Difference between revisions of "Part:BBa J31001:Design"
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The Biobricks on this part are not wildtype but the cut sites are still viable.
 
The Biobricks on this part are not wildtype but the cut sites are still viable.
  
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{| width="800px" cellspacing="2"
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{| width="850px" cellspacing="2"
 
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| style="width:200px" | Standard BioBrick Cloning Sites
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| style="width:200px" | '''Standard BioBrick Cloning Sites''' (Knight)
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| style="background:lightgrey"|<font face="courier">5'---GAATTC GCGGCCGC T TCTAGA ---insert--- T ACTAGT A GCGGCCG CTGCAG---<br>3'---CTTAAG CGCCGGCG A AGATCT ------------ A TGATCA T CGCCGGC GACGTC---<br>EcoRI  NotI  XbaI        SpeI  NotI  PstI</font>
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| style="background:lightgrey"|<font face="courier">5'---GAATTC GCGGCCGC T TCTAGA G -----insert----- T ACTAGT A GCGGCCG CTGCAG---<br>3'---CTTAAG CGCCGGCG A AGATCT C ---------------- A TGATCA T CGCCGGC GACGTC---</font>
 
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| style="width:200px" | Prefix: There is no <font color='red'>T spacer</font color> between the<font color='brown'> NotI site</font color> and the <font color='purple'>XbaI site</font color>. There is no <font color='lime'>G spacer</font color> between the <font color='purple'>XbaI</font> and the <u>coding region</u>.<br>
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| style="width:200px" | '''BBa_J31001 Cloning Sites'''
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Suffix: There is no <font color='tan'>T spacer</font color> between the <u>insert</u> and the <font color='green'>SpeI site</font color>. The <font color='gold'>T spacer</font color> between the <font color='green'>SpeI</font color> and the <font color='magenta'>NotI</font color> sites should be an A. The last ''C'' of the <font color='magenta'>NotI</font color> site is not conserved with the initial C from the <font color='cyan'>PstI site</font color>. The BB suffix currently has this sequence for the <font color='magenta'>NotI</font color> and <font color='cyan'>PstI</font color> sites <font color='magenta'>GCGGCCGc</font color><font color='cyan'>CTGCAG</font color> But it should have been: <font color='magenta'>GCGGCCG</font color><font color='purple'>''C''</font color><font color='cyan'>TGCAG</font color>
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| style="background:lightgrey" |<font face="courier">5'---GAATTC GCGGCCGC <font color='red'>*</font> TCTAGA <font color='blue'>*</font> ---Hin coding--- <font color='purple'>*</font> ACTAGT T GCGGCCGC''C''TGCAG</font></font><br><br>
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| style="background:lightgrey" | <font face="courier"><font color='blue'>GAATTC</font><font color='brown'>GCGGCCGC</font><font color='red'>-</font><font color='purple'>TCTAGA</font><font color='lime'>-</font></font>---Hin coding---<font face="courier"><font color='tan'>-</font><font color='green'>ACTAGT</font><font color='gold'>T</font><font color='magenta'>GCGGCCGC</font>''C''<font color='cyan'>TGCAG</font></font>
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'''Prefix'''<br>There is <font color='red'>no T spacer (*)</font color> between the NotI site and the XbaI site. There is <font color='blue'>no G spacer (*)</font color> between the XbaI and the Hin coding region.<br>
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'''Suffix'''<br>There is no <font color='greenn'>T spacer</font color> between the Hin coding region and the SpeI site.<br>The <font color='purple'>T spacer</font color> between the SpeI and the NotI sites should be an A. The last ''C'' of the <font color='magenta'>NotI</font color> site is not conserved with the initial C from the <font color='cyan'>PstI site</font color>. The BB suffix currently has this sequence for the <font color='magenta'>NotI</font color> and <font color='cyan'>PstI</font color> sites <font color='magenta'>GCGGCCGc</font color><font color='cyan'>CTGCAG</font color> But it should have been: <font color='magenta'>GCGGCCG</font color><font color='purple'>''C''</font color><font color='cyan'>TGCAG</font color>
 
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We compared our BioBricks with those from Tom Knight's paper,<u> Idempotent Vector Design for Standard Assembly of Biobricks</u>. As seen below
 
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[[Image:BioBricks_from_paper.png]]
 
  
 
===Data===
 
===Data===

Revision as of 06:06, 29 October 2006

DNA invertase Hin tagged with LVA


Assembly Compatibility:
  • 10
    COMPATIBLE WITH RFC[10]
  • 12
    COMPATIBLE WITH RFC[12]
  • 21
    COMPATIBLE WITH RFC[21]
  • 23
    COMPATIBLE WITH RFC[23]
  • 25
    COMPATIBLE WITH RFC[25]
  • 1000
    COMPATIBLE WITH RFC[1000]


Hin Invertase

Figure 1. 3-D structure of a Hin protein complex bound to DNA. View the [http://www.rcsb.org/pdb/explore/explore.do?structureId=1ZR4 interactive 3-D Jmol image].
 To the left is a 3-D model of the a Hin/ DNA complex crystal structure (Protein Data Bank ID 1ZR4, Li et al. 2005). A Hin protein dimer binds each HixC sequence flanking the fragment of DNA to be inverted. The two dimers (dimer 1 = leftward green and blue protein structures; dimer 2 = rightward yellow and purple protein structures) come together to form a tetrad complex where cleaved DNA ends are swapped and ligated (Richards and Johnson 2004).

Design Notes

This part is cloned in plasmid pSB1A2.

The Biobricks on this part are not wildtype but the cut sites are still viable.

Standard BioBrick Cloning Sites (Knight) 5'---GAATTC GCGGCCGC T TCTAGA G -----insert----- T ACTAGT A GCGGCCG CTGCAG---
3'---CTTAAG CGCCGGCG A AGATCT C ---------------- A TGATCA T CGCCGGC GACGTC---
BBa_J31001 Cloning Sites 5'---GAATTC GCGGCCGC * TCTAGA * ---Hin coding--- * ACTAGT T GCGGCCGCCTGCAG</font>

Prefix
There is no T spacer (*) between the NotI site and the XbaI site. There is no G spacer (*) between the XbaI and the Hin coding region.
Suffix
There is no T spacer between the Hin coding region and the SpeI site.
The T spacer between the SpeI and the NotI sites should be an A. The last C of the NotI site is not conserved with the initial C from the PstI site. The BB suffix currently has this sequence for the NotI and PstI sites GCGGCCGcCTGCAG But it should have been: GCGGCCGCTGCAG

Data

HinLVA has been assembled with a pLac promoter and RBS (see BBa_S03536) to create a HinLVA expression casette. We observe inversion of HixC-flanked segments of DNA in the presence of this casette. Inversion occurs without IPTG induction of pLac-Hin. This may be caused by read-through from the vector backbone or leaky transcription from pLac.

Figure 2. An NheI digest detects Hin-mediated flipping of a HixC-flanked pBad promoter.
Figure 3. An NheI digest detects Hin-mediated flipping of a HixC-flanked coding region (RBS-Tet).

Source

Hin invertase (BBa_J31000) from Salmonella typhimurium and the LVA degredation tag (BBa_M0040).

References

  • Li, W., Kamtekar, S., Xiong, Y., Sarkis, G.J., Grindley, N.D., Steitz, T.A. (2005) Structure of a synaptic gamma delta resolvase tetramer covalently linked to two cleaved DNAs. Science. 309: 1210-1215
  • Sanders, E.R., Johnson, R.C. (2004) Stepwise Dissection of the Hin-catalyzed Recombination Reaction from Synapsis to Resolution. J. Mol. Biol. 340: 753–766.
  • Knight, Tom. Idempotent Vector Design for Standard Assembly of Biobricks