Homework
Weekly homework submissions:
Professor Jacobson’s Questions Q1: Polymerase Error Rate vs. the Human Genome Raw polymerase error rate: DNA polymerase III (the baseline replicative polymerase) misincorporates roughly 1 in 10^4 to 10⁵ nucleotides during synthesis. I fyou factor in built-in proofreading checkpoints this error rate reduces to about 1 in 10⁷.
Week 1 HW: Principles and Practices
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.
Week 2 HW :DNA Read Write Edit
Molecular Biology 101 1. Nucleotides In Silico Several free tools let you visualize and manipulate DNA/RNA sequences on your computer. Key options: SnapGene Viewer (plasmid maps), NCBI BLAST (sequence alignment), UCSC Genome Browser (reference genomes), and Benchling (all-in-one cloud platform). Benchling is a great starting point — it’s free, browser-based, and lets you import sequences (GenBank, FASTA, or raw), view annotated maps, design primers, run in silico digests, and align sequencing data. It also supports team collaboration and version control.
Week 3: Lab Automation HTGAA 2026 — Fiona Connolly What Lab Automation Can Do for Us? Lab automation is simply automating the processes in the lab. Scripted protocols, and integrated instruments to carry out experimental procedures with ideally minimal manual intervention. Particularly in molecular biology, this typically translates to very precise , temporally and temperature controlled liquid handling across the scale from picoL to Litres. The precise transfer of reagents, cultures, or genetic constructs between wells, plates, and vessels.
Week 4 Review: Protein Design Part I
Week 4 — Protein Design Part I Foundations of protein chemistry: alphabet, structure, and design A topic guide on the amino-acid alphabet, secondary structure, chirality, β-sheet aggregation, and the principles of designing structured peptides — written as a stand-alone primer rather than a homework Q&A. This page is Part A of the Week 4 deliverable for HTGAA Spring 2026; Parts B, C, and D (sequence/structure analysis, ML protein design, MS2 L-protein engineering proposal) will be added as those sessions complete.
Week 6 & 7 Review: Genetic Circuits
Week 6 — Genetic Circuits I: Assembly Technologies Part 1 — DNA Assembly: PCR, Gibson, Golden Gate, and transformation A topic guide on the molecular-biology toolkit that underpins all of synthetic biology: amplifying DNA (PCR), cutting it (restriction enzymes), joining it (Gibson and Golden Gate), and getting it into cells (transformation). Written as a stand-alone primer rather than a homework Q&A. Part 2 (Asimov Kernel: building genetic circuits computationally) will follow as a separate page once the simulation work is complete.