Zachary Z. Sun

Learn More
Ideal cell-free expression systems can theoretically emulate an in vivo cellular environment in a controlled in vitro platform. This is useful for expressing proteins and genetic circuits in a controlled manner as well as for providing a prototyping environment for synthetic biology. To achieve the latter goal, cell-free expression systems that preserve(More)
Accelerating the pace of synthetic biology experiments requires new approaches for rapid prototyping of circuits from individual DNA regulatory elements. However, current testing standards require days to weeks due to cloning and in vivo transformation. In this work, we first characterized methods to protect linear DNA strands from exonuclease degradation(More)
A central goal of synthetic biology is to engineer cellular behavior by engineering synthetic gene networks for a variety of biotechnology and medical applications. The process of engineering gene networks often involves an iterative 'design-build-test' cycle, whereby the parts and connections that make up the network are built, characterized and varied(More)
RNA regulators are emerging as powerful tools to engineer synthetic genetic networks or rewire existing ones. A potential strength of RNA networks is that they may be able to propagate signals on time scales that are set by the fast degradation rates of RNAs. However, a current bottleneck to verifying this potential is the slow design-build-test cycle of(More)
While complex dynamic biological networks control gene expression in all living organisms, the forward engineering of comparable synthetic networks remains challenging. The current paradigm of characterizing synthetic networks in cells results in lengthy design-build-test cycles, minimal data collection, and poor quantitative characterization. Cell-free(More)
NOTE: This is a technical report for future inclusion in work pending submission, review, and publication. Therefore, this work has not been peer-reviewed and is presented as-is.. CC-BY-NC-ND 4.0 International license peer-reviewed) is the author/funder. It is made available under a The copyright holder for this preprint (which was not .
One of the fundamental challenges in implementing complex biocircuits is understanding how the spatial arrangement of biological parts impacts biocircuit behavior. We develop a set of synthetic biology parts for systematically probing the effects of spatial arrangement on levels of transcription. Our initial experimental assays prove that even the(More)
Acknowledgements This thesis would not exist without the help and support of many people. First of all, I would like to thank Prof. Sebastian Maerkl for being a great advisor during the past 5 years, for always coming up with helpful ideas when I needed them and good discussions. I would also like to thank my PhD committee for evaluating my work: Prof. I am(More)
  • 1