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

{| width="800"
 * style="background-color: #EEE"|[[Image:owwnotebook_icon.png|128px]] Project name
 * style="background-color: #F2F2F2" align="center"|  |Main project page
 * style="background-color: #F2F2F2" align="center"|  |Main project page


 * colspan="2"|
 * colspan="2"|

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:


 * }