Genomically encoded logic gates and cell-cell communication devices for the implementation of a cryptographic hashing algorithm in living cells

Cell-cell communicaon can be harnessed to distribute tasks across different cells. Applied to biocomputaon, communicaon enables cell populaons to carry out operaons too complex to be performed in a single cell. Doing so in a predictable manner requires well characterized genec parts that can signal between cells and process those signals. In this work, we develop a set of 12 logic gates encoded on the E. coli genome based on phage repressors with superior characteriscs to previous sets of transcriponal logic gates. We addionally develop a set of four cell-cell communicaon devices compable with the newly designed logic gates. To engineer large circuits, we introduce a method to paron a large genec circuit across different cells while considering the size of the circuit that can be placed in a single cell and communicaon between cells. Together, these tools were used to implement a recoded version of the MD5 hashing funcon, a historically widely used cryptography algorithm. The circuit requires 110 logic gates paroned across 65 E. coli strains, requiring a total of 0.66 Mb of recombinant DNA introduced onto their genomes with the most complex strain carrying a total of 40 recombinant genes. For each unique strain we constructed, we experimentally verified the strains can sense the appropriate input signals and compute the correct logic funcon, as indicated by a fluorescent output. To validate each cell communicates the correct signal to the next cell, we use reporter cells to measure the signal from the sender and show the reporter cells respond correctly. This work demonstrates the behavioral complexity that can be achieved with synthec cellular populaons.

Name thesis:degree_name

Doctoral

Department dc:contributor.department

Massachusetts Institute of Technology. Microbiology Graduate Program

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2023

Author dc:creator

• Padmakumar, Jai Phiroze

Advisor dc:contributor.advisor

• Voigt, Christopher A.

Statement dc:rights

• In Copyright - Educational Use Permitted
• Copyright retained by author(s)

Licence dc:rights.uri

• https://rightsstatements.org/page/InC-EDU/1.0/

Handle dc:identifier.uri

https://hdl.handle.net/1721.1/152844

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/152844