" and "bricks", and DNA hydrogels that can be used for applications across various fields of materials science. Another unique feature of DNA is its ability to bind other materials through molecular recognition which has made the use of DNA aptamer or DNA-protein conjugates highly useful for applications in biosensing and identification. The main focus of this thesis is to demonstrate the use of DNA as an invaluable tool for engineering specific nanostructures for biosensing. The first chapter introduces the basics of DNA and current research in various DNA structures and assemblies and their applications. The second and third chapters describe the self-assembly of two structurally different nanomaterials using DNA, carbon nanotubes and gold nanoparticles. In the second chapter, the successful large -scale alignment of carbon nanotubes on a surface is shown. The study goes into the factors that affect the quality of alignment, including salt concentration, length of DNA, and annealing. In the third chapter, we show how DNA can be used to engineer discrete gold nanocrystal assemblies-"nanodumbbells"- that can adopt different structural conformations through DNA interactions. By incorporating DNA aptamers in the nanoparticle structure, these nanodumbbells can be used to sense particular analytes in solution. Chapter 4 continues the study of the nanodumbbell structures and their potential use as surface -enhanced Raman spectroscopy (SERS) biosensors. A large measurable difference in Raman signal was experimentally obtained from the two distinct nanodumbbell conformations. This was compared with theoretical studies of SERS enhancement to validate the signals produced. We were also able to show the successful detection of an analyte, ATP, using the DNA-mediated probe and SERS detection method