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

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Writing to DNA Insert content here... Outline 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: