Rapid and efficient generation of sequence variants by templated synthesis

NIH Pandemic-Era Grants

Pandemic Era Grants

2023

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Principal Investigator: Harris H Wang
Organization: COLUMBIA UNIVERSITY HEALTH SCIENCES
Fiscal Year: 2023
Award: $452,375
Funding agency: National Human Genome Research Institute

PROJECT SUMMARY
The ability to synthesize gene- and pathway-sized DNA is a key tool in functional genomics. Many applications
of gene synthesis call for the generation and testing of sequence variants containing multi-site mutations. Unfor-
tunately, current approach to produce such constructs still rely on de novo synthesis, which remains slow, costly,
and ill-matched for variant generation. Here, we propose to advance the concept of template-guided gene syn-
thesis as a novel strategy to build kilobase-sized DNA constructs using an existing sequence as a template. Our
first Aim will be to advance this template-guided synthesis and mutagenesis approach by developing predictive
oligo design algorithms, optimizing experimental protocols, and implementing robotic automation. Our second
Aim will focus on extending the method to >1,000 constructs at a time with bead-based oligo capture techniques
and parallel variant assemblies in picoliter emulsion droplets. We will evaluate the performance of our platform
in an example use case through the generation of phosphomimetic variants to map cell signaling. We expect
that our template-guided synthesis platform will be able to produce multi-site sequence variants that are >5 kb
in length in a high-throughput and automated fashion. Furthermore, this approach will be up to 10-20 times
cheaper and 5-10 time faster than current de novo gene synthesis methods.

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