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Team:Michigan/Project
From 2012.igem.org
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<div class="text-panel-content"> | <div class="text-panel-content"> | ||
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| - | + | <p>HbiF and LVA degradation tag were ordered from IDT with the following specifications.</p> | |
| - | + | ||
| + | <p> <span style="background-color:#E0771B;font-family:Courier, monospace;">EcoRI</span></p> | ||
| + | <p> <span style="background-color:#E0B91B;font-family:Courier, monospace;">XbaI</span></p> | ||
| + | <p> <span style="background-color:#C8E0DB;font-family:Courier, monospace;">SpeI</span></p> | ||
| + | <p> <span style="background-color:#A9C9A4;font-family:Courier, monospace;">PstI</span></p> | ||
| + | <p> <span style="background-color:#86C67C;font-family:Courier, monospace;">AgeI</span></p> | ||
| + | <p> <span style="background-color:#CD96CD;font-family:Courier, monospace;">NgoMIV</span></p> | ||
| + | |||
| + | <p><br/>HbiF possesses an N-terminus in the (truncated) RFC10 format :</p> | ||
| + | |||
| + | <p style="font-family:Courier, monospace;"><span style="background-color:#E0771B">GAATTC</span> GCGGCCGC T <span style="background-color:#E0B91B;">TCTAG</span> [ATG]</p> | ||
| + | |||
| + | <p><br/>No extra amino acids are created by this prefix, in comparison to the standard RFC25 prefix, which creates a serine and glycine. The suffix proceeds as follows:</p> | ||
| + | |||
| + | <p style="font-family:Courier, monospace;"><span style="background-color:#86C67C;">ACCGGT</span> TAAT <span style="background-color:#C8E0DB">ACTAGT</span> A GCGGCCG <span style="background-color:#A9C9A4">CTGCAG</span> </p> | ||
| + | |||
| + | <p><br/>In order to properly attach the LVA degradation tag, the prefix of the tag sequence must be complementary to the suffix of Hbif. For this part, the prefix and suffix are reversed in comparison to above: the prefix is RFC25, and the suffix is RFC10, for reasons that are discussed below.</p> | ||
| + | |||
| + | <p><br/>Prefix:</p> | ||
| + | <p style="font-family:Courier, monospace;"><span style="background-color:#E0771B;">GAATTC</span> GCGGCCGC T <span style="background-color:#E0B91B;">TCTAGA</span> TG <span style="background-color:#CD96CD;">GCCGGC</span></p> | ||
| + | |||
| + | <p><br/>Suffix:</p> | ||
| + | |||
| + | <p style="font-family:Courier, monospace;"><span style="color:red;">(TAA TAA)</span> T <span style="background-color:#C8E0DB;">ACTAGT</span> A GCGGCCG <span style="background-color:#A9C9A4;">CTGCAG</span></p> | ||
| + | |||
| + | <p><br/>The suffix is RFC10 - we don’t need it to be RFC25 because two stop codons not in the original suffixes have been introduced before the suffix starts. LVA-mediated degradation depends on a series of amino acids at the C-terminus binding to cellular degradation machinery, and failure to abruptly halt transcription after this sequence may result in improper binding and degradation. Unlike in the RFC25 suffix, which adds linker amino acids after the protein domain ends, RFC10 adds a tyrosine before its internal stop codon, assuming translation proceeds that far - this could severely hinder binding.</p> | ||
</div> | </div> | ||
| + | <div class="text-nopanel-content" style="background-color:#e5c19f;"> | ||
| + | <p class="title">Main tasks:</p> | ||
| + | |||
| + | <ol> | ||
| + | <li>Extract Hbif and the degradation tags from their parent plasmids, place in biobrick-compatible plasmids.</li> | ||
| + | <li>Obtain RFC25-standard plasmid Bba-K157000 for use in construction.</li> | ||
| + | <li>Clone the LVA tag onto Hbif’s C-terminus.</li> | ||
| + | <li>Design primers to FimE which place an AgeI site at it’s C-terminus.</li> | ||
| + | <li>Clone the LVA tag onto the modified FimE.</li> | ||
| + | <li>Assay functionality of both. </li> | ||
| + | </ol> | ||
| + | |||
| + | </div> | ||
</div> | </div> | ||
Revision as of 00:49, 6 July 2012
Abstract
Recombinases can be used to create responsive genetic elements in biological systems. Further, it is theoretically possible to create complex control circuits using combinations of invertible DNA sequences. We utilized HbiF to augment an existing recombinase system in Escherichia coli that relied on FimE. A burst of induced, low level expression of one recombinase is expected to invert the promoter flanked by the recombinase binding sites IRR and IRL, triggering a switch from strong expression of one to another set of proteins made downstream. Induced expression of the second recombinase is expected to revert the promoter to its original orientation, triggering the original set of protein expression. The inversion will be sustained across cell divisions with little leaky protein expression and negligible performance degradation after repeated inversions. This is a heritable, binary memory system and can be used as a component in more complex systems.
HbiF and LVA degradation tag were ordered from IDT with the following specifications.
EcoRI
XbaI
SpeI
PstI
AgeI
NgoMIV
HbiF possesses an N-terminus in the (truncated) RFC10 format :
GAATTC GCGGCCGC T TCTAG [ATG]
No extra amino acids are created by this prefix, in comparison to the standard RFC25 prefix, which creates a serine and glycine. The suffix proceeds as follows:
ACCGGT TAAT ACTAGT A GCGGCCG CTGCAG
In order to properly attach the LVA degradation tag, the prefix of the tag sequence must be complementary to the suffix of Hbif. For this part, the prefix and suffix are reversed in comparison to above: the prefix is RFC25, and the suffix is RFC10, for reasons that are discussed below.
Prefix:
GAATTC GCGGCCGC T TCTAGA TG GCCGGC
Suffix:
(TAA TAA) T ACTAGT A GCGGCCG CTGCAG
The suffix is RFC10 - we don’t need it to be RFC25 because two stop codons not in the original suffixes have been introduced before the suffix starts. LVA-mediated degradation depends on a series of amino acids at the C-terminus binding to cellular degradation machinery, and failure to abruptly halt transcription after this sequence may result in improper binding and degradation. Unlike in the RFC25 suffix, which adds linker amino acids after the protein domain ends, RFC10 adds a tyrosine before its internal stop codon, assuming translation proceeds that far - this could severely hinder binding.
Main tasks:
- Extract Hbif and the degradation tags from their parent plasmids, place in biobrick-compatible plasmids.
- Obtain RFC25-standard plasmid Bba-K157000 for use in construction.
- Clone the LVA tag onto Hbif’s C-terminus.
- Design primers to FimE which place an AgeI site at it’s C-terminus.
- Clone the LVA tag onto the modified FimE.
- Assay functionality of both.
Modeling
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s, when an unknown printer took a galley of type and scrambled it to make a type specimen book. It has survived not only five centuries, but also the leap into electronic typesetting, remaining essentially unchanged. It was popularised in the 1960s with the release of Letraset sheets containing Lorem Ipsum passages, and more recently with desktop publishing software like Aldus PageMaker including versions of Lorem Ipsum.
Recombinase Characterization
Lorem Ipsum is simply dummy text of the printing and typesetting industry. Lorem Ipsum has been the industry's standard dummy text ever since the 1500s, when an unknown printer took a galley of type and scrambled it to make a type specimen book. It has survived not only five centuries, but also the leap into electronic typesetting, remaining essentially unchanged. It was popularised in the 1960s with the release of Letraset sheets containing Lorem Ipsum passages, and more recently with desktop publishing software like Aldus PageMaker including versions of Lorem Ipsum.
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