Week 3 HW: Lab Automation

Final projects were added to the slide and the python file were submitted too.

Post-Lab Questions

1.

One paper I found is “AssemblyTron: flexible automation of DNA assembly with Opentrons OT-2 lab robots” by Bryant et al. The paper describes a workflow for using an Opentrons OT-2 robot to automate DNA assembly. Instead of manually pipetting every DNA part, enzyme, and reagent, the robot can set up many assembly reactions in a more consistent way. The authors made this system because DNA assembly is a common step in synthetic biology, but it becomes slow and error-prone when many constructs have to be tested.

I think this is a useful example because it shows automation being used for a real bottleneck in biology. A lot of synthetic biology depends on building and testing many genetic designs, not just making one perfect construct. The Opentrons robot helps make that process more scalable and less dependent on repetitive manual pipetting. This is especially relevant for projects where small volume differences could affect whether a construct works or not.

2. Automation plan for my final project

For my final project, I want to synthetically produce spider silk proteins and compare which expression or assembly conditions give the best silk-like material. The part I would automate is the screening process, since spider silk production depends on many variables: DNA construct design, protein concentration, buffer composition, pH, salt concentration, and drying or assembly conditions. Instead of testing each condition by hand, I would use an Opentrons-style liquid handler to set up a 96-well plate with many small-scale reactions.

A possible workflow would be:

  1. Dispense cell-free protein synthesis master mix or expression reagents into each well.
  2. Add different spider silk protein DNA constructs to different rows or columns.
  3. Add additives or buffer conditions, such as different pH levels, salts, or crowding agents.
  4. Mix each well consistently using repeated pipetting.
  5. Incubate the plate so the silk proteins are expressed.
  6. Transfer small amounts of the expressed protein into assembly wells with different precipitation or fiber-forming conditions.
  7. Measure output using fluorescence, absorbance, viscosity, or imaging to identify which conditions give the strongest or most fiber-like material.

The main reason automation would help is that spider silk synthesis probably needs a lot of trial and error. A robot would let us test many conditions in parallel while keeping the volumes and timing more consistent. This would make it easier to see which variables actually matter, instead of worrying that the result changed because of manual pipetting differences.