Difference between revisions of "Part:BBa J31000:Design"

(→‎Design Notes)
 
(5 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
 
 
__NOTOC__
 
__NOTOC__
 
<partinfo>BBa_J31000 short</partinfo>
 
<partinfo>BBa_J31000 short</partinfo>
Line 11: Line 10:
  
 
===Biobricks===
 
===Biobricks===
−
The Biobricks attached to this part are not correct.
+
The Biobricks attached to this part are not wild type but the cut sites are still viable.
 +
 
 +
<font face=courier new><font color='blue'>GAATTC</font color><font color='brown'>GCGGCCGC</font color><font color='green'>T</font color><font color='orange'>TCTAGA</font color><font color='red'>-</font color><u>ATGGCTACTATTGGGTATATTCGGGTGTCAACAATTGACCAAAATATCGATTTACAGCGTAATGCGCTTACCAGTGCAAATTGTGACCGCATTTTTGAGGACCGTATCAGTGGCAAGATTGCAAACCGCCCCGGCCTGAAACGAGCGTTAA
 +
 
 +
AGTATGTAAATAAAGGCGATACTCTTGTCGTCTGGAAATTAGACAGACTGGGCCGCAGCGTGAAAAACCTGGTGGCGTTAATATCAGAATTACATGAACGTGGAGCTCACTTCCATTCTTTAACCGATAGTATTGATACCAGTAGCGCGATGGGGCGAT
 +
 
 +
TCTTTTTTCATGTAATGTCAGCACTGGCCGAGATGGAGCGAGAATTAATTGTCGAGCGAACCCTTGCCGGACTGGCTGCCGCCAGAGCGCAAGGACGACTGGGAGGGCGCCCTCGGGCGATCAACAAACATGAACAGGAACAGATTAGTCGGCTATTA
 +
 
 +
GAGAAAGGCCATCCTCGGCAGCAACTAGCTATTATTTTTGGTATTGGCGTATCTACCTTATACAGATATTTTCCGGCAAGCCGTATAAAAAAACGAATGAATTAA</u><font color='tan'>-</font color><font color='lime green'>ACTAGT
 +
</font color><font color='navy'>-</font color><font color='pink'>GCGGCCGC</font color><font color='cyan'>CTGCAG</font color></font face>
 +
 
 +
There is no <font color='red'>G</font color> spacer between the <font color='orange'>XbaI</font color> and the <u>insert</u>.
 +
 
 +
There is no <font color='tan'>T</font color> spacer between the <u>insert</u> and the <font color='lime green'>SpeI</font color> site.
 +
 
 +
There is no <font color='navy'>A</font color> spacer between the <font color='lime green'>SpeI</font color> site and the <font color='pink'>NotI site</font color>.
 +
 
 +
The last C of the <font color='pink'>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 <font color='pink'>NotI</font color> and <font color='cyan'>PstI</font color>:
 +
<font color='pink'>GCGGCCGc</font color><font color='cyan'>CTGCAG</font color>
 +
 
 +
But it should have been:
 +
<font color='pink'>GCGGCCG</font color><font color='purple'>C</font color><font color='cyan'>TGCAG</font color>
 +
 
 +
There is no <font color='navy'>spacer</font color> between the <font color='pink'>NotI</font color> site and the <font color='lime green'>SpeI</font color> site. There should be a T.
 +
 
 +
We compared our BioBricks with those from Tom Knight's paper,<u> Idempotent Vector Design for Standard Assembly of Biobricks</u>. As seen below
  
−
<font color='blue'>GAATTCGCGGCCGCTTCTAGA-ATGGCTACTATTGGGTATATTCGGGTGTCAACAATTG
+
[[Image:BioBricks_from_paper.png]]
−
ACCAAAATATCGATTTACAGCGTAATGCGCTTACCAGTGCAAATTGTGACCGCATTTTTGAGGACCGTATCAGTGGCAAGATTGCAAACCGCCCCGGCCTGAAACGAGCGTTAAAGTATGTAAATAAAGGCGATACTCTTGTCGTCTGGAAATTAGACAGACTGGGCCGCAGCGTGAAAAACCTGGTGGCGTTAATATCAGAATTACATGAACGTGGAGCTCACTTCCATTCTTTAACCGATAGTATTGATACCAGTAGCGCGATGGGGCGATTCTTTTTTCATGTAATGTCAGCACTGGCCGAGATGGAGCGAGAATTAATTGTCGAGCGAACCCTTGCCGGACTGGCTGCCGCCAGAGCGCAAGGACGACTGGGAGGGCGCCCTCGGGCGATCAACAAACATGAACAGGAACAGATTAGTCGGCTATTAGAGAAAGGCCATCCTCGGCAGCAACTAGCTATTATTTTTGGTATTGGCGTATCTACCTTATACAGATATTTTCCGGCAAGCCGTATAAAAAAACGAATGAATTAA-ACTAGT-GCGGCCGCCTGCAG
+
  
 
===Source===
 
===Source===
Line 21: Line 46:
  
 
===References===
 
===References===
 +
[https://dspace.mit.edu/handle/1721.1/21168|  Knight, Tom. Idempotent Vector Design for Standard Assembly of Biobricks]

Latest revision as of 14:26, 27 July 2006

DNA-invertase Hin from Salmonella typhimurium


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 into plasmid pSB1A2.

Biobricks

The Biobricks attached to this part are not wild type but the cut sites are still viable.

GAATTCGCGGCCGCTTCTAGA-ATGGCTACTATTGGGTATATTCGGGTGTCAACAATTGACCAAAATATCGATTTACAGCGTAATGCGCTTACCAGTGCAAATTGTGACCGCATTTTTGAGGACCGTATCAGTGGCAAGATTGCAAACCGCCCCGGCCTGAAACGAGCGTTAA

AGTATGTAAATAAAGGCGATACTCTTGTCGTCTGGAAATTAGACAGACTGGGCCGCAGCGTGAAAAACCTGGTGGCGTTAATATCAGAATTACATGAACGTGGAGCTCACTTCCATTCTTTAACCGATAGTATTGATACCAGTAGCGCGATGGGGCGAT

TCTTTTTTCATGTAATGTCAGCACTGGCCGAGATGGAGCGAGAATTAATTGTCGAGCGAACCCTTGCCGGACTGGCTGCCGCCAGAGCGCAAGGACGACTGGGAGGGCGCCCTCGGGCGATCAACAAACATGAACAGGAACAGATTAGTCGGCTATTA

GAGAAAGGCCATCCTCGGCAGCAACTAGCTATTATTTTTGGTATTGGCGTATCTACCTTATACAGATATTTTCCGGCAAGCCGTATAAAAAAACGAATGAATTAA-ACTAGT -GCGGCCGCCTGCAG

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

There is no T spacer between the insert and the SpeI site.

There is no A spacer between the SpeI site and the NotI site.

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 NotI and PstI: GCGGCCGcCTGCAG

But it should have been: GCGGCCGCTGCAG

There is no spacer between the NotI site and the SpeI site. There should be a T.

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

References

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