Difference between revisions of "Part:BBa K4147016"

 
Line 5: Line 5:
 
This gene target the RXLR gene of <i>P. capsici</i>. The RXLR gene encondes for RXLR effectors, a protein produced by <i>P. capsici</i> which suppresses the plant's natural defense system.
 
This gene target the RXLR gene of <i>P. capsici</i>. The RXLR gene encondes for RXLR effectors, a protein produced by <i>P. capsici</i> which suppresses the plant's natural defense system.
  
−
<!-- Add more about the biology of this part here
+
===Thermodynamic properties===
−
===Usage and Biology===
+
 
 +
In collaboration with the iGEM Tec-Monterrey 2022 team, we performed an evaluation of the siRNA sequence we designed. For this we sent the mRNA of the gene we plan to silence (RXLR of <i>P. capsici</i>). And with the help of the software they developed we obtained a hybridization Gibbs Free Energy of approximately -32.9 kcal/mol, the lower this value the better. Since it indicates that the hybridization will be a spontaneous reaction.
 +
 
 +
[[File:Gibbs.png|600px|thumb|center|alt=Gibbs Free Energy analysisi of posible siRNAs.|Free Gibbs Energy analysis of possible siRNAs that target RXLR gene of <i>P. capsici</i>. Our designed siRNA showed a Gibbs Free Energy of -32.9 kcal/mol. Which indicates that the hibridization reaction will be a spontaneous reaction.]]
 +
 
 +
Likewise, the <i>in silico</i> analysis showed a relative efficiency of hibridization of 93%. The software developed by the Tec-Monterrey 2022 team evaluates all possible siRNAs and according to the analysis of the thermodynamic properties of each siRNA assigns a value between 0 and 100, where 100 is an almost perfect site to hybridize and 0 is a bad site to hybridize.
 +
 
 +
[[File:Relative.png|600px|thumb|center|alt=Gibbs Free Energy analysisi of posible siRNAs.|Free Gibbs Energy analysis of possible siRNAs that target RXLR gene of <i>P. capsici</i>. Our designed siRNA showed a Grelative efficiency of hibridization of 93%.]]
 +
 
  
 
<!-- -->
 
<!-- -->

Revision as of 20:19, 9 October 2022


siRNA designed to target RXLR gene of P. capsici

This gene target the RXLR gene of P. capsici. The RXLR gene encondes for RXLR effectors, a protein produced by P. capsici which suppresses the plant's natural defense system.

Thermodynamic properties

In collaboration with the iGEM Tec-Monterrey 2022 team, we performed an evaluation of the siRNA sequence we designed. For this we sent the mRNA of the gene we plan to silence (RXLR of P. capsici). And with the help of the software they developed we obtained a hybridization Gibbs Free Energy of approximately -32.9 kcal/mol, the lower this value the better. Since it indicates that the hybridization will be a spontaneous reaction.

Gibbs Free Energy analysisi of posible siRNAs.
Free Gibbs Energy analysis of possible siRNAs that target RXLR gene of P. capsici. Our designed siRNA showed a Gibbs Free Energy of -32.9 kcal/mol. Which indicates that the hibridization reaction will be a spontaneous reaction.

Likewise, the in silico analysis showed a relative efficiency of hibridization of 93%. The software developed by the Tec-Monterrey 2022 team evaluates all possible siRNAs and according to the analysis of the thermodynamic properties of each siRNA assigns a value between 0 and 100, where 100 is an almost perfect site to hybridize and 0 is a bad site to hybridize.

Gibbs Free Energy analysisi of posible siRNAs.
Free Gibbs Energy analysis of possible siRNAs that target RXLR gene of P. capsici. Our designed siRNA showed a Grelative efficiency of hibridization of 93%.


Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]