Attributions#
Work by the team#
To be completed
Per-person contribution statements. The lab journal records who ran which experiment day by day; this section should summarise that by contribution area rather than reproduce it.
Reused material#
Being explicit about what we did not build ourselves.
Plasmids#
| Source | Obtained as | Used for |
|---|---|---|
pdCas9-bacteria (Addgene) |
Bacterial stab | Source of the dCas9 coding sequence, amplified out by PCR |
pSC101-T7-T3RNAP (Addgene) |
Bacterial stab | MutaT7 platform components |
| pDB series (Addgene) | Bacterial stab | Mutagenesis plasmid backbone |
pET-Duet-1 |
Laboratory stock | Expression backbone for shell constructs |
Published work this project is built on#
The project is a recombination of four existing results, and it is worth being plain that none of the underlying components are ours:
- QtEncapsulin's structure and native cargo-loading chemistry — Giessen et al., eLife 8, e46070 (2019).
- Shell permeability and single-step cargo loading — Kwon, Andreas, Jones & Giessen, bioRxiv (2026), doi:10.64898/2026.04.06.716810.
- Directed evolution of this shell, and the dominant-negative problem it raises — Siddiquee et al., bioRxiv (2026), doi:10.64898/2026.01.12.698938.
- The λN·boxB handle and evolution of an RNA-packaging capsid — Tetter et al., Science 372, 1220–1224 (2021), doi:10.1126/science.abg2822.
- Guide-truncation titration of dCas9 repression, and the kick-out model our selection depends on — Vigouroux et al., Molecular Systems Biology 14, e7899 (2018), doi:10.15252/msb.20177899.
- Continuous hypermutation for context and comparison — Diercks et al., Science 389, 618–622 (2025), doi:10.1126/science.adp9583.
Our contribution is the combination: wiring encapsulation to survival through a titratable CRISPRi circuit, and giving one shell two orthogonal handles on a ribonucleoprotein.
Protocols#
Published protocols were used and modified where our equipment differed — most substantially the Ni-NTA procedure, which was rebuilt as a hybrid of a manufacturer protocol written for pre-packed columns, a published methods section, and local practice for hand-packed columns. Modifications are documented in Protocols.
Software and infrastructure#
Plasmid design and sequence alignment in Benchling. This wiki is built with MkDocs on a bespoke theme with no external runtime dependencies.
Help from others#
To be completed
Acknowledgement of the host laboratory, the advisors who supplied training, bench space, equipment access and troubleshooting advice, and the sequencing facility. The journal records substantial day-to-day help that belongs here.