Cross-species harmonized eGFP
Sequence and Features
- 10COMPATIBLE WITH RFC
- 12COMPATIBLE WITH RFC
- 21Illegal XhoI site found at 409
- 23COMPATIBLE WITH RFC
- 25COMPATIBLE WITH RFC
- 1000COMPATIBLE WITH RFC
The part has been confirmed by sequencing and has no mutations.
Usage and Biology
This coding sequence for eGFP has been generated through the use of our cross-species codon harmonizer. This tool allows you to generate a coding sequence with equal codon usage across a range of organisms. In this case, E. coli, V. natriegens and B. subtilis were selected for the harmonization.
The goal of harmonization is to ensure similar translational rates across these species for the same construct.
The DNA sequence of the part was synthesized by IDT with flanking BpiI sites and respective Modular Cloning (MoClo) compatible coding sequence overhangs. The part was then cloned in a level 0 MoClo backbone pICH41308 and the sequence was confirmed by sequencing. The cloning protocol can be found in the modular cloning section below.
Modular Cloning (MoClo) is a system which allows for efficient one pot assembly of multiple DNA fragments. The MoClo system consists of Type IIS restriction enzymes that cleave DNA 4 to 8 base pairs away from the recognition sites. Cleavage outside of the recognition site allows for customization of the overhangs generated. The MoClo system is hierarchical. First, basic parts (promoters, UTRs, CDS and terminators) are assembled in level 0 plasmids in the kit. In a single reaction, the individual parts can be assembled into vectors containing transcriptional units (level 1). Furthermore, MoClo allows for directional assembly of multiple transcriptional units. Successful assembly of constructs using MoClo can be confirmed by visual readouts (blue/white or red/white screening). Click here for the protocol.
Note: The basic parts sequences of the Sci-Phi 29 collection in the registry contain only the part sequence and therefore contain no overhangs or restriction sites. For synthesizing MoClo compatible parts, refer to table 2.
Table 1: Overview of different level in MoClo
|Level 0||Basic||Promoters, 5’ UTR, CDS and terminators||BpiI|
|Level 1||Composite||Transcriptional units||BsaI|
|Level 2/M/P||Composite||Multiple transcriptional units||BpiI|
For synthesizing basic parts, the part of interest should be flanked by a BpiI site and its specific type overhang. These parts can then be cloned into the respective level 0 MoClo parts. For level 1, where individual transcriptional units are cloned, the overhangs come from the backbone you choose. The restriction sites for level 1 are BsaI. However, any type IIS restriction enzyme could be used.
Table 2: Type specific overhangs and backbones for MoClo. Green indicates the restriction enzyme recognition site. Blue indicates the specific overhangs for the basic parts
|Basic Part||Sequence 5' End||Sequence 3' End||Level 0 backbone|
|Promoter||NNNN GAAGAC NN GGAG||TACT NN GTCTTC NNNN||pICH41233|
|5’ UTR||NNNN GAAGAC NN TACT||AATG NN GTCTTC NNNN||pICH41246|
|CDS||NNNN GAAGAC NN AATG||GCTT NN GTCTTC NNNN||pICH41308|
|Terminator||NNNN GAAGAC NN GCTT||CGCT NN GTCTTC NNNN||pICH41276|
To test whether this eGFP has the same translational rates in these three organisms we made use of our incoherent feed forward loop which allows us to take away other biological context dependent variables.