Difference between revisions of "Part:BBa K4414040"
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__NOTOC__
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<partinfo>BBa_K4414040 short</partinfo>
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<partinfo>BBa_K4016012 short</partinfo>
  
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Respond to stimuli.
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This composite part is designed to generate cyclinE1 degradation with [[Part:BBa_K4016013]] through DocS-Coh2 interaction and VH_cyclinE1-VK_cyclinE1 folded conformation.
  
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<!-- Add more about the biology of this part here
 
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===Usage and Biology===
 
  
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==Usage and Biology==
 +
In the project this year, we used a previously described ScFv of Cyclin E as our targeting module. With our protein degradation tool, we can degrade cyclin E in a signal-dependent manner, therefore controlling the proliferation of the cells or even synchronize a set of cells at a specific phase of cell cycle.
  
−
===Characterization===
+
The design based on the high-affinity protein–protein interaction between two complementary modules: the cohesin and the dockerin. The cohesin–dockerin couple represents the interaction between two complementary families of protein modules that exhibit divergent specificities and affinities..[1]
 +
 
 +
Upregulation of cyclin E expression begins late in G1 and is maintained into S-phase.[2] It is a critical cell cycle protein in the regulated progression of normal cells to replicate their DNA. Ectopic overexpression of cyclin E results in accelerated G1 progression, chromosome instability, and a reduced requirement for growthfactors..[3]
 +
 
 +
Because expressing the full-length of ScFv might already be sufficient to trigger the dysfunction of cyclins, we designed another set of constructs that split the ScFv into VH and VK fragments, and fused these fragments on either N terminus of C terminus of Predator proteins. In this case, the small molecular induced dimerization would also trigger the reconstitution of ScFv, therefore reducing the potential effect of full-length ScFv on Cyclins.
 +
 
 +
In the design of BBa_K4016012 we link Coh2 with VH fragment by a short flexible polypeptide linker, so that it can work as a whole.
 +
 
 +
 
 +
<html>
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 +
<figure class="figure">
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<img src="https://static.igem.org/mediawiki/parts/3/3a/T--NUDT_CHINA--Part_SchematicFigure_12-13_.png" class="figure-img img-fluid rounded"  height="350px">
 +
 
 +
</figure>
 +
 
 +
</html>
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Figure 1. Schematic Figure of BBa_K4016012 and BBa_K4016013
 +
 
 +
 
 +
 
 +
 
 +
==Characterization==
 +
This part was cloned in pXQ135 plasmid and transfected into HEK293T cell lines using Invitrogen LipofectamineTM 3000.It was validated through four ways:PCR, enzyme digestion, sequencing and functional test.
 +
 
 +
===PCR===
 +
The PCR is performed with Green Taq Mix by Vazyme.
 +
 
 +
F-Prime: 5’-CTAGCGTTTAAACTTAAGCTTGCCACCATGGAGGTTCAACTGGAGGAGTCTG-3’
 +
 
 +
R-Prime: 5’- TGGATATCTGCAGAATTCTTACACGTTCACGCCGCCGTCGAT-3’
 +
 
 +
The PCR protocol is selected based on the Users Manuel. The Electrophoresis was performed on a 1% Agarose gel.
 +
 
 +
 
 +
===Enzyme Digestion===
 +
After the assembly the plasmid was transferred into the Competent E. coli DH5α). After culturing overnight in LB,we minipreped the plasmid for cutting. The cutting procedure was performed with Hind III EcoR I restriction endonuclease bought.
 +
The plasmid was cutted in a 20μL system at 37 ℃ for 2 hours. The Electrophoresis was performed on a 1％ Agarose glu.
 +
 
 +
 
 +
===Sequecing===
 +
The plasmid was sequenced correct.
  
 
<!-- -->
 
<!-- -->
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<span class='h3bb'>Sequence and Features</span>
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===Sequence and Features===
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<partinfo>BBa_K4414040 SequenceAndFeatures</partinfo>
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<partinfo>BBa_K4016012 SequenceAndFeatures</partinfo>
  
  
 
<!-- Uncomment this to enable Functional Parameter display  
 
<!-- Uncomment this to enable Functional Parameter display  
 
===Functional Parameters===
 
===Functional Parameters===
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<partinfo>BBa_K4414040 parameters</partinfo>
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<partinfo>BBa_K4016012 parameters</partinfo>
 
<!-- -->
 
<!-- -->
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==Functional test==
 +
This part (BBa_K4016012) was tested together with BBa_K4016013
 +
 +
===Method===
 +
*1. Cell transfection
 +
(1)Seed HEK293T cells into 6-well cell culture plates.
 +
 +
(2)Culture for 16 h before transfection
 +
 +
(3)Total plasmid mixes of 800ng per well are mixed thoroughly in DMEM before a polyethylenimine (PEI) solution (1 mg/ml) is added into the plasmid mixture in a ratio of 1:5 (plasmid weight/PEI weight)
 +
 +
(4)The plasmid–PEI mixture is vortexed and incubated at room temperature for 15 min. The mixture is then added into the cells and incubated for at least 6 h.
 +
 +
(5)Cells are then changed into fresh medium and culture for 18 h before subculture.
 +
 +
*2.CCK-8 assay
 +
(1)Wash HEK293T cells in 6-well plate with PBS and trypsinize prior to resuspension in fresh complete medium in a 15 ml microcentrifuge tube.
 +
 +
(2)Dispense 100ul of cell suspension (approximately 30000 cells per well) into 96 well plates.
 +
 +
(3)Apply the experiment group with blue light stimulus (480nm, stimulate 2 seconds with a 58 second-interval) for 72 h before sampling and analysis assay
 +
 +
(4)Add 10 ul CCK-8 solution to each well and incubate for 2 h in the incubator.
 +
 +
(5)Record results using microplate reader to measure the absorbance at 450 nm.
 +
 +
<html>
 +
 +
<figure class="figure">
 +
<img src="https://static.igem.org/mediawiki/parts/0/07/T--NUDT_CHINA--Part_Validation_Flourescent_72h.png
 +
" class="figure-img img-fluid rounded"  height="350px">
 +
 +
</figure>
 +
 +
</html>
 +
Figure2. Schematic representation of the experimental process of validation for BBa_K4016012 and [[Part:BBa_K4016013]]
 +
 +
 +
 +
 +
===Result===
 +
<html>
 +
 +
<figure class="figure">
 +
<img src="https://static.igem.org/mediawiki/parts/e/ee/T--NUDT_CHINA--Part_Result_12-13.png" class="figure-img img-fluid rounded"  height="350px">
 +
 +
</figure>
 +
 +
</html>
 +
Figure 3.CK8 cell proliferation assay of HEK-293 cells transfected with indicated plasmids.
 +
 +
 +
 +
===Reference===
 +
 +
[1]Jiang, Hongyu. Expression and purification of a human anti-cyclinD1 single-chain variable fragment antibody AD5 and its characterization[J]. International Journal of Molecular Medicine, 2013, 32(6):1451-1457.
 +
 +
[2]Stacey M. Ivanchuk, James T. Rutka,CHAPTER 9 - Regulation of the Cell Cycle and Interventional Developmental Therapeutics. HERBERT B. NEWTON, Handbook of Brain Tumor Chemotherapy, Academic Press, 2006, 123-140.
 +
 +
[3]Randall W. Strube , Si-Yi Chen, et al. Characterization of anti-cyclin E single-chain Fv antibodies and intrabodies in breast cancer cells: enhanced intracellular stability of novel sFv–Fc intrabodies[J].Journal of Immunological Methods, 2002, 263: 149–167.

Revision as of 13:19, 8 October 2022


VH_CyclinE1-Coh2

This composite part is designed to generate cyclinE1 degradation with Part:BBa_K4016013 through DocS-Coh2 interaction and VH_cyclinE1-VK_cyclinE1 folded conformation.


Usage and Biology

In the project this year, we used a previously described ScFv of Cyclin E as our targeting module. With our protein degradation tool, we can degrade cyclin E in a signal-dependent manner, therefore controlling the proliferation of the cells or even synchronize a set of cells at a specific phase of cell cycle.

The design based on the high-affinity protein–protein interaction between two complementary modules: the cohesin and the dockerin. The cohesin–dockerin couple represents the interaction between two complementary families of protein modules that exhibit divergent specificities and affinities..[1]

Upregulation of cyclin E expression begins late in G1 and is maintained into S-phase.[2] It is a critical cell cycle protein in the regulated progression of normal cells to replicate their DNA. Ectopic overexpression of cyclin E results in accelerated G1 progression, chromosome instability, and a reduced requirement for growthfactors..[3]

Because expressing the full-length of ScFv might already be sufficient to trigger the dysfunction of cyclins, we designed another set of constructs that split the ScFv into VH and VK fragments, and fused these fragments on either N terminus of C terminus of Predator proteins. In this case, the small molecular induced dimerization would also trigger the reconstitution of ScFv, therefore reducing the potential effect of full-length ScFv on Cyclins.

In the design of BBa_K4016012 we link Coh2 with VH fragment by a short flexible polypeptide linker, so that it can work as a whole.


Figure 1. Schematic Figure of BBa_K4016012 and BBa_K4016013



Characterization

This part was cloned in pXQ135 plasmid and transfected into HEK293T cell lines using Invitrogen LipofectamineTM 3000.It was validated through four ways:PCR, enzyme digestion, sequencing and functional test.

PCR

The PCR is performed with Green Taq Mix by Vazyme.

F-Prime: 5’-CTAGCGTTTAAACTTAAGCTTGCCACCATGGAGGTTCAACTGGAGGAGTCTG-3’

R-Prime: 5’- TGGATATCTGCAGAATTCTTACACGTTCACGCCGCCGTCGAT-3’

The PCR protocol is selected based on the Users Manuel. The Electrophoresis was performed on a 1% Agarose gel.


Enzyme Digestion

After the assembly the plasmid was transferred into the Competent E. coli DH5α). After culturing overnight in LB,we minipreped the plasmid for cutting. The cutting procedure was performed with Hind III EcoR I restriction endonuclease bought. The plasmid was cutted in a 20μL system at 37 ℃ for 2 hours. The Electrophoresis was performed on a 1％ Agarose glu.


Sequecing

The plasmid was sequenced correct.

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]



Functional test

This part (BBa_K4016012) was tested together with BBa_K4016013

Method

  • 1. Cell transfection

(1)Seed HEK293T cells into 6-well cell culture plates.

(2)Culture for 16 h before transfection

(3)Total plasmid mixes of 800ng per well are mixed thoroughly in DMEM before a polyethylenimine (PEI) solution (1 mg/ml) is added into the plasmid mixture in a ratio of 1:5 (plasmid weight/PEI weight)

(4)The plasmid–PEI mixture is vortexed and incubated at room temperature for 15 min. The mixture is then added into the cells and incubated for at least 6 h.

(5)Cells are then changed into fresh medium and culture for 18 h before subculture.

  • 2.CCK-8 assay

(1)Wash HEK293T cells in 6-well plate with PBS and trypsinize prior to resuspension in fresh complete medium in a 15 ml microcentrifuge tube.

(2)Dispense 100ul of cell suspension (approximately 30000 cells per well) into 96 well plates.

(3)Apply the experiment group with blue light stimulus (480nm, stimulate 2 seconds with a 58 second-interval) for 72 h before sampling and analysis assay

(4)Add 10 ul CCK-8 solution to each well and incubate for 2 h in the incubator.

(5)Record results using microplate reader to measure the absorbance at 450 nm.

Figure2. Schematic representation of the experimental process of validation for BBa_K4016012 and Part:BBa_K4016013



Result

Figure 3.CK8 cell proliferation assay of HEK-293 cells transfected with indicated plasmids.


Reference

[1]Jiang, Hongyu. Expression and purification of a human anti-cyclinD1 single-chain variable fragment antibody AD5 and its characterization[J]. International Journal of Molecular Medicine, 2013, 32(6):1451-1457.

[2]Stacey M. Ivanchuk, James T. Rutka,CHAPTER 9 - Regulation of the Cell Cycle and Interventional Developmental Therapeutics. HERBERT B. NEWTON, Handbook of Brain Tumor Chemotherapy, Academic Press, 2006, 123-140.

[3]Randall W. Strube , Si-Yi Chen, et al. Characterization of anti-cyclin E single-chain Fv antibodies and intrabodies in breast cancer cells: enhanced intracellular stability of novel sFv–Fc intrabodies[J].Journal of Immunological Methods, 2002, 263: 149–167.