Difference between revisions of "Part:BBa K5237006"

 
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<partinfo>BBa_K5237006 short</partinfo>
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simple staple
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===Usage and Biology===
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  <!-- Part summary -->
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  <section id="1">
 +
    <h1>Simple-Staple: TetR-Oct1</h1>
 +
    <p>The Simple Staple (Oct1-DBD-TetR fusion) is a bivalent DNA-binding protein designed to bring two DNA sequences
 +
      into
 +
      close proximity, combining the human Oct1 DNA-binding domain (Oct1-DBD) and the bacterial tetracycline repressor
 +
      protein (TetR). Oct1-DBD recognizes the octamer motif, while TetR binds specifically to the tetO
 +
      operator sequences. This Simple Staple was applied to establish a Förster Resonance Energy Transfer (FRET)-based
 +
      assay,
 +
      which was used to monitor DNA-DNA proximity in bacterial systems.</p>
 +
    <p>&nbsp;</p>
 +
  </section>
 +
  <div id="toc" class="toc">
 +
    <div id="toctitle">
 +
      <h1>Contents</h1>
 +
    </div>
 +
    <ul>
 +
      <li class="toclevel-1 tocsection-1"><a href="#1"><span class="tocnumber">1</span> <span class="toctext">Sequence
 +
            overview</span></a>
 +
      </li>
 +
      <li class="toclevel-1 tocsection-2"><a href="#2"><span class="tocnumber">2</span> <span class="toctext">Usage and
 +
            Biology</span></a>
 +
      </li>
 +
      <li class="toclevel-1 tocsetction-3"><a href="#3"><span class="tocnumber">3</span> <span class="toctext">Assembly
 +
            and part evolution</span></a>
 +
      </li>
 +
      <li class="toclevel-1 tocsection-5"><a href="#4"><span class="tocnumber">4</span> <span
 +
            class="toctext">Results</span></a>
 +
      </li>
 +
      <li class="toclevel-1 tocsection-8"><a href="#5"><span class="tocnumber">5</span> <span
 +
            class="toctext">References</span></a>
 +
      </li>
 +
    </ul>
 +
  </div>
 +
  <section id="part-collection">
 +
    <font size="5"><b>The PICasSO Toolbox </b> </font>
 +
    <p><br></p>
 +
    <div class="thumb">
 +
    <div class="thumbinner" style="width:550px"><img alt=""
 +
        src="https://static.igem.wiki/teams/5237/wetlab-results/registry-part-collection-engineering-cycle-example-overview.svg"
 +
        style="width:99%;" class="thumbimage">
 +
      <div class="thumbcaption">
 +
        <i><b>Figure 1: Example how the part collection can be used to engineer new staples</b></i>
 +
      </div>
 +
    </div>
 +
    </div>
 +
 
 +
 
 +
    <p>
 +
      <br>
 +
      The 3D organization of the genome plays a crucial role in regulating gene expression in eukaryotic cells,
 +
      impacting cellular behavior, evolution, and disease. Beyond the linear DNA sequence, the spatial arrangement of
 +
      chromatin, influenced by DNA-DNA interactions, shapes pathways of gene regulation. However, the tools to precisely
 +
      manipulate this genomic architecture remain limited, rendering it challenging to explore the full potential of the
 +
      3D genome in synthetic biology. We - iGEM Team Heidelberg 2024 - have developed PICasSO, a powerful molecular
 +
      toolbox based on various DNA-binding proteins to address this issue.
 +
 
 +
    </p>
 +
    <p>
 +
      The <b>PICasSO</b> part collection offers a comprehensive, modular platform for precise manipulation and
 +
      re-programming
 +
      of DNA-DNA interactions using protein staples in living cells, enabling researchers to recreate natural 3D genomic
 +
      interactions, such as enhancer hijacking, or to design entirely new spatial architectures for gene regulation.
 +
      Beyond its versatility, PICasSO includes robust assay systems to support the engineering, optimization, and
 +
      testing of new staples, ensuring functionality <i>in vitro</i> and <i>in vivo</i>. We took special care to include
 +
      parts crucial for testing every step of the cycle (design, build, test, learn) when engineering new parts
 +
    </p>
 +
 
 +
    <p>At its heart, the PICasSO part collection consists of three categories. (i) Our <b>DNA-binding proteins</b>
 +
      include our
 +
      finalized enhancer hijacking Cas staple as well as half staples that can be used by scientists to compose entirely
 +
      new Cas staples in the future. We also include our simple staples that serve as controls for successful stapling
 +
      and can be further engineered to create alternative, simpler and more compact staples. (ii) As <b>functional
 +
        elements</b>, we list additional parts that enhance the functionality of our Cas and Basic staples. These
 +
      consist of
 +
      protease-cleavable peptide linkers and inteins that allow condition-specific, dynamic stapling <i>in vivo</i>.
 +
      Besides staple functionality, we also include the parts to enable the efficient delivery of PICasSO's with our
 +
      interkingdom conjugation system.
 +
    </p>
 +
    <p>
 +
      (iii) As the final component of our collection, we provide parts that support the use of our <b>custom readout
 +
        systems</b>. These include components of our established FRET-based proximity assay system, enabling users to
 +
      confirm
 +
      accurate stapling. Additionally, we offer a complementary, application-oriented testing system for functional
 +
      readout via a luciferase reporter, which allows for straightforward experimental simulation of enhancer hijacking.
 +
    </p>
 +
    <p>
 +
      The following table gives a complete overview of all parts in our PICasSO toolbox. The highlighted parts showed
 +
      exceptional performance as described on our iGEM wiki and can serve as a reference. The other parts in the
 +
      collection are versatile building blocks designed to provide future iGEMers with the flexibility to engineer their
 +
      own custom Cas staples, enabling further optimization and innovation
 +
    </p>
 +
    <p>
 +
      <font size="4"><b>Our parts collection includes:</b></font><br>
 +
    </p>
 +
 
 +
    <table style="width: 90%;">
 +
      <td colspan="3" align="left"><b>DNA-binding proteins: </b>
 +
        The building blocks for engineering of custom staples for DNA-DNA interactions with a modular system ensuring
 +
        easy assembly.</td>
 +
      <tbody>
 +
        <tr bgcolor="#FFD700">
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237000" target="_blank">BBa_K5237000</a></td>
 +
          <td>fgRNA Entryvector MbCas12a-SpCas9</td>
 +
          <td>Entryvector for simple fgRNA cloning via SapI</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237001" target="_blank">BBa_K5237001</a></td>
 +
          <td>Half-Staple: dMbCas12a-Nucleoplasmin NLS</td>
 +
          <td>Staple subunit that can be combined to form a functional staple, for example with fgRNA and dCas9 </td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237002" target="_blank">BBa_K5237002</a></td>
 +
          <td>Half-Staple: SV40 NLS-dSpCas9-SV40 NLS</td>
 +
          <td>Staple subunit that can be combined to form a functional staple, for example with our fgRNA or dCas12a
 +
          </td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237003" target="_blank">BBa_K5237003</a></td>
 +
          <td>Cas-Staple: SV40 NLS-dMbCas12a-dSpCas9-Nucleoplasmin NLS</td>
 +
          <td>Functional Cas staple that can be combined with sgRNA or fgRNA to bring two DNA strands in close proximity
 +
          </td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237004" target="_blank">BBa_K5237004</a></td>
 +
          <td>Half-Staple: Oct1-DBD</td>
 +
          <td>Staple subunit that can be combined to form a functional staple, for example with TetR.<br>
 +
            Can also be combined with a fluorescent protein as part of the FRET proximity assay</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237005" target="_blank">BBa_K5237005</a></td>
 +
          <td>Half-Staple: TetR</td>
 +
          <td>Staple subunit that can be combined to form a functional staple, for example with Oct1.<br>
 +
            Can also be combined with a fluorescent protein as part of the FRET proximity assay</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237006" target="_blank">BBa_K5237006</a></td>
 +
          <td>Simple-Staple: TetR-Oct1</td>
 +
          <td>Functional staple that can be used to bring two DNA strands in close proximity</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237007" target="_blank">BBa_K5237007</a></td>
 +
          <td>Half-Staple: GCN4</td>
 +
          <td>Staple subunit that can be combined to form a functional staple, for example with rGCN4</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237008" target="_blank">BBa_K5237008</a></td>
 +
          <td>Half-Staple: rGCN4</td>
 +
          <td>Staple subunit that can be combined to form a functional staple, for example with rGCN4</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237009" target="_blank">BBa_K5237009</a></td>
 +
          <td>Mini-Staple: bGCN4</td>
 +
          <td>
 +
            Assembled staple with minimal size that can be further engineered</td>
 +
        </tr>
 +
      </tbody>
 +
      <td colspan="3" align="left"><b>Functional elements: </b>
 +
        Protease cleavable peptide linkers and inteins are used to control and modify staples for further optimization
 +
        for custom applications.</td>
 +
      <tbody>
 +
        <tr bgcolor="#FFD700">
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237010" target="_blank">BBa_K5237010</a></td>
 +
          <td>Cathepsin B-Cleavable Linker (GFLG)</td>
 +
          <td>Cathepsin B cleavable peptide linker, that can be used to combine two staple subunits ,to make responsive
 +
            staples</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237011" target="_blank">BBa_K5237011</a></td>
 +
          <td>Cathepsin B Expression Cassette</td>
 +
          <td>Cathepsin B which can be selectively express to cut the cleavable linker</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K52370012" target="_blank">BBa_K5237012</a></td>
 +
          <td>Caged NpuN Intein</td>
 +
          <td>Undergoes protein transsplicing after protease activation, can be used to create functionalized staple
 +
            units</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K52370013" target="_blank">BBa_K5237013</a></td>
 +
          <td>Caged NpuC Intein</td>
 +
          <td>Undergoes protein transsplicing after protease activation, can be used to create functionalized staple
 +
            units</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K52370014" target="_blank">BBa_K5237014</a></td>
 +
          <td>fgRNA processing casette</td>
 +
          <td>Processing casette to produce multiple fgRNAs from one transcript, can be used for multiplexing</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K52370015" target="_blank">BBa_K5237015</a></td>
 +
          <td>Intimin anti-EGFR Nanobody</td>
 +
          <td>Interkindom conjugation between bacteria and mammalian cells, as alternative delivery tool for large
 +
            constructs</td>
 +
        </tr>
 +
      </tbody>
 +
      <td colspan="3" align="left"><b>Readout Systems: </b>
 +
        FRET and enhancer recruitment to measure proximity of stapled DNA in bacterial and mammalian living cells
 +
        enabling swift testing and easy development for new systems.</td>
 +
      <tbody>
 +
        <tr bgcolor="#FFD700">
 +
          <td><a href="https://parts.igem.org/Part:BBa_K52370016" target="_blank">BBa_K5237016</a></td>
 +
          <td>FRET-Donor: mNeonGreen-Oct1</td>
 +
          <td>Donor part for the FRET assay binding the Oct1 binding cassette. Can be used to visualize DNA-DNA
 +
            proximity</td>
 +
        </tr>
 +
        <tr bgcolor="#FFD700">
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237017" target="_blank">BBa_K5237017</a></td>
 +
          <td>FRET-Acceptor: TetR-mScarlet-I</td>
 +
          <td>Acceptor part for the FRET assay binding the TetR binding cassette. Can be used to visualize DNA-DNA
 +
            proximity</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237018" target="_blank">BBa_K5237018</a></td>
 +
          <td>Oct1 Binding Casette</td>
 +
          <td>DNA sequence containing 12 Oct1 binding motifs, can be used for different assays such as the FRET
 +
            proximity assay</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237019" target="_blank">BBa_K5237019</a></td>
 +
          <td>TetR Binding Cassette</td>
 +
          <td>DNA sequence containing 12 Oct1 binding motifs, can be used for different assays such as the FRET
 +
            proximity assay</td>
 +
        </tr>
 +
        <td><a href="https://parts.igem.org/Part:BBa_K5237020" target="_blank">BBa_K5237020</a></td>
 +
        <td>Cathepsin B-Cleavable Trans-Activator: NLS-Gal4-GFLG-VP64</td>
 +
        <td>Readout system that responds to protease activity. It was used to test Cathepsin-B cleavable linker.</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237021" target="_blank">BBa_K5237021</a></td>
 +
          <td>NLS-Gal4-VP64</td>
 +
          <td>Trans-activating enhancer, that can be used to simulate enhancer hijacking. </td>
 +
        </tr>
 +
        <td><a href="https://parts.igem.org/Part:BBa_K5237022" target="_blank">BBa_K5237022</a></td>
 +
        <td>mCherry Expression Cassette: UAS, minimal Promotor, mCherry</td>
 +
        <td>Readout system for enhancer binding. It was used to test Cathepsin-B cleavable linker.</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237023" target="_blank">BBa_K5237023</a></td>
 +
          <td>Oct1 - UAS binding casette</td>
 +
          <td>Oct1 and UAS binding cassette, that was used for the simulated enhancer hijacking assay.</td>
 +
        </tr>
 +
        <tr>
 +
          <td><a href="https://parts.igem.org/Part:BBa_K5237024" target="_blank">BBa_K5237024</a></td>
 +
          <td>Minimal promoter Firefly luciferase</td>
 +
          <td>Contains Firefly luciferase controlled by a minimal promoter. It was used as a luminescence readout for
 +
            simulated enhancer hijacking.</td>
 +
        </tr>
 +
      </tbody>
 +
    </table>
 +
    </p>
 +
  </section>
 +
  <section id="1">
 +
    <h1>1. Sequence overview</h1>
 +
  </section>
 +
</body>
 +
 
 +
</html>
 +
 
 +
<!--################################-->
 
<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K5237006 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K5237006 SequenceAndFeatures</partinfo>
 +
<!--################################-->
 +
 +
<html>
 +
 +
 +
<section id="2">
 +
  <h1>2. Usage and Biology</h1>
 +
  <div class="thumb">
 +
    <div class="thumbinner" style="width:452px;"><a href="placeholder" class="image"><img alt=""
 +
          src="https://static.igem.wiki/teams/5237/picasso-iconlr-transp.svg" width="450" height="313"
 +
          class="thumbimage" style="width: 80%; height: auto;"></a>
 +
      <div class="thumbcaption">
 +
        <i><b>Figure 1</b></i><br>
 +
        <i>Lorem Ipsum</i>
 +
      </div>
 +
    </div>
 +
  </div>
 +
  <p>The Simple Staple (Oct1-DBD-TetR fusion) combines the well-characterized bacterial transcriptional repressor TetR
 +
    with
 +
    the human transcription factor Oct1-DBD, creating a versatile DNA-binding protein capable of bringing two DNA
 +
    sequences
 +
    into proximity. TetR naturally functions in gram-negative bacteria by regulating the expression of the tetA gene in
 +
    response to tetracycline. It binds selectively to palindromic tetO sequences with high affinity, forming a homodimer
 +
    that dissociates upon exposure to tetracycline, allowing gene expression (Berens & Hillen, 2004). Its
 +
    well-understood
 +
    DNA-binding properties make it a reliable component in synthetic biology, particularly in systems where controlled
 +
    DNA
 +
    interactions are crucial.</p>
 +
 +
  <p>Oct1-DBD is a component of the human transcription factor Oct1, involved in immune
 +
    regulation and stress responses. It binds specifically to the octamer motif (5'-ATGCAAAT-3') in promoter and enhancer
 +
    regions, stabilizing DNA binding through its POU-specific and POU homeodomains (Lundbäck <i>et al.</i>, 2000). Previous studies
 +
    have demonstrated that Oct1-DBD can be readily fused to other proteins, increasing solubility and preserving DNA-binding
 +
    capabilities (Park <i>et al.</i>, 2013; Stepchenko <i>et al.</i>, 2021).</p>
 +
 +
  <p>By fusing these two proteins, the Simple staple was developed to bridge DNA sequences carrying their respective binding
 +
    motifs. This bivalent DNA-binding system was successfully applied in our project to establish a FRET-based proximity
 +
    assay, enabling real-time monitoring of DNA interactions in bacterial systems. This versatile and modular approach opens
 +
    up new possibilities for synthetic gene regulation and spatial genome organization.</p>
 +
</section>
 +
<section id="3">
 +
  <h1>3. Assembly and part evolution</h1>
 +
  <p>The Oct1-DBD amino acid sequence was obtained from UniProt (<a href="https://www.uniprot.org/uniprot/P14859"
 +
      target="_blank">P14859</a>, POU domain, class 2, transcription factor 1)
 +
    and DNA binding domain extracted based on information given from Park <i>et al.</i> 2013 & 2020. TetR amino acid
 +
    sequence was obtaine from UniProt(<a href="https://www.uniprot.org/uniprotkb/P04483/entry"
 +
      target="_blank">P04483</a>). Coding sequences were codon optimized for <i>E. coli</i> and obtained through gene synthesis.
 +
    The proteins were genetically linked with a short GSGGS linker.
 +
  </p>
 +
</section>
 +
<section id="4">
 +
  <h1>4. Results</h1>
 +
  <h2><i>In vitro</i> DNA binding</h2>
 +
  <p>The Simple staple construct was modified with a C-terminal His<sub>6</sub>-tag and expressed under T7 promoter.
 +
    Protein was purified with a Ni-NTA affinity column. Fractions were analysed on a 4-15 % SDS-Page (Fig. 2). Strong bands
 +
    of the protein of interest are visible in the raw lysate indicating strong expression. Even though a strong band was seen in the flow through,
 +
    indicating unbound protein of interest, the purified fraction showed a strong band with almost no unspecific proteins co-purified. The eluate contained 1.5 mg/mL protein,
 +
    resulting in a total of &#8967; 3.34 mg purified protein.</p>
 +
    <div class="thumb">
 +
      <div class="thumbinner" style="width:200px;"><img alt="SDS-PAGE_tetR-Oct1"
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            src="https://static.igem.wiki/teams/5237/wetlab-results/bs-sds-page-tetr-oct1-fus.svg" style="width:99%;" class="thumbimage">
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          <i><b>Figure 2: SDS-PAGE analysis of the TetR-Oct1 fusion protein.</b></i> Fractions were loaded on a 4-15 % SDS-PAGE gel and stained with coomassie blue.
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          Lane 1: raw lysate, Lane 2: flow through, Lane 3: purified fraction.
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  <h1>5. References</h1>
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  <p>Wu, W., Zhang, L., Yao, L., Tan, X., Liu, X., & Lu, X. (2015). Genetically assembled fluorescent biosensor
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    for in situ detection of bio-synthesized alkanes. Scientific reports, 5, 10907. <a
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      href="https://doi.org/10.1038/srep10907" target="_blank">https://doi.org/10.1038/srep10907</a></p>
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===Functional Parameters===
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Revision as of 14:29, 28 September 2024


BBa_K5237006

Simple-Staple: TetR-Oct1

The Simple Staple (Oct1-DBD-TetR fusion) is a bivalent DNA-binding protein designed to bring two DNA sequences into close proximity, combining the human Oct1 DNA-binding domain (Oct1-DBD) and the bacterial tetracycline repressor protein (TetR). Oct1-DBD recognizes the octamer motif, while TetR binds specifically to the tetO operator sequences. This Simple Staple was applied to establish a Förster Resonance Energy Transfer (FRET)-based assay, which was used to monitor DNA-DNA proximity in bacterial systems.

 

The PICasSO Toolbox


Figure 1: Example how the part collection can be used to engineer new staples


The 3D organization of the genome plays a crucial role in regulating gene expression in eukaryotic cells, impacting cellular behavior, evolution, and disease. Beyond the linear DNA sequence, the spatial arrangement of chromatin, influenced by DNA-DNA interactions, shapes pathways of gene regulation. However, the tools to precisely manipulate this genomic architecture remain limited, rendering it challenging to explore the full potential of the 3D genome in synthetic biology. We - iGEM Team Heidelberg 2024 - have developed PICasSO, a powerful molecular toolbox based on various DNA-binding proteins to address this issue.

The PICasSO part collection offers a comprehensive, modular platform for precise manipulation and re-programming of DNA-DNA interactions using protein staples in living cells, enabling researchers to recreate natural 3D genomic interactions, such as enhancer hijacking, or to design entirely new spatial architectures for gene regulation. Beyond its versatility, PICasSO includes robust assay systems to support the engineering, optimization, and testing of new staples, ensuring functionality in vitro and in vivo. We took special care to include parts crucial for testing every step of the cycle (design, build, test, learn) when engineering new parts

At its heart, the PICasSO part collection consists of three categories. (i) Our DNA-binding proteins include our finalized enhancer hijacking Cas staple as well as half staples that can be used by scientists to compose entirely new Cas staples in the future. We also include our simple staples that serve as controls for successful stapling and can be further engineered to create alternative, simpler and more compact staples. (ii) As functional elements, we list additional parts that enhance the functionality of our Cas and Basic staples. These consist of protease-cleavable peptide linkers and inteins that allow condition-specific, dynamic stapling in vivo. Besides staple functionality, we also include the parts to enable the efficient delivery of PICasSO's with our interkingdom conjugation system.

(iii) As the final component of our collection, we provide parts that support the use of our custom readout systems. These include components of our established FRET-based proximity assay system, enabling users to confirm accurate stapling. Additionally, we offer a complementary, application-oriented testing system for functional readout via a luciferase reporter, which allows for straightforward experimental simulation of enhancer hijacking.

The following table gives a complete overview of all parts in our PICasSO toolbox. The highlighted parts showed exceptional performance as described on our iGEM wiki and can serve as a reference. The other parts in the collection are versatile building blocks designed to provide future iGEMers with the flexibility to engineer their own custom Cas staples, enabling further optimization and innovation

Our parts collection includes:

DNA-binding proteins: The building blocks for engineering of custom staples for DNA-DNA interactions with a modular system ensuring easy assembly.
BBa_K5237000 fgRNA Entryvector MbCas12a-SpCas9 Entryvector for simple fgRNA cloning via SapI
BBa_K5237001 Half-Staple: dMbCas12a-Nucleoplasmin NLS Staple subunit that can be combined to form a functional staple, for example with fgRNA and dCas9
BBa_K5237002 Half-Staple: SV40 NLS-dSpCas9-SV40 NLS Staple subunit that can be combined to form a functional staple, for example with our fgRNA or dCas12a
BBa_K5237003 Cas-Staple: SV40 NLS-dMbCas12a-dSpCas9-Nucleoplasmin NLS Functional Cas staple that can be combined with sgRNA or fgRNA to bring two DNA strands in close proximity
BBa_K5237004 Half-Staple: Oct1-DBD Staple subunit that can be combined to form a functional staple, for example with TetR.
Can also be combined with a fluorescent protein as part of the FRET proximity assay
BBa_K5237005 Half-Staple: TetR Staple subunit that can be combined to form a functional staple, for example with Oct1.
Can also be combined with a fluorescent protein as part of the FRET proximity assay
BBa_K5237006 Simple-Staple: TetR-Oct1 Functional staple that can be used to bring two DNA strands in close proximity
BBa_K5237007 Half-Staple: GCN4 Staple subunit that can be combined to form a functional staple, for example with rGCN4
BBa_K5237008 Half-Staple: rGCN4 Staple subunit that can be combined to form a functional staple, for example with rGCN4
BBa_K5237009 Mini-Staple: bGCN4 Assembled staple with minimal size that can be further engineered
Functional elements: Protease cleavable peptide linkers and inteins are used to control and modify staples for further optimization for custom applications.
BBa_K5237010 Cathepsin B-Cleavable Linker (GFLG) Cathepsin B cleavable peptide linker, that can be used to combine two staple subunits ,to make responsive staples
BBa_K5237011 Cathepsin B Expression Cassette Cathepsin B which can be selectively express to cut the cleavable linker
BBa_K5237012 Caged NpuN Intein Undergoes protein transsplicing after protease activation, can be used to create functionalized staple units
BBa_K5237013 Caged NpuC Intein Undergoes protein transsplicing after protease activation, can be used to create functionalized staple units
BBa_K5237014 fgRNA processing casette Processing casette to produce multiple fgRNAs from one transcript, can be used for multiplexing
BBa_K5237015 Intimin anti-EGFR Nanobody Interkindom conjugation between bacteria and mammalian cells, as alternative delivery tool for large constructs
Readout Systems: FRET and enhancer recruitment to measure proximity of stapled DNA in bacterial and mammalian living cells enabling swift testing and easy development for new systems.
BBa_K5237016 FRET-Donor: mNeonGreen-Oct1 Donor part for the FRET assay binding the Oct1 binding cassette. Can be used to visualize DNA-DNA proximity
BBa_K5237017 FRET-Acceptor: TetR-mScarlet-I Acceptor part for the FRET assay binding the TetR binding cassette. Can be used to visualize DNA-DNA proximity
BBa_K5237018 Oct1 Binding Casette DNA sequence containing 12 Oct1 binding motifs, can be used for different assays such as the FRET proximity assay
BBa_K5237019 TetR Binding Cassette DNA sequence containing 12 Oct1 binding motifs, can be used for different assays such as the FRET proximity assay
BBa_K5237020 Cathepsin B-Cleavable Trans-Activator: NLS-Gal4-GFLG-VP64 Readout system that responds to protease activity. It was used to test Cathepsin-B cleavable linker.
BBa_K5237021 NLS-Gal4-VP64 Trans-activating enhancer, that can be used to simulate enhancer hijacking.
BBa_K5237022 mCherry Expression Cassette: UAS, minimal Promotor, mCherry Readout system for enhancer binding. It was used to test Cathepsin-B cleavable linker.
BBa_K5237023 Oct1 - UAS binding casette Oct1 and UAS binding cassette, that was used for the simulated enhancer hijacking assay.
BBa_K5237024 Minimal promoter Firefly luciferase Contains Firefly luciferase controlled by a minimal promoter. It was used as a luminescence readout for simulated enhancer hijacking.

1. Sequence overview

Sequence and Features


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BamHI site found at 493
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]

2. Usage and Biology

Figure 1
Lorem Ipsum

The Simple Staple (Oct1-DBD-TetR fusion) combines the well-characterized bacterial transcriptional repressor TetR with the human transcription factor Oct1-DBD, creating a versatile DNA-binding protein capable of bringing two DNA sequences into proximity. TetR naturally functions in gram-negative bacteria by regulating the expression of the tetA gene in response to tetracycline. It binds selectively to palindromic tetO sequences with high affinity, forming a homodimer that dissociates upon exposure to tetracycline, allowing gene expression (Berens & Hillen, 2004). Its well-understood DNA-binding properties make it a reliable component in synthetic biology, particularly in systems where controlled DNA interactions are crucial.

Oct1-DBD is a component of the human transcription factor Oct1, involved in immune regulation and stress responses. It binds specifically to the octamer motif (5'-ATGCAAAT-3') in promoter and enhancer regions, stabilizing DNA binding through its POU-specific and POU homeodomains (Lundbäck et al., 2000). Previous studies have demonstrated that Oct1-DBD can be readily fused to other proteins, increasing solubility and preserving DNA-binding capabilities (Park et al., 2013; Stepchenko et al., 2021).

By fusing these two proteins, the Simple staple was developed to bridge DNA sequences carrying their respective binding motifs. This bivalent DNA-binding system was successfully applied in our project to establish a FRET-based proximity assay, enabling real-time monitoring of DNA interactions in bacterial systems. This versatile and modular approach opens up new possibilities for synthetic gene regulation and spatial genome organization.

3. Assembly and part evolution

The Oct1-DBD amino acid sequence was obtained from UniProt (P14859, POU domain, class 2, transcription factor 1) and DNA binding domain extracted based on information given from Park et al. 2013 & 2020. TetR amino acid sequence was obtaine from UniProt(P04483). Coding sequences were codon optimized for E. coli and obtained through gene synthesis. The proteins were genetically linked with a short GSGGS linker.

4. Results

In vitro DNA binding

The Simple staple construct was modified with a C-terminal His6-tag and expressed under T7 promoter. Protein was purified with a Ni-NTA affinity column. Fractions were analysed on a 4-15 % SDS-Page (Fig. 2). Strong bands of the protein of interest are visible in the raw lysate indicating strong expression. Even though a strong band was seen in the flow through, indicating unbound protein of interest, the purified fraction showed a strong band with almost no unspecific proteins co-purified. The eluate contained 1.5 mg/mL protein, resulting in a total of ⌇ 3.34 mg purified protein.

SDS-PAGE_tetR-Oct1
Figure 2: SDS-PAGE analysis of the TetR-Oct1 fusion protein. Fractions were loaded on a 4-15 % SDS-PAGE gel and stained with coomassie blue. Lane 1: raw lysate, Lane 2: flow through, Lane 3: purified fraction.

5. References

Wu, W., Zhang, L., Yao, L., Tan, X., Liu, X., & Lu, X. (2015). Genetically assembled fluorescent biosensor for in situ detection of bio-synthesized alkanes. Scientific reports, 5, 10907. https://doi.org/10.1038/srep10907