Directed Evolution
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Directed Evolution is an excellent starting point for any scientist interested in directed evolution. This primer aims to provide readers with the foundational knowledge and vocabulary that enables them to tackle the literature and begin designing their projects.
Directed evolution, as a field, can be challenging to start in; one of the biggest challenges to starting work in this field is that it requires a different style of thinking than many areas of chemistry. CHAPTER 1 explains this different mentality and then gives an overview of directed evolution: what it is, why it is useful, how evolution is applied in the lab, and how evolution can be applied for human benefit.
Given the diversity and quantity of methods and approaches in directed evolution, the remaining chapters focus on helping the readers find the right approach to their specific problem by outlining the basic thought process and classical methods in directed evolution. Specifically, CHAPTER 2 discusses applying directed evolution to nucleic acids. Nucleic acid evolution has several unique features that make it easier to understand conceptually, making it a good starting point for understanding how to think about and leverage evolution. CHAPTERS 3 through 6 cover approaches to evolving proteins. CHAPTER 3 discusses the strengths and weaknesses of different approaches to the diversification of proteins, giving the reader a framework for designing libraries. CHAPTERS 4, 5, and 6 introduce different approaches to sorting by applying selection pressures to find the best variant from a large complex library.
Upon completing this primer, the reader will have a theoretical basis to design and execute a directed evolution campaign. They will have the core knowledge to dive into the larger world of directed evolution and begin designing projects that leverage this powerful technique.
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Aaron M. Leconte has always been drawn to the idea of making new and potentially useful molecules. For Aaron, even after two decades, the challenging act of designing and creating a molecule that never existed before still feels powerful and profound. As an undergraduate at Carleton College, Aaron studied under Dave Alberg, learning the joys of organic synthesis. During his Ph.D. at Scripps Research in La Jolla, California, in the lab of Floyd Romesberg, Aaron shifted from making small organic molecules to using directed evolution to make proteins with new and improved functions to expand the genetic alphabet. Aaron then went on to a postdoctoral fellowship with David Liu at Harvard University, where he used a new directed evolution method (PACE) to study protein-directed evolution itself. In his independent career, Aaron works with an incredibly talented group of undergraduate student researchers at Claremont McKenna, Pitzer, and Scripps Colleges. His research group is currently using directed evolution to engineer polymerases and luciferases for applications in biomedical sciences. Aaron occasionally gets to teach a class on directed evolution to senior undergraduate students; this course and the lessons learned from teaching it form the structure and content of this primer.
Clair M. Colee has only just begun her career path in science, but her desire to create and explore has been a cornerstone of her identity from a young age. When she first learned that evolution could be used as a research tool, Clair was thrilled by the idea that molecules could be created, improved, or altered by the same principles that have shaped the natural world around us. As an undergraduate at Scripps College, Clair worked in the lab of Aaron Leconte, where she used directed evolution to alter the light emission color of luciferase for improved applications in bioluminescence imaging. Clair also had the opportunity to study under Scott Silverman as a Snyder Scholar at the University of Illinois Urbana Champaign, where she designed the components of an in vitro selection scheme used to identify novel DNA catalysts. Having just graduated from Scripps College, Clair is now pursuing a Ph.D. in chemistry—in fact, she is currently in the process of deciding between Ph.D. programs! Clair was particularly captivated by Aaron’s aforementioned class on directed evolution and hopes to continue exploring the endless methods and applications of this revolutionary field in her future research endeavors.
