We just preprinted DropSynth-Gold where we replaced PCA with Golden Gate Assembly (GGA) inside emulsion droplets, extending multiplexed gene synthesis to ~3 kb constructs assembled from up to 12 fragments while preserving the scalability of DropSynth. 1/n

Our new Science Advances paper is out! 🎉 The Plesa Lab's first, it builds on DropSynth technology as a proof of concept for large-scale synthetic gene libraries, showcasing a synthetic metagenomics approach to studying antibiotic resistance at scale. 👉 www.science.org/doi/10.1126/...

DropSynth-Gold: Golden Gate Assembly in Emulsions Extends Multiplexed Gene Libraries to Greater Lengths https://www.biorxiv.org/content/10.64898/2026.05.29.728538v1

🎥 My Variant Effects Seminar Series (VESS) talk is now on YouTube! I discuss how DropSynth-based gene synthesis reveals how bacterial DHFR variants evolve antibiotic resistance. Thanks to @varianteffect.bsky.social for the invite!

🔗 www.youtube.com/watch?v=KiA9...

#VESS #VariantEffects #DropSynth

Story time! Introducing the first of several new flavors of DropSynth gene synthesis we have been working on, cooked up by @hkalltheway.bsky.social and Sam Hinton. TLDR: We show multiple gene variants assembled per barcoded droplet and 1 kbp lengths. 1/n www.biorxiv.org/content/10.1...

⏰Abstract deadline for the Cascadia Advanced Genomic Technologies Meeting is April 30!⚠️ We're hoping this will be the first of many, catalyzing collaboration and leveraging our regional strength in advanced genomics technologies! See you there!
de-boer-lab.github.io/CAGT_meeting/

We’d love to hear your comments and feedback! Disclosure: I’m a co-founder and equity holder in @synplexity.bsky.social, which is commercializing DropSynth to empower other researchers to perform similar studies at scale. 13/n

Using β-barrel fluorescent proteins (FPs) as a model, we synthesized a large fraction of the known β-barrel FPs from
@fpbase.org (620 seqs), in two codon versions using DropSynth resulting in two large parental libraries spanning natural diversity. 4/n

Degenerate DropSynth for Simultaneous Assembly of Diverse Gene Libraries and Local Designed Mutants https://www.biorxiv.org/content/10.1101/2023.12.11.569291v1

Many GGA library assembly methods are limited by the number of orthogonal junctions that can coexist in a shared reaction. DropSynth-Gold performs each assembly in its own droplet. Library scale is determined primarily by barcode diversity, not junction diversity. 5/n

We cover a lot more in the preprint but overall we think this is a simple way to hit much larger assembly scales and could generalize to many applications beyond fusion point selection. We're quite excited about what this opens up, stay tuned for more! 12/12 www.biorxiv.org/content/10.1...

Why rebuild the wheel with every variant (wasting oligos and barcodes)? With this in mind we sought to make multiple gene variants in each droplet. With Degenerate DropSynth, it's like using a blueprint for the core and tweaking the design details. 6/n

We kept everything that makes DropSynth scalable: barcoded bead capture, emulsion compartmentalization, and pooled processing, but replaced PCA with Type IIS Golden Gate Assembly inside droplets. 3/n

Traditional DropSynth uses PCA, which becomes increasingly prone to cross-hybridization artifacts, partial assemblies, and amplification bias especially as fragment count increases. 2/n

We identified the selection of the fusion point between sensor and kinase as a major failure point. Although DropSynth could make 1536 genes, this would be quickly saturated by all the sensor and fusion variants we wanted to make. 5/n

Some background first. DropSynth is a low-cost simple method to carry out multiplexed assembly of oligos into 1,536 designed genes. We isolate gene fragments onto barcoded beads and load them into emulsions for PCA assembly. 2/n

Degenerate DropSynth for Simultaneous Assembly of Diverse Gene Libraries and Local Designed Mutants https://www.biorxiv.org/content/10.1101/2023.12.11.569291v1

DropSynth-Gold: Golden Gate Assembly in Emulsions Extends Multiplexed Gene Libraries to Greater Lengths https://www.biorxiv.org/content/10.64898/2026.05.29.728538v1