SEGASEGA_collection Version 1 (Collection)In the Standardized Genome Architecture (SEGA), genomic integration of DNA fragments is enabled by λ-Red recombineering and so-called landing pads that are a common concept in synthetic biology and typically contain features that i) enable insertion of additional genetic elements and ii) provide well-characterized functional parts such as promoters and genes, and iii) provides insulation against genome context-dependent effects. The SEGA landing pads allow for reusable homology regions and time-efficient construction of parallel genetic designs with a minimal number of reagents and handling steps. SEGA bricks, typically synthetic DNA or PCR fragments, are integrated on the genome simply by combining the two reagents (i.e. competent cells and DNA), followed by incubation steps, and successful recombinants are identified by visual inspection on agar plates. The design of the SEGA standard was heavily influenced by the Standard European Vector Architecture (SEVA). SEGA landing pads typically hosts two major genetic “control elements” that influence gene expression on the transcriptional (C1), and translational (C2) level. Furthermore, landing pads contain gadgets such as selection and counterselection markers.
SBOLDesigner CAD ToolSBOLDesigner Version 3.1 (Agent)SBOLDesigner is a simple, biologist-friendly CAD software tool for creating and manipulating the sequences of genetic constructs using the Synthetic Biology Open Language (SBOL) 2 data model. Throughout the design process, SBOL Visual symbols, a system of schematic glyphs, provide standardized visualizations of individual parts. SBOLDesigner completes a workflow for users of genetic design automation tools. It combines a simple user interface with the power of the SBOL standard and serves as a launchpad for more detailed designs involving simulations and experiments. Some new features in SBOLDesigner are the ability to add variant collections to combinatorial derivations, enumerating those collections, and the ability to view sequence features hierarchically. There are also some small changes to the way that preferences work in regards to saving a design with incomplete sequences.
Intein_assisted_Bisection_MappingIntein_assisted_Bisection_Mapping_collection Version 1 (Collection)Split inteins are powerful tools for seamless ligation of synthetic split proteins. Yet, their use remains limited because the already intricate split site identification problem is often complicated by the requirement of extein junction sequences. To address this, we augmented a mini-Mu transposon-based screening approach and devised the intein-assisted bisection mapping (IBM) method. IBM robustly revealed clusters of split sites on five proteins, converting them into AND or NAND logic gates. We further showed that the use of inteins expands functional sequence space for splitting a protein. We also demonstrated the utility of our approach over rational inference of split sites from secondary structure alignment of homologous proteins. Furthermore, the intein inserted at an identified site could be engineered by the transposon again to become partially chemically inducible, and to some extent enabled post-translational tuning on host protein function. Our work offers a generalizable and systematic route towards creating split protein-intein fusions and conditional inteins for protein activity control.
Cello E. Coli PartsEco1C1G1T1_collection Version 1 (Collection)These are the Cello parts for E. Coli circuits
BBa_K143071BBa_K143071 Version 1 (Component)AmyE integratable PoPS generator (P43-gsiB) (with CmR)
BBa_K143072BBa_K143072 Version 1 (Component)AmyE integratable PoPS generator (P43-spoVG) (with CmR)
BBa_K143073BBa_K143073 Version 1 (Component)AmyE integratable PoPS generator (Pveg-gsiB) (with CmR)
BBa_K143074BBa_K143074 Version 1 (Component)AmyE integratable PoPS generator (Pveg-spoVG) (with CmR)
BBa_J69522BBa_J69522 Version 1 (Component)tetR-repressible promoter coupled with mCherry Reporter
rTT+pRBBa_K093003 Version 1 (Component)Convergent Promoter System: Forward Module: rTT+lambda pR
Q04510+RFPBBa_K131018 Version 1 (Component)Intermediate for the Response circuit
BBa_K101016BBa_K101016 Version 1 (Component)Dually repressed promoter with sites for TetR and P22MNT binding
SBFP2BBa_K156010 Version 1 (Component)SBFP2 (strongly enhanced blue fluorescent protein)
BBa_K122016BBa_K122016 Version 1 (Component)4CL:STS with CYC1 terminator.
RBS-RFPBBa_K093005 Version 1 (Component)RFP with RBS
RBS-cIBBa_K093006 Version 1 (Component)cI repressor with RBS
oriTr/LacZBBa_K125350 Version 1 (Component)oriTr with lac promoter and lacZ
oriT/LacZBBa_K125360 Version 1 (Component)oriT with lac promoter and lacZ
BBa_K086001BBa_K086001 Version 1 (Component)modified Lutz-Bujard LacO promoter,with alternative sigma factor σ24 followed by YFP reporter
BBa_K086018BBa_K086018 Version 1 (Component)modified Lutz-Bujard LacO promoter,with alternative sigma factor σ24
BBa_K086002BBa_K086002 Version 1 (Component)modified Lutz-Bujard LacO promoter,with alternative sigma factor σ24 followed by YFP
BBa_K086019BBa_K086019 Version 1 (Component)modified Lutz-Bujard LacO promoter,with alternative sigma factor σ24
BBa_K086003BBa_K086003 Version 1 (Component)modified Lutz-Bujard LacO promoter,with alternative sigma factor σ24 followed by YFP reporter
BBa_K086020BBa_K086020 Version 1 (Component)modified Lutz-Bujard LacO promoter,with alternative sigma factor σ24
BBa_K156009BBa_K156009 Version 1 (Component)OFP (orange fluorescent protein)
BBa_K125810BBa_K125810 Version 1 (Component)slr2016 signal sequence + GFP fusion for secretion of GFP
OriTRBBa_J01003 Version 1 (Component)OriT-R (Origin of transfer for the R-plasmid nic region)
pBSEP1BBa_K090401 Version 1 (Component)Gram-positive Shuttle Vector for Episomal Expression
BBa_K142008BBa_K142008 Version 1 (Component)lacI IS mutant R197A with RBS and terminator
BBa_K142009BBa_K142009 Version 1 (Component)lacI IS mutant R197F with RBS and terminator
BBa_K142010BBa_K142010 Version 1 (Component)lacI IS mutant T276A with RBS and terminator
BBa_K142011BBa_K142011 Version 1 (Component)lacI IS mutant T276Fwith RBS and terminator
BBa_K142012BBa_K142012 Version 1 (Component)lacI IS mutant R197A T276A with RBS and terminator
BBa_K142013BBa_K142013 Version 1 (Component)lacI IS mutant R197A T276F with RBS and terminator
BBa_K142014BBa_K142014 Version 1 (Component)lacI IS mutant R197F T276A with RBS and terminator
BBa_K142015BBa_K142015 Version 1 (Component)lacI IS mutant R197F T276F with RBS and terminator
BBa_K142202BBa_K142202 Version 1 (Component)SceI with RBS (BBa_B0030) and double terminator (BBa_B0015)
BBa_K142203BBa_K142203 Version 1 (Component)T4 ligase with RBS (BBa_B0030) and double terminator (BBa_B0015)
BBa_K116510BBa_K116510 Version 1 (Component)GFP under control of pOmpf promoter(K116500+E0240)
BBa_K142047BBa_K142047 Version 1 (Component)tet-controlled LacI generator with constitutive TetR expression cassette
BBa_K142024BBa_K142024 Version 1 (Component)IPTG-on tetracycline-off pulse generator with LacI mutant (R197A) and TetR expression cassette
BBa_K142025BBa_K142025 Version 1 (Component)IPTG-on tetracycline-off pulse generator with LacI mutant (R197F) and TetR expression cassette
BBa_K142026BBa_K142026 Version 1 (Component)IPTG-on tetracycline-off pulse generator with LacI mutant (T276A) and TetR expression cassette
BBa_K142027BBa_K142027 Version 1 (Component)IPTG-on tetracycline-off pulse generator with LacI mutant (T276F) and TetR expression cassette
BBa_K142028BBa_K142028 Version 1 (Component)IPTG-on tetracycline-off pulse generator with LacI mutant (R197A, T276A)/TetR expression cassette
BBa_K142029BBa_K142029 Version 1 (Component)IPTG-on tetracycline-off pulse generator with LacI mutant (R197A, T276F)/TetR expression cassette
BBa_K142030BBa_K142030 Version 1 (Component)IPTG-on tetracycline-off pulse generator with LacI mutant (R197F, T276A)/TetR expression cassette
BBa_K142031BBa_K142031 Version 1 (Component)IPTG-on tetracycline-off pulse generator with LacI mutant (R197F, T276F)/TetR expression cassette
BBa_K116501BBa_K116501 Version 1 (Component)RpaA(regulator of phycobilisome-associated)