Difference between revisions of "Part:BBa K3697004"

Revision as of 04:43, 24 October 2020

Recombination-based Detection System for B. Subtilis (manP)

This system, once incorporated into the B. Subtilis will act as a detection system for a customizable nucleic acid sequence corresponding to the sequence with homology to the "homology arms" of the system. It acts a detection system, as when exposed to the target sequence a recombination will be triggered causing the excision of the negative selection marker that is flanked by the homology arms. More information about the specific negative selection marker used in this system can be found in the documentation for part BBa_K3697002 and more information about the specific set of homology arms used in this system can be found in the documentation for part BBa_K3697003.

Usage and Biology

This system works in B. subtilis because of the way that it integrates with the competence and genomic recombination systems in B. subtilis. A brief overview of both of these systems is given below.

The competence system in B. subtilis is driven by the expression of the ComK transcription factor[1]. This system naturally occurs in B. Subtilis when they are put on environmental stress, but strains of B. subtilis have been engineered to have inducible competence. Some examples of strains with inducible competence systems that were successfully used by the 2020 Stanford iGEM team are 1A976 and 1A1276. Both of these strains were obtained through the Bacillus Genetic Stock Center (http://www.bgsc.org/). https://attachments.office.net/owa/cneimeth%40stanford.edu/service.svc/s/GetAttachmentThumbnail?id=AAMkADRhYWU4ZjY2LWZhMTEtNDQ1YS1iZDc1LTkwOWU2OGIxNWI5YQBGAAAAAAAvKT49t%2BS9TYKBjC7pGP6%2FBwCLOV8cePSyRrxbwSrUqFI5AAAAAAEMAACLOV8cePSyRrxbwSrUqFI5AAJcEyc5AAABEgAQAMiXxCQgK1NMl1cSBRjZHe8%3D&thumbnailType=2&owa=outlook.office.com&scriptVer=20201019001.11&X-OWA-CANARY=3e_uVndpck-V1xKjBOHTU7B0fljXd9gYQdngQiDWOf3fy9-PqdvzzQtf7rtESbksyH0RKx98D48.&token=eyJhbGciOiJSUzI1NiIsImtpZCI6IjU2MzU4ODUyMzRCOTI1MkRERTAwNTc2NkQ5RDlGMjc2NTY1RjYzRTIiLCJ0eXAiOiJKV1QiLCJ4NXQiOiJWaldJVWpTNUpTM2VBRmRtMmRueWRsWmZZLUkifQ.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.nOYSOfJgdv_gVcoLJB8hp3vSNNJd9oqUXAozsk5Gpw8U4aJouEn_D-qViTwHBEREJMPNQ3h6AY0LaTqZop8CpSqECAD5YS4F9Eg-V8XMpoKL6FRQoSJ_7nw_AbeEhv5MxYRpG65qUtIP5pQwcgd8Zh7xhHiDZiipepZPAUCVypTe9c-HJlULPtjTcSG39RutfU0c2QcZK6jU7xdW4dfFWlKQh9Tx5JPPHZXXbd5j68R4pxpDSFMvmXj2h3GigO83Wnf1gImSkvq3923Z6GU7fNuOeaBVNPmC8PwZvjiGT51l2ClMBETOQObMWaHw-8grtQeKkxu6J9uCHjo9oYuHyw&animation=true [1] Turgay K, Hahn J, Burghoorn J, Dubnau D. 1998. Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor. EMBO J 17:6730–6738.

Sequence and Features

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
COMPATIBLE WITH RFC[12]
21
INCOMPATIBLE WITH RFC[21]
Illegal BglII site found at 679
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 1272
Illegal AgeI site found at 922
Illegal AgeI site found at 1016
Illegal AgeI site found at 2682
1000
INCOMPATIBLE WITH RFC[1000]
Illegal BsaI.rc site found at 822
Illegal SapI site found at 1844

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K3697004 short</partinfo>
-This system, once incorporated into the B. Subtilis will act as a detection system for a customizable nucleic acid sequence corresponding to the sequence with homology to the "homology arms" of the system. It acts a detection system, as when exposed to the target sequence a recombination will be triggered causing the excision of the negative selection marker that is flanked by the homology arms (more details on the exact negative selection marker and homology arms used in this sequence can be found in the documentation for parts BBa_K3697002 and BBa_K3697003 respectively).
+This system, once incorporated into the B. Subtilis will act as a detection system for a customizable nucleic acid sequence corresponding to the sequence with homology to the "homology arms" of the system. It acts a detection system, as when exposed to the target sequence a recombination will be triggered causing the excision of the negative selection marker that is flanked by the homology arms. More information about the specific negative selection marker used in this system can be found in the documentation for part BBa_K3697002 and more information about the specific set of homology arms used in this system can be found in the documentation for part BBa_K3697003.
-<!-- Add more about the biology of this part here
 ===Usage and Biology===
+This system works in B. subtilis because of the way that it integrates with the competence and genomic recombination systems in B. subtilis. A brief overview of both of these systems is given below.
+The competence system in B. subtilis is driven by the expression of the ComK transcription factor[1]. This system naturally occurs in B. Subtilis when they are put on environmental stress, but strains of B. subtilis have been engineered to have inducible competence. Some examples of strains with inducible competence systems that were successfully used by the 2020 Stanford iGEM team are 1A976 and 1A1276. Both of these strains were obtained through the Bacillus Genetic Stock Center (http://www.bgsc.org/).
+https://attachments.office.net/owa/cneimeth%40stanford.edu/service.svc/s/GetAttachmentThumbnail?id=AAMkADRhYWU4ZjY2LWZhMTEtNDQ1YS1iZDc1LTkwOWU2OGIxNWI5YQBGAAAAAAAvKT49t%2BS9TYKBjC7pGP6%2FBwCLOV8cePSyRrxbwSrUqFI5AAAAAAEMAACLOV8cePSyRrxbwSrUqFI5AAJcEyc5AAABEgAQAMiXxCQgK1NMl1cSBRjZHe8%3D&thumbnailType=2&owa=outlook.office.com&scriptVer=20201019001.11&X-OWA-CANARY=3e_uVndpck-V1xKjBOHTU7B0fljXd9gYQdngQiDWOf3fy9-PqdvzzQtf7rtESbksyH0RKx98D48.&token=eyJhbGciOiJSUzI1NiIsImtpZCI6IjU2MzU4ODUyMzRCOTI1MkRERTAwNTc2NkQ5RDlGMjc2NTY1RjYzRTIiLCJ0eXAiOiJKV1QiLCJ4NXQiOiJWaldJVWpTNUpTM2VBRmRtMmRueWRsWmZZLUkifQ.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.nOYSOfJgdv_gVcoLJB8hp3vSNNJd9oqUXAozsk5Gpw8U4aJouEn_D-qViTwHBEREJMPNQ3h6AY0LaTqZop8CpSqECAD5YS4F9Eg-V8XMpoKL6FRQoSJ_7nw_AbeEhv5MxYRpG65qUtIP5pQwcgd8Zh7xhHiDZiipepZPAUCVypTe9c-HJlULPtjTcSG39RutfU0c2QcZK6jU7xdW4dfFWlKQh9Tx5JPPHZXXbd5j68R4pxpDSFMvmXj2h3GigO83Wnf1gImSkvq3923Z6GU7fNuOeaBVNPmC8PwZvjiGT51l2ClMBETOQObMWaHw-8grtQeKkxu6J9uCHjo9oYuHyw&animation=true
+[1] Turgay K, Hahn J, Burghoorn J, Dubnau D. 1998. Competence in Bacillus subtilis is controlled by regulated proteolysis of a transcription factor. EMBO J 17:6730–6738.
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