Gene Construction

• Genes
• Gene Variant Sets
• Gene Libraries

Genes
As a first step, CODA recommends the creation of a Hot Rod Gene in which translational pause sites and secondary structure are removed, codon usage is modified, and specific restriction enzyme sites are added (or avoided) without altering the amino acid sequence. Adjusting these, and other unspecified parameters, can yield high levels of protein in a heterologous expression system. (See the Discovery Section for additional details.) CODA’s Hot Rod gene design methodology, utilizing proprietary bioinformatics capabilities, produces a very stable, well behaved construct that can serve as a framework for further modifications as needed.

In addition to removal of translational pause sites, the Hot Rod Gene is simultaneously modified to optimize codon usage, remove secondary structure, avoid (or create) specific restriction enzyme sites, along with numerous additional specifications, all without altering the amino acid sequence.

The SpeedPlot analysis (A) represent an over represented codon pair across an open reading frame with codon pairs having high “Z-score” values.  CODA uses Translation Engineering to reengineer the gene without altering the amino acid sequence creating a “pauseless” Hot Rod gene (B).

 

Gene Variant Sets CODA can create sets of single or multiple variants.  CODA’s proprietary technology and design allows for a cleaner and faster way to introduce mutations or deletions to the baseline Hot Rod gene.  This method presents an economical approach to obtain sets of specific gene variants.

Gene Libraries
CODA utilizes its state of the art 64-node cluster to aid with custom design.  This super computer creates genes that are “self-assembling”. A self-assembling gene allows for easy and efficient design and creation of the focused library.  CODA is able to generate libraries quickly and with high library coverage efficiency. 

Combinatorial Libraries
There are many major approaches and methods in designing combinatorial libraries.
Computational design strategies are dependent on the type of library desired.  Focused libraries are designed to meet specific criteria with the end goal in mind.  

Deletion Libraries
The yield and solubility of proteins of interest can be dramatically improved by introducing deletions or mutations to the sequence.  CODA’s unique self assembling genes make it possible to truncate one or more amino acids at a time from the N- and/or C-terminus.  Deletion methods are user defined and ensures quality with a fast delivery time.

The resulting deletion libraries contain unparalleled coverage and flexibility of design.

 

Selective Amino Acid Replacement CODA’s technology allows the creation of variants with amino acid changes at selected sites of interest

Comprehensive Amino Acid Substitution Change one position at a time with all possible amino acids.

Random or Directed Insertion/Internal Deletion CODA can randomly or directly insert any given amino acid(s).  Similarly, CODA can also delete any internal amino acid(s).