Difference between revisions of "Part:BBa K2923018:Experience"
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===Introduction===
 
===Introduction===
  
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To validate the designed constructs we decided to test two different aptazymes : Theophylline switch-off (stop auto-cleavage in presence of ligand) and Guanine switch-on (active auto-cleavage in presence of ligand). For negative control, we choose an inactive form of aptazyme : mutation at ribozyme domain. iGEM Strasbourg designed construct require the use of aptazyme linked to MS2 and PP7 stem-loops. The following results described MS2-MS2-Aptazyme-PP7-PP7 activity in in-vitro and in-vivo assays.
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To validate the designed constructs we decided to test two different aptazymes: Theophylline switch-off (stop auto-cleavage in presence of ligand) and Guanine switch-on (active auto-cleavage in presence of ligand). For negative control, we choose an inactive form of aptazyme: mutation at the ribozyme domain. iGEM Strasbourg designed construct requires the use of aptazyme linked to MS2 and PP7 stem-loops. The following results described MS2-MS2-Aptazyme-PP7-PP7 activity in in-vitro and in-vivo assays.
  
 
===In-vitro assay of BBa_K2923018===
 
===In-vitro assay of BBa_K2923018===
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In order to check MS2-MS2-Theophylline-PP7-PP7 cleavage activities, in-vitro transcription products were analyzed by 2% agarose gel with urea (Figure 1).
 
In order to check MS2-MS2-Theophylline-PP7-PP7 cleavage activities, in-vitro transcription products were analyzed by 2% agarose gel with urea (Figure 1).
  
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[[Image: Theo gel-1.jpg|300px|thumb|center| Figure 1: Aptazyme catalytic activity assay. Theophylline aptazyme were transcribed in vitro for 1h30. RNA was analyzed in an 8% polyacrylamide gel with urea. The inactive form of Theophylline aptazyme represent the whole RNA and correspond to band of 94 pb. Clived aptazyme represent the two parts of the aptazyme Theophylline (18 pb + 76 pb).
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[[Image: Theo gel-1.jpg|300px|thumb|center| Figure 1: Aptazyme catalytic activity assay. Theophylline aptazyme were transcribed in vitro for 1h30. RNA was analyzed in an 8% polyacrylamide gel with urea. The inactive form of Theophylline aptazyme represents the whole RNA and corresponds to the band of 94 pb. Cleaved aptazyme represents the two parts of the aptazyme Theophylline (18 pb + 76 pb).
 
]]
 
]]
  
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In-vitro assay show, that PP7-PP7-Theophylline-MS2-MS2 constructs have kept 100% of their ribozyme activity. Also, inactive aptazyme did not present aptazyme catalytic activity, which confirms their use as efficient negative control.
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===In-vivo: ß-galactosidase assay in the absence of ligand===
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Before to start an in vivo experiment on aptazymes, we characterized the constructs created by Berry KE and Hochschild as positive and negative controls.
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A ß-galactosidase activity positive control also called BH3 corresponds to  <partinfo>BBa_K2923000</partinfo>. A ß-galactosidase activity negative control, called BH2 correspond to empty plasmid backbone.
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Theophylline aptazyme is switch-off (self-cleaves in absence of ligand) and prevents ß-galactosidase transcription.  It was analyze in presence of its inactive form and BH2, BH3 controls (Figure 2).
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[[Image: Aptazyme Theo 0.jpg|400px|thumb|center| Figure 2:  ß-galactosidase assay on Theophylline aptazyme in absence of ligand]]
  
 
===User Reviews===
 
===User Reviews===

Revision as of 11:33, 14 October 2019

Introduction

To validate the designed constructs we decided to test two different aptazymes: Theophylline switch-off (stop auto-cleavage in presence of ligand) and Guanine switch-on (active auto-cleavage in presence of ligand). For negative control, we choose an inactive form of aptazyme: mutation at the ribozyme domain. iGEM Strasbourg designed construct requires the use of aptazyme linked to MS2 and PP7 stem-loops. The following results described MS2-MS2-Aptazyme-PP7-PP7 activity in in-vitro and in-vivo assays.

In-vitro assay of BBa_K2923018

In order to check MS2-MS2-Theophylline-PP7-PP7 cleavage activities, in-vitro transcription products were analyzed by 2% agarose gel with urea (Figure 1).

Figure 1: Aptazyme catalytic activity assay. Theophylline aptazyme were transcribed in vitro for 1h30. RNA was analyzed in an 8% polyacrylamide gel with urea. The inactive form of Theophylline aptazyme represents the whole RNA and corresponds to the band of 94 pb. Cleaved aptazyme represents the two parts of the aptazyme Theophylline (18 pb + 76 pb).

In-vitro assay show, that PP7-PP7-Theophylline-MS2-MS2 constructs have kept 100% of their ribozyme activity. Also, inactive aptazyme did not present aptazyme catalytic activity, which confirms their use as efficient negative control.

In-vivo: ß-galactosidase assay in the absence of ligand

Before to start an in vivo experiment on aptazymes, we characterized the constructs created by Berry KE and Hochschild as positive and negative controls. A ß-galactosidase activity positive control also called BH3 corresponds to BBa_K2923000. A ß-galactosidase activity negative control, called BH2 correspond to empty plasmid backbone.

Theophylline aptazyme is switch-off (self-cleaves in absence of ligand) and prevents ß-galactosidase transcription. It was analyze in presence of its inactive form and BH2, BH3 controls (Figure 2).

Figure 2: ß-galactosidase assay on Theophylline aptazyme in absence of ligand

User Reviews

UNIQda4f624b37dae585-partinfo-00000001-QINU UNIQda4f624b37dae585-partinfo-00000002-QINU