Nayan
Sapers
Closed Loop Automation For Engineering Orthogonal Translation Systems
Abstract profile. Full document pending author claim.
Authors:
Nayan Sapers, Felix Radford, George Church
Date Created:
2025-01-01
Course Title:
Professor:
Not specified
About Paper:
Orthogonal translation systems (OTSs) enable incorporation of Current progress demonstrates successful automation of RNA nonstandard amino acids (nsAAs) into proteins, expanding their production and purification with yields comparable to manual functional capabilities. Traditional OTS development relies on directed evolution with limited throughput, constraining methods. The DNA assembly pipeline combines PCR amplification, magnetic bead purification, and Gibson Assembly exploration of design space. This project develops closed-loop to construct chimeric synthetase libraries. This automation automationtoengineerchimericaminoacyl-tRNAsynthetaseswith enables construction of thousands of variants weekly, compared to unprecedented orthogonality and efficiency. approximately 100 manually. Theapproachintegratesthreeaims: completeautomationoftRNA- Future work integrates ESM-3 and AlphaFold3 for computational SCAN on Opentrons Flex, automated DNA library assembly, design of linker sequences and binding domains. The closed- and AI-guided design of novel OTSs. tRNA-SCAN is a proceduredevelopedinlabthatenablesmassivelyparallelprofiling loopoptimizationstrategycombineshigh-throughputexperimental characterization with machine learning to iteratively improve of aminoacylation specificity by converting tRNA charging designs. This integrated approach promises to overcome current states into sequenceable outputs through enzymatic modificationslimitations in OTS development, enabling reliable multi-site nsAA The automated workflow encompasses periodate oxidation, incorporation for advanced biotechnology applications. dephosphorylation, adapter ligations, reverse transcription, and library preparation.
Abstract:
Orthogonal translation systems (OTSs) enable incorporation of Current progress demonstrates successful automation of RNA nonstandard amino acids (nsAAs) into proteins, expanding their production and purification with yields comparable to manual functional capabilities. Traditional OTS development relies on directed evolution with limited throughput, constraining methods. The DNA assembly pipeline combines PCR amplification, magnetic bead purification, and Gibson Assembly exploration of design space. This project develops closed-loop to construct chimeric synthetase libraries. This automation automationtoengineerchimericaminoacyl-tRNAsynthetaseswith enables construction of thousands of variants weekly, compared to unprecedented orthogonality and efficiency. approximately 100 manually. Theapproachintegratesthreeaims: completeautomationoftRNA- Future work integrates ESM-3 and AlphaFold3 for computational SCAN on Opentrons Flex, automated DNA library assembly, design of linker sequences and binding domains. The closed- and AI-guided design of novel OTSs. tRNA-SCAN is a proceduredevelopedinlabthatenablesmassivelyparallelprofiling loopoptimizationstrategycombineshigh-throughputexperimental characterization with machine learning to iteratively improve of aminoacylation specificity by converting tRNA charging designs. This integrated approach promises to overcome current states into sequenceable outputs through enzymatic modificationslimitations in OTS development, enabling reliable multi-site nsAA The automated workflow encompasses periodate oxidation, incorporation for advanced biotechnology applications. dephosphorylation, adapter ligations, reverse transcription, and library preparation.
Source:
Harvard / Mia Russ, Tim Hammersen, April Craft / 2025
Topics:
design, closed, automation, assembly, library, orthogonal, translation, system, otss, enable, incorporation, current
