Week 3 HW.2: Post-Lab Reflection

2.1. Find and describe a published paper utilizing Opentrons or similar liquid handling automation tools.

The paper I have found: Slowpoke: An Automated Golden Gate Cloning Workflow for Opentrons OT‑2 and Flex

Slowpoke is a tool which generates Opentron protocols for DNA assembly. DNA assembly is used to assemble larger strings of DNA than can be synthesised in one go, by joining together oligonucleotides.

It provides facilities to automate:

  1. Golden Gate Cloning - automates the DNA assembly reaction setup, E. Coli transformation, and plating.
  2. Colony PCR - automates colony PCR screening of resulting transformants.

Users provide for:

  1. Golden Gate Cloning

    1. Genetic toolkit map - e.g. MoClo YTK, STK plate layout
    2. Custom parts map
    3. Combination file

  2. Colony PCR

    1. Colony template positions
    2. PCR deck maps
    3. Reaction recipes.

The robot protocol automates the full pipeline of assembly, transformation, plating and colony PCR:

  1. DNA and enzyme buffer extraction.
  2. Golden gate reaction.
  3. Transformation.
  4. Plating.
  5. Colony PCR.

It is compatible with multiple MoClo/Golden Gate toolkits (YTK, STK, and extensible to others).

Manual steps still required:

  • Colony picking - most labour-intensive step.
  • Sealing PCR plates in OT-2 thermocycler module.
  • Transferring PCR tubes to benchtop thermocycler.
  • Incubation, strain storage, and plasmid purification - still accounts for a lot of time.

https://github.com/Tom-Ellis-Lab/Slowpoke

2.2. Describe your intended automation use for your final project, including pseudocode, scripts, or implementation plans.

I intend to use a cloud lab platform to screen an array of biosensor constructs that I have designed, synthesised, and expressed using cell-free protein synthesis (CFPS).