Homework
Weekly homework submissions:
Week 1 HW: Principles and Practices
- Biological Engineering Application / Tool Idea: Low-cost, field-deployable waterborne pathogen detection kit for rural and urban areas in South Asia. Why: Waterborne diseases like cholera, typhoid, and hepatitis A are major health challenges in South Asia. Current testing infrastructure is centralized, expensive, and slow. A portable, easy-to-use kit allows local health workers to identify contaminated water and prevent outbreaks. Conceptual Design:
Week 2 HW: DNA Read, Write, and Edit
Professor Jacobson 1. Polymerase and error rate Nature’s machinery for copying DNA is DNA polymerase. The error rate of typical polymerases is approximately 1 in 104 to 106 nucleotides depending on the enzyme. The human genome is ~3 billion base pairs (3 × 109 bp). Without correction, polymerase errors would result in thousands of mistakes per genome replication. Biology solves this via proofreading and mismatch repair mechanisms, which reduce the effective error rate to ~1 in 109 bp, ensuring accurate genome replication. 2. Coding DNA for human proteins On average, a human protein has ~300 amino acids. Each amino acid can be encoded by 1–6 codons (degeneracy of the genetic code). There are theoretically many different DNA sequences that could code for the same protein. In practice, not all codons work equally well due to: Codon usage bias (some codons are translated more efficiently) mRNA secondary structure affecting translation Regulatory sequences overlapping coding regions Dr. LeProust 1. Most commonly used method for oligo synthesis Solid-phase phosphoramidite synthesis is the standard method. Nucleotides are added one at a time to a growing DNA chain attached to a solid support, using cycles of deprotection, coupling, capping, and oxidation. This method is highly automated and used commercially. Citation: PMC article on oligo synthesis 2. Why oligos >200 nt are difficult Error accumulation: Each added nucleotide can fail, and errors compound with longer chains. Practical limit: High-purity oligos become impossible above ~200 nt. Chemical constraints: Steric hindrance and protecting group limitations reduce efficiency. 3. Why a 2000 bp gene cannot be synthesized directly 2000 bp is far beyond the ~200 nt limit of direct chemical synthesis. Long genes are instead assembled from short oligos using methods like PCR assembly or Gibson assembly. Direct synthesis of a 2 kb gene would yield mostly truncated or error-prone products. George Church Option Chosen: 10 essential amino acids and Lysine Contingency Essential amino acids in most animals: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine. (Arginine can be conditionally essential in children or certain species.) Lysine Contingency: