Difference between revisions of "RFC25 "Freiburg standard" parts"

(→‎Binding proteins)
(→‎Fluorescent proteins)
 
(67 intermediate revisions by the same user not shown)
Line 1: Line 1:
−
=Reptorter proteins=
+
<span style="background:#32CD32">'''[[Collections|< Back to BioBrick collection]]'''</span><br>
 +
<span style="background:#32CD32">'''[[Assembly_standard_25|< RFC25 assembly standard description]]'''</span><br>
 +
 
 +
=RFC25 BioBrick parts=
 +
==RFC25 compatible BioBrick backbones==
 +
[[File:RFC25Backbone.png|thumb|right|300px|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K801100'>pSB1C3-RFP_Generator (BBa_K801100)</A></HTML>]]
 +
 
 +
For the cloning of RFC25 BioBricks into the Parts Registry compatible backbone the plasmid <HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K801100'>pSB1C3-RFP_Generator (BBa_K801100)</A></HTML> can be used.<br>
 +
<br><br><br><br><br><br><br><br><br><br>
 +
 
 
==Fluorescent proteins==
 
==Fluorescent proteins==
 
{| class="wikitable"
 
{| class="wikitable"
−
!colspan="6"|Fluorescent proteins
+
!colspan="6"|[[RFC25_"Freiburg_standard"_parts#Fluorescent_proteins| Fluorescent proteins (click for all RFC25 parts)]]
 
|-
 
|-
 
|Protein
 
|Protein
Line 10: Line 19:
 
|Emission [nm]
 
|Emission [nm]
 
|Quantum Yield
 
|Quantum Yield
 +
|-
 +
|Cerulean
 +
|style="background:Cyan" |Cyan
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_I757009'>BBa_I757009</A></HTML>
 +
|433
 +
|475
 +
|0.62
 +
|-
 +
|eCFP
 +
|style="background:Cyan" |Cyan
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159302'>BBa_K1159302</A></HTML>
 +
|439
 +
|476
 +
|0.40
 
|-
 
|-
 
|GFP
 
|GFP
−
|<span style="background:Lime; color:white;"> Green </span>
+
|style="background:Lime" |Green  
 
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K648013'>BBa_K648013</A></HTML>
 
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K648013'>BBa_K648013</A></HTML>
 +
|484
 +
|507
 +
|0.60
 +
|-
 +
|GFP
 +
|style="background:Lime" |Green
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K863120'>BBa_K863120</A></HTML>
 +
|484
 +
|507
 +
|0.60
 +
|-
 +
|GFP
 +
|style="background:Lime" |Green
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K823039'>BBa_K823039</A></HTML>
 
|484
 
|484
 
|507
 
|507
Line 19: Line 56:
 
|-
 
|-
 
|sfGFP
 
|sfGFP
−
|<span style="background:Lime; color:white;"> Green </span>
+
|style="background:Lime" |Green
 
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1321337'>BBa_K1321337</A></HTML>
 
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1321337'>BBa_K1321337</A></HTML>
 
|485
 
|485
Line 26: Line 63:
 
|-
 
|-
 
|Dronpa (photoactivatable)
 
|Dronpa (photoactivatable)
−
|<span style="background:Lime; color:white;"> Green </span>
+
|style="background:GreenYellow" |GreenYellow
−
|BBa_K1680006
+
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1680006'>BBa_K1680006</A></HTML>
 
|503
 
|503
 
|518
 
|518
−
|
+
|0.85
 +
|-
 +
|mVenus
 +
|style="background:Yellow" |Yellow
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_I757008'>BBa_I757008</A></HTML>
 +
|515
 +
|528
 +
|0.57
 
|-
 
|-
 
|sYFP2
 
|sYFP2
−
|<span style="background:Yellow; color:black;"> Yellow </span>
+
|style="background:Yellow" |Yellow
 
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159301'>BBa_K1159301</A></HTML>
 
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159301'>BBa_K1159301</A></HTML>
 
|514
 
|514
Line 39: Line 83:
 
|0.61
 
|0.61
 
|-
 
|-
−
|eCFP
+
|mRFP
−
|<span style="background:DeepPink; color:black;"> Cyan </span>
+
|style="background:Red" |Red
−
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159302'>BBa_K1159302</A></HTML>
+
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1351021'>BBa_K1351021</A></HTML>
−
|439
+
|584
−
|476
+
|607
−
|0.40
+
|0.25
 
|-
 
|-
 
|mRFP
 
|mRFP
−
|<span style="background:red; color:black;"> Red </span>
+
|style="background:Red" |Red
 
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1615089'>BBa_K1615089</A></HTML>
 
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1615089'>BBa_K1615089</A></HTML>
 
|584
 
|584
 
|607
 
|607
 
|0.25
 
|0.25
 +
|-
 +
|mKate2
 +
|style="background:Red" |Red
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K823029'>BBa_K823029</A></HTML>
 +
|588
 +
|633
 +
|0.4
 +
|-
 +
|colspan="6"|Values for the fluorescent proteins were taken from [http://www.microscopyu.com/articles/livecellimaging/fpintro.html| microscopyu.com].
 
|}
 
|}
−
 
−
Values for the fluorescent proteins were taken from http://www.microscopyu.com/articles/livecellimaging/fpintro.html.
 
  
 
==Luciferases==
 
==Luciferases==
  
 
{| class="wikitable"
 
{| class="wikitable"
−
!colspan="4"|Luciferases
+
!colspan="6"|[[RFC25_"Freiburg_standard"_parts#Luciferases| Luciferases (click for all RFC25 parts)]]
 
|-
 
|-
 
|Protein
 
|Protein
Line 66: Line 117:
 
|-
 
|-
 
|Firefly luciferase
 
|Firefly luciferase
−
|
+
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/BBa_K525999'>BBa_K525999</A></HTML>
 
|61
 
|61
 
|-
 
|-
 
|''Renilla'' luciferase
 
|''Renilla'' luciferase
−
|
+
|not available yet
 
|36  
 
|36  
 
|-
 
|-
Line 78: Line 129:
 
|-
 
|-
 
|''Gaussia'' luciferase
 
|''Gaussia'' luciferase
−
|
+
|not available yet
 
|
 
|
 
|-
 
|-
 
|}
 
|}
  
−
==Transmembrane Domains==
+
==Transmembrane domains==
 +
 
 +
==Optogenetic parts==
  
 
==Linker domains==
 
==Linker domains==
 
{| class="wikitable"
 
{| class="wikitable"
−
!colspan="4"|Linker
+
!colspan="6"|[[RFC25_"Freiburg_standard"_parts#Linker| Linker (click for all RFC25 parts)]]
 
|-
 
|-
 
|Protein
 
|Protein
Line 96: Line 149:
 
|Short Linker
 
|Short Linker
 
|(Gly-Gly-Ser-Gly)
 
|(Gly-Gly-Ser-Gly)
−
|BBa_K243004
+
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K243004'>BBa_K243004</A></HTML>
 
|4
 
|4
 
|-
 
|-
 
|Middle Linker  
 
|Middle Linker  
 
|2x (Gly-Gly-Ser-Gly)
 
|2x (Gly-Gly-Ser-Gly)
−
|BBa_K243005
+
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K243005'>BBa_K243005</A></HTML>
 
|8
 
|8
 
|-
 
|-
 
|Long Linker
 
|Long Linker
 
|3x (Gly-Gly-Ser-Gly)
 
|3x (Gly-Gly-Ser-Gly)
−
|BBa_K243006
+
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K243006'>BBa_K243006</A></HTML>
 
|12
 
|12
 
|-
 
|-
−
|
+
|}
−
|
+
 
−
|
+
==Catalytic proteins==
−
|
+
{| class="wikitable"
 +
!colspan="6"|[[RFC25_"Freiburg_standard"_parts#Catalytic_proteins| Catalytic proteins (click for all RFC25 parts)]]
 
|-
 
|-
−
|
+
|Erythromycin Esterase Type II
−
|
+
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159000'>BBa_K1159000</A></HTML>
−
|
+
|-
−
|
+
|Laccase
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159002'>BBa_K1159002</A></HTML>
 +
|-
 +
|Laccase TVEL5
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1615067'>BBa_K1615067</A></HTML>
 +
|-
 +
|TEV Protease
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159100'>BBa_K1159100</A></HTML>
 +
|-
 +
|Thermonuclease
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159105'>BBa_K1159105</A></HTML>
 +
|-
 +
|Heroin Esterase
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1615045'>BBa_K1615045</A></HTML>
 +
|-
 +
|CRE recombinase
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1680007'>BBa_K1680007</A></HTML>
 +
|-
 +
|Monoamine Oxidase A
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1615022'>BBa_K1615022</A></HTML>
 +
|-
 +
|Endo-β-Galactosidase
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1483001'>BBa_K1483001</A></HTML>
 +
|-
 +
|α-Galactosidase
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1483002'>BBa_K1483002</A></HTML>
 +
|-
 +
|Acetylgalactosamindase
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1483000'>BBa_K1483000</A></HTML>
 +
|-
 +
|2-oxoglutarate oxygenase/decarboxylase
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1065000'>BBa_K1065000</A></HTML>
 +
|-
 +
|}
 +
==Transcription regulators==
 +
{| class="wikitable"
 +
!colspan="6"|[[RFC25_"Freiburg_standard"_parts#Transcription_regulators| Transcription regulators (click for all RFC25 parts)]]
 +
|-
 +
|VP16
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1150001'>BBa_K1150001</A></HTML>
 
|-
 
|-
 
|}
 
|}
−
 
−
==Catalytic domains==
 
−
Erythromycin Esterase Type II
 
−
BBa_K1159000
 
−
 
−
Laccase
 
−
BBa_K1159002
 
−
 
−
Laccase TVEL5
 
−
BBa_K1615067
 
−
 
−
TEV Protease
 
−
BBa_K1159100
 
−
 
−
Thermonuclease
 
−
BBa_K1159105
 
−
 
−
Heroin Esterase
 
−
BBa_K1615045
 
−
 
−
CRE recombinase
 
−
BBa_K1680007
 
−
 
−
Monoamine Oxidase A
 
−
BBa_K1615022
 
−
 
 
==Split proteins==
 
==Split proteins==
−
TEV Protease
+
{| class="wikitable"
−
BBa_K1159101
+
!colspan="6"|[[RFC25_"Freiburg_standard"_parts#Split_proteins| Split proteins (click for all RFC25 parts)]]
−
BBa_K1159102
+
|-
−
 
+
|TEV Protease
−
SpyCatcher/SpyTag
+
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159101'>BBa_K1159101</A></HTML>
−
BBa_K1159200
+
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159102'>BBa_K1159102</A></HTML>
−
BBa_K1159201
+
|-
−
 
+
|SpyCatcher/SpyTag
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159200'>BBa_K1159200</A></HTML>
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159201'>BBa_K1159201</A></HTML>
 +
|-
 +
|}
 
==Binding proteins==
 
==Binding proteins==
−
Fluorescein-Binding Anticalin  
+
{| class="wikitable"
−
BBa_K1159003
+
!colspan="6"|[[RFC25_"Freiburg_standard"_parts#Binding_proteins| Binding proteins (click for all RFC25 parts)]]
 +
|-
 +
|Fluorescein binding Anticalin  
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159003'>BBa_K1159003</A></HTML>
 +
|-
 +
|Digoxigenin binding Anticalin
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K243003'>BBa_K243003</A></HTML>
 +
|-
 +
|HER2 binding DARPin
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K404302'>BBa_K404302</A></HTML>
 +
|-
 +
|HER2 binding Affibody
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_I757009'>BBa_K404302</A></HTML>
 +
|-
 +
|Nickel Binding Protein
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1321009'>BBa_K1321009</A></HTML>
 +
|-
 +
|Cellulose binding Domain
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K863110'>BBa_K863110</A></HTML>
 +
|}
  
−
Nickel Binding Protein (NiBP)
+
==Protease cleavage sites==
−
BBa_K1321009
+
{| class="wikitable"
 +
!colspan="6"|[[RFC25_"Freiburg_standard"_parts#Protease_cleavage_sites| Protease cleavage sites (click for all RFC25 parts)]]
 +
|-
 +
|Name
 +
|Sequence
 +
|BioBrick
 +
|-
 +
|TEV cleavage site
 +
|G-ENLYFQS-G
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159318'>BBa_K1159318</A></HTML>
 +
|-
 +
|}
  
−
==Protein tags==
+
==Affinity tags==
−
''Strep''-tag II an N-part
+
{| class="wikitable"
−
BBa_K549018
+
!colspan="6"|[[RFC25_"Freiburg_standard"_parts#Affinity_tags| Affinity tags (click for all RFC25 parts)]]
−
 
+
|-
−
</html><groupparts>iGEM011 LMU-Munich</groupparts><html>
+
|HA tag
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1150016'>BBa_K1150016</A></HTML>
 +
|-
 +
|His<sub>6</sub>-tag
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_I757013'>BBa_I757013</A></HTML>
 +
|-
 +
|SpyTag
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K1159020'>BBa_K1159020</A></HTML>
 +
|-
 +
|''Strep''-tag II as N-part
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K549018'>BBa_K549018</A></HTML>
 +
|-
 +
|''Strep''-tag II
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_J18916'>BBa_J18916</A></HTML>
 +
|-
 +
|cMyc-tag
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K823036'>BBa_K823036</A></HTML>
 +
|-
 +
|3x FLAG tag
 +
|<HTML><A class='part_link' HREF='https://parts.igem.org/wiki/index.php/Part:BBa_K823034'>BBa_K823034</A></HTML>
 +
|}

Latest revision as of 20:39, 16 May 2016

< Back to BioBrick collection
< RFC25 assembly standard description

RFC25 BioBrick parts

RFC25 compatible BioBrick backbones

pSB1C3-RFP_Generator (BBa_K801100)

For the cloning of RFC25 BioBricks into the Parts Registry compatible backbone the plasmid pSB1C3-RFP_Generator (BBa_K801100) can be used.










Fluorescent proteins

Fluorescent proteins (click for all RFC25 parts)
Protein Color BioBrick Excitation [nm] Emission [nm] Quantum Yield
Cerulean Cyan BBa_I757009 433 475 0.62
eCFP Cyan BBa_K1159302 439 476 0.40
GFP Green BBa_K648013 484 507 0.60
GFP Green BBa_K863120 484 507 0.60
GFP Green BBa_K823039 484 507 0.60
sfGFP Green BBa_K1321337 485 510 0.65
Dronpa (photoactivatable) GreenYellow BBa_K1680006 503 518 0.85
mVenus Yellow BBa_I757008 515 528 0.57
sYFP2 Yellow BBa_K1159301 514 527 0.61
mRFP Red BBa_K1351021 584 607 0.25
mRFP Red BBa_K1615089 584 607 0.25
mKate2 Red BBa_K823029 588 633 0.4
Values for the fluorescent proteins were taken from [http://www.microscopyu.com/articles/livecellimaging/fpintro.html| microscopyu.com].

Luciferases

Luciferases (click for all RFC25 parts)
Protein BioBrick Size [kDa]
Firefly luciferase BBa_K525999 61
Renilla luciferase not available yet 36
NanoLuc luciferase BBa_K1159001 19
Gaussia luciferase not available yet

Transmembrane domains

Optogenetic parts

Linker domains

Linker (click for all RFC25 parts)
Protein Sequence BioBrick Length [residues]
Short Linker (Gly-Gly-Ser-Gly) BBa_K243004 4
Middle Linker 2x (Gly-Gly-Ser-Gly) BBa_K243005 8
Long Linker 3x (Gly-Gly-Ser-Gly) BBa_K243006 12

Catalytic proteins

Catalytic proteins (click for all RFC25 parts)
Erythromycin Esterase Type II BBa_K1159000
Laccase BBa_K1159002
Laccase TVEL5 BBa_K1615067
TEV Protease BBa_K1159100
Thermonuclease BBa_K1159105
Heroin Esterase BBa_K1615045
CRE recombinase BBa_K1680007
Monoamine Oxidase A BBa_K1615022
Endo-β-Galactosidase BBa_K1483001
α-Galactosidase BBa_K1483002
Acetylgalactosamindase BBa_K1483000
2-oxoglutarate oxygenase/decarboxylase BBa_K1065000

Transcription regulators

Transcription regulators (click for all RFC25 parts)
VP16 BBa_K1150001

Split proteins

Split proteins (click for all RFC25 parts)
TEV Protease BBa_K1159101 BBa_K1159102
SpyCatcher/SpyTag BBa_K1159200 BBa_K1159201

Binding proteins

Binding proteins (click for all RFC25 parts)
Fluorescein binding Anticalin BBa_K1159003
Digoxigenin binding Anticalin BBa_K243003
HER2 binding DARPin BBa_K404302
HER2 binding Affibody BBa_K404302
Nickel Binding Protein BBa_K1321009
Cellulose binding Domain BBa_K863110

Protease cleavage sites

Protease cleavage sites (click for all RFC25 parts)
Name Sequence BioBrick
TEV cleavage site G-ENLYFQS-G BBa_K1159318

Affinity tags

Affinity tags (click for all RFC25 parts)
HA tag BBa_K1150016
His6-tag BBa_I757013
SpyTag BBa_K1159020
Strep-tag II as N-part BBa_K549018
Strep-tag II BBa_J18916
cMyc-tag BBa_K823036
3x FLAG tag BBa_K823034