Synthetic biology is a research field that involves the design and synthesis of genes and genomes. It has a wide range of applications in building gene circuits, activating biochemical pathways and metabolic engineering. Over the last decade, there has been rapid progress in developing efficient DNA synthesis technologies that improve the overall quality of the constructed DNA. Currently, there are several different methods available for successful DNA assembly of long genes. However, these methods have certain drawbacks such as presence of restriction sites (scars) within the assembled sequences or multi-step reaction process to assemble a high-number of fragments. Thus, new DNA assembly methods are applied in this work that overcome these challenges.

This thesis discusses an overview of current advancements in synthetic biology with a focus on DNA assembly design tools, methods and applications. A computational tool is presented that helps in the rational design of DNA fragments based on thermodynamic analysis. The designed DNA fragments can be assembled using different techniques such as modified Gibson Assembly and no-erosion ligation based assembly method. The software predictions are validated for assembly of a high-number of DNA fragments using the two methods for a few genes. In addition, a collaborative bioinformatics project that reveals functional changes among scallop opsins after gene duplication events based on protein structure modeling is also part of this work.