This guide walks you through using AutoNA for mRNA optimization. Follow the step-by-step workflow to design sequences with improved translation efficiency, cellular stability, and protein output. If you need additional help, contact our support team at founders@atombioworks.com.
Getting Started with AutoNA
Start with your CDS
Provide a coding sequence (start codon → stop codon) that you want to optimize.
Set objectives
Choose optimization targets and constraints (tiers may limit objective count).
Generate
AutoNA proposes design candidates and scores them with interpretable plots.
Compare & export
Review summaries, benchmarks, and sequence files for downstream experiments.
Detailed Instructions
Step 1: Prepare Your Coding Sequence
Before starting, make sure your coding sequence (CDS) meets these requirements:
- Must begin with a start codon (ATG)
- Must end with a stop codon (TAA, TAG, or TGA)
- Length must be divisible by 3 (complete codons)
- Maximum length: 2,000 nucleotides (recommended: ≤1,500 nt)
Step 2: Configure Optimization Objectives
Depending on your user tier, you can select from these optimization strategies:
- Translation Efficiency: Optimize ribosome binding and translation initiation
- Half-life: Maximize cellular stability of the mRNA
- Protein Abundance: Optimize for maximum protein output
Step 3: Generate Optimized Sequences
After setting your parameters:
- Click "Generate Sequences"
- AutoNA will process your request using the mRNAutilus engine
- Wait for the job to complete (processing time depends on sequence length)
Step 4: Analyze and Export Results
Once your job is complete:
- Review the performance plots for each optimized sequence
- Compare against baseline references
- Export sequences in your preferred format for downstream applications
- Share results with collaborators if needed