Team:Freiburg/Notebook/10 June

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===??.Labday===
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{{:Team:Freiburg/Templates/header}}
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<html>
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<div id="notebook-page-header">
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<div id="notebook-back" width="100px" >
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<a href="https://2011.igem.org/Team:Freiburg/Notebook/9_June">Previous entry</a>
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</div>
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<div id="notebook-title">
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<a href="https://2011.igem.org/Team:Freiburg/Notebook"> 10 June </a>
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</div>
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<div id="notebook-next">
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<a href="https://2011.igem.org/Team:Freiburg/Notebook/11_June">Next entry</a>
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==Miniprep==
==Miniprep==
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Miniprep of parts from 8th of june and DNA concentration was measured with NanoDrop 2000c.
Miniprep of parts from 8th of june and DNA concentration was measured with NanoDrop 2000c.
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{{:Team:Freiburg/Templates/footer}}
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==3A-assembly: Digestion==
 +
 +
'''Investigators: Sophie, Theo, Sandra'''
 +
 +
Digestion of RBS and promotor to create a promotor-RBS library.
 +
 +
 +
{| cellpadding="10" cellspacing="0" border="1"
 +
|
 +
|sample
 +
|name
 +
|-
 +
|Promotor
 +
|BBa_J23104
 +
|S1
 +
|-
 +
|Promotor
 +
|BBa_J23110
 +
|S2
 +
|-
 +
|Promotor
 +
|BBa_J23116
 +
|S3
 +
|-
 +
|RBS
 +
|BBa_B0034
 +
|S4
 +
|-
 +
|RBS
 +
|BBa_B0032
 +
|S5
 +
|-
 +
|RBS
 +
|BBa_B0031
 +
|S6
 +
|-
 +
|Vector
 +
|pSB1C3
 +
|S7
 +
|}
 +
 +
 +
Enzymes used for digestion:
 +
 +
{| cellpadding="10" cellspacing="0" border="1"
 +
|
 +
|enzyme 1
 +
|enzyme 2
 +
|-
 +
|promotor (S1-S3)
 +
|EcoRI
 +
|SpeI
 +
|-
 +
|RBS (S4-S6)
 +
|Xbal
 +
|PstI
 +
|-
 +
|Vector (S7)
 +
|EcoRI
 +
|PstI
 +
|}
 +
<br/>
 +
 +
==<span style="color:grey;">Protein modelling for the precipitator</span>==
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'''Investigators: Rüdiger'''
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 +
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3cvr bacterial ligase<br/>
 +
 +
 +
FSELQLNRLNLSSLPDNLPPQ<br/>
 +
 +
ITVLEITQNALISLPELPAS<br/>
 +
 +
LEYLDACDNRLSTLPELPAS<br/>
 +
 +
LKHLDVDNNQLTXLPELPAL<br/>
 +
 +
LEYINADNNQLTXLPELPTS
 +
 +
LEVLSVRNNQLTFLPELPES
 +
 +
EIFFRCRENRITHIPENILSLDP
 +
 +
 +
Extracted ideal consensus, by consensus sequence and 3d rational analysis:
 +
 +
LEVLDVSNNQLTSLPDNLPAS
 +
 +
 +
N-Terminal Hagfish 2z66
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CPSRCSCSGTEIRCNSKGLTSVPTGIPSSATRLELESNKLQSLPHGVFDK
 +
LTQLTK
 +
Consensus: xLxxLxxLxL
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C-Terminal Hagfish 2z62
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LKELALDTNQLKSVPDGIFDR
 +
LTSLQKIWLHTNPWDCSCPRIDY
 +
LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP
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LxxLxLxxNxLx Consensus
 +
 +
 +
 +
Sequences 1-6 sent to I-Tasser for 3D structure prediction:
 +
Rational1:
 +
LxALHCSxNxLxSLPxxLPxx LxHLACSxNxLxSLPxxLPxx
 +
 +
CPSRCSCSGTEIRCNSKGLTSVPTGIPSS
 +
ATRLELESNKLQSLPHGVFDK
 +
LTALHKSNNQLTSLPDNLPAS
 +
LEHLAVSNNQLTSLPDNLPAS
 +
LEALHVSNNQLTSLPDNLPAS
 +
LEHLAVSNNQLTSLPDNLPAS
 +
LEALHVSNNQLTSLPDNLPAS
 +
LEHLAVSNNQLTSLPDNLPAS
 +
LKELALDTNQLKSVPDGIFDR
 +
LTSLQKIWLHTNPWDCSCPRIDY
 +
LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP
 +
 +
 +
 +
Rational2:
 +
LxxLxCSxNHLHSLPxxLPxx
 +
 +
 +
CPSRCSCSGTEIRCNSKGLTSVPTGIPSS
 +
ATRLELESNKLQSLPHGVFDK
 +
LTQLTKSNNHLHSLPDNLPAS
 +
LEVLDVSNNHLHSLPDNLPAS
 +
LEVLDVSNNHLHSLPDNLPAS
 +
LEVLDVSNNHLHSLPDNLPAS
 +
LEVLDVSNNHLHSLPDNLPAS
 +
LEVLDVSNNHLHSLPDNLPAS
 +
LKELALDTNQLKSVPDGIFDR
 +
LTSLQKIWLHTNPWDCSCPRIDY
 +
LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP
 +
 +
 +
Rational3:
 +
LxxLxCSxNxLxSLPHHLPxx
 +
 +
CPSRCSCSGTEIRCNSKGLTSVPTGIPSS
 +
ATRLELESNKLQSLPHGVFDK
 +
LTQLTKSNNQLTSLPHHLPAS
 +
LEVLDVSNNQLTSLPHHLPAS
 +
LEVLDVSNNQLTSLPHHLPAS
 +
LEVLDVSNNQLTSLPHHLPAS
 +
LEVLDVSNNQLTSLPHHLPAS
 +
LEVLDVSNNQLTSLPHHLPAS
 +
LKELALDTNQLKSVPDGIFDR
 +
LTSLQKIWLHTNPWDCSCPRIDY
 +
LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP
 +
 +
 +
 +
Rational4:
 +
LxxLxCSxNxLxSLPxHLPHx
 +
 +
CPSRCSCSGTEIRCNSKGLTSVPTGIPSS
 +
ATRLELESNKLQSLPHGVFDK
 +
LTQLTKSNNQLTSLPDHLPHS
 +
LEVLDVSNNQLTSLPDHLPHS
 +
LEVLDVSNNQLTSLPDHLPHS
 +
LEVLDVSNNQLTSLPDHLPHS
 +
LEVLDVSNNQLTSLPDHLPHS
 +
LEVLDVSNNQLTSLPDHLPHS
 +
LKELALDTNQLKSVPDGIFDR
 +
LTSLQKIWLHTNPWDCSCPRIDY
 +
LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP
 +
 +
 +
Rational5:
 +
LHxLxCSxNxLxSLPxxLPxH
 +
LHVLDVSNNQLTSLPDNLPAH
 +
 +
 +
CPSRCSCSGTEIRCNSKGLTSVPTGIPSS
 +
ATRLELESNKLQSLPHGVFDK
 +
LHQLTKSNNQLTSLPDNLPAH
 +
LHVLDVSNNQLTSLPDNLPAH
 +
LHVLDVSNNQLTSLPDNLPAH
 +
LHVLDVSNNQLTSLPDNLPAH
 +
LHVLDVSNNQLTSLPDNLPAH
 +
LHVLDVSNNQLTSLPDNLPAH
 +
LKELALDTNQLKSVPDGIFDR
 +
LTSLQKIWLHTNPWDCSCPRIDY
 +
LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP
 +
 +
 +
 +
Rational6:
 +
LHHLxCSxNxLxSLPxxLPxx
 +
LHHLDVSNNQLTSLPDNLPAS
 +
 +
 +
CPSRCSCSGTEIRCNSKGLTSVPTGIPSS
 +
ATRLELESNKLQSLPHGVFDK
 +
LHHLTKSNNQLTSLPDNLPAS
 +
LHHLDVSNNQLTSLPDNLPAS
 +
LHHLDVSNNQLTSLPDNLPAS
 +
LHHLDVSNNQLTSLPDNLPAS
 +
LHHLDVSNNQLTSLPDNLPAS
 +
LHHLDVSNNQLTSLPDNLPAS
 +
LHHLDVSNNQLTSLPDNLPAS
 +
LKELALDTNQLKSVPDGIFDR
 +
LTSLQKIWLHTNPWDCSCPRIDY
 +
LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP

Latest revision as of 01:18, 22 September 2011


This is the wiki page
of the Freiburger student
team competing for iGEM 2011.
Thank you for your interest!

Miniprep

Investigators: Jakob, Julia


Comments: Trafo was performed on 8th of june and plates were incubated over night at 37°C. Clones were picked to do a miniprep.


Miniprep of parts from 8th of june and DNA concentration was measured with NanoDrop 2000c.

                       

3A-assembly: Digestion

Investigators: Sophie, Theo, Sandra

Digestion of RBS and promotor to create a promotor-RBS library.


sample name
Promotor BBa_J23104 S1
Promotor BBa_J23110 S2
Promotor BBa_J23116 S3
RBS BBa_B0034 S4
RBS BBa_B0032 S5
RBS BBa_B0031 S6
Vector pSB1C3 S7


Enzymes used for digestion:

enzyme 1 enzyme 2
promotor (S1-S3) EcoRI SpeI
RBS (S4-S6) Xbal PstI
Vector (S7) EcoRI PstI


Protein modelling for the precipitator

Investigators: Rüdiger


3cvr bacterial ligase


FSELQLNRLNLSSLPDNLPPQ

ITVLEITQNALISLPELPAS

LEYLDACDNRLSTLPELPAS

LKHLDVDNNQLTXLPELPAL

LEYINADNNQLTXLPELPTS

LEVLSVRNNQLTFLPELPES

EIFFRCRENRITHIPENILSLDP


Extracted ideal consensus, by consensus sequence and 3d rational analysis:

LEVLDVSNNQLTSLPDNLPAS


N-Terminal Hagfish 2z66 CPSRCSCSGTEIRCNSKGLTSVPTGIPSSATRLELESNKLQSLPHGVFDK LTQLTK Consensus: xLxxLxxLxL C-Terminal Hagfish 2z62 LKELALDTNQLKSVPDGIFDR LTSLQKIWLHTNPWDCSCPRIDY LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP LxxLxLxxNxLx Consensus


Sequences 1-6 sent to I-Tasser for 3D structure prediction: Rational1: LxALHCSxNxLxSLPxxLPxx LxHLACSxNxLxSLPxxLPxx

CPSRCSCSGTEIRCNSKGLTSVPTGIPSS ATRLELESNKLQSLPHGVFDK LTALHKSNNQLTSLPDNLPAS LEHLAVSNNQLTSLPDNLPAS LEALHVSNNQLTSLPDNLPAS LEHLAVSNNQLTSLPDNLPAS LEALHVSNNQLTSLPDNLPAS LEHLAVSNNQLTSLPDNLPAS LKELALDTNQLKSVPDGIFDR LTSLQKIWLHTNPWDCSCPRIDY LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP


Rational2: LxxLxCSxNHLHSLPxxLPxx


CPSRCSCSGTEIRCNSKGLTSVPTGIPSS ATRLELESNKLQSLPHGVFDK LTQLTKSNNHLHSLPDNLPAS LEVLDVSNNHLHSLPDNLPAS LEVLDVSNNHLHSLPDNLPAS LEVLDVSNNHLHSLPDNLPAS LEVLDVSNNHLHSLPDNLPAS LEVLDVSNNHLHSLPDNLPAS LKELALDTNQLKSVPDGIFDR LTSLQKIWLHTNPWDCSCPRIDY LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP


Rational3: LxxLxCSxNxLxSLPHHLPxx

CPSRCSCSGTEIRCNSKGLTSVPTGIPSS ATRLELESNKLQSLPHGVFDK LTQLTKSNNQLTSLPHHLPAS LEVLDVSNNQLTSLPHHLPAS LEVLDVSNNQLTSLPHHLPAS LEVLDVSNNQLTSLPHHLPAS LEVLDVSNNQLTSLPHHLPAS LEVLDVSNNQLTSLPHHLPAS LKELALDTNQLKSVPDGIFDR LTSLQKIWLHTNPWDCSCPRIDY LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP


Rational4: LxxLxCSxNxLxSLPxHLPHx

CPSRCSCSGTEIRCNSKGLTSVPTGIPSS ATRLELESNKLQSLPHGVFDK LTQLTKSNNQLTSLPDHLPHS LEVLDVSNNQLTSLPDHLPHS LEVLDVSNNQLTSLPDHLPHS LEVLDVSNNQLTSLPDHLPHS LEVLDVSNNQLTSLPDHLPHS LEVLDVSNNQLTSLPDHLPHS LKELALDTNQLKSVPDGIFDR LTSLQKIWLHTNPWDCSCPRIDY LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP


Rational5: LHxLxCSxNxLxSLPxxLPxH LHVLDVSNNQLTSLPDNLPAH


CPSRCSCSGTEIRCNSKGLTSVPTGIPSS ATRLELESNKLQSLPHGVFDK LHQLTKSNNQLTSLPDNLPAH LHVLDVSNNQLTSLPDNLPAH LHVLDVSNNQLTSLPDNLPAH LHVLDVSNNQLTSLPDNLPAH LHVLDVSNNQLTSLPDNLPAH LHVLDVSNNQLTSLPDNLPAH LKELALDTNQLKSVPDGIFDR LTSLQKIWLHTNPWDCSCPRIDY LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP


Rational6: LHHLxCSxNxLxSLPxxLPxx LHHLDVSNNQLTSLPDNLPAS


CPSRCSCSGTEIRCNSKGLTSVPTGIPSS ATRLELESNKLQSLPHGVFDK LHHLTKSNNQLTSLPDNLPAS LHHLDVSNNQLTSLPDNLPAS LHHLDVSNNQLTSLPDNLPAS LHHLDVSNNQLTSLPDNLPAS LHHLDVSNNQLTSLPDNLPAS LHHLDVSNNQLTSLPDNLPAS LHHLDVSNNQLTSLPDNLPAS LKELALDTNQLKSVPDGIFDR LTSLQKIWLHTNPWDCSCPRIDY LSRWLNKNSQKEQGSAKCSGSGKPVRSIICP

Retrieved from "http://2011.igem.org/Team:Freiburg/Notebook/10_June"