Difference between revisions of "Part:BBa K3726038:Design"

Latest revision as of 19:15, 19 October 2021

CDS_Lv0_MCGII

Assembly Compatibility:

10
INCOMPATIBLE WITH RFC[10]
Illegal EcoRI site found at 1099
Illegal EcoRI site found at 1540
Illegal EcoRI site found at 3299
Illegal EcoRI site found at 4415
Illegal EcoRI site found at 4499
Illegal EcoRI site found at 7554
Illegal PstI site found at 1684
Illegal PstI site found at 1783
Illegal PstI site found at 2368
Illegal PstI site found at 3326
Illegal PstI site found at 3554
Illegal PstI site found at 5064
Illegal PstI site found at 6078
12
INCOMPATIBLE WITH RFC[12]
Illegal EcoRI site found at 1099
Illegal EcoRI site found at 1540
Illegal EcoRI site found at 3299
Illegal EcoRI site found at 4415
Illegal EcoRI site found at 4499
Illegal EcoRI site found at 7554
Illegal NheI site found at 4638
Illegal PstI site found at 1684
Illegal PstI site found at 1783
Illegal PstI site found at 2368
Illegal PstI site found at 3326
Illegal PstI site found at 3554
Illegal PstI site found at 5064
Illegal PstI site found at 6078
21
INCOMPATIBLE WITH RFC[21]
Illegal EcoRI site found at 1099
Illegal EcoRI site found at 1540
Illegal EcoRI site found at 3299
Illegal EcoRI site found at 4415
Illegal EcoRI site found at 4499
Illegal EcoRI site found at 7554
Illegal BglII site found at 41
Illegal BglII site found at 2081
Illegal BglII site found at 3445
Illegal BamHI site found at 2179
Illegal BamHI site found at 2194
Illegal BamHI site found at 5893
Illegal BamHI site found at 6351
Illegal BamHI site found at 7324
Illegal XhoI site found at 871
Illegal XhoI site found at 1516
Illegal XhoI site found at 1990
Illegal XhoI site found at 4520
Illegal XhoI site found at 5187
Illegal XhoI site found at 5320
23
INCOMPATIBLE WITH RFC[23]
Illegal EcoRI site found at 1099
Illegal EcoRI site found at 1540
Illegal EcoRI site found at 3299
Illegal EcoRI site found at 4415
Illegal EcoRI site found at 4499
Illegal EcoRI site found at 7554
Illegal PstI site found at 1684
Illegal PstI site found at 1783
Illegal PstI site found at 2368
Illegal PstI site found at 3326
Illegal PstI site found at 3554
Illegal PstI site found at 5064
Illegal PstI site found at 6078
25
INCOMPATIBLE WITH RFC[25]
Illegal EcoRI site found at 1099
Illegal EcoRI site found at 1540
Illegal EcoRI site found at 3299
Illegal EcoRI site found at 4415
Illegal EcoRI site found at 4499
Illegal EcoRI site found at 7554
Illegal PstI site found at 1684
Illegal PstI site found at 1783
Illegal PstI site found at 2368
Illegal PstI site found at 3326
Illegal PstI site found at 3554
Illegal PstI site found at 5064
Illegal PstI site found at 6078
Illegal NgoMIV site found at 1627
Illegal NgoMIV site found at 3016
Illegal NgoMIV site found at 3190
Illegal NgoMIV site found at 3340
Illegal NgoMIV site found at 6514
Illegal AgeI site found at 3641
1000
COMPATIBLE WITH RFC[1000]

Design Notes

In the upstream region the bases taatc corresponds with 5bp a spacer sequence to improve ribosomal translation, while AATG overhang creates an start codon that forces translation initiation of the downstream coding sequence.

In the downstream region, the extra “aa” bases allow the creation of an additional stop codon (TAA) at the end of the upstream coding sequence, ending the translation of the desired CDS in accordance with the Marburg Collection design guidelines.

The transcription initiation rate for each RBS element has been specifically adjusted to achieve optimal expression of the desired enzyme within the operon. The relative translation initiation rates for the operon can be observed in the picture below. Where this operon corresponds with the enzymes: ppc_CDS, gcl_CDS , CDS_mtkA , CDS_mtkB , CDS_mcl.

This polycistronic CDS sequence has been assembled following a modified procedure for golden gate domestication. To know more about the design process of this polycistronic lv.0 parts, visit the iGEM MADRID_UCM 2021 wiki page https://2021.igem.org/Team:MADRID_UCM/Design .

Source

Gibson assembly using this synthesized basic parts: "BBa_K3726029""BBa_K3726030" "BBa_K3726031""BBa_K3726032""BBa_K3726033"" BBa_K3726034""BBa_K3726035""BBa_K3726036""BBa_K3726037"

References

H. Yu, X. Li, F. Duchoud, D. Chuang and J. Liao, "Augmenting the Calvin–Benson–Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway", 2021.

@@ Line 1: / Line 1: @@
+__NOTOC__
+<partinfo>BBa_K3726038 short</partinfo>
+<partinfo>BBa_K3726038 SequenceAndFeatures</partinfo>
+===Design Notes===
+In the upstream region the bases taatc corresponds with 5bp a spacer sequence to improve ribosomal translation, while AATG overhang creates an start codon that forces translation initiation of the downstream coding sequence.
+In the downstream region, the extra “aa”  bases allow the creation of an additional stop codon (TAA) at the end of the upstream coding sequence, ending the translation of the desired CDS in accordance with the Marburg Collection design guidelines.
+The transcription initiation rate for each RBS element has been specifically adjusted to achieve optimal expression of the desired enzyme within the operon. The relative translation initiation rates for the operon can be observed in the picture below. Where this operon corresponds with the enzymes:  ppc_CDS, gcl_CDS , CDS_mtkA , CDS_mtkB , CDS_mcl.
+https://static.igem.org/mediawiki/parts/thumb/9/92/T--MADRID_UCM--RBSMCGII.png/800px-T--MADRID_UCM--RBSMCGII.png
+This polycistronic CDS sequence has been assembled following a modified procedure for golden gate domestication. To know more about the design process of this polycistronic lv.0 parts, visit the iGEM MADRID_UCM 2021 wiki page
+https://2021.igem.org/Team:MADRID_UCM/Design .
+===Source===
+Gibson assembly using this synthesized basic parts: "BBa_K3726029""BBa_K3726030"
+"BBa_K3726031""BBa_K3726032""BBa_K3726033"" BBa_K3726034""BBa_K3726035""BBa_K3726036""BBa_K3726037"
+===References===
+H. Yu, X. Li, F. Duchoud, D. Chuang and J. Liao, "Augmenting the Calvin–Benson–Bassham cycle by a synthetic malyl-CoA-glycerate carbon fixation pathway", 2021.