Vectors - Revision history

Axel: /* Plant */

2008-12-28T23:16:54Z

Plant

←Older revision		Revision as of 23:16, 28 December 2008
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	==Plant==		==Plant==
	[http://www.cambia.org/daisy/cambia/lab/materials.html CAMBIA Plant Transformation Vectors]		[http://www.cambia.org/daisy/cambia/lab/materials.html CAMBIA Plant Transformation Vectors]
		+
		+	[http://www.psb.ugent.be/gateway/index.php Gateway compatible binary plant vectors]

	==Other==		==Other==

Axel: /* Plant */

2008-12-28T23:14:53Z

Plant

←Older revision		Revision as of 23:14, 28 December 2008
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	==Plant==		==Plant==
-	[http://www.cambia.org/daisy/cambia/~~materials~~/~~vectors~~.html CAMBIA Plant Transformation Vectors]	+	[http://www.cambia.org/daisy/cambia/lab/materials.html CAMBIA Plant Transformation Vectors]

	==Other==		==Other==

Reshma P. Shetty at 18:46, 19 January 2008

2008-01-19T18:46:53Z

←Older revision		Revision as of 18:46, 19 January 2008
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	==Plant==		==Plant==
	[http://www.cambia.org/daisy/cambia/materials/vectors.html CAMBIA Plant Transformation Vectors]		[http://www.cambia.org/daisy/cambia/materials/vectors.html CAMBIA Plant Transformation Vectors]
		+
		+	==Other==
		+	See [[Gateway cloning system]].

	[[Category:DNA]]		[[Category:DNA]]

Reshma P. Shetty at 22:00, 20 December 2007

2007-12-20T22:00:26Z

←Older revision		Revision as of 22:00, 20 December 2007
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	==General information==		==General information==

-	~~===Stringent vs. relaxed replication===~~	+	===Online vector databases===
-	Plasmid replication control is usually controlled by balancing the levels of a positive and a negative regulator of replication. For some plasmids (pMB1/colE1 replicons) the positive regulator is an RNA and in others (e.g. pSC101) it is a protein. Plasmids with a protein positive regulator will not replicate in the abscence of protein production - ''stringent control'' (although not the same as the stringent response due to a shortage of loaded tRNAs). Plasmids with an RNA positive regulator will continue to replicate in the abscence of protein production. This is termed ''relaxed control''. High yields of plasmid may be obtained by halting protein production (via chloroamphenicol) when the culture reaches a high density and then continuing incubation for a number of hours. This might be of practical relevance when prepping the 1 and 3 series of Synthetic Biology plasmids.--[[User:Bcanton\|BC]] 19:05, 3 Sep 2005 (EDT)	+
-		+
-	===Online ~~Vector Databases~~===	+
	You can often find vector information at [http://www.ncbi.nlm.nih.gov/ NCBI,] either directly or in their list of vectors screened for contamination of new sequence at [http://www.ncbi.nlm.nih.gov/VecScreen/replist.html Vecscreen].		You can often find vector information at [http://www.ncbi.nlm.nih.gov/ NCBI,] either directly or in their list of vectors screened for contamination of new sequence at [http://www.ncbi.nlm.nih.gov/VecScreen/replist.html Vecscreen].

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	*Has some built-in features for annotation (a few genes, many restriction enzymes). Allows you to make custom "feature libraries" for annotating sequences		*Has some built-in features for annotation (a few genes, many restriction enzymes). Allows you to make custom "feature libraries" for annotating sequences
	*Can edit features found, unlike Plasmapper --[[User:Melissali\|mel]] 18:50, 12 June 2007 (EDT)		*Can edit features found, unlike Plasmapper --[[User:Melissali\|mel]] 18:50, 12 June 2007 (EDT)
-
-	~~===Nomenclature===~~
-	~~<biblio>~~
-	~~#Novick-BacteriolRev-1976 pmid=1267736~~
-	~~</biblio>~~

	==''Escherichia coli''==		==''Escherichia coli''==
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	==Plant==		==Plant==
	[http://www.cambia.org/daisy/cambia/materials/vectors.html CAMBIA Plant Transformation Vectors]		[http://www.cambia.org/daisy/cambia/materials/vectors.html CAMBIA Plant Transformation Vectors]
		+
		+	[[Category:DNA]]

Reshma P. Shetty at 21:51, 20 December 2007

2007-12-20T21:51:44Z

←Older revision		Revision as of 21:51, 20 December 2007
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	==''Escherichia coli''==		==''Escherichia coli''==

-	~~===Information===~~	+	See [[Escherichia coli/Vectors]].
-		+
-	*[[~~Bacterial artificial chromosomes]]~~	+
-	*[[F plasmids]]	+
-	*[[Synthetic Biology:Vectors \| Synthetic Biology vectors]]	+
-		+
-	~~====Common vectors====~~	+
-	~~{\|border="1"~~	+
-	\|-	+
-	~~\|Plasmid~~	+
-	~~\|Replicon~~	+
-	~~\|Copy number~~	+
-	\|-	+
-	~~\|pBR322<cite>Bolivar-Gene-1977</cite> and its derivatives~~	+
-	~~\|pMB1~~	+
-	~~\|15-20~~	+
-	\|-	+
-	~~\|pUC vectors~~	+
-	~~\|pMB1~~	+
-	~~\|500-700~~	+
-	\|-	+
-	~~\|pACYC and its derivatives~~	+
-	~~\|p15A<cite>Chang-JBacteriol-1978</cite>~~	+
-	~~\|10-12~~	+
-	\|-	+
-	~~\|pSC101 and its derivatives~~	+
-	~~\|pSC101<cite>Cohen-JBacteriol-1977</cite>~~	+
-	\|5	+
-	\|-	+
-	~~\|ColE1~~	+
-	~~\|ColE1<cite>Bazaral-J-Mol-Biol-1968,Hershfield-Proc-Natl-Acad-Sci-USA-1974</cite>~~	+
-	~~\|15-20~~	+
-	\|}	+
-		+
-	~~===Replicon Compatibility===~~	+
-	{\| border="1" cellpadding="4" cellspacing="0" style="border:#c9c9c9 1px solid; margin: 1em 1em 1em 0; border-collapse: collapse; width:710px" <!-- This line here formats your table for you. Change the code to change the formatting of your table.-->	+
-	~~\| align="center" style="background:#f0f0f0;"\|'''Incompatibility group'''~~	+
-	~~\| align="center" style="background:#f0f0f0;"\|'''Negative control element'''~~	+
-	~~\| align="center" style="background:#f0f0f0;"\|'''Comment'''~~	+
-	\|-	+
-	~~\| colE1<cite>Bazaral-J-Mol-Biol-1968,Hershfield-Proc-Natl-Acad-Sci-USA-1974</cite>, pMB1~~	+
-	~~\| RNAI~~	+
-	\| controls processing of pre-RNAII into primer. pUC is derived from pBR322 (a single mutation in the pBR322 Primer RNA and deletion of the rop gene) which is derived from a pMB1 replicon, and cannot co-reside with the colE1 incompatibility group.	+
-	\|-	+
-	~~\| IncFII, pT181~~	+
-	~~\| RNA~~	+
-	~~\| controls synthesis of RepA protein~~	+
-	\|-	+
-	~~\| P1, F, R6K, pSC101<cite>Cohen-JBacteriol-1977</cite>, p15A<cite>Chang-JBacteriol-1978</cite>~~	+
-	~~\| iterons~~	+
-	~~\| sequesters RepA protein~~	+
-	\|}	+
-		+
-	~~Replication origins in different incompatibility groups are compatible. Replication origins in the same incompatibility group are not.~~	+
-		+
-	~~Some sets of vectors with compatible origins are available as a part of the [http://www.emdbiosciences.com/html/NVG/DuetTable.html Novagen Duet system]. (from [[User:Tk \| TK]])~~	+
-		+
-	~~====Reference====~~	+
-	~~<biblio>~~	+
-	~~#MolecularCloning isbn=0-87969-577-3~~	+
-	~~#Anderson-Annu-Rev-Microbiol-1968 pmid=4879515~~	+
-	~~// Discusses transferable drug resistance in ''~~Escherichia coli~~'' (i.e. plasmids with resistance markers)~~	+
-	~~#Cohen-Proc-Natl-Acad-Sci-USA-1973a pmid=4576014~~	+
-	~~// Discusses generation of plasmids by sharing DNA, their transformation and replication.~~	+
-	~~#Cohen-Proc-Natl-Acad-Sci-USA-1973b pmid=4594039~~	+
-	~~// Discusses use of vector to propagate other DNA fragments~~	+
-	~~#Chang-JBacteriol-1978 pmid=149110~~	+
-	~~// p15A origin~~	+
-	~~#Cohen-JBacteriol-1977 pmid=334752~~	+
-	~~// pSC101 origin~~	+
-	~~#Bolivar-Gene-1977 pmid=344137~~	+
-	~~// vector pBR322~~	+
-	~~#Bazaral-J-Mol-Biol-1968 pmid=4939624~~	+
-	~~//original discovery of ColE1 plasmid~~	+
-	~~#Hershfield-Proc-Natl-Acad-Sci-USA-1974 pmid=4610576~~	+
-	~~// use of ColEI as a vector~~	+
-	~~</biblio>~~	+
-		+
-	~~===Individual vector links===~~	+
-	~~''Note: searching for cloning vector <insert vector name> when looking for vector sequences in NCBI Entrez Nucleotide search. It helps to cut down on the number of hits.''~~	+
-		+
-	*[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=6691170 pUC19]	+
-	*[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=1817728 pBeloBAC11]	+
-	*[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=4878025 pBACe3.6]	+
-	*[http://www.ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=9507713 F plasmid]	+
-	*pSCANS [http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=Nucleotide&cmd=Retrieve&list_uids=6689911&dopt=GenBank genbank] [http://genome.bnl.gov/Vectors~~/pscans.php vector info~~] ~~[http://www.genome.bnl.gov/Protocols/pscans.shtml cookbook~~]	+
-	*[http://www.~~ncbi.nlm.nih.gov/entrez/viewer.fcgi?db=nucleotide&val=42704 pSC101 replication origin]~~	+
-		+
-	~~===Other references===~~	+
-	*[http://www.emdbiosciences.com/g.asp?f=NVG/pETtable.html Novagen pET vector table]	+
-	**table with links to properties/sequences of pET vectors	+
-	**note: slow to load	+

	==Yeast==		==Yeast==

Reshma P. Shetty: /* ''Escherichia coli'' */

2007-12-20T21:49:57Z

''Escherichia coli''

←Older revision		Revision as of 21:49, 20 December 2007
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	\|-		\|-
	\|ColE1		\|ColE1
-	\|ColE1<cite>Bazaral-J-Mol-Biol-1968</cite>	+	\|ColE1<cite>Bazaral-J-Mol-Biol-1968,Hershfield-Proc-Natl-Acad-Sci-USA-1974</cite>
	\|15-20		\|15-20
	\|}		\|}
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	\| align="center" style="background:#f0f0f0;"\|'''Comment'''		\| align="center" style="background:#f0f0f0;"\|'''Comment'''
	\|-		\|-
-	\| colE1<cite>Bazaral-J-Mol-Biol-1968</cite>, pMB1	+	\| colE1<cite>Bazaral-J-Mol-Biol-1968,Hershfield-Proc-Natl-Acad-Sci-USA-1974</cite>, pMB1
	\| RNAI		\| RNAI
	\| controls processing of pre-RNAII into primer. pUC is derived from pBR322 (a single mutation in the pBR322 Primer RNA and deletion of the rop gene) which is derived from a pMB1 replicon, and cannot co-reside with the colE1 incompatibility group.		\| controls processing of pre-RNAII into primer. pUC is derived from pBR322 (a single mutation in the pBR322 Primer RNA and deletion of the rop gene) which is derived from a pMB1 replicon, and cannot co-reside with the colE1 incompatibility group.
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	// vector pBR322		// vector pBR322
	#Bazaral-J-Mol-Biol-1968 pmid=4939624		#Bazaral-J-Mol-Biol-1968 pmid=4939624
-	//~~plasmid~~ ColE1	+	//original discovery of ColE1 plasmid
		+	#Hershfield-Proc-Natl-Acad-Sci-USA-1974 pmid=4610576
		+	// use of ColEI as a vector
	</biblio>		</biblio>

Reshma P. Shetty: /* ''Escherichia coli'' */

2007-12-20T21:46:32Z

''Escherichia coli''

←Older revision		Revision as of 21:46, 20 December 2007
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	\|-		\|-
	\|ColE1		\|ColE1
-	\|ColE1	+	\|ColE1<cite>Bazaral-J-Mol-Biol-1968</cite>
	\|15-20		\|15-20
	\|}		\|}
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	\| align="center" style="background:#f0f0f0;"\|'''Comment'''		\| align="center" style="background:#f0f0f0;"\|'''Comment'''
	\|-		\|-
-	\| colE1, pMB1	+	\| colE1<cite>Bazaral-J-Mol-Biol-1968</cite>, pMB1
	\| RNAI		\| RNAI
	\| controls processing of pre-RNAII into primer. pUC is derived from pBR322 (a single mutation in the pBR322 Primer RNA and deletion of the rop gene) which is derived from a pMB1 replicon, and cannot co-reside with the colE1 incompatibility group.		\| controls processing of pre-RNAII into primer. pUC is derived from pBR322 (a single mutation in the pBR322 Primer RNA and deletion of the rop gene) which is derived from a pMB1 replicon, and cannot co-reside with the colE1 incompatibility group.
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	#Bolivar-Gene-1977 pmid=344137		#Bolivar-Gene-1977 pmid=344137
	// vector pBR322		// vector pBR322
		+	#Bazaral-J-Mol-Biol-1968 pmid=4939624
		+	//plasmid ColE1
	</biblio>		</biblio>

Reshma P. Shetty: /* ''Escherichia coli'' */

2007-12-20T21:35:49Z

''Escherichia coli''

←Older revision		Revision as of 21:35, 20 December 2007
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	\|Copy number		\|Copy number
	\|-		\|-
-	\|pBR322 and its derivatives	+	\|pBR322<cite>Bolivar-Gene-1977</cite> and its derivatives
	\|pMB1		\|pMB1
	\|15-20		\|15-20
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	// Discusses use of vector to propagate other DNA fragments		// Discusses use of vector to propagate other DNA fragments
	#Chang-JBacteriol-1978 pmid=149110		#Chang-JBacteriol-1978 pmid=149110
-	// ~~Early reference for~~ p15A origin	+	// p15A origin
	#Cohen-JBacteriol-1977 pmid=334752		#Cohen-JBacteriol-1977 pmid=334752
-	// ~~Early reference for~~ pSC101 origin	+	// pSC101 origin
		+	#Bolivar-Gene-1977 pmid=344137
		+	// vector pBR322
	</biblio>		</biblio>

Reshma P. Shetty: /* ''Escherichia coli'' */

2007-12-20T21:32:06Z

''Escherichia coli''

←Older revision		Revision as of 21:32, 20 December 2007
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	\|-		\|-
	\|pACYC and its derivatives		\|pACYC and its derivatives
-	\|p15A	+	\|p15A<cite>Chang-JBacteriol-1978</cite>
	\|10-12		\|10-12
	\|-		\|-
	\|pSC101 and its derivatives		\|pSC101 and its derivatives
-	\|pSC101	+	\|pSC101<cite>Cohen-JBacteriol-1977</cite>
	\|5		\|5
	\|-		\|-
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	\| controls synthesis of RepA protein		\| controls synthesis of RepA protein
	\|-		\|-
-	\| P1, F, R6K, pSC101, p15A	+	\| P1, F, R6K, pSC101<cite>Cohen-JBacteriol-1977</cite>, p15A<cite>Chang-JBacteriol-1978</cite>
	\| iterons		\| iterons
	\| sequesters RepA protein		\| sequesters RepA protein
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	#Cohen-Proc-Natl-Acad-Sci-USA-1973b pmid=4594039		#Cohen-Proc-Natl-Acad-Sci-USA-1973b pmid=4594039
	// Discusses use of vector to propagate other DNA fragments		// Discusses use of vector to propagate other DNA fragments
		+	#Chang-JBacteriol-1978 pmid=149110
		+	// Early reference for p15A origin
		+	#Cohen-JBacteriol-1977 pmid=334752
		+	// Early reference for pSC101 origin
	</biblio>		</biblio>

Reshma P. Shetty: /* Reference */

2007-12-20T20:31:35Z

Reference

←Older revision		Revision as of 20:31, 20 December 2007
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	#Cohen-Proc-Natl-Acad-Sci-USA-1973a pmid=4576014		#Cohen-Proc-Natl-Acad-Sci-USA-1973a pmid=4576014
	// Discusses generation of plasmids by sharing DNA, their transformation and replication.		// Discusses generation of plasmids by sharing DNA, their transformation and replication.
		+	#Cohen-Proc-Natl-Acad-Sci-USA-1973b pmid=4594039
		+	// Discusses use of vector to propagate other DNA fragments
	</biblio>		</biblio>