Difference between revisions of "Part:BBa K2904030"
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| − | + | ==<strong>Design</strong>== | |
| + | |||
| + | ===Background of 2019 OUC-China's project——RiboLego=== | ||
| + | <p> | ||
| + | Due to context-dependent performance and limited dynamic range, the widespread application of riboswitches is currently restricted. By replacing its original ORF with a new one, the structure of an aptamer domain can be subtly disrupted, resulting in a loss of ligand response. So riboswitch is still not be considered as a ‘plug and play' device. To tackle these problems, our project focuses on a standardized design principle to be used for modular and tunable riboswitch. The modular riboswitch we defined consists of the original riboswitch, Stabilizer and Tuner. Stabilizer can protect the structure of riboswitch from damage while Tuner can reduce the expression probability of fusion protein and make improvement of riboswitch function. | ||
| + | </p> | ||
| + | |||
| + | ===The construction of this part=== | ||
| + | |||
| + | After successfully constructing modular kinetic riboswitches, we then want to demonstrate that our guideline can also apply to the thermodynamic riboswitch, which can response to temperature based on conformation changes. Therefore, we selected a thermodynamic switch named Four U that performed well and designed a modular Four U riboswitch containing the original switch, Stabilizer and Tuner A. Using docking matrix, we selected the first 132bp of RFP as Stabilizer because RFP can express under the control of Four U. | ||
| + | |||
| + | ==<strong>Result</strong>== | ||
| + | To validate this new thermodynamic switch, we engineered a device including a constitutive promoter(BBa_J23119), the modular Four U riboswitch and sfGFP. After construction, the circuit was transformed into DH5αZ1. Given that the temperature threshold of Four U is 37℃, we set the culture temperature to 28℃, 37℃ and 42℃ in liquid LB medium respectively. We can observe a noticeable difference when cultured for 30 hours. Though centrifugation, the recombination strain at 37°C and 42°C shows green while the strain at 28°C shows no fluorescence. | ||
| + | [[Image:T--OUC-China--dpzz.png|center|thumb|350px|'''Figure1: The results of liquid test show the working effect of modular Four U in different temperature.''' ]] | ||
| + | <br/> | ||
| + | The above qualitative experiments are not enough to verify the effect of modular Four U, so we tested the fluorescence intensity by microplate reader to measure the expression level of the reporter protein legulated by FourU element as temperature-controlled switch. We still set three culture temperatures: 28°C, 30°C and 37°C. After overnight culture, we choose 5 time points (8h, 24h, 30h, 36h, 48h) to test fluorescence intensity of sfGFP protein. The results demonstrate that moduar FourU element is a useful thermodynamic riboswitch and works very well! | ||
| + | [[Image:T--OUC-China--030microplate.jpg|center|thumb|400px|'''Figure2: The results of microplate reader show the working effect of modular Four U element in different temperature.''' ]] | ||
| + | <p> | ||
| + | <br> | ||
| + | <br> | ||
<!-- Add more about the biology of this part here | <!-- Add more about the biology of this part here | ||
Latest revision as of 11:14, 21 October 2019
Modular Four U riboswitch
Design
Background of 2019 OUC-China's project——RiboLego
Due to context-dependent performance and limited dynamic range, the widespread application of riboswitches is currently restricted. By replacing its original ORF with a new one, the structure of an aptamer domain can be subtly disrupted, resulting in a loss of ligand response. So riboswitch is still not be considered as a ‘plug and play' device. To tackle these problems, our project focuses on a standardized design principle to be used for modular and tunable riboswitch. The modular riboswitch we defined consists of the original riboswitch, Stabilizer and Tuner. Stabilizer can protect the structure of riboswitch from damage while Tuner can reduce the expression probability of fusion protein and make improvement of riboswitch function.
The construction of this part
After successfully constructing modular kinetic riboswitches, we then want to demonstrate that our guideline can also apply to the thermodynamic riboswitch, which can response to temperature based on conformation changes. Therefore, we selected a thermodynamic switch named Four U that performed well and designed a modular Four U riboswitch containing the original switch, Stabilizer and Tuner A. Using docking matrix, we selected the first 132bp of RFP as Stabilizer because RFP can express under the control of Four U.
Result
To validate this new thermodynamic switch, we engineered a device including a constitutive promoter(BBa_J23119), the modular Four U riboswitch and sfGFP. After construction, the circuit was transformed into DH5αZ1. Given that the temperature threshold of Four U is 37℃, we set the culture temperature to 28℃, 37℃ and 42℃ in liquid LB medium respectively. We can observe a noticeable difference when cultured for 30 hours. Though centrifugation, the recombination strain at 37°C and 42°C shows green while the strain at 28°C shows no fluorescence.
The above qualitative experiments are not enough to verify the effect of modular Four U, so we tested the fluorescence intensity by microplate reader to measure the expression level of the reporter protein legulated by FourU element as temperature-controlled switch. We still set three culture temperatures: 28°C, 30°C and 37°C. After overnight culture, we choose 5 time points (8h, 24h, 30h, 36h, 48h) to test fluorescence intensity of sfGFP protein. The results demonstrate that moduar FourU element is a useful thermodynamic riboswitch and works very well!
Sequence and Features
- 10COMPATIBLE WITH RFC[10]
- 12COMPATIBLE WITH RFC[12]
- 21COMPATIBLE WITH RFC[21]
- 23COMPATIBLE WITH RFC[23]
- 25COMPATIBLE WITH RFC[25]
- 1000COMPATIBLE WITH RFC[1000]