Difference between revisions of "Part:BBa K4390008"

Latest revision as of 08:37, 12 October 2022

JUMP C part spacer

This part is not compatible with BioBrick RFC10 assembly but is compatible with the iGEM Type IIS Part standard which is also accepted by iGEM.

This part already includes the 5' and 3' JUMP C-part fusion sites, so when making composite parts using this part do not add the 5' and 3' JUMP C-part fusion sites (TTCG and GCTT).

Usage and Biology

DNA assembly is the cornerstone of synthetic biology, and fast and reliable assembly is a necessity for this. Modular cloning with Type IIS restriction enzymes allows us to quickly assemble many complex multipart constructs from libraries of basic parts. The JUMP vector platform is compatible with the PhytoBrick standard, and vectors are compatible with BioBrick architecture as well as Standard European Vector Architecture (SEVA), and uses single stranded DNA overhangs (fusion sites) generated by BsmBI and BsaI digestion for ordered assembly. There are six different JUMP part types, corresponding to different elements of a transcriptional unit, the Promoter, Ribosome Binding Site (RBS), N-terminus, Open Reading Frame (ORF), C-terminus, and terminator. Figure 1 shows the fusion sites between these part types, and that basic parts can also take up more than one part by adopting a 5’ fusion site of one part and the 3’ fusion site of another.

Figure 1: JUMP fusion sites. Adapted from Valenzuela-Ortega and French 2020. The second and third lines demonstrate how a basic part can adopt fusion sites for different basic parts and be used in assembly as such.

We have designed a series of parts, so called fillers, which allow for assembly compatibility when one particular part is not desired. The parts are flanked with fusion sites for the part type, and two nucleotides to prevent a frameshift, by having the 3’ fusion site’s 4 nucleotides generate two codons together.

One example of how this is useful is with tags. Usually, an untagged control would need to be produced in the experiment as well, so instead of ordering multiple parts with different types, the fillers can be used. We used this to drastically reduce the number of parts we needed to order, and hence improved our modularity by using few parts to make many assemblies.

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
COMPATIBLE WITH RFC[1000]

@@ Line 3: / Line 3: @@
 <partinfo>BBa_K4390008 short</partinfo>
-This part functions to fill in the space where a C part is meant to go in a JUMP assembly. Effectively, it has C part fusion sites flanking the sequence either side, with as few nucleotides in between as possible to prevent a frameshift mutation
+'''This part is not compatible with BioBrick RFC10 assembly but is compatible with the iGEM Type IIS Part standard [[Help:Standards/Assembly/Type_IIS|which is also accepted by iGEM.]]'''
+'''This part already includes the 5' and 3' JUMP C-part fusion sites, so when making composite parts using this part do not add the 5' and 3' JUMP C-part fusion sites (TTCG and GCTT).'''
+==Usage and Biology==
+DNA assembly is the cornerstone of synthetic biology, and fast and reliable assembly is a necessity for this. Modular cloning with Type IIS restriction enzymes allows us to quickly assemble many complex multipart constructs from libraries of basic parts. The JUMP vector platform is compatible with the PhytoBrick standard, and vectors are compatible with BioBrick architecture as well as Standard European Vector Architecture (SEVA), and uses single stranded DNA overhangs (fusion sites) generated by BsmBI and BsaI digestion for ordered assembly. There are six different JUMP part types, corresponding to different elements of a transcriptional unit, the Promoter, Ribosome Binding Site (RBS), N-terminus, Open Reading Frame (ORF), C-terminus, and terminator. Figure 1 shows the fusion sites between these part types, and that basic parts can also take up more than one part by adopting a 5’ fusion site of one part and the 3’ fusion site of another.
+[[File:JUMP fusionsites.png|800px|cc]]
+''Figure 1: JUMP fusion sites. Adapted from ''Valenzuela-Ortega and French 2020. ''The second and third lines demonstrate how a basic part can adopt fusion sites for different basic parts and be used in assembly as such.''
+We have designed a series of parts, so called fillers, which allow for assembly compatibility when one particular part is not desired. The parts are flanked with fusion sites for the part type, and two nucleotides to prevent a frameshift, by having the 3’ fusion site’s 4 nucleotides generate two codons together.
+One example of how this is useful is with tags. Usually, an untagged control would need to be produced in the experiment as well, so instead of ordering multiple parts with different types, the fillers can be used. We used this to drastically reduce the number of parts we needed to order, and hence improved our modularity by using few parts to make many assemblies.
 <!-- Add more about the biology of this part here
-===Usage and Biology===
 <!-- -->