Difference between revisions of "Part:BBa J31001:Design"

(→‎References)
(→‎Biobricks)
Line 13: Line 13:
 
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.
  
−
<font color='blue'>GAATTC</font color><font color='brown'>GCGGCCGC</font color><font color='red'>-</font color><font color='pink'>TCTAGA</font color><font color='lime'>-</font color><u>TGGCTACTATTGGGTATATTCGGGTGTCAACAATTGACCAAAATATCGATTTACAGCGTAATGCGCTTACCAGTGCAAATTGTGACCGCATTTTTGAGGACCGTATCAGTGGCAAGATTGCAAACCGCCCCGGCCTGAAA
+
{|
−
CGAGCGTTAAAGTATGTAAATAAAGGCGATACTCTTGTCGTCTGGAAATTAGACAGACTGGGCCGCAGCGTGAAAAACCTGGTGGCGTTAATATCAGAATTACATGAACGTGGAGCTCACTTCCATTCTTTAACCGATAG
+
|-
 +
| style="width:200px"| BioBrick Prefix:
 +
| <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"><u>TGGCTACTATTGGGTATATTCGGGTGTCAACAATTGACCAAAATATCGAT<br>
 +
TTACAGCGTA ATGCGCTTACCAGTGCAAATTGTGACCGCATTTTTGAGG<br>
 +
ACCGTATCAGTGGCAAGATTGCAAACCGCCCCGGCCTGAAACGAGCGTTA<br>
 +
AAGTATGTAAATAAAGGCGATACTCTTGTCGTCTGGAAATTAGACAGACT<br>
 +
GGGCCGCAGCGTGAAAAACCTGGTGGCGTTAATATCAGAATTACATGAACGT<br>GGAGCTCACTTCCATTCTTTAACCGATAG
 
TATTGATACCAGTAGCGCGATGGGGCGATTCTTTTTTCATGTAATGTCAGCACTGGCCGAGATGGAGCGAGAATTAATTGTCGAGCGAACCCTTGCCGGACTGGCTGCCGCCAGAGCGCAAGGACGACTGGGAGGGCG
 
TATTGATACCAGTAGCGCGATGGGGCGATTCTTTTTTCATGTAATGTCAGCACTGGCCGAGATGGAGCGAGAATTAATTGTCGAGCGAACCCTTGCCGGACTGGCTGCCGCCAGAGCGCAAGGACGACTGGGAGGGCG
 
CCCTCGGGCGATCAACAGACATGAACAGGAACAGATTAGTCGGCTATTAGAGAAAGGCCATCCTCGGCAGCAACTAGCTATTATTTTTGGTATTGGCGTATCTACCTTATACAGATATTTTCCGGCAAGCCGTATAAAAA
 
CCCTCGGGCGATCAACAGACATGAACAGGAACAGATTAGTCGGCTATTAGAGAAAGGCCATCCTCGGCAGCAACTAGCTATTATTTTTGGTATTGGCGTATCTACCTTATACAGATATTTTCCGGCAAGCCGTATAAAAA
−
AACGAATGAATAGGCCTGCTGCAAACGACGAAAACTACGCTTTAGTAGCTTA</u><font color='tan'>-</font color><font color='green'>ACTAGT</font color><font color='gold'>T</font color><font color='magenta'>GCGGCCGC</font color>''C''<font color='cyan'>TGCAG</font color>
+
AACGAATGAATAGGCCTGCTGCAAACGACGAAAACTACGCTTTAGTAGCTTA</u>
 +
| BioBrick Suffix:
 +
| <font color='tan'>-</font color><font color='green'>ACTAGT</font color><font color='gold'>T</font color><font color='magenta'>GCGGCCGC</font color>''C''<font color='cyan'>TGCAG</font></font>
 +
|}
  
−
There is no <font color='red'>T spacer</font color> between the<font color='brown'> NotI site</font color> and the <font color='pink'>XbaI site</font color>.
+
 
 +
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='pink'>XbaI</font color> and the <u>insert</u>.
 
There is no <font color='lime'>G spacer</font color> between the <font color='pink'>XbaI</font color> and the <u>insert</u>.

Revision as of 19:07, 26 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]


Design Notes

This part is cloned in plasmid pSB1A2.

Biobricks

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

BioBrick Prefix: GAATTCGCGGCCGC-TCTAGA-
Hin coding: TGGCTACTATTGGGTATATTCGGGTGTCAACAATTGACCAAAATATCGAT

TTACAGCGTA ATGCGCTTACCAGTGCAAATTGTGACCGCATTTTTGAGG
ACCGTATCAGTGGCAAGATTGCAAACCGCCCCGGCCTGAAACGAGCGTTA
AAGTATGTAAATAAAGGCGATACTCTTGTCGTCTGGAAATTAGACAGACT
GGGCCGCAGCGTGAAAAACCTGGTGGCGTTAATATCAGAATTACATGAACGT
GGAGCTCACTTCCATTCTTTAACCGATAG TATTGATACCAGTAGCGCGATGGGGCGATTCTTTTTTCATGTAATGTCAGCACTGGCCGAGATGGAGCGAGAATTAATTGTCGAGCGAACCCTTGCCGGACTGGCTGCCGCCAGAGCGCAAGGACGACTGGGAGGGCG CCCTCGGGCGATCAACAGACATGAACAGGAACAGATTAGTCGGCTATTAGAGAAAGGCCATCCTCGGCAGCAACTAGCTATTATTTTTGGTATTGGCGTATCTACCTTATACAGATATTTTCCGGCAAGCCGTATAAAAA AACGAATGAATAGGCCTGCTGCAAACGACGAAAACTACGCTTTAGTAGCTTA

BioBrick Suffix: -ACTAGTTGCGGCCGCCTGCAG


There is no T spacer between the NotI site and the XbaI site.

There is no G spacer between the XbaI and the insert.

There is no T spacer between the insert 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

We compared our BioBricks with those from Tom Knight's paper, Idempotent Vector Design for Standard Assembly of Biobricks. As seen below

BioBricks from paper.png

Source

Salmonella typhimurium and the the Hin part without LVA.

References

Knight, Tom. Idempotent Vector Design for Standard Assembly of Biobricks