Team:Penn State/Codon Optimization Design


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Bidirectional Promoters Overview

Codon Optimization

The genetic code is a degenerate one; there are more 3-part combinations of nucleotides than there are amino acids. The topic of codon optimization-that is, the cell's preference for one codon sequence over another in translation-has been heavily researched in an effort to determine the optimal genetic sequences for an organism. This project looks at the effects of repeated amino acid sequences of varying lengths and codons and their effect on the cell.

Codon Optimization

Sample navigation menu:

Overview | Design | Results

Initial Design

To test the effect of repeated codon sequences on cell protein expression, we altered a plasmid available in the Richard lab to contain a promoter, ribosome binding site, and an AHL leader sequence, followed by a non-coding repeated sequence placeholder flanked by restriction enzyme sites. A mCherry and GFP reporter allowed us to test each repeated codon sequence.


The initial construct was partially assembled by a Ph.D student formerly working in the Richard Lab at Penn State named Mike Speer. This project was designed by Mr. Speer, but never completed. The Penn State iGEM team worked closely with Mr. Speer to successfully complete the initial construct.


This part was assembled using Amplified Insert Assembly, a technique developed in the Richard Lab by the 2011 Penn State iGEM team. AIA utilizes the complementary sticky ends left by certain restriction enzymes to ligate inserts and vectors with benign scars.