Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
HW1 Ultra-efficient DNA Synthesis Machine My research is on designing a DNA synthesis machine that can reduce the cost and time to produce long strands of arbitrary DNA sequences. Right now we’re aiming for megabase strands of DNA but the goal of the project is to eventually get to the Gb range and establish a technology that can scale and improve similar to transistors in Moore’s Law. For context, I work mostly on the mechanical side and hope to learn more about the biochemistry and synthetic biology in general from this class.
Week 10 HW: Imaging and Measurement
HW10 General homework questions Work in progress, check back later
Week 11 HW: Bioproduction and Cloud Labs
HW11 Part A At some point during the global artwork process, I drew a little turtle in the bottom left of the top left plate. It later evolved into the border for the 2026 media lab side of the design but some of the pixels still exist. I loved seeing the artwork evolve over time and seeing what each person created and how, sometimes, people would join together asynchronously to complete designs. I wished the cooldown time was a little less; the 20-second period was more fun for individual creations but the longer time was better for collaboration and competition.
Week 2 HW: DNA Read, Write, and Edit
HW2 Part 1: Benchling & In-silico Gel Art This week, we made gel electrophoresis art using Lambda phage DNA and ten restriction enzymes. Gel electrophoresis uses a positive charge to pull negatively charged DNA through a conductive gel. Longer strands move slower and shorter strands move faster meaning that different lengths of DNA fragments will appear as different bars in your gel. To use this in an artistic context we take our input Lambda DNA and cut it to different lengths using different restriction enzymes which allows us to have coarse control over where these bars end up and thus we can make art with it. I have decided to really commit to my favorite animal, turtles, this semester and try to have a turtle-inspired theme to all of my projects. In an ideal world this is what I wanted my gel art to look like.
HW3 Lab Preparation: Opentrons Artwork This week, we programmed the Opentrons liquid handling robot to create fluorescent protein masterpieces. I was really looking forward to this lab and even did last week homework about expressing GFP in E.Coli. Rather than using the GFP, I found we used a variety of different colors of superfluorescent proteins. Ronan’s webtool [1] made it really easy to visualize a design, and we could even upload images to serve as a template for our designs. I decided to go all in on turtles and make a turtles all the way down image featuring a turtle with a globe for its shell. This was the original image, from my collection of Turtle CADS:
Week 4 HW: Protein Design Part I
HW4 Conceptual Questions Here are my answers to the conceptual questions: [1] How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) ~3x1024 molecules from (500g/(100g/mol))x6.02x1023 [2] Why do humans eat beef but do not become a cow, eat fish but do not become fish?
Week 5 HW: Protein Design Part II
HW5 Part A Part 1: Generate Binders with PepMLM I started by getting the SOD1 sequence from UniProt: MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ Then I added the A4V mutation which changed it to: MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
Week 6 HW: Genetic Circuits Part I
HW6 PCR and DNA Assembly What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The Phusion High-Fidelity PCR Master Mix contains a high-fidelity DNA polymerase for accurate DNA replication, dNTPs as the building blocks for new DNA strands, a buffer to maintain optimal reaction conditions, and magnesium ions which act as a cofactor for the polymerase. Together, these components enable efficient and precise DNA amplification.
Week 7 HW: Genetic Circuits Part II
HW7 Intracellular Artificial Neural Networks What advantages do IANNs have over traditional genetic circuits, whose input/output behaviors are Boolean functions? Intracellular Artificial Neural Networks use continuous analog signals instead of binary ones, which allows them to understand complex inputs like concentrations as opposed to just noting presence. They can use this to perform thresholding, enabling more complex reactions with fewer components. Overall, they are more scalable and better at multi-input sensing than regular genetic circuits.
HW9 General homework questions Explain the main advantages of cell-free protein synthesis over traditional in vivo methods, specifically in terms of flexibility and control over experimental variables. Name at least two cases where cell-free expression is more beneficial than cell production. Cell-free gives more flexibility and control because it operates in a system where you can directly control concentrations of DNA, ions, and cofactors. This allows rapid prototyping and expression of toxic or non-natural proteins without killing your host cell. It is especially beneficial for producing toxic proteins and for quickly testing genetic circuits.