Week 2 HW.5: DNA Read/Write/Edit
DNA Read
(i) What DNA would you want to sequence (e.g., read) and why? This could be DNA related to human health (e.g. genes related to disease research), environmental monitoring (e.g., sewage waste water, biodiversity analysis), and beyond (e.g. DNA data storage, biobank).
No idea. Possibly my basil plant.
(ii) In lecture, a variety of sequencing technologies were mentioned. What technology or technologies would you use to perform sequencing on your DNA and why?
I would use long-read sequencing (1–100+ kb). Even though it is more expensive, it would provide greater accuracy.
The way that DNA sequencing works currenly is by taking DNA, lysing it, and then reassembling fragments based on probabilistic approaches. The “read length” refers to how large these fragments are in terms of base pairs. A fragment of length = 1 bp would be near useless, since there is no way to “place” it probabilistically within the greater genome. A fragment of length = 150bp map well because apparently the human genome is largely non-repetitive at that scale.
Short-read sequencing is a read of 50–600 bp. Long-read sequencing is 1-100 kb.
Technologies:
- Polymerase-based sequencing
- Enzymatic digest sequencing
- Nanopore sequencing
- DNA microarrays
DNA Write
(i) What DNA would you want to synthesize (e.g., write) and why?
I have no idea.
(ii) What technology or technologies would you use to perform this DNA synthesis and why?
- Recombinant DNA synthesis
- Oligonucleotide synthesis - can make complex motifs, extremely large DNA molecules (1kbp+)
DNA Edit
(i) What DNA would you want to edit and why?
I have no idea. Potentially plant DNA. I don’t know anything about what DNA plants have. I would like to figure out how to increase the growth speed, change the bark texture. Or even doing experiments on yeast. Perhaps I could figure out the enzymes/proteins and what DNA/genes code for it, and then edit that.
(ii) What technology or technologies would you use to perform these DNA edits and why?
CRISPR-Cas9