Bird of Prey Handbook Overview
Bird of Prey (BoP) is an innovative technology for constructing standardized DNA vectors, from simple single gene constructs to complex multi-effector and multigenic systems. It simplifies DNA design, making it accessible for researchers at all levels to study gene expression, disease mechanisms, and therapeutic applications. With BoP, you can build vectors tailored to your specific research needs, enabling new discoveries in the fields of gene therapy, synthetic biology, and regenerative medicine.
Why Choose Bird of Prey?
- Efficiency: Bird of Prey streamlines the complex process of vector assembly, reducing the time needed to go from design to functional construct.
- Flexibility: From single-gene vectors to multigenic constructs, BoP gives researchers the tools they need to tailor their experiments.
- Precision: With Bird of Prey’s standardized system, the risk of error in gene assembly is greatly reduced, ensuring more consistent results.
- Cost-Effectiveness: Traditional gene synthesis methods can be expensive and time-consuming. BoP’s plug-and-play system lowers costs by simplifying the assembly process.
How It Works
BoP is built on a system of modular DNA elements, where each component of a gene – from promoters to effectors – can be easily swapped or combined to create different constructs. This flexibility allows for customized genetic designs that can be scaled from basic to complex projects.
Example Workflow:
- Start with Pre-Designed Modules: BoP offers a library of transcription units (TUs) and effectors that are ready for immediate use. Pick the ones that best suit your research goals.
- Modify and Combine: Using BoP’s standardized enzyme sites, researchers can easily digest and ligate DNA fragments, combining multiple genes into a single vector.
- Test and Iterate: Once your vector is built, it’s ready to be tested in cells. With BoP’s modular design, modifying your constructs is simple – allowing for quick iterations based on your results.
Glossary
Elements of a Bird of Prey Gene
- E Domain | see definition for “Effector/Effector (E) Domain”
- Effector (E) Domain | a domain within OspreyBio transcription units containing an effector, which is a bioactive RNA (bioRNA) or a Protein (encoded by an Open Reading Frame (ORF) that can exert an “Effect” on a biological system
- Effector Linker | an element within the effector domain of OspreyBio vectors that maintains the ability to add additional effectors within the transcription unit using an IRES shuttle
- P Domain | see definition for “Transcription Processor/Transcription Processing (P) Domain”
- R Domain | see definition for “Transcription Regulator/Transcription Regulator (R) Domain”
- Transcription Processor/Transcription Processing (P) Domain | a downstream domain within OspreyBio transcription units that contains elements that control where the TU’s effector is expressed
- Transcription Unit (TU) | a segment of DNA used to produce a single RNA molecule; all OspreyBioTU’scontain a transcription regulator (R) domain, an effector (E) domain containing a green fluorescent protein, and a transcription processing (P) domain
- Transcription Unit Linker (TUL) | a domain within OspreyBio vectors that maintains the ability to add additional transcription units within a single vector
- Transcription Regulator/Transcription Regulator (R) Domain | an upstream domain within OspreyBio transcription units that contains elements that control where the TU’s effector is expressed
Enzymes & Use Cases
- AgeI | 3' Flank of P | the enzyme at which editors can isolate the transcription unit from the transcription unit linker or in a P domain modification event
- AseI | The “Linearizer” | the enzyme at which Bird of Prey vectors can be cut for linearization to make identification of a long transcription unit in a gel easier
- KasI | 5' Flank of P/3' Flank of EL & E Domain | used to move the entire Effector domain in either Mono-Effectors or Multi-Effectors
- NotI | 3' Flank of TUL | used to release a mono-transcription unit or multi-transcription unit from the vector backbone, or when linking multiple transcription units (XhoI/NotI)
- PvuI | 5' Flank of E/3' Flank of R | used when subcloning an Effector in to the 3' domain of an IRES shuttle vector; compatible cohesive end with PacI in the 5' flank of the IRES GFP
- SalI | 5' Flank of R | used to release an entire transcription unit from the vector backbone or when adding a second transcription unit by subvloningSalI into the primary transcription unit linker’s XhoI; compatible cohesive end with XhoI
- ScaI | 5' Flank of EL | allows for the insertion of bioRNA and IRES/ORF combinations; used when subcloning an Effector into the 5' domain of an IRES shuttle vector; compatible cohesive end with EcoRV in the 3' flank of the IRES RFP
- XhoI | 5' Flank of TUL | used to open the transcription unit linker to insert a monogene or multigene into the transcription unit linker at XhoI/NotI; a compatible cohesive end with SalI