<NYI NYI TUN> — HTGAA Spring 2026
About me
I am Nyi Nyi Tun. I am glad to be a part of wonderful HTGAA 2026 course. I am exciting to explore on synthetic biology. I am based in Japan.
Contact info
https://www.linkedin.com/in/nyi-nyi-tun-9027b0213/
Subsections of <NYI NYI TUN> — HTGAA Spring 2026
Homework
Weekly homework submissions:
Week 2 Lecture Pre Homework under Professor Jacobson Section Q: Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase? A: The error rate of polymerase is approximately 1 error per 10⁵ nucleotides. Q. How does this compare to the length of the human genome. A: The haploid human genome is about:3 × 10⁹ base pairs (3 billion). If polymerase copied the genome with no additional safeguards, it falls on the order of ~30,000 errors per cell division.
Subsections of Homework
Week 01 HW: #Writeup
Week 2 Lecture Pre Homework under Professor Jacobson Section
Q: Nature’s machinery for copying DNA is called polymerase. What is the error rate of polymerase?
A: The error rate of polymerase is approximately 1 error per 10⁵ nucleotides.
Q. How does this compare to the length of the human genome.
A: The haploid human genome is about:3 × 10⁹ base pairs (3 billion). If polymerase copied the genome with no additional safeguards, it falls on the order of ~30,000 errors per cell division.
Q. How does biology deal with that discrepancy?
A. Biology solves the discrepancy by refusing to rely on any single line of defense.
Q. How many different ways are there to code (DNA nucleotide code) for an average human protein?
A. Each amino acid position can be encoded in ~3 different ways on average.
Q. In practice what are some of the reasons that all of these different codes don’t work to code for the protein of interest?
A. Reasons are as follows:
- Codon bias and tRNA availability (speed & accuracy)
- Translation kinetics and co-translational folding
- mRNA secondary structure etc.
Week 2 Lecture Pre Homework under Professor Dr. LeProust Section
Q. What’s the most commonly used method for oligo synthesis currently?
A. The most commonly used method today for synthesizing custom short DNA (or RNA) oligonucleotides in labs and biotech is ‘Solid-phase phosphoramidite chemical synthesis’
Q. Why is it difficult to make oligos longer than 200nt via direct synthesis?
A. Because small inefficiencies compound brutally with length. Chemical oligo synthesis is a game of percentages, and after ~200 cycles the math just stops being kind.
Q. Why can’t you make a 2000bp gene via direct oligo synthesis?
A. Because chemical DNA synthesis breaks down long before we get anywhere near 2000 bases — not for one reason, but because multiple failure modes pile up and become overwhelming. At that length, the process doesn’t just get inefficient; it becomes fundamentally unusable.
Week 2 Lecture Pre Homework under George Church Section Section
Q. What are the 10 essential amino acids in all animals and how does this affect your view of the “Lysine Contingency”?
A. “Essential” here means animals cannot synthesize them de novo and must obtain them from diet. The 10 essential amino acids in (essentially) all animals are
- Histidine
- Isoleucine
- Leucine
- Lysine
- Methionine
- Phenylalanine
- Threonine
- Tryptophan
- Valine
- Arginine
The lysine contingency (as usually framed) is the idea that: Life’s chemistry — especially the genetic code and amino acid set — is strongly shaped by historical accidents, and could have been very different.
Reference
OpenAI. (2026). ChatGPT (Feb 10 version) [Large language model]. https://chat.openai.com/
Week 01 HW: principles-and-practices
