Homework — DNA Read, Write, and Edit

Warning

Document every step of your in‑silico and lab work — sketches, screenshots, notes, failures, and fixes. Your write‑up should help others reproduce your process.

Part 0 — Basics of Gel Electrophoresis

  • Watch the week’s lecture and recitation videos. (Bootcamp is optional.)

Part 1 — Benchling & In‑silico Gel Art

Use the Gel Art: Restriction Digests and Gel Electrophoresis protocol as a guide.

  1. Create a free account at benchling.com
  2. Import Lambda DNA from NEB.
  3. Simulate digests with enzymes: EcoRI, HindIII, BamHI, KpnI, EcoRV, SacI, SalI.
  4. Design a banding pattern inspired by Paul Vanouse’s Latent Figure Protocol.

Part 2 — Wet‑lab Gel Art

Info
Optional for Committed Listeners with lab access; mandatory for MIT/Harvard students. Documentation due at the start of class Feb 18.

Perform the experiment you designed in Part 1 per the Gel Art protocol.

Part 3 — DNA Design Challenge

Info
Mandatory for MIT/Harvard students and Committed Listeners; due at the start of class Feb 18.
  • Choose a protein of interest and obtain the amino‑acid sequence (NCBI/UniProt/other).
  • Reverse translate to DNA.
  • Continue per recitation guidance (gRNA design, editor choice, etc.).

Gel art example