Engineering genetic codes to control the evolution of so-encoded biological systems
Abstract/Contents
- Abstract
- All life on Earth reads DNA into proteins using the same genetic code or a close variant. But what if it didn't? Here, I introduce a theory of genetic codes and their effect on the evolution of so-encoded genetic systems. I propose a class of genetic codes that penalize mutations by introducing "null codons" that cannot be readily translated and cause the ribosome to stall. I show that these "fail-safe" codes, in theory, slow the evolution of so-encoded organisms. They are "intrinsically" biocontained, being outcompeted by native species upon release or escape. I show experimentally that we can build decoders capable of reading differently-encoded DNA using defined in vitro translation systems with code-specific synthetic tRNAs. Finally, I learned design principles for encoding DNA in different genetic codes by recoding the φX174 bacteriophage genome. I propose concrete steps to further advance fail-safe code engineering, specifically to routinize the building of defined synthetic biological systems up to whole living cells.
Description
| Type of resource | text |
|---|---|
| Form | electronic resource; remote; computer; online resource |
| Extent | 1 online resource. |
| Place | California |
| Place | [Stanford, California] |
| Publisher | [Stanford University] |
| Copyright date | 2023; ©2023 |
| Publication date | 2023; 2023 |
| Issuance | monographic |
| Language | English |
Creators/Contributors
| Author | Calles, Jonathan Elias |
|---|---|
| Degree supervisor | Endy, Andrew D |
| Thesis advisor | Endy, Andrew D |
| Thesis advisor | Brophy, Jennifer |
| Thesis advisor | Covert, Markus |
| Degree committee member | Brophy, Jennifer |
| Degree committee member | Covert, Markus |
| Associated with | Stanford University, School of Engineering |
| Associated with | Stanford University, Department of Bioengineering |
Subjects
| Genre | Theses |
|---|---|
| Genre | Text |
Bibliographic information
| Statement of responsibility | Jonathan Elias Calles. |
|---|---|
| Note | Submitted to the Department of Bioengineering. |
| Thesis | Thesis Ph.D. Stanford University 2023. |
| Location | https://purl.stanford.edu/gk649bs9723 |
Access conditions
- Copyright
- © 2023 by Jonathan Elias Calles
- License
- This work is licensed under a Creative Commons Attribution 3.0 Unported license (CC BY).
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