User:Pakpoom Subsoontorn/Notebook/Genetically Encoded Memory/2008/10/10: Difference between revisions

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Name: L5, Host: Mycobacterium smegmatis
Name: L5, Host: Mycobacterium smegmatis
Name: TP901, Host: Lactococcus lactis
*Action: tyrosine integrase
*Structure:
length:: 485 aa.
crystal structure is unknown.
*Target sequence: attB:: has two inverted repeated sequence (core-type) flanking an overlap region.
attP:: has core-type sites and overlap region, without an arm-type site.
Minimal attB and attP site is <56 bps
*Mechanism:
*Excision: Excisionase has already been indentified.
*Usage:
Integration works in E.coli, mammalian cell and in vitro.


==questions/notes==
==questions/notes==

Revision as of 03:12, 9 November 2008

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Summary Note on site-specific recombinase system

  • Insert content here...

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

Site Specific recombinases

(see more experiment detail)










Name: L5, Host: Mycobacterium smegmatis

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

Database

Reference

  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

improved genomic integration at a native human sequence. Nucl Acids Res, 29 5044-5051

  1. Grainge I & Sherratt DJ (2007), Site-Specific recombination. Molecular Genetics of Recombination, Springer


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