The BioBricks Foundation:Standards/Technical/Formats - Revision history

Lucas Schirmer: /* BBF RFC 12: Tom Knight's BB-2 proposal */ changed PstI site from CTCGAG to CTGCAG according to original BBFRFC12.txt

2012-04-17T09:12:09Z

BBF RFC 12: Tom Knight's BB-2 proposal: changed PstI site from CTCGAG to CTGCAG according to original BBFRFC12.txt

2011-03-27T17:55:11Z

Disadvantages

←Older revision		Revision as of 17:55, 27 March 2011
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	===Disadvantages===		===Disadvantages===
	* BglII and BamHI cannot be heat-inactivated		* BglII and BamHI cannot be heat-inactivated
-	**~~but because their mixed site is inactive, they need not be inactivated for successful ligation.~~	+	**Not compatible with current 3A assembly method
	* incompatible to BBa format		* incompatible to BBa format
	* incompatible to BioFusion format		* incompatible to BioFusion format

2011-03-25T18:50:13Z

Disadvantages

←Older revision		Revision as of 18:50, 25 March 2011
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	===Disadvantages===		===Disadvantages===
-	* BglII cannot be heat-inactivated ~~-- current 3A standard assembly won't work~~	+	* BglII and BamHI cannot be heat-inactivated
		+	**but because their mixed site is inactive, they need not be inactivated for successful ligation.
	* incompatible to BBa format		* incompatible to BBa format
	* incompatible to BioFusion format		* incompatible to BioFusion format

2009-12-08T21:30:15Z

BBF RFC 20

←Older revision		Revision as of 21:30, 8 December 2009
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	* a single mutation (at the fused region) can upset the setup?		* a single mutation (at the fused region) can upset the setup?

-	== [[BBF RFC 20]] ==	+	== [http://hdl.handle.net/1721.1/44962 BBF RFC 20] ==
	This is near identical to RFC 10 but provides a transition plan from moving from using PstI to SbfI which is a 8-bp cutter that is compatible with PstI and includes the PstI in it.		This is near identical to RFC 10 but provides a transition plan from moving from using PstI to SbfI which is a 8-bp cutter that is compatible with PstI and includes the PstI in it.

2009-12-08T21:29:45Z

[http://hdl.handle.net/1721.1/45138 BBF RFC 10: Tom Knight's original BioBrick assembly standard

←Older revision		Revision as of 21:29, 8 December 2009
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-	== [http://hdl.handle.net/1721.1/45138 BBF RFC 10: Tom Knight's original BioBrick assembly standard ==	+	== [http://hdl.handle.net/1721.1/45138 BBF RFC 10]: Tom Knight's original BioBrick assembly standard ==

	This is the format used by most iGEM teams and most BioBricks in the MIT registry.		This is the format used by most iGEM teams and most BioBricks in the MIT registry.

2009-12-08T21:29:34Z

Biobrick alpha format (BBa) (RFC10)

←Older revision		Revision as of 21:29, 8 December 2009
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-	== ~~Biobrick alpha format (BBa)~~ [~~[The_BioBricks_Foundation~~:~~BBFRFC10\|(RFC10)]]~~ ==	+	== [http://hdl.handle.net/1721.1/45138 BBF RFC 10: Tom Knight's original BioBrick assembly standard ==

-	This is the format used by most ~~iGem~~ teams and most BioBricks in the MIT registry.	+	This is the format used by most iGEM teams and most BioBricks in the MIT registry.

	<table>		<table>

2009-12-08T21:28:07Z

←Older revision		Revision as of 21:28, 8 December 2009
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	</table>		</table>

-	== The Berkeley (BBb) Format (now called BglBricks) ==	+	==[http://hdl.handle.net/1721.1/46747 BBF RFC 21]: The Berkeley (BBb) Format (now called BglBricks) ==
	BBb is used by several researchers at UC Berkeley and is based on idempotent assembly with BamHI and BglII restriction enzymes. In a nutshell, most plasmids look like this:		BBb is used by several researchers at UC Berkeley and is based on idempotent assembly with BamHI and BglII restriction enzymes. In a nutshell, most plasmids look like this:

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	* incompatible to BioFusion format		* incompatible to BioFusion format

-	== Tom Knight's ~~BBb~~ proposal ==	+	==[http://hdl.handle.net/1721.1/45139 BBF RFC 12]: Tom Knight's BB-2 proposal ==

	Tom Knight has recently proposed to replace BBa by the following format:		Tom Knight has recently proposed to replace BBa by the following format:

2009-05-26T07:29:42Z

Fusion / BioFusion format conversion strategies

←Older revision		Revision as of 07:29, 26 May 2009
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	</sub>		</sub>
	-->		-->
-	=====Fusion -> BioFusion conversion vectors=====	+	===== [http://hdl.handle.net/1721.1/44961 BBF RFC 24]: Fusion -> BioFusion conversion vectors=====

-	Construction vectors with a modified Freiburg prefix / suffix ~~could bring~~ a protein part in frame with BioFusion parts and remove the STOP between the AgeI and SpeI site. Restriction / ligation with AgeI + NaeI can (theoretically) transfer Fusion parts into this conversion vector which can then be used for normal BioFusion cloning (at the cost of adding a T G before and after the part).	+	Construction vectors with a modified Freiburg prefix / suffix brings a protein part in frame with BioFusion parts and remove the STOP between the AgeI and SpeI site. Restriction / ligation with AgeI + NaeI can (theoretically) transfer Fusion parts into this conversion vector which can then be used for normal BioFusion cloning (at the cost of adding a T G before and after the part).
	NaeI is an isoschizomer to NgoMIV but generates blunt ends which should allow for a directional transfer.		NaeI is an isoschizomer to NgoMIV but generates blunt ends which should allow for a directional transfer.
	<table>		<table>

2009-05-26T07:28:21Z

Biofusion (Silver lab)

←Older revision		Revision as of 07:28, 26 May 2009
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	* May be confusing to mix RFC 10/RFC 20 parts		* May be confusing to mix RFC 10/RFC 20 parts

-	== ~~Biofusion~~ (Silver lab) ==	+	== [http://hdl.handle.net/1721.1/32535 BBF RFC 23] (aka Biofusion, Silver lab) ==

	The Silver lab modified the classic 1.0 format to allow for protein fusions:		The Silver lab modified the classic 1.0 format to allow for protein fusions:

2009-05-26T07:27:18Z

BBF RFC 25: Fusion parts (Freiburg iGem2007 team)

←Older revision		Revision as of 07:27, 26 May 2009
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	* not possible to preserve native protein start (but equivalent to BBa coding part could be constructed)		* not possible to preserve native protein start (but equivalent to BBa coding part could be constructed)

-	== [[BBF RFC 25]]: Fusion parts (Freiburg iGem2007 team) ==	+	== [http://hdl.handle.net/1721.1/45140 BBF RFC 25] (aka Fusion parts, Freiburg iGem2007 team) ==

	The Freiburg iGem2007 team proposed an extension of BBa, which would enable protein fusions but alleviate the disadvantages of the Biofusion format. Two restriction sites are added within the standard BBA sites. These additional sites provide compatible ends, can be employed using the same cloning strategy as for the standard restriction sites, and code for amino acids suited for linkers:		The Freiburg iGem2007 team proposed an extension of BBa, which would enable protein fusions but alleviate the disadvantages of the Biofusion format. Two restriction sites are added within the standard BBA sites. These additional sites provide compatible ends, can be employed using the same cloning strategy as for the standard restriction sites, and code for amino acids suited for linkers: