Scalable and cost-efficient custom gene library assembly from oligopools
- 1Department of Biochemistry, University of Wisconsin–Madison, Madison, WI, USA
- 2Microsoft Research, Cambridge, MA, USA
- 3Department of Biomedical Engineering, Duke University, Durham, NC, USA
Abstract
Advances in metagenomics, deep learning, and generative protein design have enabled broad in silico exploration of sequence space, but experimental characterization is still constrained by the cost and scalability of DNA synthesis. Here, we present OMEGA (Oligo-based Multiplexed Efficient Gene Assembly), a low-cost, accessible method for assembling hundreds to thousands of full-length genes in parallel using standard laboratory techniques. OMEGA computationally fragments target genes into short, high-fidelity Golden Gate-compatible oligonucleotides that can be ordered as a pooled library and assembled across multiplexed subpools. We systematically optimized the number of fragments per gene and orthogonal ligation sites per reaction and determine that OMEGA can assemble up to 2.6-kilobase constructs using as many as 70 Golden Gate sites. To validate the approach, we assembled and functionally screened a library of 810 natural and synthetic green fluorescent protein variants, recovering 94 to 97% of target sequences with high uniformity. OMEGA enables precision library construction at scale, with per-gene costs as low as $1.50, and offers a broadly applicable solution for bridging computational protein design with high-throughput experimental validation. We have developed OMEGA as an open-source software package and an easy-to-use Colab notebook to facilitate community adaptation.
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BibTeX
@article{freschlin2026scalable,
title = {{Scalable and cost-efficient custom gene library assembly from oligopools}},
author = {Chase R. Freschlin and Kevin K. Yang and Philip A. Romero},
journal = {Science Advances},
year = {2026},
month = may,
doi = {10.1126/sciadv.ady2279},
url = {https://doi.org/10.1126/sciadv.ady2279},
note = {CC BY},
}
RIS
TY - JOUR
TI - Scalable and cost-efficient custom gene library assembly from oligopools
AU - Chase R. Freschlin
AU - Kevin K. Yang
AU - Philip A. Romero
PY - 2026
DA - 2026/05/22
JO - Science Advances
DO - 10.1126/sciadv.ady2279
UR - https://doi.org/10.1126/sciadv.ady2279
AB - Advances in metagenomics, deep learning, and generative protein design have enabled broad in silico exploration of sequence space, but experimental characterization is still constrained by the cost and scalability of DNA synthesis. Here, we present OMEGA (Oligo-based Multiplexed Efficient Gene Assembly), a low-cost, accessible method for assembling hundreds to thousands of full-length genes in parallel using standard laboratory techniques. OMEGA computationally fragments target genes into short, high-fidelity Golden Gate-compatible oligonucleotides that can be ordered as a pooled library and assembled across multiplexed subpools. We systematically optimized the number of fragments per gene and orthogonal ligation sites per reaction and determine that OMEGA can assemble up to 2.6-kilobase constructs using as many as 70 Golden Gate sites. To validate the approach, we assembled and functionally screened a library of 810 natural and synthetic green fluorescent protein variants, recovering 94 to 97% of target sequences with high uniformity. OMEGA enables precision library construction at scale, with per-gene costs as low as $1.50, and offers a broadly applicable solution for bridging computational protein design with high-throughput experimental validation. We have developed OMEGA as an open-source software package and an easy-to-use Colab notebook to facilitate community adaptation.
SN - 2375-2548
ER -