User:Pakpoom Subsoontorn/Notebook/Genetically Encoded Memory

Project Description/Abstract

Notes

• Our review paper on genetically encoded memory (in preparation)
• Summary note on site-specific recombinase

Outline

1. Application
2. Grand Challenges
3. Start-up experiments
4. Review Articles

Project List

• Synthetic Jumping DNA from Integrase/excisionase system
• Implementing N-bit memory with DNA recombination
• Engineering cell-cycle reporter
• Quantitative functional profiles (Database) of site-specific recombinase
• Expanding Integrase/excisionase library

Conceptual questions

• In the abstract level, how could we live with imperfect efficiency? No matter writing mechanism we choose in the end, the fraction of cells whose genome is actually rewritten will likely to be significantly less than a hundred percent.
• What are the common/ different challenges between writing memory to DNA versus gene therapy/ transgenic?
• Why reaction line DNA integration is irreversible but mostother don't?

TO DO List

• reading
• Write up the detail structure and mechanism of integrase
• Take a look at how virus hijack a host and take control of host machinery (i.e. look at Covert's large

scale viral-bacterial models). May be the first step for engineering a cell it to modify the virus to control the cell the way we want.

• discuss HT-in vivo protein evolution project with Jennifer, James, Quake's pp
• Maybe I should start focusing on specific memory encoding problem..like counting the number of cell cycle.

..many signaling protein rise and fall in each cell cycle, so as the copy number of genome..we might be able to make use of them.

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