Difference between revisions of "Part:BBa K2918061"

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<partinfo>BBa_K2918061 short</partinfo>
 
<partinfo>BBa_K2918061 short</partinfo>
  
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<span class='h3bb'>Sequence and Features</span>
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Φ29 bacteriophage origin of replication (OriR)
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<partinfo>BBa_K2918061 SequenceAndFeatures</partinfo>
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===Usage and Biology===
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<span class='h3bb'>Sequence and Features</span><partinfo>BBa_K2918061 SequenceAndFeatures</partinfo>
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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, but the presence of multiple copies of the same ribozyme in different genes may result in homologous recombination <html><a href="#Lou2012">(Lou et al., 2012)</a></html>. With that in mind, we, from TU Delft 2019, have designed Type IIS parts of both ribozymes and RBS for modular assembly in any combination desired.
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Unfortunately, junction sequences such as Type IIS overhangs between ribozyme and RBS can also influence translation rates. To achieve scarless modular cloning of ribozymes and RBS, the strategy illustrated below can be adopted.  
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The part has been confirmed by sequencing and there are no mutations.
  
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<html><a href="#Lou2012">Lou et al., 2012</a></html> have screened and identified a series of ribozymes for insulating genetic circuits. All of these ribozymes contain conserved 3’ ends  (ACCTCTACAAATAATTTT<b>GTTT</b>AA) and the 4 highlight nucleotides can be used as a fusion site identified as compatible to Type IIS cloning. In the RBS sequence, AA should be added upstream in order to complement the incomplete ribozyme sequence when assembled.
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===Usage and Biology===
  
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===Strain Construction===
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The Φ29 replication mechanism is a unique protein-primed based replication of a linear plasmid. Protein primed replication, unlike the conventional DNA or RNA primed mechanism, greatly simplifies the design of replication systems. The Φ29 replication can be established by using four simple proteins: Φ29 DNA polymerase (DNAP/p2),terminal protein <html><a href="https://parts.igem.org/Part:BBa_K2918001"> (TP/p3)</a></html>, single stranded binding protein <html><a href="https://parts.igem.org/Part:BBa_K2918002"> (SSB/p5)</a></html> and double stranded binding protein <html><a href="https://parts.igem.org/Part:BBa_K2918003"> (DSB/p6)</a></html>.
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The DNA sequence of the part was synthesized by IDT with flanking BsaI sites and AATG 3' overhang. The RBS was then cloned along with an altered ribozyme [https://parts.igem.org/Part:BBa_K2918012/ RiboJ] in a level 0 MoClo backbone [http://www.addgene.org/47992/ pICH41246] and the sequence was confirmed by sequencing. The cloning protocol can be found in the modular cloning section below. Click <html><a href="http://2019.igem.org/Team:TUDelft/Experiments" target="_blank">here</a></html> for the detailed protocol.
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The replication process begins by binding of the Φ29 DNA polymerase and terminal protein complex at the origins of replication (OriR and OriL), which flank the protein-primed linear plasmid <html><a href="#Nies2018">(Nies et al, 2018)</a></html>. The double stranded DNA binding proteins <html><a href="https://parts.igem.org/Part:BBa_K2918003 (DSB/p6)</a></html> aid in the process of replication and bind more intensely at the origins of replication (OriR and OriL), destabilizing the region and facilitating strand displacement. Single stranded binding proteins bind to the displaced DNA strand preventing strand switching of the DNA polymerase and protecting the linear plasmid from host nucleases <html><a href="#Nies2018">(Nies et al, 2018)</a></html>.
  
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===Modular Cloning===
 
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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).
 
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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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Insert Φ29 replication animation/image!
  
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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. The complete sequence of our parts including backbone can be found <html><a href="http://2019.igem.org/Team:TUDelft/Experiments" target="_blank">here</a>.</html></b>
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The Φ29 replication system is promising in many ways:
  
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-The Φ29 DNA Polymerase has the highest processivity of all known single subunit DNA polymerases <html><a href="#Blanco1988">(Blanco et al, 1988)</a></html>, and can be used for whole genome amplification. <br>
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-The Φ29 machinery along with cell free expression systems can be used to establish the three dogmas of biology in-vitro. Setting the basis for artificial cell development. <br>
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-The existing DNA-protein covalent bonds offer many possibilities to engineer the terminal proteins with functional peptide
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sequences. <br>
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-We envision that the unique configuration of the double-stranded, protein-capped linear replicon will be a basis for many
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new engineered protein-DNA complexes.<br>
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-Orthogonal replication not only enables replication independent from the host, but the ability to engineer the orthogonal
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DNA polymerase’s fidelity without introducing mutations in the cell’s genome makes in vivo directed evolution a
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possibility. <br>
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===Characterization===
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        <b>Table 1:</b> Overview of different level in MoClo
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to be edited
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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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                <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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===Strain Construction===
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            <tr>        <td>Level 1</td>
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The DNA sequence of the part was synthesized by IDT and cloned by restriction-ligation in <html><a href="http://www.addgene.org/47998/pICH41308"> pICH47732 </a></html> and the sequence was confirmed by sequencing. The cloning protocol can be found in the MoClo section below.
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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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                    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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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.
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        <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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            <tr>
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                <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>
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            </tr>
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                    Promoter
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                </td>
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                <td>NNNN <span style="color:limegreen">GAAGAC</span> NN <span style="color:dodgerblue">GGAG</span></td>
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                <td><span style="color:dodgerblue">TACT</span> NN <span style="color:limegreen">GTCTTC</span> NNNN</td>
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                <td>pICH41233</td>
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            <tr>        <td>5’ UTR</td>
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                <td>NNNN <span style="color:limegreen">GAAGAC</span> NN <span style="color:dodgerblue">TACT</span></td>
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                <td><span style="color:dodgerblue">AATG</span> NN <span style="color:limegreen">GTCTTC</span> NNNN</td>
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                <td>pICH41246</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>
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                <td><span style="color:dodgerblue">GCTT</span> NN <span style="color:limegreen">GTCTTC</span> NNNN</td>
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                <td>pICH41308</td>
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                    Terminator</td>
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                <td>NNNN <span style="color:limegreen">GAAGAC</span> NN <span style="color:dodgerblue">GCTT</span></td>
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                <td><span style="color:dodgerblue">CGCT</span> NN <span style="color:limegreen">GTCTTC</span> NNNN</td>
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                <td>pICH41276</td>
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===References===
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<li>
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<a id="Lou2012" href="https://www.nature.com/articles/nbt.2401" target="_blank">
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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>
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Revision as of 17:59, 17 October 2019

Φ29 Right origin of replication (OriR)

Φ29 bacteriophage origin of replication (OriR)

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 there are no mutations.

Usage and Biology

The Φ29 replication mechanism is a unique protein-primed based replication of a linear plasmid. Protein primed replication, unlike the conventional DNA or RNA primed mechanism, greatly simplifies the design of replication systems. The Φ29 replication can be established by using four simple proteins: Φ29 DNA polymerase (DNAP/p2),terminal protein (TP/p3), single stranded binding protein (SSB/p5) and double stranded binding protein (DSB/p6). The replication process begins by binding of the Φ29 DNA polymerase and terminal protein complex at the origins of replication (OriR and OriL), which flank the protein-primed linear plasmid (Nies et al, 2018). The double stranded DNA binding proteins (Nies et al, 2018).


Insert Φ29 replication animation/image!

The Φ29 replication system is promising in many ways:

-The Φ29 DNA Polymerase has the highest processivity of all known single subunit DNA polymerases (Blanco et al, 1988), and can be used for whole genome amplification.
-The Φ29 machinery along with cell free expression systems can be used to establish the three dogmas of biology in-vitro. Setting the basis for artificial cell development.
-The existing DNA-protein covalent bonds offer many possibilities to engineer the terminal proteins with functional peptide sequences.
-We envision that the unique configuration of the double-stranded, protein-capped linear replicon will be a basis for many new engineered protein-DNA complexes.
-Orthogonal replication not only enables replication independent from the host, but the ability to engineer the orthogonal DNA polymerase’s fidelity without introducing mutations in the cell’s genome makes in vivo directed evolution a possibility.




Characterization

to be edited

Strain Construction

The DNA sequence of the part was synthesized by IDT and cloned by restriction-ligation in pICH47732 and the sequence was confirmed by sequencing. The cloning protocol can be found in the MoClo section below.