New Biological Pathways

Through synthetic biology, our species is now learning to give biology instructions by using microscopic – often designed – biological components, allowing biology to conduct highly specialized forms of work previously unseen in nature. In this thesis, I propose and develop three new biological pathways which can perform three different categories of work i) information retrieval ii) information storage and iii) information editing. For information retrieval, I propose repurposing viral capsid proteins to perform non-destructive transcriptomic measurements. We demonstrate that this approach allows for live-cell transcriptomics, and we longitudinally measure the transcriptional responses of the same living human cells after stimulation with TNFa. For information storage, I propose and develop trans-splicing as a strategy to barcode the introduction of genetic elements en masse, and show that cell transcriptomes can be reliably barcoded for facile information storage. For information editing, I propose and develop a new RNA splicing machine – the splice editor – which can edit long stretches of mRNA sequences. I demonstrate that this CRISPR/Cas13 guided editor can perform exon replacement, which may one day lead to a new class of therapeutics. Altogether, this thesis showcases three new biological pathways, and demonstrates that living biological systems can be instructed to perform various kinds of complex, biological work.

Name thesis:degree_name

Doctoral

Department dc:contributor.department

Massachusetts Institute of Technology. Department of Biological Engineering

Grantor dc:publisher

Massachusetts Institute of Technology

Year dc:date.issued

2022

Author dc:creator

• Borrajo, Jacob

Advisor dc:contributor.advisor

• Blainey, Paul

Statement dc:rights

• In Copyright - Educational Use Permitted
• Copyright MIT

Licence dc:rights.uri

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

Handle dc:identifier.uri

https://hdl.handle.net/1721.1/152489

OAI identifier oai:identifier

oai:dspace.mit.edu:1721.1/152489