Difference between revisions of "Part:BBa J31006:Design"

Revision as of 17:06, 29 October 2006

tetracycline resistance protein TetA(C) (backwards) [cf. BBa_J31007]

Assembly Compatibility:

10
COMPATIBLE WITH RFC[10]
12
INCOMPATIBLE WITH RFC[12]
Illegal NheI site found at 1043
21
INCOMPATIBLE WITH RFC[21]
Illegal BamHI site found at 897
23
COMPATIBLE WITH RFC[23]
25
INCOMPATIBLE WITH RFC[25]
Illegal NgoMIV site found at 343
Illegal NgoMIV site found at 503
Illegal NgoMIV site found at 871
1000
COMPATIBLE WITH RFC[1000]

Design Notes

It was cloned into PsB1A2 plasmids.

Biobricks

The Biobricks on this part are not wild type, 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 T TCTAGA * --Hin coding-- * ACTAGT T GCGGCCGCCTGCAG--
3'--CTTAAG CGCCGGCG * AGATCT * -------------- * TGATCA A CGCCGGCGGACGTC--

Prefix
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 A spacer between the SpeI and the NotI has changed to a T.
There is an extra C between the NotI site and the PstI site

5'GAATTC GCGGCCGC T TCTAGA - aatccagctccaccgggccgaggtacgtggcgctgcgttgcgcccctccgtctgttccatatcccgccgcggatgttaggtacggttgggcaaggtacac gagcggctccgccgtatttagcggcactgctagtcgccaggttactagcttcaatccgaccattctcggcgctcgctaggaacttcgacagggactacca gcagtagatggacggacctgtcgtaccggacgttgcgcccgtagggctacggcggccttcgctcttcttagtattaccccttccggtaggtcggagcgca gcgcttgcggtcgttctgcatcgggtcgcgcagccggcggtacggccgctattaccggacgaagagcggctttgcaaaccaccgccccggtcactgcttc cgaactcgctcccgcacgttctaaggcttatggcgttcgctgtccggctagtagcagcgcgaggtcgctttcgccaggagcggcttttactgggtctcgc gacggccgtggacaggatgctcaacgtactatttcttctgtcagtattcacgccgctgctatcagtacggggcgcgggtggccttcctcgactgacccaa cttccgagagttcccgtagccagctgcgagagggaatacgctgaggacgtaatccttcgtcgggtcatcatccaactccggcaactcgtggcggcggcgt tccttaccacgtacgttcctctaccgcgggttgtcagggggccggtgccccggacggtggtatgggtgcggctttgttcgcgagtactcgggcttcaccg ctcgggctagaaggggtagccactacagccgctatatccgcggtcgttggcgtggacaccgcggccactacggccggtgctacgcaggccgcatctccta ggtgtcctgcccacaccagcggtactagcgcatcagctatcaccgaggttcatcgcttcgctcgtcctgacccgccgccggtttcgccagcctgtcacga ggctcttgcccacgcgtatctttaacgtagttgcgtatatcgcgatcgtcgtgcggtatcactgaccgctacgacagccttacctgctatagggcgttct ccgggccgtcatggccgtattggttcggatacggatgtcgtaggtcccactgccacggctcctactgctactcgcgtaacaatctaaagta - ACTAGT A GCGGCCG CTGCAG

EcoRI NotI Spacer XbaI Missing G spacer Coding Region Missing T spacer SpeI Spacer NotI PstI

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

Source

PsB1AT3

References

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

@@ Line 1: / Line 1: @@
 __NOTOC__
 <partinfo>BBa_J31006 short</partinfo>
@@ Line 12: / Line 11: @@
 ===Biobricks===
 The Biobricks on this part are not wild type, but the cut sites are still viable.
+{| width="800px" cellspacing="5"
+|- valign="top"
+| style="width:180px" | '''Standard BioBrick Cloning Sites''' (Knight)
+| 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>
+|- valign="top"
+| style="width:180px" | '''BBa_J31001 Cloning Sites'''
+| style="background:lightgrey" |<font face="courier">5'--GAATTC GCGGCCGC T TCTAGA <font color='blue'>*</font> --Hin coding-- <font color='purple'>*</font> ACTAGT <font color='darkgreen'>T</font> GCGGCCG<font color='magenta'>C</font>CTGCAG--<br>3'--CTTAAG CGCCGGCG <font color='red'>*</font> AGATCT <font color='blue'>*</font> -------------- <font color='purple'>*</font> TGATCA <font color='darkgreen'>A</font> CGCCGGC<font color='magenta'>G</font>GACGTC--</font><br><br>
+'''Prefix'''<br>There is <font color='blue'>no G spacer (*)</font> between the XbaI and the Hin coding region.<br>
+'''Suffix'''<br>There is <font color='purple'>no T spacer (*)</font> between the Hin coding region and the SpeI site.<br>The A spacer between the SpeI and the NotI has changed to a <font color='darkgreen'>T</font>.<br>There is an extra <font color='magenta'>C</font> between the NotI site and the PstI site
+|}
 <font size='4'>5'</font size><font color='blue'>GAATTC</font color><font color='pink'> GCGGCCGC</font color><font color='gold'> T</font color> <font color='orange'> TCTAGA</font color><font color='red'> -</font color> <u>aatccagctccaccgggccgaggtacgtggcgctgcgttgcgcccctccgtctgttccatatcccgccgcggatgttaggtacggttgggcaaggtacac