Team:EPF-Lausanne/Our Project/TetR mutants/MITOMI data

From 2011.igem.org

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(Wildtype TetR)
 
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Using the <html> <a href="https://2011.igem.org/Team:EPF-Lausanne/Tools/MITOMI">MITOMI</a></html> technique we determined the DNA binding landscape of the wild type TetR. To do so, we first designed and generated the library of double-stranded DNA sequences that cover all possible single base substitutions within the TetO operator sequence. Based on that library we measured the dissociation constants of the mutant to all the tetO-like sequences of the library. Then, we determined the specificity of the mutant to the Tet operator sequence, expressed as a position-weight matrix (PWM).
Using the <html> <a href="https://2011.igem.org/Team:EPF-Lausanne/Tools/MITOMI">MITOMI</a></html> technique we determined the DNA binding landscape of the wild type TetR. To do so, we first designed and generated the library of double-stranded DNA sequences that cover all possible single base substitutions within the TetO operator sequence. Based on that library we measured the dissociation constants of the mutant to all the tetO-like sequences of the library. Then, we determined the specificity of the mutant to the Tet operator sequence, expressed as a position-weight matrix (PWM).
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The WebLogo we obtained for the wild-type is:
+
The enoLOGO we obtained for the wild-type is:
[[File:EPFL2011_WTTetR_WebLogo.png|700px]]
[[File:EPFL2011_WTTetR_WebLogo.png|700px]]
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'''WebLogo reference:'''<p>
+
'''enoLOGO reference:'''<p>
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
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Using the <html> <a href="https://2011.igem.org/Team:EPF-Lausanne/Tools/MITOMI">MITOMI</a></html> technique we determined the DNA binding landscape of the TetR V36F mutant. To do so, first we designed and generated the library of double stranded DNA sequences that cover all possible single base substitution within the tetO operator sequence. Based on that library we measured the dissociation constants of the mutant to variable tetO-like sequences and determined the specificity of the mutant to the tet operator sequence (expressed as a PWM).
Using the <html> <a href="https://2011.igem.org/Team:EPF-Lausanne/Tools/MITOMI">MITOMI</a></html> technique we determined the DNA binding landscape of the TetR V36F mutant. To do so, first we designed and generated the library of double stranded DNA sequences that cover all possible single base substitution within the tetO operator sequence. Based on that library we measured the dissociation constants of the mutant to variable tetO-like sequences and determined the specificity of the mutant to the tet operator sequence (expressed as a PWM).
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The WebLogo we obtained for the V36F mutant:
+
The enoLOGO we obtained for the V36F mutant:
[[File:EPFL2011_MITOMI_WebLogo_V36F.png|700px]]
[[File:EPFL2011_MITOMI_WebLogo_V36F.png|700px]]
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'''WebLogo reference:'''<p>
+
'''enoLOGO reference:'''<p>
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
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The WebLogo we obtained for the E37A W43S T141A mutant:
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The enoLOGO we obtained for the E37A W43S T141A mutant:
[[File:EPFL2011_WebLogo_EA37WS43TA41.png|700px]]
[[File:EPFL2011_WebLogo_EA37WS43TA41.png|700px]]
-
'''WebLogo reference:'''<p>
+
'''enoLOGO reference:'''<p>
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
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The WebLogo we obtained for the P39K mutant:
+
The enoLOGO we obtained for the P39K mutant:
[[File:EPFL2011_P39K_WebLogo.png|700px]]
[[File:EPFL2011_P39K_WebLogo.png|700px]]
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Using the <html> <a href="https://2011.igem.org/Team:EPF-Lausanne/Tools/MITOMI">MITOMI</a></html> technique we determined the DNA binding landscape of the TetR Y42F mutant. To do so, first we designed and generated the library of double stranded DNA sequences that cover all possible single base substitution within the tetO operator sequence. Based on that library we measured the dissociation constants of the mutant to variable tetO-like sequences and determined the specificity of the mutant to the tet operator sequence (expressed as a PWM). For the Y42F mutant we observed the decrease of the specificity compared to the wild-type tetR sequence.
Using the <html> <a href="https://2011.igem.org/Team:EPF-Lausanne/Tools/MITOMI">MITOMI</a></html> technique we determined the DNA binding landscape of the TetR Y42F mutant. To do so, first we designed and generated the library of double stranded DNA sequences that cover all possible single base substitution within the tetO operator sequence. Based on that library we measured the dissociation constants of the mutant to variable tetO-like sequences and determined the specificity of the mutant to the tet operator sequence (expressed as a PWM). For the Y42F mutant we observed the decrease of the specificity compared to the wild-type tetR sequence.
-
The WebLogo we obtained for the Y42F mutant:
+
The enoLOGO we obtained for the Y42F mutant:
[[File:EPFL2011_WebLogo_Y42F.png|700px]]
[[File:EPFL2011_WebLogo_Y42F.png|700px]]
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-
'''WebLogo reference:'''<p>
+
'''enoLOGO reference:'''<p>
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
Line 347: Line 347:
Using the <html> <a href="https://2011.igem.org/Team:EPF-Lausanne/Tools/MITOMI">MITOMI</a></html> technique we determined the DNA binding landscape of the TetR P39Q Y42M mutant. To do so, first we designed and generated the library of double stranded DNA sequences that cover all possible single base substitution within the tetO operator sequence. Based on that library we measured the dissociation constants of the mutant to variable tetO-like sequences and determined the specificity of the mutant to the tet operator sequence (expressed as a PWM). For the P39Q Y42M mutant we observed the decrease of the specificity compared to the wild-type tetR sequence.
Using the <html> <a href="https://2011.igem.org/Team:EPF-Lausanne/Tools/MITOMI">MITOMI</a></html> technique we determined the DNA binding landscape of the TetR P39Q Y42M mutant. To do so, first we designed and generated the library of double stranded DNA sequences that cover all possible single base substitution within the tetO operator sequence. Based on that library we measured the dissociation constants of the mutant to variable tetO-like sequences and determined the specificity of the mutant to the tet operator sequence (expressed as a PWM). For the P39Q Y42M mutant we observed the decrease of the specificity compared to the wild-type tetR sequence.
-
The WebLogo we obtained for the P39Q Y42M mutant:
+
The enoLOGO we obtained for the P39Q Y42M mutant:
[[File:EPFL2011_P39QY42M_WebLogo.png|700px]]
[[File:EPFL2011_P39QY42M_WebLogo.png|700px]]
-
'''WebLogo reference:'''<p>
+
'''enoLOGO reference:'''<p>
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.
enoLOGOS: a versatile web tool for energy normalized sequence logos.
enoLOGOS: a versatile web tool for energy normalized sequence logos.

Latest revision as of 21:49, 26 October 2011