Week 2 HW

Part 1

Hi. I used the KPNI enzyme repeatedly in the virtual digest. Is it possible to re-use enzymes? I think not. The DNA will have already been cut up.

Part 3

I chose the protein phytochrome, which is found in plants and which detects red light. I chose phytochrome because I wanted to use a protein that’s found in plants. Initially I thought about choosing a protein that’s in asparagus. I learned that asparagus is green because of chlorophyll not because of a protein.

Codon optimization might be useful for speeding up protein production. I chose to optimize codon usage for spreading earthmoss because I like moss.

A cell-dependent way to produce phytochrome is:

  • put the DNA into a plasmid
  • put the plasmid into spreading earthmoss (how???? I wonder if putting the plasmid into water and putting the water onto the earthmoss would work)

5.1 DNA Read

i) The DWORF gene because it’s short. I am imagining that a shorter gene will be easier for me to read. AI prompts: “what’s the shortest dna sequence found in nature?” and “can you name me the functional genes that encode for short peptides” ii)Next generation sequencing by synthesis because I want to see the colors light up one by one as the DNA is synthesized.

  1. I don’t know.
  2. Input: Human DNA. Preparation: I don’t know.
  3. Add adaptors to end of DNA sequence. Denature DNA to get one strand. Make nucleotides have fluorescent tags. Polymerase will make the complementary strand. A camera takes images of what’s happening.
  4. Short single-stranded nucleotide sequences.

5.2 DNA Write

i) A genetic circuit so I can learn what it is. When light is detected, light up. ii) Chip based DNA synthesis. involving….a silicon wafer….optical addressing…. I don’t yet understand how manipulating protons related to synthesizing DNA..~~– I don’t know what the limitations of this technology are.

5.3 DNA Edit

i) Edit the DNA of the green algae that sits on lakes to see if it can send light into the water below it. Why? To see if something that grows with light can also emit light.