Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    Project Propalsal: A small, low-cost desktop platform that combines short DNA synthesis with cell-free expression. Users (students, community labs, small clinics) design short DNA sequences through a web interface, send them to a benchtop “DNA printer,” and immediately test them in a cell-free system. This pushes “personal fabrication” into biology and could support education and grassroots innovation, but raises serious questions about biosecurity, safety, and equity when DNA writing becomes cheap and widely accessible.

  • Week 2 HW: DNA Read, Write, & Edit

    3.1 Choose your protein I chose Green Fluorescent Protein (GFP) from the jellyfish Aequorea victoria. Reasons: -Classic reporter protein in molecular biology and imaging -Small, monomeric, and widely used as a fusion tag sp|P42212|GFP_AEQVI Green fluorescent protein OS=Aequorea victoria OX=6100 GN=GFP PE=1 SV=1 MSKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTL VTTFSYGVQCFSRYPDHMKQHDFFKSAMPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLV NRIELKGIDFKEDGNILGHKLEYNYNSHNVYIMADKQKNGIKVNFKIRHNIEDGSVQLAD HYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHMVLLEFVTAAGITHGMDELYK 3.2 Reverse translate (protein → DNA) reverse translation of sp|P42212|GFP_AEQVI Green fluorescent protein OS=Aequorea victoria OX=6100 GN=GFP PE=1 SV=1 to a 714 base sequence of most likely codons. atgagcaaaggcgaagaactgtttaccggcgtggtgccgattctggtggaactggatggc gatgtgaacggccataaatttagcgtgagcggcgaaggcgaaggcgatgcgacctatggc aaactgaccctgaaatttatttgcaccaccggcaaactgccggtgccgtggccgaccctg gtgaccacctttagctatggcgtgcagtgctttagccgctatccggatcatatgaaacag catgatttttttaaaagcgcgatgccggaaggctatgtgcaggaacgcaccatttttttt aaagatgatggcaactataaaacccgcgcggaagtgaaatttgaaggcgataccctggtg aaccgcattgaactgaaaggcattgattttaaagaagatggcaacattctgggccataaa ctggaatataactataacagccataacgtgtatattatggcggataaacagaaaaacggc attaaagtgaactttaaaattcgccataacattgaagatggcagcgtgcagctggcggat cattatcagcagaacaccccgattggcgatggcccggtgctgctgccggataaccattat ctgagcacccagagcgcgctgagcaaagatccgaacgaaaaacgcgatcatatggtgctg ctggaatttgtgaccgcggcgggcattacccatggcatggatgaactgtataaa

  • Week 3 HW: LabAutomation

    1. Reference paper: HYDRA – hydrogels by robotic automation Citation Torchia, E. et al. Fabrication of cell culture hydrogels by robotic liquid handling automation for high-throughput drug testing. Communications Engineering, 4, 222 (2025). What they did This paper introduces HYDRA (HYDrogels by Robotic liquid-handling Automation), a method to fabricate thin, planar hydrogel films directly inside standard 96- and 384-well plates using liquid-handling robots.

  • Week 4 HW: ProteinDesign

    Part A. Conceptual Questions Question: 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.) Answer: 5 mol × 6.02 × 10²³ ≈ 3 × 10²⁴ amino acid molecules. So eating 500 g of meat gives you on the order of 10²⁴ (about three septillion) amino acid molecules.

  • Week 5 HW: Protein Design II

    Part 1 1. Retrieve SOD1 sequence and introduce A4V MATKVCVVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ

  1. PepMLM-generated 12-aa peptides + known binder (lower = higher model confidence in the binder). ID Peptide (12 aa) Source Perplexity (PepMLM) P1 WHSPVAAARLKE PepMLM 11.721713 P2 KRYGAAAARHKK PepMLM 11.211369 P3 WRYPVAGLALKE PepMLM 13.068802 P4 WHSPPAAVALGE PepMLM 12.159801 Ref FLYRWLPSRRGG known SOD1 binder N/A Observation (PepMLM confidence by perplexity): Among generated candidates, P2 (KRYGAAAARHKK) has the lowest perplexity (highest PepMLM confidence), while P3 (WRYPVAGLALKE) has the highest perplexity (lowest confidence among the four).

  • Week 6 HW: Genetic Circuits Part I: Assembly Technologies

    Answers to Questions About This Week’s Lab Protocol 1. What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? Phusion High-Fidelity PCR Master Mix typically contains several important components: Phusion DNA polymerase, dNTPs, reaction buffer, and MgCl2. The polymerase synthesizes new DNA strands and has proofreading activity, which lowers the error rate compared with standard Taq polymerase. The dNTPs provide the nucleotide building blocks needed to make the new DNA strands. The buffer maintains the proper chemical environment, including pH and salt concentration, for the enzyme to work efficiently. MgCl2 is an essential cofactor that allows the polymerase to function properly. In this lab, the master mix is provided as a 2X mix, so only template DNA, primers, and water are added separately. (neb.com)