Difference between revisions of "Part:BBa K3994009"
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HrpS is a key functional factor under PttB344 promoter (Figure 1). And this sequence is inserted into plasmid. Its sequence is shown in Figure 2.
 
HrpS is a key functional factor under PttB344 promoter (Figure 1). And this sequence is inserted into plasmid. Its sequence is shown in Figure 2.
  
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[[File:T--Shanghai Metro Utd--BBa K4005001-figure2a.png|500px|thumb|center|Figure 2a. SDS-PAGE assey of protein and Freeze-dried powder of the ANG protein..]]
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[[File:T--NOFLS YZ--BBa K3994009-Figure1.png|500px|thumb|center|Figure 1. Boolean gate logic circuit/AND circuit construction...]]
  
  
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[[File:T--NOFLS YZ--BBa K3994009-Figure2.png|500px|thumb|center|Figure 2. PttB344_HrpS_PJ23105_ttrR, sensing S4O62- to release the substance S...]]
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The profiles of every basic part are as follows:
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=== BBa_K3994003 ===
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==== Name: HrpS ====
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==== Base Pairs: 912bp ====
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==== Origin: Pseudomonas syringae, genome ====
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==== Properties: A coding sequence of HrpS protein ====
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=== Usage and Biology ===
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This codes for HrpS protein. HrpR protein binds to HrpS protein forming a complex and then triggering the transcription of promoter hrpL. This functions like a AND logic gate.
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=== BBa_K3994012 ===
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==== Name: PttB344 ====
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==== Base Pairs: 85bp ====
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==== Origin: Synthetic ====
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==== Properties: A coding sequence of promoter ttB344. ====
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=== Usage and Biology ===
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This is a sequence of PttB344. PttrB185-269 is a minimal TtrR activated promoter when TtrR is phosphorylated by TtrS after TtrS sensing tetrathionate.
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=== Experimental approach ===
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==== Recombinant Plasmid Construction ====
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[[File:T--NOFLS YZ--BBa K3994001-Figure1.png|500px|thumb|center|Figure 3. The electrophoresis results of enzyme digestion and PCR...]]
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Lane 1 and 2: Plasmid pSU2718-p15A digested by Xba1 and BamH1.
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Lane 3: Part 2, PttB344_HrpS_PJ23105_ttrR, got by PCR method with size of 2060bp.
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This step is used to get the plasmids pSU2718-p15A digested by enzyme Xba1 and BamH1and gene PttB344_HrpS_PJ23105_ttrR by PCR method for later in the process. Therefore, channel 1 and 2 were plasmids pSU2718-p15A digested by enzyme Xba1 and BamH1. And channel 3 were gene PttB344_HrpS_PJ23105_ttrR got by PCR. Clean-up the product to obtain pSU2718-p15A backbone and PttB344_HrpS_PJ23105_ttrR-fragment.
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T4 DNA ligase is used to connect pSU2718-p15A backbone and PttB344_HrpS_PJ23105_ttrR-fragment to get plasmid pSU2718-part2.
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[[File:T--NOFLS YZ--BBa K3994001-Figure2.png|500px|thumb|center|Figure 4 E-coil having the desired pSU2718-part2 (Left) and control (Right)...]]
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[[File:T--NOFLS YZ--BBa K3994001-Figure5.0.png|500px|thumb|center|Figure 5. The electrophoresis result of enzyme digestion identification...]]
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[[File:T--NOFLS YZ--BBa K3994001-Figure3.png|500px|thumb|center|Figure 5. The electrophoresis result of enzyme digestion identification...]]
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Lane 1: Plasmid pSU2718-p15A digested by EcoR1.
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Lane 2 to 5: Recombinant plasmid pSU2718-part2 digested by EcoRI. We got two bands with size of 2803bp and 1544bp.
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The results show that we got the correct plasmid. And the plasmid was sent to sequence.
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[[File:T--NOFLS YZ--BBa K3994001-Figure3.png|500px|thumb|center|Figure 6 The result of sequencing for plasmid pSU2718-part2...]]
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Sequencing feedback shows we have obtained the correct plasmids which is consistent with their DNA profiles.
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=== Proof of function ===
 
<!-- Add more about the biology of this part here
 
<!-- Add more about the biology of this part here
 
===Usage and Biology===
 
===Usage and Biology===

Revision as of 09:56, 19 October 2021


PttB344_HrpS_PJ23105_ttrR

promoter

Profile

Name: PttB344_HrpS_PJ23105_ttrR

Base Pairs: 2040 bp

Origin: Synthetic

Properties: A biosensor releasing fluorescence only when detecting the IBD marker.

Usage and Biology

Background

Inflammatory bowel disease (IBD) is a chronic intestinal inflammatory disease of unknown etiology, including ulcerative colitis (CD) and Crohn’s disease (CD). This chronic disease, which is prone to repeated deterioration, currently lacks unified diagnostic and treatment standards, and is posing a great threat to public health. Drug therapy (anti-inflammatory drugs) is the preferred treatment for IBD. However, studies in the past 10 years have found that 30-50% of IBD patients do not respond to anti-TNF treatment. In addition, after long-term use of anti-inflammatory drugs, the patient's intestinal microbial status changes over time, and the effect may be lost due to drug resistance. Therefore, we need to seek help from other treatments for IBD. HrpR protein binds to HrpS protein forming a complex and then triggering the transcription of promoter hrpL. It can sense S4O62- to release the substance S


Construct design

HrpS is a key functional factor under PttB344 promoter (Figure 1). And this sequence is inserted into plasmid. Its sequence is shown in Figure 2.

Figure 1. Boolean gate logic circuit/AND circuit construction...


Figure 2. PttB344_HrpS_PJ23105_ttrR, sensing S4O62- to release the substance S...


The profiles of every basic part are as follows:

BBa_K3994003

Name: HrpS

Base Pairs: 912bp

Origin: Pseudomonas syringae, genome

Properties: A coding sequence of HrpS protein

Usage and Biology

This codes for HrpS protein. HrpR protein binds to HrpS protein forming a complex and then triggering the transcription of promoter hrpL. This functions like a AND logic gate.

BBa_K3994012

Name: PttB344

Base Pairs: 85bp

Origin: Synthetic

Properties: A coding sequence of promoter ttB344.

Usage and Biology

This is a sequence of PttB344. PttrB185-269 is a minimal TtrR activated promoter when TtrR is phosphorylated by TtrS after TtrS sensing tetrathionate.

Experimental approach

Recombinant Plasmid Construction

Figure 3. The electrophoresis results of enzyme digestion and PCR...


Lane 1 and 2: Plasmid pSU2718-p15A digested by Xba1 and BamH1.

Lane 3: Part 2, PttB344_HrpS_PJ23105_ttrR, got by PCR method with size of 2060bp.


This step is used to get the plasmids pSU2718-p15A digested by enzyme Xba1 and BamH1and gene PttB344_HrpS_PJ23105_ttrR by PCR method for later in the process. Therefore, channel 1 and 2 were plasmids pSU2718-p15A digested by enzyme Xba1 and BamH1. And channel 3 were gene PttB344_HrpS_PJ23105_ttrR got by PCR. Clean-up the product to obtain pSU2718-p15A backbone and PttB344_HrpS_PJ23105_ttrR-fragment. T4 DNA ligase is used to connect pSU2718-p15A backbone and PttB344_HrpS_PJ23105_ttrR-fragment to get plasmid pSU2718-part2.


Figure 4 E-coil having the desired pSU2718-part2 (Left) and control (Right)...


Figure 5. The electrophoresis result of enzyme digestion identification...


Figure 5. The electrophoresis result of enzyme digestion identification...

Lane 1: Plasmid pSU2718-p15A digested by EcoR1.

Lane 2 to 5: Recombinant plasmid pSU2718-part2 digested by EcoRI. We got two bands with size of 2803bp and 1544bp.

The results show that we got the correct plasmid. And the plasmid was sent to sequence.


Figure 6 The result of sequencing for plasmid pSU2718-part2...

Sequencing feedback shows we have obtained the correct plasmids which is consistent with their DNA profiles.

Proof of function

Sequence and Features


Assembly Compatibility:
  • 10
    INCOMPATIBLE WITH RFC[10]
    Illegal XbaI site found at 25
    Illegal XbaI site found at 175
    Illegal PstI site found at 13
  • 12
    INCOMPATIBLE WITH RFC[12]
    Illegal NheI site found at 839
    Illegal NheI site found at 862
    Illegal PstI site found at 13
  • 21
    INCOMPATIBLE WITH RFC[21]
    Illegal BglII site found at 1893
    Illegal BamHI site found at 31
  • 23
    INCOMPATIBLE WITH RFC[23]
    Illegal XbaI site found at 25
    Illegal XbaI site found at 175
    Illegal PstI site found at 13
  • 25
    INCOMPATIBLE WITH RFC[25]
    Illegal XbaI site found at 25
    Illegal XbaI site found at 175
    Illegal PstI site found at 13
    Illegal AgeI site found at 553
    Illegal AgeI site found at 1106
    Illegal AgeI site found at 1112
    Illegal AgeI site found at 1247
  • 1000
    COMPATIBLE WITH RFC[1000]