Difference between revisions of "Part:BBa K2918029"

Revision as of 22:09, 18 October 2019

OriL-GFP-Kan-OriR

Linear plasmid for replication by Φ29 replication machinery.

Sequence and Features

Assembly Compatibility:

10
INCOMPATIBLE WITH RFC[10]
Illegal EcoRI site found at 664
Illegal EcoRI site found at 2056
12
INCOMPATIBLE WITH RFC[12]
Illegal EcoRI site found at 664
Illegal EcoRI site found at 2056
Illegal NheI site found at 956
21
INCOMPATIBLE WITH RFC[21]
Illegal EcoRI site found at 664
Illegal EcoRI site found at 2056
Illegal BamHI site found at 873
23
INCOMPATIBLE WITH RFC[23]
Illegal EcoRI site found at 664
Illegal EcoRI site found at 2056
25
INCOMPATIBLE WITH RFC[25]
Illegal EcoRI site found at 664
Illegal EcoRI site found at 2056
1000
COMPATIBLE WITH RFC[1000]

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

Overview

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

Usage and Biology

The Φ29 replication mechanism involves replication of a protein-primed based replication linear DNA. Protein primed replication, unlike the conventional DNA or RNA primed mechanism, do not depend on specific sequences of DNA/RNA and 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 (DSB/p6) 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 (Nies et al, 2018). The replication mechanism is depicted in the Figure 1.

Figure 1: Overview of phi 29 replication mechanism

Strain Construction

The construct was assembled by golden gate assembly based modular cloning system. First, the individual transcriptional units were cloned into level 1 destination vectors [http://www.addgene.org/47998/pICH47732] and [http://www.addgene.org/47998/pICH47742] by BpiI based golden gate assembly. The multi-transcriptional unit construct was assembled by a BsaI based golden gate. The assembly was a one-pot restriction-ligation reaction where the individual level 1 constructs were added along with the destination vector [http://www.addgene.org/47998/pICH8031] and the construct was confirmed by sequencing. The cloning protocol can be found in the MoClo 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. The complete sequence of our parts including backbone can be found here.

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

@@ Line 12: / Line 12: @@
 ===Overview===
-<p>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 replication, greatly simplifies the design of replication systems. The Φ29 replication begins at origins of replication (OriR and OriL) on two sides of a linear protein primed linear DNA <html><a href="#Nies2018">(Nies et al, 2018)</a></html>.The Φ29 replication can be established by using four simple proteins: Φ29 DNA polymerase (DNAP/p2),terminal protein [https://parts.igem.org/Part:BBa_K2918001 (TP/p3)],single stranded binding protein [https://parts.igem.org/Part:BBa_K2918002 (SSB/p5)] and double stranded binding protein [https://parts.igem.org/Part:BBa_K2918003 (DSB/p6)].
+The part has been confirmed by sequencing and there are no mutations.
-The replication process begins by binding of the Φ29 DNA polymerase and terminal protein complex at the origins of replication <html><a href="#Nies2018">(Nies et al, 2018)</a></html>.The Φ29 DNA polymerase is a single subunit protein known to have high processivity, it has been shown to synthesize upto 70 kilobase pairs of DNA <html><a href="#Blanco1988">(Blanco et al, 1988)</a></html>. The double stranded DNA binding proteins [https://parts.igem.org/Part:BBa_K2918003 (DSB/p6)] aid in the process of replication and binds 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>.</p>
-Insert Φ29 replication animation/image!
+===Usage and Biology===
-The Φ29 replication system is promising in many ways:
+The Φ29 replication mechanism involves replication of a protein-primed based replication linear DNA. Protein primed replication, unlike the conventional DNA or RNA primed mechanism, do not depend on specific sequences of DNA/RNA and 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>.
+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>. The replication mechanism is depicted in the Figure 1.
+<div><ul>
+<center>
+   <li style="display: inline-block;"> [[File:T--TUDelft--replicationpartstest.jpg|thumb|none|550px|<b>Figure 1:</b> Overview of phi 29 replication mechanism]] </li>
+</center>
+    </ul></div>
--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>
--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>
--The existing DNA-protein covalent bonds offer many possibilities to engineer the terminal proteins with functional peptide
-sequences. <br>
--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.<br>
--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. <br>
 ===Strain Construction===