Open-Synth is an open-source platform for de novo oligonucleotide synthesis using Digital Microfluidics (EWOD) and enzymatic catalysis. A project by Glyxon Biolabs.
Current DNA synthesis is a centralized, logistics-heavy bottleneck that limits innovation in independent labs. Open-Synth addresses this by building a decentralized Enzymatic DNA Synthesis (EDS) platform.
Our Hypothesis: A modified murine Terminal Deoxynucleotidyl Transferase (TdT), coupled with a Car9 silica-binding domain, enables controlled, single-nucleotide addition on a digital microfluidics (EWOD) chip. By manipulating 300µm magnetic beads within the OpenDrop V4.2 system, we aim to produce high-fidelity oligos on-demand, bypassing expensive global logistics.
Open-Synth is built upon the OpenDrop ecosystem developed by Gaudi Labs.
- Core Hardware: OpenDrop V4.2 – An open-source Electrowetting-on-Dielectric (EWOD) controller.
- Frugal Innovation: By leveraging Gaudi Labs' modular design, we empower scientists in the Global South to generate silencing triggers locally, reducing dependence on international shipments.
Our platform utilizes a recombinant version of murine TdT, expressed in E. coli with a 6xHis-Car9 dual-tag.
- Car9 (Silica Binding Domain): Facilitates high-affinity attachment of the purified protein to silica-coated magnetic nanobeads.
- Programmatic Synthesis: The Mag-nano + TdT complex is integrated into the EWOD system, exposed to sequential baths of activation and inhibition buffers for programmatic serial reaction.
- Sustainability: Magnetic beads and enzymes are designed for high recovery and multi-cycle reusability.
Figure 1: Digital Microfluidic (EWOD) cartridge architecture optimized for reagent transport.
Figure 2: Close-up of the Open-Synth interface based on the Gaudi Labs OpenDrop platform.
Figure 3: Structural model of the recombinant TdT-Car9 fusion protein and vector map.
Success is defined by the synthesis of functional 20-40mer DNA oligonucleotides, validated as templates for in vitro transcription or PCR-generated dsDNA probes.
- Ultimate Metric: The successful induction of known phenotypes in C. elegans (e.g., unc-22 or gfp silencing) using Open-Synth generated probes.
- Next Steps: Automating the synthesis of RNAi libraries for real-time functional genomics.
Open-Synth is a catalyst for a decentralized network of researchers. We aim to:
- Share Protocols: Open-access workflows for TdT purification and EWOD synthesis cycles.
- Open Resources: Collaborative development of digital microfluidic "scripts" for the OpenDrop platform.
- Community-Led Bio: Empowering the Global South to iterate biological designs outside traditional institutional silos.
- Palluk et al. (2018): De novo DNA synthesis using TdT-dNTP conjugates. Nature Biotech.
- Houchaimi (2024): Automated DNA assembly on digital microfluidic devices. RIT Thesis.
- Ashley et al. (2023): TdT applications in biotechnology and DNA nanotechnology. PubMed.
- U.S. Patent 11,851,651: Scalable methods for biopolymer synthesis using EWOD systems.
This project is executed by a high-level technical team with international research experience:
- David J. Castillo, PhD (Project Lead): Founder of Glyxon Biolabs. Specialist in molecular biophysics and frugal science hardware.
- Contact: glyxonbiolabs@gmail.com
- Carlos Barba-Ostria, PhD (Biosynthesis): Expert in protein engineering and enzymatic systems (USFQ).
- Contact: cbarba@usfq.edu.ec
- Biological Validation: Strategic collaboration with Dr. Rosa Navarro’s Lab (IFC-UNAM), providing access to specialized C. elegans and microinjection facilities.
- Contact: rnavarro@ifc.unam.mx
For technical inquiries, community partnerships, or to join the Digital Biology network, please open an Issue in this repository or contact Glyxon Biolabs at: glyxonbiolabs@gmail.com | www.glyxon.com
Empowering Decentralized Science through Open Infrastructure.