Difference between revisions of "Part:BBa J63010:Design"

Revision as of 14:51, 29 October 2006

Protein fusion vector (Silver lab standard)

Assembly Compatibility:

10
INCOMPATIBLE WITH RFC[10]
Plasmid lacks a prefix.
Plasmid lacks a suffix.
Illegal EcoRI site found at 3246
Illegal XbaI site found at 3261
Illegal SpeI site found at 1
Illegal PstI site found at 15
12
INCOMPATIBLE WITH RFC[12]
Plasmid lacks a prefix.
Plasmid lacks a suffix.
Illegal EcoRI site found at 3246
Illegal SpeI site found at 1
Illegal PstI site found at 15
Illegal NotI site found at 8
Illegal NotI site found at 3252
21
INCOMPATIBLE WITH RFC[21]
Plasmid lacks a prefix.
Plasmid lacks a suffix.
Illegal EcoRI site found at 3246
23
INCOMPATIBLE WITH RFC[23]
Plasmid lacks a prefix.
Illegal EcoRI site found at 3246
Illegal XbaI site found at 3261
25
INCOMPATIBLE WITH RFC[25]
Plasmid lacks a prefix.
Plasmid lacks a suffix.
Illegal EcoRI site found at 3246
Illegal XbaI site found at 3261
Illegal SpeI site found at 1
Illegal PstI site found at 15
Illegal NgoMIV site found at 2825
1000
INCOMPATIBLE WITH RFC[1000]
Plasmid lacks a prefix.
Plasmid lacks a suffix.
Illegal BsaI.rc site found at 1393
Illegal SapI site found at 310

Design Notes

This plasmid was designed to permit in-frame assembly of protein fusions. Although it contains the standard biobrick ends (EcoRI, XbaI, SpeI, PstI), a part immediately follows the XbaI restriction site and immediately precedes a SpeI site. These changes form a [http://hdl.handle.net/1721.1/32535 revised biobrick assembly strategy - biofusion assembly], which remains compatible with standard biobricks and uses the standard biobricks assembly methods. However, unlike the standard biobricks assembly, when two parts in this plasmid are fused, six nucleotides (ACTAGA) separate the two parts, thus keeping the coding sequences in-frame.

Like the biobrick standard, parts cannot contain EcoRI, XbaI, SpeI or PstI restriction sites.
An additional design criteria is that a part should not begin with the nucleotides TC. If a part did, the XbaI site would be methylated by DamI and thus digestion at this site would be blocked.

Source

Synthetized DNA from Blue Heron.

References

[http://hdl.handle.net/1721.1/32535 1. Ira Phillips and Pam Silver. "A New Biobrick Assembly Strategy Designed for Facile Protein Engineering." DSpace at MIT].

@@ Line 7: / Line 7: @@
 ===Design Notes===
-This plasmid was designed to permit in-frame assembly of protein fusions. Although it contains the standard biobrick ends (EcoRI, XbaI, SpeI, PstI), a part immediately follows the XbaI restriction site and immediately precedes a SpeI site. These changes form a [http://hdl.handle.net/1721.1/32535 revised biobrick assembly strategy], which remains compatible with standard biobricks and uses the standard biobricks assembly methodology. However, unlike the standard biobricks assembly, when two parts in this plasmid are fused, six nucleotides (ACTAGA) separate the two parts, thus keeping the coding sequences in-frame.
+This plasmid was designed to permit in-frame assembly of protein fusions. Although it contains the standard biobrick ends (EcoRI, XbaI, SpeI, PstI), a part immediately follows the XbaI restriction site and immediately precedes a SpeI site. These changes form a [http://hdl.handle.net/1721.1/32535 revised biobrick assembly strategy - biofusion assembly], which remains compatible with standard biobricks and uses the standard biobricks assembly methods. However, unlike the standard biobricks assembly, when two parts in this plasmid are fused, six nucleotides (ACTAGA) separate the two parts, thus keeping the coding sequences in-frame.
 *Like the biobrick standard, parts cannot contain EcoRI, XbaI, SpeI or PstI restriction sites.
 *An additional design criteria is that a  part should not begin with the nucleotides TC. If a part did, the XbaI site would be methylated by DamI and thus digestion at this site would be blocked.