GeneOptimizer® Process for Multi-parameter Gene Optimization

The power of custom gene synthesis is the ability to design your DNA without the constraints of traditional cloning. Equally important to most researchers, however, is obtaining high yield of mRNA and ultimately protein from synthetic genes. We developed GeneOptimizer® software to maximize expression of synthetic genes in all commonly used expression systems.
It is a proprietary software loaded with a sophisticated algorithm that considers all relevant transcription and translation optimization parameters in a single operation and delivers a DNA sequence configured with your specifications, optimized for maximum performance in your system (Figure 1). Years of research have gone into the algorithms that drive GeneOptimizer® software, and we continue to update its features based on new developments in biological research.

Publication Download

A recently published study about mammalian gene expression, proves the reliability of the GeneOptimizer® approach. Key highlights of the study:     

  • 86% of optimized genes showed higher expression than the corresponding wildtype
  • 100% of optimized genes showed expression, 12% of wildtype genes did not
  • Protein expressed from optimized genes was soluble and showed full functional activity


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Sequence optimization using the GeneOptimizer® software process is included as an optional step with all GeneArt® Gene Synthesis services. To take advantage, select your expression host when setting up a request using our online customer portal. The online software will then guide you through the project setup process, including online sequence optimization. Alternatively, you can request GeneOptimizer® sequence analysis using the same online customer portal.



Figure 1 - The GeneOptimizer® Software tool optimizes sequences for maximum transcription/translation.

How It works

Using our online customer portal, design your synthetic gene by uploading your sequence, selecting your expression system, and specifying your cloning vector and sequence details, such as start/stop codons, 3’/5’ untranslated regions, and inclusion/exclusion of restriction enzymes sites and immunomodulatory CpG motifs. Once you submit your request, GeneOptimizer® software generates as many as 500,000 optimized variants of your target sequence in an evolutionary approach that addresses the most important sequence parameters in parallel. It then selects one optimized DNA sequence that best suits your research requirements.


GeneOptimizer® sequence processing includes the following:
 

  • Identification of the best way to incorporate your requested sequence elements
  • Elimination of cryptic splice sites and RNA destabilizing sequence elements for increased RNA stability
  • Addition of RNA stabilizing sequence elements
  • Codon optimization and G/C content adaptation for your expression system
  • Intron removal
  • Avoidance of stable RNA secondary structures

Results in Up to a 100-Fold Increase in Expression

The GeneOptimizer® process has been shown to help deliver massive increases in protein yield; due to a combination of factors that, together, stabilize mRNA and maximize translational efficacy (Figure 2). Some customers have reported up to a 100-fold increase in expression yields compared to unoptimized gene sequence.
Figure 2 - Sequence optimization using the GeneArt® GeneOptimizer® process significantly increases expression. Reference: Graf M. et al (2000), J Virol 2000 Nov; 74(22): 10822–10826