Difference between revisions of "Part:BBa K2918023"

Revision as of 18:00, 3 October 2019

Weak T7 promoter - Universal RBS - Φ29 DSB (p6) - WT T7 terminator

This part consists of a T7 promotor, a universal Ribosome Binding Site (RBS), a Coding DNA Sequence (CDS) coding for the DSB p6 and a Wild Type T7 terminator.

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
INCOMPATIBLE WITH RFC[25]
Illegal AgeI site found at 292
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI site found at 68
Illegal BsaI.rc site found at 94

Overview

The replication of DNA and its conversion into functional proteins are vital processes in all living systems. DNA is copied during the replication process. The bacteriophage Φ29 contains a DNA replication machinery which replicates the linear plasmid by itself. This process is called orthogonal replication and can be beneficially used. The desired gene can be expressed in other hosts without interfering with the genome of its host. Our Sci-Phi 29 tool is based on the Φ29 DNA replication system and its four proteins. The terminal proteins (TP) cap the linear DNA, protect the linear DNA and are the starting point for the Φ29 DNA polymerase (DNAP/p2). DNAP binds to the TP and replicates the DNA. During the replication, single and double stranded DNA is protected by respectively single stranded DNA binding proteins (SSB/p5) and double stranded DNA binding proteins (DSB/p6).

Strain Construction

Identification of the DSB protein

For identifying our constructs we used PURE(Protein synthesis Using Recombinant Elements) system. This is an E.coli based cell-free protein synthesis system and it contains all the elements to make in vitro translation-transcription possible. A 10-μL reaction consists of 0.5 μL enzym solution, 1 μL ribosome solution, 0.5 μL Green Lyse, 5 nM DNA and RNAse-free milliQ for filling up the volume. The proteins were identified by an 18% SDS-PAGE gel and mass spectrometry.

SDS-PAGE

Figure

An SDS-PAGE was carried out for the DSB protein with 3 different promoter strengths: Wild-Type, 0.5 and 0.1. For a control PURE solution without any DNA was used. As can be concluded from the figure, in the sample containing the p6 protein a band can be found at the expected height(13kb). The band is also absent in the control, indicating that the p6 protein was successfully produced in the PURE system using this construct.

Mass Spectrometry

In addition to the SDS-PAGE, the identity of the proteins was also confirmed by mass spectrometry. To do this, a sequence unique to the DSB’s amino acid sequence were chosen and screened for their presence in the PURE system. For the p6 the peptide sequences are: GEPVQVVSVEPNTEVYELPVEK and FLEVATVR. Data was normalized to the presence of the EF-TU protein, which can be found in the same amount in all PURE system solutions.

Figure

The peak areas of the resulting mass spectrographs shown in Figure ? reflect the occurrence of a given sequence in the sample. The unique peptides that were screened for were only present in each protein expected to contain the sequence.

Hence, it can be concluded that the results were positive and the identity of the proteins could be verified by mass spectrometry.

In Vitro replication

Toxicity

Our sci-phi29 tool is based on four components of the Φ29 bacteriophage: DNAP, TP, p5 and p6. However, overexpression of these proteins are toxic for the cell. In order to determine the optimal expression levels of the proteins in live cells, we carried out viability assays in E.coli BL21(DE3)PlysS. The results are shown in the graphs below…

@@ Line 23: / Line 23: @@
 Figure
-An SDS-PAGE was carried out for the DSB protein with 3 different promoter strengths: Wild-Type, 0.5 and 0.1. For a control PURE solution without any DNA was used. The
+An SDS-PAGE was carried out for the DSB protein with 3 different promoter strengths: Wild-Type, 0.5 and 0.1. For a control PURE solution without any DNA was used. As can be concluded from the figure, in the sample containing the p6 protein a band can be found at the expected height(13kb). The band is also absent in the control, indicating that the p6 protein was successfully produced in the PURE system using this construct.
 <b>Mass Spectrometry </b>
-In addition to the SDS-PAGE, the identity of the proteins was also confirmed by mass spectrometry. To do this, a sequence unique to the DSB’s amino acid sequence were chosen and screened for their presence in the PURE system. For the p6 the peptide sequences are: <i>GEPVQVVSVEPNTEVYELPVEK</i> and <i>FLEVATVR</i>
+In addition to the SDS-PAGE, the identity of the proteins was also confirmed by mass spectrometry. To do this, a sequence unique to the DSB’s amino acid sequence were chosen and screened for their presence in the PURE system. For the p6 the peptide sequences are: <i>GEPVQVVSVEPNTEVYELPVEK</i> and <i>FLEVATVR</I>. Data was normalized to the presence of the EF-TU protein, which can be found in the same amount in all PURE system solutions.
 Figure