An AI-native experimental laboratory for autonomous biomolecular engineering
1.Researchers introduce AutoDNA, an AI-native autonomous laboratory that performs complex biomolecular experiments—such as DNA synthesis and sequencing—entirely without human intervention, achieving performance comparable to expert scientists.
2.Unlike prior systems that rely on predefined heuristics and workflows, AutoDNA uses a multi-agent architecture co-designed with instruments and models, enabling closed-loop experimentation via continuous “design-experiment-optimize” cycles.
3.AutoDNA supports diverse nucleic acid functions including synthesis, transcription, amplification, and sequencing. It powers applications like diagnostics, drug development, and DNA data storage, serving even non-expert users through natural language commands.
4.The system features intelligent agents with specialized roles: experiment planning, hypothesis generation, literature mining, reagent management, hardware abstraction, and real-time execution. Agents collaborate autonomously, guided by LLM-based reasoning.
5.The Program Developer Agent converts technical specs of lab instruments into AI-native “atomic services”—Python objects described in natural language—bridging AI models with physical hardware in an interpretable way.
6.In an end-to-end nucleic acid test, AutoDNA autonomously designed and executed an RPA-based assay. It generated, corrected, and ran all control code, matching the accuracy and diagnostic output of human-executed protocols.
7.For enzymatic DNA synthesis, AutoDNA autonomously explored a multi-objective optimization space (yield, time, reagents) across 5 iterations. It selected buffers, added surfactants, and tuned reaction conditions, reaching a stepwise yield of 97.7%.
8.The system handled over 9,300 individual hardware steps with no human input. Sequencing validated synthesis quality, showing error rates consistent with expert-controlled experiments. Main errors were deletions, likely from bead aggregation.
9.AutoDNA supports concurrent execution of multiple experiments. It dynamically monitors hardware status and reroutes tasks across equivalent instruments to avoid conflicts—tripling throughput and significantly improving instrument utilization.
10.In a multi-user scenario, AutoDNA autonomously resolved resource contention by rerouting a thermal incubation step to an alternative instrument (thermocycler), reducing total experiment time by 169 minutes compared to queue-based scheduling.
11.AutoDNA also supports a full DNA data storage pipeline: encoding data into DNA, synthesizing strands, sequencing them back, and decoding. It completed an end-to-end read-write cycle with 78 strands in 162.9 hours and perfect data recovery.
12.This work showcases the first fully AI-native lab for autonomous, multi-objective, and multi-user biomolecular engineering, marking a shift from AI-assistive to AI-native scientific research platforms.
📜Paper:
arxiv.org/abs/2507.02379
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