Difference between revisions of "Part:BBa K2243027"

Revision as of 14:42, 1 November 2017

Bxb1 attB_836R_Bxb1 attP

To test the influence of attBP sites of Bxb1 to terminator ECK120010836 (abbreviation: 836) in the reverse direction.

Usage and Biology

Usage

We constructed this part to characterize the recombination efficiency of the recombinase Bxb1 gp35 (BBa_K2243012). It consists of the terminator ECK120010836 (abbreviation: 836) in the reverse direction flanked by attB and attP sites of recombinase Bxb1 gp35. Upon recombination, the orientation of the terminator changes. As a result, expression of downstream sequence is blocked.

Biology

The attP site of Mycobacteriophage Bxb1 is used to integrate phage DNA at the host attB site of Mycobacterium smegmatis, generating the recombinant junctions attL and attR. DNA cleavage and re-ligation occur at the central crossover region at attB and attP, which allows the sequence to be flipped, excised, or inserted between recognition sites. We obtained the terminator, attB and attP sites by oligo synthesis.

Characterization

We first characterized the terminator strength using the following formula:

Ts=〖GFP〗of the random sequence/〖[GFP]〗with the terminator

Terminator Strength Induced with 0.1mM IPTG

Terminator Strength Induced with 1mM IPTG

And we sifted out 6 desirable unidirectional terminators without potential cryptic promotor in both orientations.

Terminator Strength Induced with 0.1M IPTG

Forward and Reverse Terminator Strength Ratio Induced with 0.1mM and 1mM IPTG

Terminator Reference Table

Media:Peking_trt.xlsx

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
INCOMPATIBLE WITH RFC[1000]
Illegal SapI site found at 22

@@ Line 21: / Line 21: @@
 ===Characterization===
-. We first characterized the terminator strength using the following formula:
+We first characterized the terminator strength using the following formula:
 Ts=〖GFP〗of the random sequence/〖[GFP]〗with the terminator
+[[File:Peking_TS_0.1mM.png|800px|thumb|center|Terminator Strength Induced with 0.1mM IPTG]]
+[[File:Peking_TS_1mM.png|800px|thumb|center|Terminator Strength Induced with 1mM IPTG]]
 And we sifted out 6 desirable unidirectional terminators without potential cryptic promotor in both orientations.
-[[File:Peking IPTG 0.1M.png|200px|thumb|center|Terminator Strength Induced with 0.1M IPTG]]
+[[File:Peking ratio.png|600px|thumb|center|Terminator Strength Induced with 0.1M IPTG]]
+[[File:Peking TS good terminators.png|600px|thumb|center|Forward and Reverse Terminator Strength Ratio Induced with 0.1mM and 1mM IPTG]]
-[[File:Peking IPTG 1M.png|200px|thumb|center|Terminator Strength Induced with 1M IPTG]]
-. We then characterized the inversion efficiency.
+<!-- -->
+Terminator Reference Table
-We transformed the testing system and expression system of corresponding recombinase into one single cell to see if the inversions happened, and if the leakage expression of recombinases would impact the system. In the end, couples of terminators and recombinases with near complete inversions and minimal leakage were selected.
+[[Media:Peking_trt.xlsx]]
-Microplate spectrophotometer was used to conduct preliminary measurements. Bacterial culture was added into 96-well plate(200ul for each well). OD600 and fluorescence intensity were measured. Background OD600 and fluorescence of plate, culture medium ,and autofluorescence should be eliminated through setting control groups. Fluorescence intensity/OD600 was cauculated using the net fluorescence intensity and net OD600. The transcription barrier strength of attBP/Terminator can be characterized quantitatively referring to the Ts formula.