Team:Penn State/Codon Optimization

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   <div id="desc">
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     <h2>Codon Optimization</h2>
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     <h3>Codon Optimization</h3></br>
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     <p>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. </p>  
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     <p>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. </p>  
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     <h2>Codon Optimization</h2>
     <h2>Codon Optimization</h2>
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     <a class="activemaintab" href="http://2012.igem.org/Team:Penn_State/Bidirectional_Promoters_Overview">Overview</a>
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     <a class="activemaintab" href="http://2012.igem.org/Team:Penn_State/Codon_Optimization">Overview</a>
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     <span class="hide"> | </span> <a class="maintab" href="http://2012.igem.org/Team:Penn_State/Codon_Optimization_Design">Design</a>
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<h3>Background</h3>
<h3>Background</h3>
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     <p>Before we can make a protein, we need an mRNA to carry the information about the order of the amino acids.  
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     <p>All of the proteins around us, with few exceptions, are made up of 20 fundamental building blocks of life - amino acids. Different arrangements and combinations of these basic building blocks give us the diversity of proteins that we see. Messenger RiboNucleic Acids (mRNA) is in essence a "photocopy" of DNA that codes for a gene. mRNA carry codons, which are groups of three bases that code for a single amino acid. There are 64 possible combinations of codons (4 x 4 x 4 = 64), but these combinations are degenerate, so there can be more than one codon that codes for the same amino acid.  
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But before we can make mRNA we need to know where the genes are in the DNA of a cell. Before RNA polymerase can
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make a copy it needs to bind to the DNA. This is assisted by a variety of factors, other proteins, that look for
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a specific sequence in the DNA. This sequence is called a promoter because it promotes the transcription of the
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DNA into RNA by the RNA polymerase. These sequences are generally upstream, or ahead, of a gene's coding sequence.  
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</p>
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<h3>The Problem</h3>
<h3>The Problem</h3>
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<p>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.
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<p>We have mentioned how these can be a number of codons that can code for the same Amino Acid, and subsequently, a number of tRNA molecules that can carry a given Amino Acid. In nature, and in many organisms, only a select few of these tRNA and codon combinations are used instead of all sequences that code for the same amino acid. This is called codon bias.
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</p>
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<h3>The Objective</h3>
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<p>Our goal for this project is to see which codons are preferred, or biased. We also want to investigate if this bias can change over time, different circumstances, or stresses.  
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     <h3>Projects</h3>
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       <li><a href="http://2012.igem.org/Team:Penn_State/MSC_Overview">Multiple Start Codons</a></li>
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       <li><a href="http://2012.igem.org/Team:Penn_State/Multiple_Start_Codons">Multiple Start Codons</a></li>
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       <li><a href="http://2012.igem.org/Team:Penn_State/Bidirectional_Promoters_Overview">Bidirectional Promoters</a></li>
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       <li><a href="http://2012.igem.org/Team:Penn_State/Bidirectional_Promoters">Bidirectional Promoters</a></li>
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       <li><a href="http://2012.igem.org/Team:Penn_State/Codon_Optimization_Overview">Codon Optimization</a></li>
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       <li><a href="http://2012.igem.org/Team:Penn_State/Codon_Optimization">Codon Optimization</a></li>
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Latest revision as of 03:07, 27 October 2012

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

Background

All of the proteins around us, with few exceptions, are made up of 20 fundamental building blocks of life - amino acids. Different arrangements and combinations of these basic building blocks give us the diversity of proteins that we see. Messenger RiboNucleic Acids (mRNA) is in essence a "photocopy" of DNA that codes for a gene. mRNA carry codons, which are groups of three bases that code for a single amino acid. There are 64 possible combinations of codons (4 x 4 x 4 = 64), but these combinations are degenerate, so there can be more than one codon that codes for the same amino acid.

The Problem

We have mentioned how these can be a number of codons that can code for the same Amino Acid, and subsequently, a number of tRNA molecules that can carry a given Amino Acid. In nature, and in many organisms, only a select few of these tRNA and codon combinations are used instead of all sequences that code for the same amino acid. This is called codon bias.

The Objective

Our goal for this project is to see which codons are preferred, or biased. We also want to investigate if this bias can change over time, different circumstances, or stresses.