Synthetic biology is a new area of biological research that combines science and engineering. Synthetic biology encompasses many different approaches, methodologies and disciplines, and many different definitions exist. What they all have in common, however, is that they see synthetic biology as the design and construction of new biological functions and systems not found in nature. This volume of Methods in Enzymology has been split into 2 parts and covers topics such as measuring and engineering central dogma processes, mathematical and computational methods and next-generation DNA assembly and manipulation.