Week 07 — Genetic Circuits Part II

Genetic circuits illustration

We continue Genetic Circuits with emphasis on regulatory logic, toggle switches, and practical pathways for implementing and testing circuits in cells.

  • Date: Tue Mar 18. Slides: will be posted after class. Recording: Zoom
  • Warning This homework is based on the Week 7 Lab. It’s a good week to start honing final projects and focusing on developing / researching protocols. Key Link Week 7 — Homework & Lab Google Doc Questions 1–3 (mandatory for all students) How do endoribonucleases (ERNs) work to decrease protein levels? Name 2 differences between how ERNs work and how proteases work. How does Lipofectamine 3000 work? How does DNA get into human cells and how is it expressed? Explain what poly‑transfection is and why it’s useful when building neuromorphic circuits. Questions 4–6 (added Mar 19; optional for MIT/Harvard, mandatory for Committed Listeners) Genetic Toggle Switches Provide a detailed explanation of the mechanism behind genetic toggle switches, including how bi‑stability is established and maintained. Describe at least one induction method used to switch states, including molecular signals or environmental factors involved. Note limitations. How many “switches” can we potentially chain? Is there a metabolic cost? Natural Genetic Circuit Example Identify and describe in detail a naturally occurring genetic circuit, emphasizing its biological function, components, and regulatory interactions. Synthetic Genetic Circuit Select and critically analyze a synthetic genetic circuit previously engineered by researchers (e.g., pDAWN). Provide details about its construction, components, intended function, and performance. Discuss potential limitations or improvements suggested in subsequent literature or experimental data.
  • Date: Wed Mar 19. Slides: will be shared after class. Recording: Zoom
  • Tip This week’s lab focuses on genetic circuit design and testing workflows. Document your design rationale, parts selection, and test plans. Objective Translate design principles into an actionable workflow: from selecting promoters/regulators to drafting test plans for toggle switches or related motifs. Concepts You’ll Learn Regulatory logic & bi‑stability Design strategies for toggle/switch constructs Practical testing plans and documentation
  • Gibson Assembly Recap (protocol) — Google Doc pDAWN optogenetic system — Addgene Synthetic gene circuits review — overview (2024)