Difference between revisions of "Part:BBa K3924031"
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===Validation based on protein expression level=== | ===Validation based on protein expression level=== | ||
After getting the synthetic plasmid, we test it by DNA sequencing and the result showed correctness of the sequence. Then we transformed the plasmid into BL21 chemocompetent cells and expressed miniSOG successfully. We first test the expression of miniSOG by Coomassie bright blue staining and the result is below (Fig. 1). <br/> | After getting the synthetic plasmid, we test it by DNA sequencing and the result showed correctness of the sequence. Then we transformed the plasmid into BL21 chemocompetent cells and expressed miniSOG successfully. We first test the expression of miniSOG by Coomassie bright blue staining and the result is below (Fig. 1). <br/> | ||
| − | [[Image: T--Tsinghua--Coomassie_of_miniSOG.png|'''Figure 1: The Coomassie dyeing result''']] | + | [[Image: T--Tsinghua--Coomassie_of_miniSOG.png|center|600px|thumb|'''Figure 1: The Coomassie dyeing result''']] |
===Validation based on protein activity=== | ===Validation based on protein activity=== | ||
Then the purified miniSOG was used to test it labelling ability and the results of labelling strongly suggested the protein activity of miniSOG (Fig. 2). Under blue light illumination, miniSOG can catalyze labelling of RNA with biotin-NH2 probes. After the reaction, RNA clean & concentrator kit (Zymo) was used to get rid of excess biotin-NH2 probes and dot-plot assay was used for color development using streptavidin-HRP followed by substrates (see protocol for experimental details). This result is in line with the results reported by previous literature<sup>[1]</sup>, and we established a relatively fixed work flow for labelling assay during these initial experiments.<br/> | Then the purified miniSOG was used to test it labelling ability and the results of labelling strongly suggested the protein activity of miniSOG (Fig. 2). Under blue light illumination, miniSOG can catalyze labelling of RNA with biotin-NH2 probes. After the reaction, RNA clean & concentrator kit (Zymo) was used to get rid of excess biotin-NH2 probes and dot-plot assay was used for color development using streptavidin-HRP followed by substrates (see protocol for experimental details). This result is in line with the results reported by previous literature<sup>[1]</sup>, and we established a relatively fixed work flow for labelling assay during these initial experiments.<br/> | ||
| − | [[Image: T--Tsinghua--Labelling_of_miniSOG.png|'''Figure 2: The non-specific labelling of RNA using miniSOG ''']] | + | [[Image: T--Tsinghua--Labelling_of_miniSOG.png|center|600px|thumb|'''Figure 2: The non-specific labelling of RNA using miniSOG ''']] |
To prepare for the subsequent test of specific markers, we tested the sensitivity of miniSOG RNA labelling ability after verifying its activity (Fig. 3). From this test, the result shows, when the RNA concentration is above 200ng/ul, miniSOG can significantly label RNA. Therefore, the RNA concentration of 200ng/ul is used as the standard line for detection in our later experiments. | To prepare for the subsequent test of specific markers, we tested the sensitivity of miniSOG RNA labelling ability after verifying its activity (Fig. 3). From this test, the result shows, when the RNA concentration is above 200ng/ul, miniSOG can significantly label RNA. Therefore, the RNA concentration of 200ng/ul is used as the standard line for detection in our later experiments. | ||
| − | [[Image: T--Tsinghua--Labelling_of_miniSOG in RNA gradient.png|'''Figure 3: The result of miniSOG RNA labelling sensitivity test''']] | + | [[Image: T--Tsinghua--Labelling_of_miniSOG in RNA gradient.png|center|600px|thumb|'''Figure 3: The result of miniSOG RNA labelling sensitivity test''']] |
==Reference== | ==Reference== | ||
[1] Wang, P., Tang, W., Li, Z., Zou, Z., Zhou, Y., Li, R., Xiong, T., Wang, J., & Zou, P. (2019). Mapping spatial transcriptome with light-activated proximity-dependent RNA labeling. Nat. Chem. Biol., 15(11), 1110–1119. https://doi.org/10.1038/s41589-019-0368-5 <br/> | [1] Wang, P., Tang, W., Li, Z., Zou, Z., Zhou, Y., Li, R., Xiong, T., Wang, J., & Zou, P. (2019). Mapping spatial transcriptome with light-activated proximity-dependent RNA labeling. Nat. Chem. Biol., 15(11), 1110–1119. https://doi.org/10.1038/s41589-019-0368-5 <br/> | ||
Revision as of 12:26, 21 October 2021
miniSOG, mutagenesis from Arabidopsis phototropin 2
Sequence and Features
- 10INCOMPATIBLE WITH RFC[10]Illegal EcoRI site found at 43
- 12INCOMPATIBLE WITH RFC[12]Illegal EcoRI site found at 43
Illegal NheI site found at 4 - 21INCOMPATIBLE WITH RFC[21]Illegal EcoRI site found at 43
Illegal BamHI site found at 37
Illegal XhoI site found at 364 - 23INCOMPATIBLE WITH RFC[23]Illegal EcoRI site found at 43
- 25INCOMPATIBLE WITH RFC[25]Illegal EcoRI site found at 43
- 1000COMPATIBLE WITH RFC[1000]
Profile
Name: miniSOG
Base Pairs: 372bp
Origin: Arabidopsis thaliana
Properties: A mutagenesis phototropin protein which can generate ROS after being exposed to blue light
Usage and Biology
miniSOG was engineered by-site specific mutagenesis from Arabidopsis phototropin 2, which naturally binds FMN but does not generate ROS [1]-[3]. By mutation, it can generate ROS after being exposed to blue light and ROS can oxidize guanosine into an intermediate, which could be attacked by primary amine to form covalent bond with NH2-containing probes which could be used to label RNA.
Design and Construction
For this part, we got the amino acid sequence thanks to a grant from the Peng Zou lab, Peking University. Then we optimized the protein codon and synthesized the sequence by company.
Functional Verification
Validation based on protein expression level
After getting the synthetic plasmid, we test it by DNA sequencing and the result showed correctness of the sequence. Then we transformed the plasmid into BL21 chemocompetent cells and expressed miniSOG successfully. We first test the expression of miniSOG by Coomassie bright blue staining and the result is below (Fig. 1).
Validation based on protein activity
Then the purified miniSOG was used to test it labelling ability and the results of labelling strongly suggested the protein activity of miniSOG (Fig. 2). Under blue light illumination, miniSOG can catalyze labelling of RNA with biotin-NH2 probes. After the reaction, RNA clean & concentrator kit (Zymo) was used to get rid of excess biotin-NH2 probes and dot-plot assay was used for color development using streptavidin-HRP followed by substrates (see protocol for experimental details). This result is in line with the results reported by previous literature[1], and we established a relatively fixed work flow for labelling assay during these initial experiments.
To prepare for the subsequent test of specific markers, we tested the sensitivity of miniSOG RNA labelling ability after verifying its activity (Fig. 3). From this test, the result shows, when the RNA concentration is above 200ng/ul, miniSOG can significantly label RNA. Therefore, the RNA concentration of 200ng/ul is used as the standard line for detection in our later experiments.
Reference
[1] Wang, P., Tang, W., Li, Z., Zou, Z., Zhou, Y., Li, R., Xiong, T., Wang, J., & Zou, P. (2019). Mapping spatial transcriptome with light-activated proximity-dependent RNA labeling. Nat. Chem. Biol., 15(11), 1110–1119. https://doi.org/10.1038/s41589-019-0368-5
[2] Ding, T., Zhu, L., Fang, Y., Liu, Y., Tang, W., & Zou, P. (2020). Chromophore-Assisted Proximity Labeling of DNA Reveals Chromosomal Organization in Living Cells. Angew. Chem. Int. Ed., 59(51), 22933–22937. https://doi.org/10.1002/anie.202005486
[3] Ruiz-González, R., Cortajarena, A. L., Mejias, S. H., Agut, M., Nonell, S., & Flors, C. (2013). Singlet oxygen generation by the genetically encoded tag miniSOG. J. Am. Chem. Soc., 135(26), 9564–9567. https://doi.org/10.1021/ja4020524