Custom DNA designs: how to vibe-code full-scale app in the two years
Daniil N. Bratashov1,2; 1Moscow Institute of Physics and Technology, Moscow, Russia; 2Saratov State university, Saratov, Russia
Abstract
Modern synthetic biology allows to design long custom DNA structures up to small genome level. One of the critical requirements for the design of complex structures is development of algorithms to split the long DNA sequence into smaller parts - synthons and oligonucleotides. The algorithm should provide multi-parametric constrained optimization trying to satisfy as possible the biological and synthetic constrains of DNA synthesis and assembly. We have designed the DNA-split program to make the basic construction of complex genetic assemblies, do the DP optimizations of dividing the full DNA into parts and single oligos and providing the full CAD/CAM/automation capabilities for DNA synthesis. The validation of algorithms was done with the tandem fluorescent dyes cassette modelling, optimization and wet lab synthesis in both the manual and automatic modes. The majority of algorithms was developed with the help of LLM codegeneration, code review, agentic workflow up to liquid handlers automatic protocol descriptions.
Speaker
Daniil Bratashov
MIPT, Saratov state university
Russia
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