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 10^{4 to 10}6 nucleotides depending on the enzyme.

The human genome is ~3 billion base pairs (3 × 10^9 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 10^9 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:

Fictional mechanism in Jurassic Park where engineered organisms cannot make lysine and therefore depend on an external supply.
In reality, lysine is already essential, but organisms can survive in nature because lysine is widely available in food.
This highlights that engineered dependencies could theoretically control survival, but natural environmental availability must be considered.

Citation: