Difference between revisions of "Part:BBa K2289000"
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Aptazyme:
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==Aptazyme==
 
An aptazyme is a ssDNA molecule thay can recognize a ligand and catalyze a reaction. The funcionality of this molecule depends on three modules; an aptamer, for  
 
An aptazyme is a ssDNA molecule thay can recognize a ligand and catalyze a reaction. The funcionality of this molecule depends on three modules; an aptamer, for  
 
recognition of the ligand, a DNAzyme, for catalize the reaction and linkers, fundamental parts that can bind specific zones of the Aptazyme, and with that those  
 
recognition of the ligand, a DNAzyme, for catalize the reaction and linkers, fundamental parts that can bind specific zones of the Aptazyme, and with that those  
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This part consists on an Aptazyme that can recognise Saxitoxin (STX) and that can catalyse a chromogenic reaction.  
 
This part consists on an Aptazyme that can recognise Saxitoxin (STX) and that can catalyse a chromogenic reaction.  
  
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Modules:
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==Modules==
  
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STX M30f Aptamer (<BBA_K2289004 href=”https://parts.igem.org/Part:BBa_K2289004”> </a>)
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=== STX M30f Aptamer ([https://parts.igem.org/Part:BBa_K2289004 Part:BBa_K2289004]) ===
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It is an aptamer for saxitoxin, developed by Zheng et. al. 2015, this aptamer was selected by apool of aptamers. It has a dissociation constant (Kd)  
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of 0,133 uM.
  
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HRP-Mimicking DNAzyme (<BBa_K1614007 href=”https://parts.igem.org/Part:BBa_K1614007”> </a>):
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=== HRP-Mimicking DNAzyme ([https://parts.igem.org/Part:BBa_K1614007 Part:BBa_K1614007]) ===
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It is a DNAzyme developed by Travascio et. al. 1998. This DNAzyme, just as its name says, it imitates the horseradish peroxidase catalytic activity, and
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it has been demonstrated that works well with a chromogenic reactant, ABTS. This DNAzyme needs Hemin to act as a catalyst, it adopts a G-cuadruplex
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conformation that allows hemin to form a complex, that, at the same time enables the DNAzyme to catalyse the reaction (see Figure 3).
  
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J_X linker:
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=== J_X linker ===
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These are linkers generated by the JAWS software developed by Team Heidelberg 2015. Each linker binds to a specific zone of the molecule, allowing the
 +
inactive conformation of the Aptazyme. Those were calculated by the software to allow both conformations of the Aptazyme, the inactive one, and the active
 +
in the presence of the ligand.
  
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All in one:
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==All in one==
  
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Primal fold:
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=== Inactive fold ===
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We expect that the molecule folding is the same
  
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In the presence of the toxin:
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=== In the presence of the toxin ===
  
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Dynamics:
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=== Dynamics and kinetics ===
  
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here

Revision as of 02:29, 29 October 2017


STX Aptazyme J_1

This part is a noncoding single-stranded DNA Aptazyme, this molecule combines 3 modules, an HRP-mimicking DNAzyme, an aptamer for recognition of Saxitoxin (related to the red tide) and linkers.


Aptazyme

An aptazyme is a ssDNA molecule thay can recognize a ligand and catalyze a reaction. The funcionality of this molecule depends on three modules; an aptamer, for recognition of the ligand, a DNAzyme, for catalize the reaction and linkers, fundamental parts that can bind specific zones of the Aptazyme, and with that those can act as kidnappers of the catalytic zone of the molecule. The linkers are fundamental, because they are placed in such a way that when the aptamer is not interacting with the ligand, the linkers are kidnapping the DNAzyme, altering the conformation of the DNAzyme (see Figure 1a).

When the aptamer interacts with the ligand, a conformational change takes place in the molecule, this conformational change promote the movement of the linkers from the original place, and in consecuense the DNAzyme is released, with that the DNAzyme can take the catalytic conformation and can catalyse the reaction (see Figure 1b).

This part consists on an Aptazyme that can recognise Saxitoxin (STX) and that can catalyse a chromogenic reaction.

Modules

=== STX M30f Aptamer (Part:BBa_K2289004) === It is an aptamer for saxitoxin, developed by Zheng et. al. 2015, this aptamer was selected by apool of aptamers. It has a dissociation constant (Kd) of 0,133 uM.

=== HRP-Mimicking DNAzyme (Part:BBa_K1614007) === It is a DNAzyme developed by Travascio et. al. 1998. This DNAzyme, just as its name says, it imitates the horseradish peroxidase catalytic activity, and it has been demonstrated that works well with a chromogenic reactant, ABTS. This DNAzyme needs Hemin to act as a catalyst, it adopts a G-cuadruplex conformation that allows hemin to form a complex, that, at the same time enables the DNAzyme to catalyse the reaction (see Figure 3).

=== J_X linker === These are linkers generated by the JAWS software developed by Team Heidelberg 2015. Each linker binds to a specific zone of the molecule, allowing the inactive conformation of the Aptazyme. Those were calculated by the software to allow both conformations of the Aptazyme, the inactive one, and the active in the presence of the ligand.

All in one

=== Inactive fold === We expect that the molecule folding is the same

=== In the presence of the toxin ===

=== Dynamics and kinetics ===

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]