Dynamic DNA Strand Displacement Circuits Thesis by David Yu Zhang In Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy California Institute of Technology Pasadena, California 2010 (Defended May 14, 2010) c 2010 David Yu Zhang All Rights Reserved ii Acknowledgements When I started my graduate career–actually, even about one year before I finished my graduate career–I had no idea how anything I did would fit into a grander vision of science and technology. You see, a graduate student’s mark of success is somewhat different from a professor’s: A grad student’s good day is to get his data to agree with his data from yesterday, and to get both to agree with his model (after some model tinkering). A professor’s good day is to get his funding agency to agree with his research, and to get the world to agree with his genius. For me, after a somewhat lengthy undergrad detour into transcriptional circuitry work, I had figured out the trick to being a successful graduate student: work with the simplest, most well-understood system possible, and work around anything you don’t understand. I think my adviser, Erik Winfree, partially realized what I was doing, and started nagging me from fairly early on to develop a “deeper understanding” of the science that I did, and also to confront rather than avoid some of the harder problems. It wasn’t easy (as testified by the 2 and a half years it took to write the manuscript in chapter 2), but in the end I feel more like a scientist than a lab technician because of the experience. So, it is with great humbleness and appreciation that I first give thanks to my Ph.D. adviser, Erik Winfree. Paul Rothemund, Rebecca Schulman, and Jongmin Kim have provided me with invalu- able advice, both scientific and personal, and I feel that I would not be where I am today without their assistance. Paul inspired me to deal with my own adversities with poise by relating to me his past troubles, as well as the ways he dealt with them. Rebecca was and is an endless source of useful information, advice, and encouragement–she was the one who encouraged me to apply for the Hertz despite my undergrad GPA, and she is the one who helped me regain my self confidence in the last few turbulent years of my undergraduate education. Jongmin acted as my SURF co-mentor when I was an undergrad, and taught iii me a number of techniques, both in science and in Starcraft. All three of you were great advisers to me, and I am sure all of your future students will feel the same! I thank my research collaborators, Bernard Yurke, Andrew Turberfield, Georg Seelig, David Soloveichik, Rizal Hariadi, and Lulu Qian. Working with you all has been a wonderful and enlightening experience, and I look forward to future work together. I thank my other labmates, Nadine Dabby, Joseph Schaeffer, Peng Yin, and Sungwook Woo. Lab would be a much more boring place without your presence. I give special thanks to Karolyn Knoll, our administrative assistant, for making day-to- day life about a hundred times easier. Thank you Karolyn, for your help ordering reagents and fixing machines and scheduling travel and so on, and thank you for the cookies. Siping Han, Robert Barish, and Xiaoyan Robert Bao have been three of my best friends during my time here at Caltech, and I thank them for providing not only amusing personal stories, but also intelligent minds that I could bounce ideas off. I am confident that they will become great scientists, and look forward to talking to and working with them in the future. I thank Niles Pierce, Richard Murray, Zhen-Gang Wang, Scott Fraser, Joel Burdick, and Shuki Bruck, the members of my thesis committee, for their guidance. At the time, I wasn’t so happy that they assigned me three whole textbooks to read (and to be honest, I only finished one of them), but in retrospect, I agree that this was important for my development as a scientist. I am very grateful to the Fannie and John Hertz Foundation, not only for providing me with a nice stipend, but more importantly for providing me with a community of peers who are as excited by science and technology as I am. No other organization I belong to or know of has a stronger sense of unity, and I am proud to be a Hertz Fellow. My father, mother, and little sister Wendy deserve special thanks for putting up with me as long as they have. I am terrible at keeping in touch at a distance, and it is only through their tireless effort that I still feel that I have a family. Finally, I would like to thank my fiancee Sherry Xi Chen, who has made me a much happier man in the three years since we met. iv Abstract Nucleic acids, the “NA” in DNA and RNA, have long been known to be vitally important molecules within biological cells and organisms. However, they are interesting for more than just their known roles in biology: their predictable Watson-Crick base pairing properties allow nucleic acids to be powerful nanoscale engineering tools. Additionally, nucleic acid- based devices are particularly attractive as biotechnological tools, because nucleic acids naturally exist within all life, and thus nucleic acid devices more easily function in cellular environments. It is for these reasons that nucleic acids have emerged as a frequent star in recent synthetic biology, biotechnology, and nanotechnology research papers. This thesis is a collection of 6 experimental papers, 3 theoretical papers, and 1 review paper that demonstrate and characterize novel nucleic acid-based devices such as catalysts, logic gates, and allosteric switches. Particular effort was placed in ensuring that all the designs are generalizable in sequence and that all the devices are modular in nature; this allows many different components to be integrated into higher-complexity devices. The works presented in this thesis were designed using only non-covalent changes to nucleic acid complexes and structures via Watson-Crick base pairing–i.e. hybridization, branch migration, and dissociation. These three primitives are sufficient to construct an endless variety of circuits and devices, much like how resistors, capacitors, and inductors al- low complex electrical circuits. One advantage of devices, reactions, and circuits engineered using only Watson-Crick interactions is their robustness to their environmental conditions. While enzymatic reactions require specific temperatures, salt conditions, and co-factors, nucleic acid hybridization works reliably in a variety of different solutions. These works are not meant to be final, optimized designs for devices, but rather demon- strations of the wide range of possibilities afforded by nucleic acid engineering and of prob- lems that can be practically solved with dynamic nucleic acid devices in the near future. v Contents Acknowledgements iii Abstract v 1. DNA as an Engineering Material 1 2. A Survey of the Field 14 3. Kinetics of Strand Displacement Reactions 42 4. Amplification and Transduction of DNA Signals 95 5. Robustness and Specificity of the DNA Catalyst 132 6. Allosteric Control 166 7. Digital Nucleic Acid Concentration Sensor 181 8. Characterizing Cooperative Hybridization 203 9. Fixed Gain and Linear Classification 227 10. Towards Self Replication 243 A1. Domain-based Sequence Design of DNA 263 vi Chapter 1: DNA as an Engineering Material Author’s Note: This chapter is a semi-technical introduction to DNA for the general reader. For the technical reader, a review of the field is presented in Chapter 2. For better or for worse, DNA biology and technology possess more lay recognition than most other sciences. Humanity’s ancient and general fascination with the heredity of traits almost guaranteed that genetics would blossom as a center-stage scientific discipline even before the structure of DNA was fully unraveled. In recent times, DNA has been popularized by films such as Jurassic Park, and nowadays most public high school curricula teach of DNA being the “master molecule of the cell.” Given the scope and promise of DNA biotechnology, it should come as no surprise that technical improvements are improving at a rate as fast as or faster than improvements in the other great technology of our lifetime–silicon transistors. In a rough equivalent of Moore’s Law, the prices of DNA synthesis and sequencing are dropping exponentially in time (Fig. 1-1). What does come as a surprise to most who hear about my research for the first time, is the fact that I and others in my field are using DNA quite differently than the way it is used in biology. Geneticists and microbiologists primarily use synthetic DNA as a method of granting a cell the blueprints for constructing a protein that the cell would otherwise not have, using the cellular machinery for transcription and translation to process the introduced DNA. We biomolecular engineers instead use DNA as a basic programmable 1 FIG. 1-1: Carlson’s Law. The price of DNA oligonucleotide and gene synthesis has been dropping exponentially over the past 20 years. Image by Robert Carlson, http://www.synthesis.cc/2008/11/gene- synthesis-cost-update.html. building block, with which we can build all sorts of useful and complex devices at the nanoscale, independent of the cell’s mechanisms. The use of naturally existing objects in ways different than their natural use is hardly a new concept; this idea dates back as far as the Stone Age, when humans used the bones of dead animals for axes and other tools.