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Compartmentalization of DNA-Based Molecular Computing Elements Using Lipid Bilayers Aurora Fabry-Wood University of New Mexico

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Compartmentalization of DNA-Based Molecular Computing Elements Using Lipid Bilayers Aurora Fabry-Wood University of New Mexico University of New Mexico UNM Digital Repository Biomedical Engineering ETDs Engineering ETDs Summer 7-2018 Compartmentalization of DNA-Based Molecular Computing Elements Using Lipid Bilayers Aurora Fabry-Wood University of New Mexico Follow this and additional works at: https://digitalrepository.unm.edu/bme_etds Part of the Biomedical Engineering and Bioengineering Commons, and the Diagnosis Commons Recommended Citation Fabry-Wood, Aurora. "Compartmentalization of DNA-Based Molecular Computing Elements Using Lipid Bilayers." (2018). https://digitalrepository.unm.edu/bme_etds/20 This Dissertation is brought to you for free and open access by the Engineering ETDs at UNM Digital Repository. It has been accepted for inclusion in Biomedical Engineering ETDs by an authorized administrator of UNM Digital Repository. For more information, please contact [email protected]. Aurora Fabry-Wood Candidate Biomedical Engineering Department This dissertation is approved, and it is acceptable in quality and form for publication: Approved by the Dissertation Committee: Steven W. Graves, PhD, Chairperson Darko Stefanovic, PhD Matthew R. Lakin, PhD Nick J. Carroll, PhD Menake Piyasena, PhD Compartmentalization of DNA-Based Molecular Computing Elements Using Lipid Bilayers By Aurora Fabry-Wood BS, Biology, University of Arizona, 2004 MS, Biomedical Engineering, University of New Mexico, 2015 DISSERTATION Submitted in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Engineering The University of New Mexico Albuquerque, New Mexico July 2018 ii ACKNOWLEDGEMENTS I would first like to thank my committee for their support and the knowledge they shared along the way. Professor Steven W. Graves, who served as chairman of the committee, was always there to remind me of my ultimate goal. He managed me like a champion and I will forever appreciate that. My co-advisor Professor Darko Stefanovic continuously expected excellence, which drove me to succeed. His requests for big picture objectives helped me to keep a broader audience in mind. Professor Matthew R. Lakin working with you has improved my technical writing skills, by orders of magnitude. “The United States and Great Britain are two countries separated by a common language,” said George Bernard Shaw. Thank you, Matt, for imparting some of your British eloquence on this American chick. Professor Nick J. Carroll I greatly appreciate your presence in the lab, I hope you never forget the value of that. Also, you always recognize my various skills in the lab – thank you so much for that. Finally, thank you Professor Menake Piyasena, of New Mexico Tech, for your valuable research. Silica microspheres would not have been a part of my dissertation without your publications on the topic. I consider myself very lucky to have had such an exceptional group of mentors. Professor Milan Stojanovic, Dr. Stevan Pecic and Dr. Kyung-Ae (Kasi) Yang at Columbia University also contributed significantly to this work. Prof. Stojanovic provided continuous advice and was always a pleasure to work. Dr. Pecic synthesized the OPV compound described in Chapter 6 and provided very useful feedback regarding the click chemistry. Dr. Yang advised on the aptamers presented in Chapter 7. iii Additionally, there were a number of professors that did not serve on my committee, but whose support deserves acknowledgement. Professor Andrew P. Shreve whose dedication as an instructor and overall knowledge base is very inspiring. Professor Eva Chi for being such an intelligent and composed mentor. Professor David G. Whitten for his wealth of experience and publishing expertise. I had the privilege of working with a number of exceptional undergraduates and I would like to take a moment to appreciate their dedication and hard work. Nick A. Baker, who worked with our group for 2 years, you made my first couple of years as a undergrad mentor super fun. Madalyn E. Fetrow, who has been with the lab for the last 3 years, we are lucky to have you. Ayomide Oloyede, who has been with the group for the last year, you are a joy to work with. I would also like to acknowledge the amazing group of graduate students who were with me along the way. Thank you, Katie Schroeder (not technically a grad student but with us along the way), Heather Mendez, Jennifer Fetzer and Dr. Nadiezda Fernandez-Oropeza for being such amazing ladies and for all the kindness you brought to our group. Thank you, Frank Fencl for being my graduate school twin and for all the laughter you bring. Thank you, Adan Myers y Gutierrez for countless discussions and being such a great travel buddy. Thanks also to Dr. Albert Perry III, Dr. Harry Pappas, Dr. Loreen Stromberg, Dr. Kent Coombs, Dr. Matthew Rush, Adeline Fanni, and Kiersten Lenz for general awesomeness. iv DEDICATION This body of work is dedicated to my parents Larry Wood, Elizabeth Fabry and my Official Step-Pop James Mahoney. My mother whose support and love is unparalleled. My father who diligently taught me the physics of this planet and solar system. And Jim for his endless commitment to his family and to this planet we all call home. To all three of them for brining me up in the Grand Canyon, on the Mogollon Rim, and in the midst of the loving, intelligent and adventurous Homeward Bound community. A community which to this day inspires me and keeps me honest. I would also like to dedicate this to my sisters, brothers and many friends. Sagi your compassion deserves a Nobel Prize and I absolutely respect you. Dawn you are an amazing sister and a better mother, love you big sis’. Kyra I am so lucky to have your enduring friendship. Tevis your curiosity is inspiring. Donovan you have the biggest heart, and sweetest family. Finally, I dedicate this work to the many amazing people who have graced my life. v Compartmentalization of DNA-Based Molecular Computing Elements Using Lipid Bilayers By Aurora Fabry-Wood BS, Biology, University of Arizona, 2004 MS, Biomedical Engineering, University of New Mexico, 2015 PhD, Biomedical Engineering, University of New Mexico, 2018 ABSTRACT This dissertation will present a progression from the detection of double- stranded DNA using a combination of toehold-mediated strand displacement and DNAzyme reactions in dilute saline solutions, to the generation of separate compartments to allow standardization of DNA computing elements, by protecting from complementary strands. In well-mixed solutions complementary regions vi cause spurious interactions. Importantly, these compartments also provide protection from nucleases. Along the way we will also explore the use of silica microsphere supported lipid bilayers to run compartmentalized DNA reactions on a fluid surface and the design of a molecule capable of DNA-based transmembrane signal transduction. vii Table of Contents ACKNOWLEDGEMENTS .................................................................................................. iii DEDICATION .................................................................................................................... v Compartmentalization of DNA-Based Molecular Computing Elements Using Lipid Bilayers .......................................................................................................................... vi By Aurora Fabry-Wood .................................................................................................. vi ABSTRACT ...................................................................................................................... vi Table of Contents ................................................................................................................ viii TABLE OF FIGURES ....................................................................................................... xiii TABLE OF FIGURES (cont.) ............................................................................................ xiv TABLE OF TABLES .......................................................................................................... xv CHAPTER 1 - INTRODUCTION .......................................................................................... 1 1.1 A Need for Improved Arbovirus Diagnostics ..................................................................... 1 1.2 Molecular Scale Computers as a Solution ......................................................................... 4 1.3 Limitations Associated with Solution Phase DNA-Based Molecular Computing Systems . 9 1.4 Spatially Organizing DNA-based Molecular Computing Systems to Address These Limitations ........................................................................................................................... 14 1.5 Present Studies ............................................................................................................... 18 1.6 References ...................................................................................................................... 20 CHAPTER 2 - GOALS AND OVERVIEW OF WORK............................................................ 25 CHAPTER 3 - A UNIFIED SENSOR ARCHITECTURE FOR ISOTHERMAL DETECTION OF DOUBLE-STRANDED DNA, OLIGONUCLEOTIDES, AND SMALL MOLECULES ................... 29 3.1 Abstract .......................................................................................................................... 30 3.2 Introduction, Results, Discussion, Conclusions and Future Directions ............................ 30 3.3 Experimental Section .....................................................................................................
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