Week 2 HW: DNA Read, Write, and Edit

Week 2 Lecture Preparation

Professor Jacobson

1. What is the error rate of polymerase and how does biology handle it?
DNA polymerases typically have an error rate of about 10⁻⁷ to 10⁻⁸ per base after proofreading. The human genome has around 3 billion base pairs, so without correction there would be many mutations each replication cycle. Biology solves this discrepancy through proofreading mechanisms in polymerases and additional mismatch repair systems, which reduce the effective mutation rate.

2. How many ways are there to code for an average human protein? Why don’t all of them work?
Because of the degeneracy of the genetic code, many amino acids are encoded by multiple codons. For an average protein of a few hundred amino acids, there are astronomically many possible DNA sequences that could encode it. However, not all sequences work well because of factors like codon bias, mRNA secondary structure, GC content, regulatory sequences, and effects on translation efficiency and protein folding.

Dr. LeProust

1. Most commonly used method for oligo synthesis
The most common method is phosphoramidite solid-phase chemical synthesis.

2. Why is it difficult to make oligos longer than 200 nt?
Each synthesis step has a small error rate. As the oligo length increases, these errors accumulate, leading to a low proportion of full-length, correct sequences.

3. Why can’t you make a 2000 bp gene directly?
Because the cumulative error rate would be extremely high. Instead, shorter oligos are synthesized and then assembled into longer DNA fragments using techniques like PCR assembly or Gibson assembly.

George Church Question

Essential amino acids and the lysine contingency

The ten essential amino acids in animals are: histidine, isoleucine, leucine, lysine, methionine, phenylalanine, threonine, tryptophan, valine, and (in some contexts) arginine.

The lysine contingency refers to engineering organisms that depend on an external supply of lysine to survive. Since lysine is essential and cannot be synthesized by animals, this creates a biological containment strategy. It reduces the risk of engineered organisms surviving outside controlled environments.