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DNA2.0 Unlocks The Secrets Of Optimized Gene Design: Company Identifies Codon Choice Design Principles for Optimal Protein Expression
Date:9/14/2009

To achieve high levels of protein expression, many researchers have abandoned cloning in favor of synthetic genes, which can be acquired in a couple of weeks at a reasonable cost. Unlike a natural gene, a synthetic gene can be designed to use any codon to encode each amino acid. This has the potential to be a huge advantage, as most researchers have come to accept that "codon optimization" can affect protein expression. DNA2.0 has produced a set of gene optimization design algorithms that allow the company to reliably offer expression yields up to 50 times greater than competing approaches.

Menlo Park, Calif (PRWEB) September 14, 2009 -- DNA2.0, the leading gene synthesis and protein engineering company, today announced the results of breakthrough research that has enabled the company to identify the design principle by which codons may be chosen to optimize protein expression. DNA2.0's research, which is funded by a grant from the National Science Foundation, has produced a set of design algorithms that allow the company to reliably offer expression yields up to 50 times greater than competing approaches. The paper, "Design Parameters to Control Synthetic Gene Expression in Escherichia coli" appears today in the publication, PLoS ONE (http://dx.plos.org/10.1371/journal.pone.0007002).

To achieve high levels of protein expression, many researchers have abandoned cloning in favor of synthetic genes, which can be acquired in a couple of weeks at a reasonable cost. Unlike a natural gene, a synthetic gene can be designed to use any codon to encode each amino acid. This has the potential to be a huge advantage, as most researchers have come to accept that "codon optimization" can affect protein expression. However, since a protein can be encoded by many alternative nucleic acid sequences, a gene design strategy is required to predict the sequence that will result in optimal expression. For example, a 300 amino acid protein of average amino acid composition could be encoded by more than a googol (10100) different gene sequences.

Several different approaches to optimization--including codon sampling, codon pair optimization and codon frequency matching--have been based primarily on analysis of genomic sequences rather than hypothesis-driven experiments and have proven to be hit-or-miss. However, DNA2.0's research has uncovered the elements in gene design that fundamentally determine the protein expression yields that can be obtained from a DNA sequence. The results are contrary to some of the most widely held assumptions, in particular DNA2.0 has found that the common practice of using the codons that are used most highly in the native genes of an organism can actually reduce expression.

"Our systematic analysis of gene design parameters in this study has allowed us to identify codon usage within a gene as a critical determinant of protein expression levels in E. coli," said Dr. Mark Welch, Director of Gene Design for DNA2.0 and corresponding author for the paper. "We propose a biochemical basis for this, as well as design algorithms to ensure high protein production from synthetic genes. Replication of this methodology has already allowed us to derive design algorithms for several additional expression systems."

Researchers at DNA2.0 synthesized two sets of ~40 genes, one encoding phi29 polymerase, the other a single chain antibody; both are commercially valuable proteins. Expression of the genes was measured in E. coli: levels ranged from undetectable to 30% of cellular protein. Correlation of sequences with expression levels led to the conclusion that protein expression strongly depends on codon choice. Surprisingly, the favored codons were not those most abundant in highly expressed native E. coli genes, rather they were those codons read by tRNAs that are most highly charged during amino acid starvation.

"DNA2.0 has discovered the 'Rosetta stone' for determining the best codon choices, which means that we can design genes for our customers that are guaranteed for high expression yields," said Jeremy Minshull, president of DNA2.0. "The PLoS ONE publication nicely complements the broad and fundamental patents we were recently awarded for this technology; peer review is essential for scientific credibility, and none of our competitors can come close to this."

Together with the recently released pJexpress E. coli expression vectors, DNA2.0's patented gene optimization technology offers the most integrated and efficient path from virtual sequence to expressed protein. While many other gene synthesis companies offshore manufacturing to areas of the world with lax IP protection, all DNA2.0 genes are made at the company's state-of-the-art facility in Menlo Park, thus ensuring the greatest security for patented or confidential sequences. DNA2.0 guarantees researchers high quality synthetic genes, delivered on time, every time.

About DNA2.0:
Founded in 2003, DNA2.0 is the leading synthetic genomics company. It is the fastest provider of synthetic genes, based in the US with a global customer base encompassing academia, government and the pharmaceutical, chemical, agricultural and biotechnology industries. DNA2.0 has provided genes to thousands of customers, for whom it has synthesized many millions of base pairs. DNA2.0 explores novel applications for synthetic genes and is exploiting the synergy between highly efficient gene synthesis process and new protein optimization technologies. The tools and applications brought to market by DNA2.0 are transforming biology into an engineering discipline. The company is privately held and is headquartered in Menlo Park, Calif. For more information, please visit www.DNA20.com.

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