Protein coding sequences/DNA modification

Restriction enzymes

A restriction enzyme or restriction endonuclease is an enzyme that either nicks or cuts double-stranded DNA at specific recognition nucleotide sequences known as a restriction site. Many restriction sites are actually palindromic sequences in which the restriction enzyme cleaves within the recognition site. However, some restriction enzymes, known as offset cutters, cleave at a position a few nucleotides away from the recognition site. Most restriction enzymes are sensitive to the methylation state of the recognition site and won't cleave if the site is methylated. (There are also some enzymes, like DpnI, that specifically cleave methylated recognition sites.)

In synthetic biology, restriction enzymes and restriction enzyme sites are most commonly used for assembly of genetic parts into devices and systems.

Note that the DNA ligases below adhere to Assembly standard 21.

*More...*
Name	Protein	Description	Direction	Uniprot	KEGG	E.C.	Recognition sequence
BBa_K112116		a~BamHI
BBa_K112117		a~BglII
BBa_I716210		BamHI endonuclease without start codon
BBa_K112106		BglII endonuclease
BBa_K112107		BglII endonuclease without stop codon
BBa_K112123		BglII restriction enzyme

Samantha Liang, as a member of the 2007 UC Berkeley iGEM team, constructed the restriction enzyme protein coding sequence BBa_I716210.

Madhvi Venkatesh, Bing Xia and the [http://2008.igem.org/Team:UC_Berkeley 2008 UC Berkeley iGEM team], constructed several restriction enzyme protein coding sequences BBa_K112106-BBa_K112108 and BBa_K112117.

References

[http://rebase.neb.com/rebase/rebase.html Rebase] - the official restriction enzyme database

DNA Ligases

DNA ligase can link together two DNA strands that have double-strand break. In synthetic biology, DNA ligase is most commonly used during assembly of genetic parts and devices.

Note that the DNA ligases below adhere to Assembly standard 21.

*More...*
Name	Protein	Description	Tag	KEGG	Length	Status
BBa_K525740		DNA ligase from Escherichia coli (LigA) with His-tag			2037	Not in stock
BBa_K525730		DNA ligase from Escherichia coli (LigA) with PT7 and RBS			2055	Not in stock
BBa_K2916000		ArgRS protein equipped with a 10x HIS affinity tag			1800	Not in stock
BBa_K3832000	aroG	aroG (Mutant S211F)		EC 2.5.1.54	1053
BBa_K112114		a~Ligase!			1468	It's complicated
BBa_K3757000	CtAEP1	CtAEP1			1450
BBa_K525710		DNA ligase from Escherichia coli (LigA) with PT7, RBS and His-tag	His-tag		2064	In stock
BBa_K525010		Fusion Protein of S-Layer SbpA and LigA with His-Tag	His-tag		5226	Not in stock
BBa_K525009		Fusion Protein of S-Layer SgsE and LigA with His-Tag	His-tag		4434	Not in stock
BBa_K2916003		GlyRS protein equipped with a 6x HIS affinity tag			3032	Not in stock

Bing Xia and the [http://2008.igem.org/Team:UC_Berkeley 2008 UC Berkeley iGEM team], constructed several ligase protein coding sequences BBa_K112111-BBa_K112114.

Recombinases

A recombinase is an enzyme that catalyzes the exchange of short pieces of DNA between two long DNA strands, particularly the exchange of homologous regions.

For details on the different recombination systems available via the Registry, see Recombination.

Note that some of the recombinase protein coding sequences listed below adhere to Assembly standard 21.

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Name	Protein	Description	Direction	KEGG	UniProt	E.C.	Length
BBa_K1680008		Δ1-19 Cre recombinase					972
BBa_K2460001		φBT1 integrase					1845
BBa_K2460004		φRv1 integrase					1470
BBa_K3120003		A human codon-optimized SpCas9					4101
BBa_K112115		a~Cre					1036
BBa_I716212		Cre (GTG start)					1032
BBa_I716213		Cre (TTG start)					1032
BBa_J61047		Cre DNA recombinase					1037
BBa_K1680007		Cre recombinase					1029
BBa_K112122		Cre with stop codon					1032
BBa_K1680019		Cre-dronpa fusion					1764
BBa_K1680020		Cre-dronpa fusion					1782
BBa_K1680018		Cre-Dronpa fusion					1746
BBa_K1680017		Cre-Dronpa Fusion					1728
BBa_J31001	Hin-LVA	DNA invertase Hin tagged with LVA		stm:STM2772	P03013	none	612
BBa_J31000	Hin	DNA-invertase Hin from Salmonella typhimurium		stm:STM2772	P03013	none	573
BBa_K1680024		Dronpa caged Cre with NLS					2487
BBa_K1680023		Dronpa caged Cre with NLS					2469
BBa_K1680022		Dronpa caged Cre with NLS					2451
BBa_K1680021		Dronpa caged Cre with NLS					2433
BBa_I11021	Xis lambda	excisionase from E. coli phage lambda (removes prophage from host genome)	Forward	none	P03699	none	280
BBa_I11031	Xis P22	excisionase from E. coli phage P22 (removes prophage from host genome)	Forward	none	P04889	none	412
BBa_K137007		fimE					558
BBa_K1015001		Flippase(FLP)					1272
BBa_K313002		flpe DNA recombinase					1272
BBa_I11020	Int lambda	integrase from E. coli phage lambda	Forward	none	P03700	none	1132
BBa_I11030	Int P22	integrase from E. coli phage P22	Forward	none	P04890	none	1225
BBa_K3254009		Integrase Int10					1446
BBa_K3254006		Integrase Int5					1659
BBa_K3254007		Integrase Int7					1389
BBa_K3254008		Integrase Int8					1386
BBa_K907000		Mycobacterium Phage Bxb1 gp35, DNA integrase					1503
BBa_K907001		Mycobacterium Phage Bxb1 gp47, DNA excisionase					768
BBa_K3254018		original sequence of phiC31 integrase gene					1842
BBa_K361000		Rci site-specific recombinase					1155
BBa_J70007		recT recombination gene from Spiroplasma citri					858
BBa_K108022		RuvA					612
BBa_K108023		RuvB					1011
BBa_K108024		RuvC					522
BBa_K2460007		TG1 integrase					1923
BBa_K112001	Xis	Xis from bacteriophage lambda, assembly standard 21					216
BBa_K112217		{a~ihfA!} The ihf alpha gene ready to have rbs attached with stop codon, BBb format					304
BBa_K112223		{a~ihfB!} The ihf beta gene ready to have rbs attached and stop codon, BBb format					289
BBa_K112211		{a~int!} The integrase gene with rbs ready to be attached with stop codon, BBb format					1075
BBa_K112204		{a~xis!} The bacteriophage lambda xis gene ready to have rbs attached and stop codon; assembly stand					223
BBa_K112219		{ihfB!} The ihf beta gene with start and stop codons, BBb format					285
BBa_K112207		{int!} The integrase gene with start and stop codon, BBb format					1071
BBa_K112200		{xis!} from bacteriophage lambda; assembly standard 21					219

Karmella Haynes, Malcolm Campbell and the [http://2006.igem.org/Davidson_2006 2006 Davidson College/Missouri Western iGEM team], designed and constructed the Hin recombinase parts BBa_J31000 and BBa_J31001. You can read more about the 2006 Davidson/Missouri Western project in their open-access paper [http://www.jbioleng.org/content/2/1/8 Engineering bacteria to solve the Burnt Pancake Problem] published in the Journal of Biological Engineering Haynes.

Molly Allen and the [http://2008.igem.org/Team:UC_Berkeley 2008 UC Berkeley iGEM team], constructed several ihf alpha integrase protein coding sequences such as BBa_K112211, BBa_K112217, and BBa_K112223 listed above.

Qi Liu and the [http://2008.igem.org/Team:Tsinghua 2008 Tsinghua iGEM team] designed and constructed the RuvABC resolvasome parts BBa_K108022-BBa_K108024.

Chromatin proteins

Chromatin is the complex combination of DNA, RNA, and protein that makes up chromosomes. It is found inside the nuclei of eukaryotic cells, and within the nucleoid in prokaryotic cells. It is divided between heterochromatin (condensed) and euchromatin (extended) forms. Protein associated with chromatin are listed here.

Note that several of the protein coding sequences below, except BBa_Y00073 and BBa_Y00029, adhere to Assembly standard 28.

*More...*
Name	Protein	Description	Length	Status
BBa_Y00073		S. pombe gene SPCC126.04c, coded for S. cerevisiae expression	1094	It's complicated
BBa_Y00029		S. pombe homolog of S.cerevisiae SGF29, recoded for expression in S.c.	794	It's complicated
BBa_K106001		Sir4, Aar1 AD part	4077	It's complicated
BBa_K106002		Sir2, Aar1 AB part	1686	It's complicated
BBa_K106003		Sir2, Aar1 BD part	1686	It's complicated
BBa_K106011	Sas2	Sas2 histone acetyltransferase, Aar1 AB part	1017	It's complicated
BBa_K106012	Sas2	Sas2 histone acetyltransferase, Aar1 BD part	1014	It's complicated
BBa_K106013	Esa1	Esa1 histone acetyltransferase, Aar1 BD part	1338	It's complicated
BBa_K106692		Sir3, AarI A!D part (A!D variant!)	2937	It's complicated

Natalie Kuldell, an instructor at MIT, designed and constructed the chromatin protein parts BBa_Y00073 and BBa_Y00029.

Ryan Quan, Willis Wong, and Andrew Horowitz and the [http://2008.igem.org/Team:UCSF 2008 UCSF iGEM team] designed and constructed many of the chromatin protein parts listed above.