Difference between revisions of "Part:BBa K2918013"

 
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__NOTOC__
 
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<partinfo>BBa_K2918013 short</partinfo>
 
<partinfo>BBa_K2918013 short</partinfo>
  
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BioBrick BBa_B0032 (RBS) along with ribozyme (SarJ).
  
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<!-- Add more about the biology of this part here
 
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===Usage and Biology===
 
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<span class='h3bb'>Sequence and Features</span>
 
<span class='h3bb'>Sequence and Features</span>
 
<partinfo>BBa_K2918013 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K2918013 SequenceAndFeatures</partinfo>
  
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The part has been confirmed by sequencing and has no mutations.
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===Usage and Biology===
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Many promoter parts contain sequences downstream of the Transcription Start Site (such as operators or assembly fusion sites) resulting in extra unintended sequences in the transcript. These additional sequences are shown to significantly affect gene expression levels, disrupting the modularity and predictability of synthetic parts <html><a href="#Lou2012">(Lou et al., 2012)</a></html>. Therefore, to insulate the translation rates of the part from the use of different promoters, ribozymes can be used for their self cleavage properties and remove these sequences upstream of mRNA. By the inclusion of ribozymes in 5’ UTR parts, outputs of genetic circuits will be insulated from genetic context. The presence of multiple copies of the same ribozyme in different genes may result in homologous recombination and hence a series of ribozymes have been engineered <html><a href="#Lou2012">(Lou et al., 2012)</a></html>.
 +
This BioBrick consists of <html><a href="https://parts.igem.org/Part:BBa_K2918039">SarJ</a> and <html><a href="https://parts.igem.org/Part:BBa_B0032">BBa_B0032</a></html>.
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===Strain Construction===
 +
The DNA sequence of the part was synthesized by IDT with flanking BpiI sites and respective Modular Cloning (MoClo) compatible 5' UTR overhangs. The RBS was then cloned in a level 0 MoClo backbone <html><a href="http://www.addgene.org/47992">pICH41246</a></html> and the sequence was confirmed by sequencing. The cloning protocol can be found in the modular cloning section below.
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===Modular Cloning===
 +
Modular Cloning (MoClo) is a system which allows for efficient one pot assembly of multiple DNA fragments. The MoClo system consists of Type IIS restriction enzymes that cleave DNA 4 to 8 base pairs away from the recognition sites. Cleavage outside of the recognition site allows for customization of the overhangs generated. The MoClo system is hierarchical. First, basic parts (promoters, UTRs, CDS and terminators) are assembled in level 0 plasmids in the kit. In a single reaction, the individual parts can be assembled into vectors containing transcriptional units (level 1). Furthermore, MoClo allows for directional assembly of multiple transcriptional units. Successful assembly of constructs using MoClo can be confirmed by visual readouts (blue/white or red/white screening).
 +
For the protocol, you can find it <html><a href="http://2019.igem.org/Team:TUDelft/Experiments" target="_blank">here</a>.</html>
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 +
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<b>Note: The basic parts sequences of the Sci-Phi 29 collection in the registry contain only the part sequence and therefore contain no overhangs or restriction sites. For synthesizing MoClo compatible parts, refer to table 2. </b>
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<html>
 +
    <style>
 +
 +
        #tabletu {
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            background-color: transparent;
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            border-collapse: collapse;
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            width:80%;
 +
        }
 +
 +
        #tabletu td, th {
 +
            border: 1px solid #000000;
 +
            padding: 8px;
 +
        }
 +
 +
        #tabletu th {
 +
            padding: 8px;
 +
            text-align: left;
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            border: 1px solid #000000; 
 +
            background-color: rgba(0,110,167,1);
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            color: white;
 +
        }
 +
 +
    </style>
 +
 +
    <body>
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        <b>Table 1:</b> Overview of different level in MoClo
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        <table id="tabletu">
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            <tr>
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                <th>Level
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                </th>
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                <th>Basic/Composite
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                </th>
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                <th>
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                    Type</th>
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                <th>Enzyme</th>
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            </tr>
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            <tr>
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                <td>
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                    Level 0
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                </td>
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                <td>Basic</td>
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                <td>Promoters, 5’ UTR, CDS and terminators</td>
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                <td>BpiI</td>
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 +
            </tr>
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            <tr>        <td>Level 1</td>
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                <td>Composite</td>
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                <td>Transcriptional units</td>
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                <td>BsaI</td>
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            </tr>
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            <tr>
 +
                <td>
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                    Level 2/M/P</td>
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                <td>Composite</td>
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                <td>Multiple transcriptional units</td>
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                <td>BpiI</td>
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            </tr>
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 +
 +
        </table>
 +
 +
 +
    </body>
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</html>
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 +
For synthesizing basic parts, the part of interest should be flanked by a <span style="color:limegreen">BpiI site</span> and its <span style="color:dodgerblue">specific type overhang</span>. These parts can then be cloned into the respective level 0 MoClo parts. For level 1, where individual transcriptional units are cloned, the overhangs come from the backbone you choose. The restriction sites for level 1 are BsaI. However, any type IIS restriction enzyme could be used.
 +
 +
 +
 +
<html>
 +
    <style>
 +
 +
        #tabletu {
 +
            background-color: transparent;
 +
            border-collapse: collapse;
 +
            width:100%;
 +
        }
 +
 +
        #tabletu td, th {
 +
            border: 1px solid #000000;
 +
            padding: 8px;
 +
        }
 +
 +
        #tabletu th {
 +
            padding: 8px;
 +
            text-align: left;
 +
            border: 1px solid #000000; 
 +
            background-color: rgba(0,110,167,1);
 +
            color: white;
 +
        }
 +
 +
 +
    </style>
 +
 +
    <body>
 +
        <b>Table 2:</b> Type specific overhangs and backbones for MoClo. Green indicates the restriction enzyme recognition site. Blue indicates the specific overhangs for the basic parts
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        <table id="tabletu">
 +
            <tr>
 +
                <th>Basic Part
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                </th>
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                <th>Sequence 5' End
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                </th>
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                <th>
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                    Sequence 3' End</th>
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                <th>Level 0 backbone</th>
 +
            </tr>
 +
            <tr>
 +
                <td>
 +
                    Promoter
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                </td>
 +
                <td>NNNN <span style="color:limegreen">GAAGAC</span> NN <span style="color:dodgerblue">GGAG</span></td>
 +
                <td><span style="color:dodgerblue">TACT</span> NN <span style="color:limegreen">GTCTTC</span> NNNN</td>
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                <td>pICH41233</td>
 +
 +
            </tr>
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            <tr>        <td>5’ UTR</td>
 +
                <td>NNNN <span style="color:limegreen">GAAGAC</span> NN <span style="color:dodgerblue">TACT</span></td>
 +
                <td><span style="color:dodgerblue">AATG</span> NN <span style="color:limegreen">GTCTTC</span> NNNN</td>
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                <td>pICH41246</td>
 +
            </tr>
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            <tr>
 +
                <td>
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                    CDS</td>
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                <td>NNNN <span style="color:limegreen">GAAGAC</span> NN <span style="color:dodgerblue">AATG</span></td>
 +
                <td><span style="color:dodgerblue">GCTT</span> NN <span style="color:limegreen">GTCTTC</span> NNNN</td>
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                <td>pICH41308</td>
 +
            </tr>
 +
            <tr>
 +
                <td>
 +
                    Terminator</td>
 +
                <td>NNNN <span style="color:limegreen">GAAGAC</span> NN <span style="color:dodgerblue">GCTT</span></td>
 +
                <td><span style="color:dodgerblue">CGCT</span> NN <span style="color:limegreen">GTCTTC</span> NNNN</td>
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                <td>pICH41276</td>
 +
            </tr>
 +
 +
 +
        </table>
 +
 +
 +
    </body>
 +
</html>
 +
 +
===References===
 +
<html>
 +
<ul>
 +
<li>
 +
<a id="Lou2012" href="https://www.nature.com/articles/nbt.2401" target="_blank">
 +
Lou, C., Stanton, B., Chen, Y.-J., Munsky, B., & Voigt, C. A. (2012). Ribozyme-based insulator parts buffer synthetic circuits from genetic context. <i>Nature Biotechnology</i>, 30(11), 1137–1142.</a>
 +
</li>
 +
</ul>
 +
</html>
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
−
<partinfo>BBa_K2918013 parameters</partinfo>
+
<partinfo>BBa_K2918014 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Latest revision as of 17:53, 6 December 2019

BBa_B0032 RBS and SarJ

BioBrick BBa_B0032 (RBS) along with ribozyme (SarJ).

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]

The part has been confirmed by sequencing and has no mutations.

Usage and Biology

Many promoter parts contain sequences downstream of the Transcription Start Site (such as operators or assembly fusion sites) resulting in extra unintended sequences in the transcript. These additional sequences are shown to significantly affect gene expression levels, disrupting the modularity and predictability of synthetic parts (Lou et al., 2012). Therefore, to insulate the translation rates of the part from the use of different promoters, ribozymes can be used for their self cleavage properties and remove these sequences upstream of mRNA. By the inclusion of ribozymes in 5’ UTR parts, outputs of genetic circuits will be insulated from genetic context. The presence of multiple copies of the same ribozyme in different genes may result in homologous recombination and hence a series of ribozymes have been engineered (Lou et al., 2012). This BioBrick consists of SarJ and BBa_B0032.

Strain Construction

The DNA sequence of the part was synthesized by IDT with flanking BpiI sites and respective Modular Cloning (MoClo) compatible 5' UTR overhangs. The RBS was then cloned in a level 0 MoClo backbone pICH41246 and the sequence was confirmed by sequencing. The cloning protocol can be found in the modular cloning section below.

Modular Cloning

Modular Cloning (MoClo) is a system which allows for efficient one pot assembly of multiple DNA fragments. The MoClo system consists of Type IIS restriction enzymes that cleave DNA 4 to 8 base pairs away from the recognition sites. Cleavage outside of the recognition site allows for customization of the overhangs generated. The MoClo system is hierarchical. First, basic parts (promoters, UTRs, CDS and terminators) are assembled in level 0 plasmids in the kit. In a single reaction, the individual parts can be assembled into vectors containing transcriptional units (level 1). Furthermore, MoClo allows for directional assembly of multiple transcriptional units. Successful assembly of constructs using MoClo can be confirmed by visual readouts (blue/white or red/white screening). For the protocol, you can find it here.


Note: The basic parts sequences of the Sci-Phi 29 collection in the registry contain only the part sequence and therefore contain no overhangs or restriction sites. For synthesizing MoClo compatible parts, refer to table 2.


Table 1: Overview of different level in MoClo

Level Basic/Composite Type Enzyme
Level 0 Basic Promoters, 5’ UTR, CDS and terminators BpiI
Level 1 Composite Transcriptional units BsaI
Level 2/M/P Composite Multiple transcriptional units BpiI

For synthesizing basic parts, the part of interest should be flanked by a BpiI site and its specific type overhang. These parts can then be cloned into the respective level 0 MoClo parts. For level 1, where individual transcriptional units are cloned, the overhangs come from the backbone you choose. The restriction sites for level 1 are BsaI. However, any type IIS restriction enzyme could be used.


Table 2: Type specific overhangs and backbones for MoClo. Green indicates the restriction enzyme recognition site. Blue indicates the specific overhangs for the basic parts

Basic Part Sequence 5' End Sequence 3' End Level 0 backbone
Promoter NNNN GAAGAC NN GGAG TACT NN GTCTTC NNNN pICH41233
5’ UTR NNNN GAAGAC NN TACT AATG NN GTCTTC NNNN pICH41246
CDS NNNN GAAGAC NN AATG GCTT NN GTCTTC NNNN pICH41308
Terminator NNNN GAAGAC NN GCTT CGCT NN GTCTTC NNNN pICH41276

References