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

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Summary Note on site-specific recombinase system

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Classification
Keywords for classification, which can be overlapped
 * By Structure
 * Tyrosine recombinase
 * Serine recombinase
 * Large Serine recombinase
 * By Function
 * Integrase
 * Excisionase
 * Invertase
 * Resolvase
 * Transposase
 * other stuffs
 * Integron

Methods

 * Discovering new site-specific recombinase
 * Characterizing protein domains
 * DNA binding domain
 * Catalytic domain
 * Finding the target-site
 * Minimal specific sequence for targeting
 * Looking into recombination mechanism
 * DNA topologies
 * Protein-DNA interaction
 * Chronology of events
 * Chemistry at active site
 * Evaluating Efficiency
 * Recombination yield
 * Specificity

questions/notes

 * play with bacteriophage and microbial genome database, look for recombinase genes
 * look at Tn4451 mechanism for boosting up integration, Lyras and Rood 2000

Reference
improved genomic integration at a native human sequence. Nucl Acids Res, 29 5044-5051
 * 1) Groth AC & Calos MP (2004), Phage Integrases: Biology and Applications. J.Mol.Biol. 335:667-678
 * 2) Sclimenti CR, Thyagarajan B & Calos MP, Directed evolution of a recombinase for
 * 1) Grainge I & Sherratt DJ (2007), Site-Specific recombination. Molecular Genetics of Recombination, Springer


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