User:Pakpoom Subsoontorn/Notebook/Genetically Encoded Memory/2008/10/16

From OpenWetWare
Jump to navigationJump to search
Owwnotebook icon.png Project name Report.pngMain project page
Resultset previous.pngPrevious entry      Next entryResultset next.png

Writing to DNA

  • Insert content here...


  • Goal: To change to sequence of DNA at a specific locations
  • Approaches:
    • Site-specific double-stranded break
    • Error-prone DNA polymerase
    • Site-specific recombinases
      • Classification by functions (analogous): transposase, invertase, resolvase, integrase
      • Classification by structures (homologous): tyrosine recombinase, serine recombinase
  • Site-specific double-stranded break
    • DSB activate repairing mechanism, especially homologous recombination
    • custom-made Zn-finger binding protein
  • Error-prone DNA polymerase
    • targeted by ORI on plasmid
    • invivo directed evolution
  • Site-specific recombinase: by function and by structures
    • transposase
    • invertase
    • resolvase
    • integrase
    • excisionase
    • Tyrosine-recombinase, Serine recombinase (comparison)
  • Engineering perspective: what do engineer wanna know
    • reversibility/ efficiency
    • specificity
    • speed
    • modularity (for protein engineer)
  • Data-management
    • Goal: to have a well-organized system to compare/contrast these machinery
    • Demand: what information do we want as an engineer
    • Supply: what kind of information exist
      • our parallel experiment
      • literature: (reference system, split rawdata and inference)
        • public database like PDB, GenBank
        • review paper
        • experimental paper
  • how should our "table" look like
    • need to take into account uncertainity of inference
    • capture the recurring pattern of experiment / raw data
  • The Database project..for site-specific recombinase..and maybe other DNA-writer
    • Need more quantitative information, more standardized information
    • source of information: literature + parallel experiment
    • What do we need in our table: