Difference between revisions of "Part:BBa K4830025"

 
(→‎Characterization)
 
(5 intermediate revisions by the same user not shown)
Line 5: Line 5:
 
TLR-76 pegRNA - prime editing guide RNA (pegRNA) targeting the premature stop codon instilled in an eGFP. The TLR-76 pegRNA is used in the improved Traffic Light Reporter (TLR) assay for prime editing adapted from the TLR paper in the References.
 
TLR-76 pegRNA - prime editing guide RNA (pegRNA) targeting the premature stop codon instilled in an eGFP. The TLR-76 pegRNA is used in the improved Traffic Light Reporter (TLR) assay for prime editing adapted from the TLR paper in the References.
  
−
<!-- Add more about the biology of this part here
 
 
===Usage and Biology===
 
===Usage and Biology===
 +
Prime editing is an innovative technology for genome editing that enables the installation of the wide spectrum of gene modifications such as 12 possible base-to-base conversions, small insertions, and deletions, without requiring double-stranded breaks or donor DNA templates. This technology provides high versatility and target specificity, offering the potential to revolutionize medicine by providing novel tools for treating genetic diseases.
  
 +
Prime editing relies on specialized prime editors, which usually consist of reverse transcriptase enzyme fused to nickase Cas9, and prime editing guide RNA containing a spacer that specifies the target site. It also includes a scaffold and 3’ extension containing a primer binding site (PBS) and an RT template encoding the desired edit. To initiate prime editing, PE creates a single-strand break in the DNA at the target site to allow reverse transcriptase to access the DNA and synthesize a new DNA strand using pegRNA as a template. Then the information from the edited strand is copied to the complementary strand through the cell’s natural repair pathways.
 +
 +
eGFP is a green fluorescent protein derived from Aequorea victoria. It has an excitation maxima of 488nm, and emission maxima of 509nm.
 +
 +
===Characterization===
 +
The pegRNA in combination with ngRNA were used to test the efficiency of the Prime Editor containing the alternative Reverse Trancriptases. The pegRNA served as template to install the edit. 3 plasmids containing PE, pegRNA and ngRNA were trasfected into HEK293T cells, and editing efficiency was evaluated 72hr after transfection using flow cytometry by evaluating either the mean fluorescence intensity of the enhanced green fluorescent protein (eGFP), or the percentage of cells containing the eGFP.
 +
 +
TLR-76 pegRNA (BBa_K4830025) was co-transfected with 777BFP ngRNA (BBa_K4830026). The targeting sequence was the premature stop codon found on the eGFP requiring a complex edit (BBa_K4830029). Initial testing were performed on two different cell lines containing the integrated sequence. HEK293T TLR WT is a heterogeneous cell line containing the integrated sequence, while HEK293T 1D10 is a homogeneous cell line derived from the former.
 +
 +
<html>
 +
<div class = "middle">
 +
<img src = "https://static.igem.wiki/teams/4830/wiki/tlr-wtassay.png" style = "width:768px;height:440px">
 +
</div>
 +
</html>
 +
Fig. 1 Bar graph shows the P3 FITC-H Mean (indicating the mean fluorescence intensity of eGFP), and scatter points denote the P3% Parent (indicating the percentage of cell containing correctly edited wild-type eGFP). Results from initial testing with TLR WT cell line.
 
<!-- -->
 
<!-- -->
−
<span class='h3bb'>Sequence and Features</span>
+
 
 +
 
 +
<html>
 +
<div class = "middle">
 +
<img src = "https://static.igem.wiki/teams/4830/wiki/tlr-1d10assay.png" style = "width:768px;height:440px">
 +
</div>
 +
</html>
 +
Fig. 2 Bar graph shows the P3 FITC-H Mean (indicating the mean fluorescence intensity of eGFP), and scatter points denote the P3% Parent (indicating the percentage of cell containing correctly edited wild-type eGFP). Results from initial testing with TLR 1D10 cell line.
 +
<!-- -->
 +
 
 +
===Sequence and Features===
 +
The sequence contains the spacer, gRNA scaffold and RTTPBS.
 
<partinfo>BBa_K4830025 SequenceAndFeatures</partinfo>
 
<partinfo>BBa_K4830025 SequenceAndFeatures</partinfo>
  

Latest revision as of 11:56, 12 October 2023


TLR-76 pegRNA

TLR-76 pegRNA - prime editing guide RNA (pegRNA) targeting the premature stop codon instilled in an eGFP. The TLR-76 pegRNA is used in the improved Traffic Light Reporter (TLR) assay for prime editing adapted from the TLR paper in the References.

Usage and Biology

Prime editing is an innovative technology for genome editing that enables the installation of the wide spectrum of gene modifications such as 12 possible base-to-base conversions, small insertions, and deletions, without requiring double-stranded breaks or donor DNA templates. This technology provides high versatility and target specificity, offering the potential to revolutionize medicine by providing novel tools for treating genetic diseases.

Prime editing relies on specialized prime editors, which usually consist of reverse transcriptase enzyme fused to nickase Cas9, and prime editing guide RNA containing a spacer that specifies the target site. It also includes a scaffold and 3’ extension containing a primer binding site (PBS) and an RT template encoding the desired edit. To initiate prime editing, PE creates a single-strand break in the DNA at the target site to allow reverse transcriptase to access the DNA and synthesize a new DNA strand using pegRNA as a template. Then the information from the edited strand is copied to the complementary strand through the cell’s natural repair pathways.

eGFP is a green fluorescent protein derived from Aequorea victoria. It has an excitation maxima of 488nm, and emission maxima of 509nm.

Characterization

The pegRNA in combination with ngRNA were used to test the efficiency of the Prime Editor containing the alternative Reverse Trancriptases. The pegRNA served as template to install the edit. 3 plasmids containing PE, pegRNA and ngRNA were trasfected into HEK293T cells, and editing efficiency was evaluated 72hr after transfection using flow cytometry by evaluating either the mean fluorescence intensity of the enhanced green fluorescent protein (eGFP), or the percentage of cells containing the eGFP.

TLR-76 pegRNA (BBa_K4830025) was co-transfected with 777BFP ngRNA (BBa_K4830026). The targeting sequence was the premature stop codon found on the eGFP requiring a complex edit (BBa_K4830029). Initial testing were performed on two different cell lines containing the integrated sequence. HEK293T TLR WT is a heterogeneous cell line containing the integrated sequence, while HEK293T 1D10 is a homogeneous cell line derived from the former.

Fig. 1 Bar graph shows the P3 FITC-H Mean (indicating the mean fluorescence intensity of eGFP), and scatter points denote the P3% Parent (indicating the percentage of cell containing correctly edited wild-type eGFP). Results from initial testing with TLR WT cell line.


Fig. 2 Bar graph shows the P3 FITC-H Mean (indicating the mean fluorescence intensity of eGFP), and scatter points denote the P3% Parent (indicating the percentage of cell containing correctly edited wild-type eGFP). Results from initial testing with TLR 1D10 cell line.

Sequence and Features

The sequence contains the spacer, gRNA scaffold and RTTPBS.


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]