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Gene Design

Designing genes de novo liberates scientists from the constraints of naturally occurring nucleotide sequences. However, the enormous number of base pair combinations that all code for the same amino acid sequence can be daunting. On average, each amino acid is represented by three different codons. For a small protein of only 200 amino acids, then, there are around 3200 (or ~2.5*1094) nucleotide sequences to choose from. GenScript's original gene design software (OptimumGeneTM) focuses on the need for codon concentrations that results in high levels of heterologous protein expression. Our proprietary design algorithm balances a host of relevant factors to produce the most effective gene sequence possible. The following is a brief description of GenScript's gene design strategy (OptimumGeneTM).

1. Selecting a codon usage table: The large number of genomic sequences now available has made it possible to derive the codon usage for any organism. GenScript can design genes based on the codon usage tendencies of any requested organism. For proteins that are to be expressed in more than one host, GenScript can create hybrid codon usage tables. Codons below the selected threshold in either host are replaced, and the frequencies for the remaining codons can be calculated using either the frequencies for the most restrictive organism or using the mean value for each codon.

2. Eliminating unfavorable and uneven GC content: The strength of the guanine-cytosine bond can lead to undesirable mRNA secondary structures. The most effective candidate sequences will have more favorable GC content.

3. Avoiding unfavorable mRNA secondary structures: Overly stable mRNA secondary structures, particularly at the 5' end of the transcript, have been implicated in reduced gene expression. The potential of a transcribed mRNA to adopt such a structure can be identified using free energy calculations. Candidate sequences containing significant mRNA secondary structures can then be screened out.

4. Adding or removing restriction sites: The presence or absence of selected restriction sites is often important to facilitate subsequent gene manipulations such as swapping between vectors, exchanging protein domains, and adding or removing peptide tags or fusion partners. Candidate sequences can be tested to ensure the correct placement or elimination of restriction sites.

5. Other constraints: Additional constraints that can be used to filter the gene synthesis solutions include adding or removing polyadenylation signals and other regulatory elements, adding or removing immuno-stimulatory or immuno-suppressive elements (for DNA vaccines), RNA methylation signals, selenocystein incorporation signals and other factors, depending on the biological system used and specific application or concern.

6. Additional features of our gene design (OptimumGeneTM) service:

  • Manipulation of restriction enzyme cutting sites: These sites can be added or removed during the design process to facilitate future manipulation of the construct.
  • Design of fusion proteins: Any epitope tag sequences (e.g, HIS tag and GST tag) or protease cutting site can be incorporated into the designed gene for the expession of a fusion protein. The delivered synthetic gene construct is ready for expression and purification without further manipulation.
  • Creation of gene variants (mutant forms): Multiple variant forms (or variant library) can be designed for functional study and screening.
gene design

Note: You may use our secure web server or to submit sequence for optimization and synthesis. In your message, please include:

  • Protein or ORF DNA sequence.
  • Intended host expression system.
  • Restriction enzyme cutting sites at both ends.
  • Restriction enzyme cutting sites that you want to avoid in the optimized sequence.
  • Restriction enzyme cutting sites that you want to keep in the original sequence.

Reference

  • Frank Gronlund Jorgensen, et al. Heterogeneity in Regional GC Content and Differential Usage of Codons and Amino Acids in GC-Poor and GC-Rich Regions of the Genome of Apis mellifera. Molecular Biology and Evolution. Dec 2006.
  • P Roy, et al. Effect of mRNA secondary structure on the efficiency of translational initiation by eukaryotic ribosomes. European Journal of Biochemistry. 1990; 191(3): 647-652.
  • Svetlana A. Shabalina, et al. A periodic pattern of mRNA secondary structure created by the genetic code. Nucleic Acids Res. 2006; 34: 2428-2437.
  • Satya RV, et al. A pattern matching algorithm for codon optimization and CpG motif-engineering in DNA expression vectors. Proc IEEE Comput Soc Bioinform Conf. 2003; 2: 294-305.
  • Kim CH, et al. Codon optimization for high-level expression of human erythropoietin (EPO) in mammalian cells. Gene. 1997; 199: 293-301.

How to Order Synthetic Genes:

Orders can be placed by phone, , fax or online with a formal PO (Purchase Order) or credit card. Our customer service representatives are available 24 hours Monday through Friday. You may contact us anytime for assistance. For privacy protection, please submit your gene sequences via our secure online ordering system.

Order online Order online: https://www.genscript.com/ssl-bin/order_gene
Order by email Order by email: gene@genscript.com
Order by phone Order by phone: 1-877-436-7274 (Toll-Free) 1-732-885-9188
Order by fax Order by fax: 1-732-210-0262 1-732-885-5878