Team:Penn State/Codon Optimization


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Bidirectional Promoters Overview

Codon Optimization

The genetic code is a degenerative 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

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Overview | Design | Results


Before we can make a protein, we need an mRNA to carry the information about the order of the amino acids. But before we can make mRNA we need to know where the genes are in the DNA of a cell. Before RNA polymerase can make a copy it needs to bind to the DNA. This is assisted by a variety of factors, other proteins, that look for a specific sequence in the DNA. This sequence is called a promoter because it promotes the transcription of the DNA into RNA by the RNA polymerase. These sequences are generally upstream, or ahead, of a gene's coding sequence.

The Problem

Not all promoters cause RNA polymerase to transcribe downstream in the expected "forward direction". Some promoters can cause RNA polymerase to go in the opposite direction from what is expected, or go in both directions. This is what we are trying to find out; do different promoters go in different directions, and what is the directional preference of different promoters.