Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
Question 1: First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. DNA is the rulebook of life! Imagine it as small lego pieces, building up the entire empire of a human body. But, what if we can pick out the lego pieces and assemble them in different, never-thought-before ways, to unlock new functions and outcomes ?! This is the potential of engineering synthetic genetic circuits! I am intrigued by the possibility of engineering our desired outcome by designing genetic circuits that can alter or control it.
Week 2 HW: DNA Read-Write-Edit - Pre Lecture Prep
Pre-Lecture Prep Homework Questions from Professor Jacobson: 1 Machinery of nature, for copying DNA is called polymerase. What is the error rate of polymerase? How does this compare to the length of the human genome. How does biology deal with that discrepancy? The error rate for the error correcting polymerase is approximately 1 in 10^6 base pairs. The human genome is about 3 billion base pairs in lenght, meaning that without correction, a single round of replication can result in approximately 3000 errors per cell division.
Week 2 HW: DNA Read-Write-Edit - Post Lecture Learnings
Part 0: Basics of Gel Electrophoresis Attend or watch all lecture and recitation videos. Optionally watch bootcamp. Status: Completed. Part 1: Benchling & In-silico Gel Art See this week’s lab protocol “Gel Art: Restriction Digests and Gel Electrophoresis” for details. Overview: 1 Make a free account at benchling.com 2 Import the Lambda DNA. 3 Simulate Restriction Enzyme Digestion with the following Enzymes: a EcoRI b HindIII c BamHI d KpnI e EcoRV f SacI g SalI 4 Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. 5 You might find Ronan’s website a helpful tool for quickly iterating on designs!
Assignment: Python Script for Opentrons Artwork I used the GUI coordinates to prepare this code: Post Lab Questions: One of the great parts about having an automated robot is being able to precisely mix, deposit, and run reactions without much intervention, and design and deploy experiments remotely.