Difference between revisions of "Team:Rice/DrylabAnalysis"

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                 <p><br />
 
                     Existing RNA thermometers operate around 37°C and do not exhibit significant conformational changes between 25°C and 30°C. As most plants will die
 
                     Existing RNA thermometers operate around 37°C and do not exhibit significant conformational changes between 25°C and 30°C. As most plants will die
 
                     at 37°C, it was necessary to design thermometers that experienced conformational change between 25°C. We chose to design thermometers by finding optimal  
 
                     at 37°C, it was necessary to design thermometers that experienced conformational change between 25°C. We chose to design thermometers by finding optimal  
 
                     candidates using a genetic algorithm, as the complexity of RNA folding made it difficult to rationally design thermometers.
 
                     candidates using a genetic algorithm, as the complexity of RNA folding made it difficult to rationally design thermometers.
 
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  </div><h2 style = "background-color:#26849cff!important;"> RNA thermometer design </h2> </br>
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  </div><h2 style = "background-color:#1f9ec1!important;"> RNA Thermometer Design </h2> </br>
 
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<p>In essence, RNA thermometers are a form of temperature dependent translational regualtion. At low temperatures, there is a higher probability of more base pairs forming what is known as a "stem-loop structure". At higher temperatures, the thermometers "melt", meaning there is a decreased likilook of base pairs forming. </p>
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<p>In essence, RNA thermometers are a form of temperature dependent translational regulation. At low temperatures, there is a higher probability of more base pairs forming what is known as a "stem-loop structure". At higher temperatures, the thermometers "melt", meaning there is a decreased likelihood of base pairs forming. </p>
 
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             <h2>Percentage base pair optimization algorithm</h2>
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             <h2>Percentage base pair optimization algorithm</h2>
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             <ol>
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             <ol>
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                 <li>
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                 <li>
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                     <p>
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                     <p>
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                         For each base of the complement of the context containing the RBS, create three other
−
                         For each base of the complement of the context containing the RBS, create three other
+
                         permutations which have that base mutated. All of these permutations combined form the initial
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                         permutations which have that base mutated. All of these permutations combined form the initial
+
                         population. The baseline is defined as the full sequence containing the context before the
−
                         population. The baseline is defined as the full sequence containing the context before the
+
                         variable region, the variable region which is the complement of the RBS-containing context, and
−
                         variable region, the variable region which is the complement of the RBS-containing context, and
+
                         the RBS-containing context.
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                         the RBS-containing context.
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                     </p>
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                 </li>
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                 <li>
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                 <li>
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                     <p>
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                     <p>
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                         Calculate the base pairing probabilities at the two given temperatures for each test sequence
−
                         Calculate the base pairing probabilities at the two given temperatures for each test sequence
+
                         using the NuPack command <code>pairs -T TEMP -pseudo -material rna sequencename.</code>
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                         using the NuPack command <code>pairs -T TEMP -pseudo -material rna sequencename.</code>
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                     </p>
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                     </p>
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                 </li>
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                 </li>
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                 <li>
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                 <li>
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                     <p>
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                     <p>
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                         The output of the command consists in part of a list of every base and the base(s) which it has
−
                         The output of the command consists in part of a list of every base and the base(s) which it has
+
                         a > 0.001 probability of base pairing with by position number. Find the base pairings where one
−
                         a > 0.001 probability of base pairing with by position number. Find the base pairings where one
+
                         of the bases is in the RBS-containing region and add up the probabilities corresponding to that
−
                         of the bases is in the RBS-containing region and add up the probabilities corresponding to that
+
                         base pairing. The nature of this NuPack command should prevent duplicates. Then, subtract the
−
                         base pairing. The nature of this NuPack command should prevent duplicates. Then, subtract the
+
                         probability that these bases are unpaired.
−
                         probability that these bases are unpaired.
+
                     </p>
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                 </li>
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                     <p>
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                     <p>
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                         Subtract the number of base pairings at 30°C from the number of base pairings at 25°C. We want
−
                         Subtract the number of base pairings at 30°C from the number of base pairings at 25°C. We want
+
                         to maximize the number of RBS-base pairings that disappear as the temperature increases from
−
                         to maximize the number of RBS-base pairings that disappear as the temperature increases from
+
                         25°C to 30°C (for reference, the command I use for the minimum free energy calculation is
−
                         25°C to 30°C (for reference, the command I use for the minimum free energy calculation is
+
                         <code>mfe -T TEMP -pseudo -material rna sequencename</code>)
−
                         <code>mfe -T TEMP -pseudo -material rna sequencename</code>)
+
                     </p>
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                     </p>
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                 </li>
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                 </li>
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                 <li>
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                 <li>
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                     <p>
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                     <p>
+
                         Using the library DEAP, select 50 individuals through the tournament selection method.
−
                         Using the library DEAP, select 50 individuals through the tournament selection method.
+
                     </p>
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                     </p>
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                 </li>
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                 </li>
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             </ol>      
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             </ol>
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</div>
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        </div>
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     </div>
 
     </div>

Revision as of 06:53, 20 October 2019


Existing RNA thermometers operate around 37°C and do not exhibit significant conformational changes between 25°C and 30°C. As most plants will die at 37°C, it was necessary to design thermometers that experienced conformational change between 25°C. We chose to design thermometers by finding optimal candidates using a genetic algorithm, as the complexity of RNA folding made it difficult to rationally design thermometers.





RNA Thermometer Design


In essence, RNA thermometers are a form of temperature dependent translational regulation. At low temperatures, there is a higher probability of more base pairs forming what is known as a "stem-loop structure". At higher temperatures, the thermometers "melt", meaning there is a decreased likelihood of base pairs forming.

The stem-loop structure of the thermometer was created by taking the complement of the ribosome binding site(RBS) and surrounding the nucleotides and introducing mutations into the sequence. The resulting altered sequence is known as the variable region. Mutating this region serves a two prong purpose. First off, it ensures that the RBS will be locked into the structure of the thermometer, rendering it inaccessible to the ribosome at low temperatures. Secondly, it allows us to optimize for the targeted melting temperature.

Percentage base pair optimization algorithm

  1. For each base of the complement of the context containing the RBS, create three other permutations which have that base mutated. All of these permutations combined form the initial population. The baseline is defined as the full sequence containing the context before the variable region, the variable region which is the complement of the RBS-containing context, and the RBS-containing context.

  2. Calculate the base pairing probabilities at the two given temperatures for each test sequence using the NuPack command pairs -T TEMP -pseudo -material rna sequencename.

  3. The output of the command consists in part of a list of every base and the base(s) which it has a > 0.001 probability of base pairing with by position number. Find the base pairings where one of the bases is in the RBS-containing region and add up the probabilities corresponding to that base pairing. The nature of this NuPack command should prevent duplicates. Then, subtract the probability that these bases are unpaired.

  4. Subtract the number of base pairings at 30°C from the number of base pairings at 25°C. We want to maximize the number of RBS-base pairings that disappear as the temperature increases from 25°C to 30°C (for reference, the command I use for the minimum free energy calculation is mfe -T TEMP -pseudo -material rna sequencename)

  5. Using the library DEAP, select 50 individuals through the tournament selection method.