Difference between revisions of "Part:BBa K4815017"
(→‎Sequence and Features)
 
(3 intermediate revisions by the same user not shown)
Line 1: Line 1:
 
__NOTOC__
 
__NOTOC__
−
<partinfo>BBa_K4815016 short</partinfo>
+
<partinfo>BBa_K4815017 short</partinfo>
 
===Description===
 
===Description===
−
The functional promoter sequence (about 223 bp) generated by our AI model Pymaker is inserted into the dual-fluorescence reporter system for characterization and we describe it as pDualPH6. Random DNA yields diverse expression levels in a yeast promoter library, while we can use the episomal dual reporter system expressing a constitutive red fluorescent protein (RFP) and a variable yellow fluorescent protein (YFP) to quantify promoter activity. By adpoting the log(YFP/RFP) measured using flow cytometry, we can detect the expression rate of our synthesized promoters. The advantage of this system is its ability to eliminate the influence of plasmid copy number and the growth status of the bacterial host, thereby providing a more direct measurement of the relative expression strength of the synthesized promoters by the Pymaker.
+
The functional promoter sequence (about 223 bp) generated by our AI model Pymaker is inserted into the dual-fluorescence reporter system for characterization and we describe it as pDualPH7. Random DNA yields diverse expression levels in a yeast promoter library, while we can use the episomal dual reporter system expressing a constitutive red fluorescent protein (RFP) and a variable yellow fluorescent protein (YFP) to quantify promoter activity. By adpoting the log(YFP/RFP) measured using flow cytometry, we can detect the expression rate of our synthesized promoters. The advantage of this system is its ability to eliminate the influence of plasmid copy number and the growth status of the bacterial host, thereby providing a more direct measurement of the relative expression strength of the synthesized promoters by the Pymaker.
 
===Loci===
 
===Loci===
−
pDualPH6 consists two parts: the synthesized core promoter and the pDual reporter scaffold. The synthesized core promoter is an 80 bp sequence generated by the Pymaker and is seated at approximately -170 to -90 upstream to the codon (which is the presumed transcription start site-TSS and is where most transcription factors binding sites lie).  
+
pDualPH7 consists two parts: the synthesized core promoter and the pDual reporter scaffold. The synthesized core promoter is an 80 bp sequence generated by the Pymaker and is seated at approximately -170 to -90 upstream to the codon (which is the presumed transcription start site-TSS and is where most transcription factors binding sites lie).  
 
The pDual reporter scaffold can link the core promoter with the codon and provide restriction sites of BamH I and Xho I which make it possible for the plasmids with the scaffold to be inserted by various core promoter sequences at ease.   
 
The pDual reporter scaffold can link the core promoter with the codon and provide restriction sites of BamH I and Xho I which make it possible for the plasmids with the scaffold to be inserted by various core promoter sequences at ease.   
  
Line 11: Line 11:
  
 
===Sequence and Features===
 
===Sequence and Features===
−
<partinfo>BBa_K4815016 SequenceAndFeatures</partinfo>
+
<partinfo>BBa_K4815017 SequenceAndFeatures</partinfo>
 +
<p>Ori: the origin of replication</p>
 +
<p>AmpR:have resistence to the ampicillin</p>
 +
<p>CEN: be related to the centromere</p>
 +
<p>ARS:autonomously replication sequences</p>
 +
<p>URA3: can express uracil and can be chose on the uracil defective medium(SC-URA)</p>
  
 
===Composition===
 
===Composition===
−
We link PYPH6 to the plasmid framework by double enzyme digestion assay and ligation assay, the figure bellow shows the success in the assembly process. In the process PYPH6 is extracted from pDualPH6-pDual mcherry-yeGFP High6 and be inserted into pDual-H6-LTB-eGFP.  
+
We link PYPH7 to the plasmid framework by double enzyme digestion assay and ligation assay, the figure bellow shows the success in the assembly process. In the process PYPH7 is extracted from pDualPH7-pDual mcherry-yeGFP High7 and be inserted into pDual-H7-LTB-eGFP.  
 
<html>
 
<html>
 
<style> .image-container {display: flex; justify-content: center; } .image-container img { margin: 0 10px;} </style> <div class="image-container"> <img src="https://static.igem.wiki/teams/4815/wiki/result/9.png" alt="Image 1" width = 20%> <img src="https://static.igem.wiki/teams/4815/wiki/result/12.png" alt="Image 2" width=60%> </div> </html>
 
<style> .image-container {display: flex; justify-content: center; } .image-container img { margin: 0 10px;} </style> <div class="image-container"> <img src="https://static.igem.wiki/teams/4815/wiki/result/9.png" alt="Image 1" width = 20%> <img src="https://static.igem.wiki/teams/4815/wiki/result/12.png" alt="Image 2" width=60%> </div> </html>
Line 20: Line 25:
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
−
<partinfo>BBa_K4815016 parameters</partinfo>
+
<partinfo>BBa_K4815017 parameters</partinfo>
 
<!-- -->
 
<!-- -->

Latest revision as of 08:30, 12 October 2023

pDualPH7-pDual mcherry-yeGFP High 7

Description

The functional promoter sequence (about 223 bp) generated by our AI model Pymaker is inserted into the dual-fluorescence reporter system for characterization and we describe it as pDualPH7. Random DNA yields diverse expression levels in a yeast promoter library, while we can use the episomal dual reporter system expressing a constitutive red fluorescent protein (RFP) and a variable yellow fluorescent protein (YFP) to quantify promoter activity. By adpoting the log(YFP/RFP) measured using flow cytometry, we can detect the expression rate of our synthesized promoters. The advantage of this system is its ability to eliminate the influence of plasmid copy number and the growth status of the bacterial host, thereby providing a more direct measurement of the relative expression strength of the synthesized promoters by the Pymaker.

Loci

pDualPH7 consists two parts: the synthesized core promoter and the pDual reporter scaffold. The synthesized core promoter is an 80 bp sequence generated by the Pymaker and is seated at approximately -170 to -90 upstream to the codon (which is the presumed transcription start site-TSS and is where most transcription factors binding sites lie). The pDual reporter scaffold can link the core promoter with the codon and provide restriction sites of BamH I and Xho I which make it possible for the plasmids with the scaffold to be inserted by various core promoter sequences at ease.

Usage and Biology

We used a synthetic promoter to drive the expression of the YeGFP gene on the same plasmid, while the TEF1 promoter was used in the reverse orientation to drive the expression of the mCherry gene. Additionally, we incorporated a lactose-inducible switch to enhance safety. We utilized flow cytometry to monitor the two fluorescence signals excited by different light channels and analyzed the corresponding data. We plotted the natural logarithm of the ratio of GFP to mCherry (ln(GFP/mCherry)) as a frequency distribution graph to showcase the relative expression strength of different promoters in yeast.

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal EcoRI site found at 396
    Illegal XbaI site found at 3677
    Illegal SpeI site found at 1351
    Illegal PstI site found at 991
    Illegal PstI site found at 2232
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal EcoRI site found at 396
    Illegal NheI site found at 3443
    Illegal SpeI site found at 1351
    Illegal PstI site found at 991
    Illegal PstI site found at 2232
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal EcoRI site found at 396
    Illegal BglII site found at 1963
    Illegal BamHI site found at 3640
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal EcoRI site found at 396
    Illegal XbaI site found at 3677
    Illegal SpeI site found at 1351
    Illegal PstI site found at 991
    Illegal PstI site found at 2232
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal EcoRI site found at 396
    Illegal XbaI site found at 3677
    Illegal SpeI site found at 1351
    Illegal PstI site found at 991
    Illegal PstI site found at 2232
    Illegal NgoMIV site found at 1862
  • 1000
    INCOMPATIBLE WITH RFC[1000]
    Illegal BsaI site found at 2922
    Illegal BsaI.rc site found at 4317
    Illegal SapI site found at 4808
    Illegal SapI site found at 5408
    Illegal SapI.rc site found at 2769

Ori: the origin of replication

AmpR:have resistence to the ampicillin

CEN: be related to the centromere

ARS:autonomously replication sequences

URA3: can express uracil and can be chose on the uracil defective medium(SC-URA)

Composition

We link PYPH7 to the plasmid framework by double enzyme digestion assay and ligation assay, the figure bellow shows the success in the assembly process. In the process PYPH7 is extracted from pDualPH7-pDual mcherry-yeGFP High7 and be inserted into pDual-H7-LTB-eGFP.

Image 1 Image 2