dsRED (BBa_E1010) compatible with Genabler assembly
dsRED (BBa_E1010) part with inward facing EarI recognition sites at the ends
To be compatible with Genabler assembly, the part has inward-facing EarI sites at the ends. When assembled by BioBrick assembly, five N-terminal residues MetAlaSerSerSer- and one C-terminal Ala residue will be added to the original sequence of BBa_E1010.
IP-Free TannenRFP (Red Fluorescent Protein)
This sequence is fully synthetic, (non-Aequorea) and is codon optimized for expression in E. coli.
This synthetic part was created through a gene engineering and synthesis project at DNA 2.0.
Monomeric Red Fluorescent Protein from Discosoma striata
Mutant of the Biobrick BBa_E1010, in order to make it compatible with the Freiburg-Standard, two AgeI-Restriction sites were deleted monomeric RFP: Red Fluorescent Protein. Excitation peak: 584 nm Emission peak: 607 nm
The Biobrick has the Following Prefix and Suffix: Gatcgaattccgcggccgcttctagataaggaggagccggc Gatcctgcagcggccgctactagtattaaccggt
pCusC mKate2. copper sensitive promoter with RFP reporter gene
This part is the SNAP-mCHERRY UNIT of cyclebow including a SNAP UNIT and a mCHERRY UNIT. The SNAP UNIT, which can be cut off by CRE, includes an sv40 nuclear location sequence (NLS), a covalent labeling of fusion proteins named SNAP-tag?? and an sv40 terminator flanked by homodromous recognition site of recombinase CRE named loxP. The mCHERRY UNIT, which can be cut off by VIKA, includes a degradation tag named DBOX, a fluorescent gene mCherry and an sv40 terminator flanked by homodromous recognition site of recombinase VIKA named Vox. You may use this part to: 1) Test the cut-off efficiency of recombinase CRE and VIKA; 2) Estimate the time needed for genome repair because mCherry can only be expressed after the cut off of SNAP UNIT and genome repair; 3) Fast cut off this part by transient transfecting recombinase gene into nucleus; 4) When there is no CRE, you can use this part as the SNAP UNIT, which can help localize proteins in vivo with BLOCK and dye from NEB company.
The SNAP-tag?? was brought from NEB company. NLS and sv40 terminator were got from commercial plasmid: pentry nls GFP/pcdna3.1. The sequence of Vox and DBOX was retrieved from Addgene and got through denovo synthesis. mCHERRY was got from commercial plasmid: pentry dcas9 mcherry bira.
pTet + RBS + mRFP1 + Transcriptional terminator
This part codifies for a red fluorescent protein (BBa_K081014). It??s regulated by a TetR repressible promoter (R0040).
mRFP: Monomeric red fluorescent protein engineered to enhance photoresistance (BBa_E1010). It was used the part BBa_K081014. ptet: Based in the TetR repressible promoter of operon for resistance against tetracycline (BBa_R0040).
UV Mutation Optimized RFP (Improved Expression)
RFP sequence, based on E1010, with the number of possible pyrimidine dimer-forming sites reduced to the maximum possible extent. Altered from BBa_K1673101 to increase effective expression approximately 40%
Sequence produced by the Vanderbilt iGEM 2015 mutation optimization software.
mCherry fluorescent protein - Rights owned by Clontech. Sequence is commercially available from Clontech. Sequence obtained through PCR amplification, with BioBrick prefix and suffix added through in-house designed primers.
PstI site within the mCherry sequence - has to be assembled using BioBrick assembly in such an order that any successive digestions will not require PstI, otherwise the mCherry sequence will be cut as well as the site of interest.
Lactose/IPTG inducible promoter with RFP reporter tagged with DAS-ssrA degradation tag followed by terminator. The tagged RFP is degraded within cell, thus provides better temporal resolution of red fluorescence and promoter activity. Presence of SspB is crucial for effective protein degradation.
Part was assembled using BrickClip assembly (BBF RFC104) using other biobrick parts as templates. BrickClip assembly is a special case of more general Paperclip assembly method.[1]
**highly** engineered mutant of red fluorescent protein from Discosoma striata (coral) with barcode
Constantin Ahlmann-Eltze, Charlotte Bunne, Magdalena Büscher, Jan Gleixner, Max Horn, Anna Huhn, Nils Klughammer, Jakob Kreft, Elisabeth Schäfer, Carolin Schmelas, Silvan Schmitz, Max Waldha
This part is essentially identical to <partinfo>BBa_E1010</partinfo>, but has a point mutation in the barcode. Barcodes are discontinued, but composite parts using this part will have the mutated barcode.
RFP sequence, based on E1010, with the number of oxidation-prone sites reduced to the minimum possible amount.
This is the coding sequence for mCherry with AB ends for Aar1 cloning.
Since this is an BD part, there is no ATG but there is a stop codon. For more information on AarI cloning, please refer to the UCSF 2008 igem page.
The dTomato protein is a fluorescent dimer protein that emits orange-red light when it is excited by green-yellow light. It is preferable to use ??? especially in self-made fluorometry tests ??? because the excitation wavelengths and the emission wavelengths do not overlap as much as in other fluorescent proteins. The dTomato excitation peak is at 554 nm and 50% of it is at 510 nm. The emission peak is at 581 nm and the 50% emission peak is at 629 nm. Characterization has been made with the Anderson promoters BBa_J23101 (this construct) and BBa_J23110 (construct BBa_K1688011)
dTomato was derived from a monomeric mutant of the anthozoan coral RFP, DsRed.
mRFP (DsRed) derived, altered to be a biobrick by removing a PstI site and adding in the ends.
Made a point mutation to eliminate a PstI site in the middle and then added BioBrick ends using PCR. Sequenced using primers that bind to the pSB1A2 plasmid on either side of the brick.
mCherry from Roger Y. Tsien's lab, altered to be BioBrick compatible
RFP (BBa_1491008) with 6X His Tag for easier protein purification. Original sequence was codon optimized for E.coli by IDT Codon optimization tool.
His tag for easier protein purification and codon optimized for E.coli.
The dTomato protein is a fluorescent dimer protein that emits orange-red light when it is excited by green-yellow light. It is preferable to use ??? especially in self-made fluorometry tests ??? because the excitation wavelengths and the emission wavelengths do not overlap as much as in other fluorescent proteins. The dTomato excitation peak is at 554 nm and 50% of it is at 510 nm. The emission peak is at 581 nm and the 50% emission peak is at 629 nm.
Partially optimized RFP sequence, based on E1010. Has a 4% reduction in the number of possible pyrimidine dimer-forming sites.
RFP sequence, based on E1010, with the number of possible pyrimidine dimer-forming sites reduced to the maximum possible extent.
Lactose/IPTG inducible promoter with RBS, RFP reporter tagged with LAA-ssrA degradation tag and terminator. The tagged RFP is actively degraded within cell, thus provides better temporal resolution of red fluorescence and promoter activity.
Part was assembled using BrickClip assembly (BBF RFC 104) using other biobrick parts as templates. BrickClip assembly is a special case of more general Paperclip assembly method.[1]
Naringenin sensor (FdeR) with mKate as reporter
Sascha Hein, Niklas Hummel, Sebastian Barthel, Thomas Dohmen
We modified the naringenin biosensor from Siedler et al. by elimination of one EcoRI restriction site and by changing the native ribosomal binding site into the strong RBS Bba_B0034. Based on this reporter protein and 3 different fluorescence proteins, we designed 3 new biosensors for in vivo detection and determination of naringenin. The natural source of FdeR is Herbaspirillum seropedicae. You can use our reporter for measuring naringenin concentrations in your samples. Depending on which fluorophor you want to detect, you can use one of three biosensors: GFP fluorescence K1497020 mKate (DsRed variant) fluorescence K1497021 CFP fluorescence K1497022
The mCHERRY UNIT: mCherry flanked by Vox
This part is the mCHERRY UNIT of cyclebow system including a degradation tag named DBOX, a fluorescent gene mCherry and an sv40 terminator flanked by homodromous recognition site of recombinase VIKA named Vox. The whole part can be cut off by VIKA. You may use this part to: 1) Provide fluorescent red which can be quickly cut off by transient transfecting recombinase gene into nucleus; 2) Use it as a part of the flp-out system[5]. 5. Voutev, R. and E.J. Hubbard, A "FLP-Out" system for controlled gene expression in Caenorhabditis elegans. Genetics, 2008. 180(1): p. 103-19.
The sequence of Vox and DBOX was retrieved from Addgene and got through denovo synthesis. mCHERRY and sv40 terminator were got from commercial plasmid: pentry dcas9 mcherry bira and pentry nls GFP/pcdna3.1, respectfully.
This part is the SNAP-mCHERRY-CYAN UNIT of cyclebow including a SNAP UNIT, a mCHERRY UNIT and a plain CYAN. The SNAP UNIT, which can be cut off by CRE, includes an sv40 nuclear location sequence (NLS), a covalent labeling of fusion proteins named SNAP-tag?? and an sv40 terminator flanked by homodromous recognition site of recombinase CRE named loxP. The mCHERRY UNIT, which can be cut off by VIKA, includes a degradation tag named DBOX, a fluorescent gene mCherry and an sv40 terminator flanked by homodromous recognition site of recombinase VIKA named Vox. You may use this part to: 1) Test the cut-off efficiency of recombinase CRE and VIKA; 2) Estimate the time needed for genome repair because mCherry can only be expressed after the cut off of SNAP UNIT and genome repair; 3) Fast cut off this part by transient transfecting recombinase gene into nucleus; 4) When there is no CRE, you can use this part as the SNAP UNIT, which can help localize proteins in vivo with BLOCK and dye from NEB company.
The SNAP-tag?? was brought from NEB company. NLS and sv40 terminator were got from commercial plasmid: pentry nls GFP/pcdna3.1. The sequence of Vox and DBOX was retrieved from Addgene and got through denovo synthesis. mCHERRY was got from commercial plasmid: pentry dcas9 mcherry bira. CYAN was got from commercial plasmid: puc18 cfp-yfp.
RFP sequence, based on E1010, with the number of possible pyrimidine dimer-forming sites increased to the maximum possible amount.
Sequence produced by the Vanderbilt iGEM 2015 mutation optimization software
This is N-terminal of mCherry, that can be used in Bimolecular Fluorescence Complementation system (BiFC).
PartsRegistry J06505, originally from Discosoma sp.
The dTomato protein is a fluorescent dimer protein that emits orange-red light when it is excited by green-yellow light. It is preferable to use ??? especially in self-made fluorometry tests ??? because the excitation wavelengths and the emission wavelengths don't overlap as much as in other fluorescent proteins. The dTomato excitation peak is at 554 nm and 50% of it is at 510 nm. Also, its emission peak is at 581 nm and its 50% emission at 629 nm (Figure 1). Characterization has been made with the Anderson promoters BBa_J23101 and (construct BBa_K1688010) and BBa_J23110 (construct BBa_K1688011).
It was derived from a monomeric mutant of the anthozoan coral RFP, DsRed
The second portion of the RFP gene, after the HixC insertion point.
Lactose/IPTG inducible promoter with RBS, RFP reporter tagged with LVA-ssrA degradation tag and terminator. The tagged RFP is actively degraded within cell, thus provides better temporal resolution of red fluorescence and promoter activity. This part can be considered as improved version of BBa_J04451 as it does not contain StuI restriction site coding for additional 'RP' residues between RFP and LVA tag.
KillerRed is a red fluorescent protein that produces reactive oxygen species (ROS) in the presence of yellow-orange light (540-585 nm). KillerRed is engineered from Aequorea victoria GFP (avGFP) to be phototoxic. It has been shown that KillerRed produces superoxide radical anions by reacting with water. Superoxide reacts with the chromophore of KillerRed, causing it to become dark, which ultimately gives rise to a bleaching effect. KillerRed is spectrally similar to mRFP1 with a similar brightness. KillerRed is oligomeric and may form large aggregates. This sequence is codon optimized for mammalian cells and has 14 rare proline codons for E. coli (CCC) and one rare arginine codon (AGA). Codon optimization should be taken into consideration if large amounts of the protein are required. Expression on a high-copy plasmid has produced detectable fluorescent signal, however.
This sequence is not codon optimized for E. coli.
Engineered from avGFP. Provided by the Bruchez lab at Carnegie Mellon
Lactose/IPTG inducible promoter wuth RFP reporter tagged with AAV-ssrA degradation tag followed by terminator. The tagged RFP is actively degraded within cell, thus provides better temporal resolution of red fluorescence and promoter activity. Part was assembled using BrickClip assembly (BBF RFC 104) using other biobrick parts as templates. BrickClip assembly is a special case of more general Paperclip assembly method.[1] Reference [1] Trubitsyna, M., Michlewski, G., Cai, Y., Elfick, A. & French, C. E. PaperClip: rapid multi-part DNA assembly from existing libraries. Nucleic Acids Res. 1???8 (2014). doi:10.1093/nar/gku829
Since this is an AB part, there is an ATG but no stop codon. For more information on AarI cloning, please refer to the UCSF 2008 igem page.
mRFP derivative. Ex548nm/Em562. yeast codon optimized.
Contains N- and C-terminal linker sequences (with homology to biobrick parts BBa_E2060 (mCherry), BBa_E2020 (Cerulean CFP), and BBa_E2030 (Venus YFP) to facilitate color swapping in yeast. Adds N-"MATSG" and "GSGTA"-C. to published amino acid sequence. Double TAATAA stop codon. Missing EcoRI, HindIII, NotI, NdeI, XhoI, RsrII, BamHI, NcoI, BglI, SpeI, XbaI, and PstI. except for 5' and 3' ends no significant sequence identity runs to mCherry (BBa_E2060).
Shaner et al, 2004. Nat Biotech (22):1567-1571
The part is basically a sequence encoding red florescent protein. With specially designed primers, it can be fused with its previous signal protein, yebF.
It is RFC23 compatible, with specially designed prefix.
Obtaining this sequence, we designed primers to take the sequence from IGEM distributed part, BBa_E1010.
'''The dTomato protein is a fluorescent dimer protein that emits orange-red light when it is excited by green-yellow light. The excitation wavelengths and the emission wavelengths don't overlap as much as in other fluorescent proteins, which makes it preferable to use ??? especially in self‑made fluorometry tests.'''
mCherry (BBa_J06504) compatible with Genabler assembly
mCherry (BBa_J0654) part with inward facing EarI recognition sites at the ends compatible with Genabler assembly.
To be compatible with Genabler assembly, the part has inward-facing EarI sites at the ends. When assembled by BioBrick assembly, five N-terminal residues MetAlaSerSerSer- and one C-terminal Ala residue will be added to the original sequence of BBa_E0040.
mCherry is based on the BioBrick BBa_J06504.
Highly engineered monomeric mutant of RFP. Improved version of part BBa_E1010 to remove illegal AgeI sites and add RFC25 prefix and suffix.
Codon optimised for E. coli. RFC 25 compatible.
mRFP highly engineered variant originally from Discosoma striata.
A SV40 nuclear localization signal was added to the phototoxic protein KillerRed.