20.109:Module 1:RefactorM13

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Discoverers

  • Rebecca Adams (BsmBI site, rbs-g10)
  • Andrew Ji
  • Bryan Hernandez
  • Amirah Khan
  • Stephanie Nix
  • Mathangi Radha

Designers

Annotation

We'll need to annotate the M13K07 DNA sequence that's online here.

  • Kevin T.L. Vogelsang: (gene VI, HpaI restriction site)
  • Bryan Hernandez: BBa_m1307, gene VIII, and AhdI site
  • Jen Logan: (promoter g5, PvuI site)
  • Aditya Kohli: BBa_M13508 (rbs-g8), AccI site
  • Kate Broadbent: BBa_M13507 (rbs-g7), BamHI site
  • Matt Gethers: BBa_13102 (Gene 2 Promoter) and BssSI Site
  • Jerzy Szablowski: MscI site [5080-5085], BBa_M13505 (rbs-g5) [827-842]
  • Neil Zimmerman: HindIII site (7402-7407), BBa_M13503 (g3 RBS: 1563-1578)
  • Amirah Khan: BBa_M13103 (Gene 3 Promoter: 1500-1547) and BsrGI site (1021-1025)
  • Sophie Wong: BBa_M13108 (Gene 8 Promoter: 1155-1201), Pst1 site (8079/8083)
  • Han Zhu: BBa_M13502 (Gene 2 RBS: 8252-8267), TliI site (7922/7926)
  • Andrew Ji: BBa_M13504 (Gene 4 RBS: 4204-4219), BstBI site (6518/6520)
  • Iny Jhun: BBa_M13001 (Geme 1: 3196-4242, PacI (4131-4138)
  • Tiffany Guo: BBa_M13501 (Gene 1 RBS: 8252-8267), SgrAI (5867-5871)
  • Mathangi Radha: BBa_M13106 (Gene 6 Promoter: 2716-2764), NgoMIV (5613/5617)
  • Mike Lee: BBa_M13003 (Gene 3 ORF: 1579-2853); ApaLI site (4743-4748)
  • Emzo de los Santos: BBa_M13005 (Gene 5 ORF: 843-1106), SacI site (6951/6956)
  • David Ying: BBa_M13101 (Gene 1 Promoter: 3086-3132), SacII site (6030-6035)
  • Dawn Spelke: BBa_M13104 (Gene 4 Promoter: 4055-4103), NruI site (7865/7870)
  • Stephanie Nix: BBa_M13110 (g10 promoter: 381-428), XhoI site (7922/7926)
  • Michael Oh: Bba_M13506 (rbs-g6: 2840-2855), SwaI site (8202-8209)
  • Jen Chao: BBa_M13509 (gene 9 RBS) ,EcoNI site (7611-7612)
  • Mary Hatch: BBa_M13504 (gene 4 RBS), BBa_M13511 (gene 11 RBS), DrdI site (5763/5765)

Design Thoughts

Suggested redesign ideas from "for next time" assignment M1D2

moved to discussion page for M1D3

Clean up work on wild-type genes

genetic element promoter RBS coding
start synthesis with
gII BBa_M13102
(need 5' UTR?) 		BBa_M13502 BBa_M13002'
(modified to remove gene 10 promoter)
gX BBa_M13110
(need 5' UTR?) 		BBa_M13510 BBa_M13010'
(modified to remove gene 5 promoter)
gV BBa_M13105
(need 5' UTR?) 		BBa_M13505 BBa_M13005
gVII BBa_M13507 BBa_M13007'
(modified to remove overlap with gene 9 dwnstm)
gIX BBa_M13509 BBa_M15009'
(modified to remove overlap with gene 8 dwnstm)
gVIII BBa_M13108
(need 5' UTR?) 		BBa_M13508 BBa_M13008
Transcriptional terminator (if M13K07 part, then need to modify to remove gene 3 promoter)
gIII BBa_M13103 BBa_M13503 BBa_M13003'
(modified to remove gene 6 promoter, change GTG start?)
gVI BBa_M13106 BBa_M13506 BBa_M13006'
(modified to remove gene 1 promoter)
gI BBa_M13101 BBa_M13501 BBa_M13001'
(modified to remove gene 11 RBS, gene 4 promoter, RBS, start)
gXI BBa_M13511 BBa_M13011'
(modified to remove gene 4 promoter, RBS, start)
gIV BBa_M13104
(need 5' UTR?) 		BBa_M13504 BBa_M13004'
M13K07 ori/KanR/p15a ori
end synthesis


Note: modified parts would need to be codon varied to remove direct repeats (for cases in which internal parts are unstuffed).

Please add your thoughts about this M13.1 sketch and the class redesign ideas.
All ideas are welcome.
Preceed your comments with 4"~"s to allow for attribution.
Nkuldell 11:37, 23 February 2007 (EST) I don't think we want to make M13 an integrating phage based on work of [Derbise, et al]

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