Team:Heidelberg/Notebook/material

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Contents

Material

Buffers & Solution

SM 50 mM Tris, pH 7.5
20 mM MgSO4
50 mM NaCl
0.01 % gelatine
Tethering buffer, pH 7.0 10 mM potassium phosphate
(K2HPO4 : KH2PO4 = 1 :1 )
100 µM EDTA
1 µM L-Methionine
10 mM lactic acid
M63 salt 3 g/l KH2PO4
9 g/l K2HPO4
4 g/l (NH4)2SO4
0.5 g/l FeSO4
Amino acid mix 5 g/l L-threonine
5 g/l L-histidin
5 g/l L-leucine
5 g/l L-methionine
M9 salts 64 g/l Na2HPO4 x 7H2O
15 g/l KH2PO4
2.5 g/l NaCl
5 g/l NH4Cl

Kits

Kit supplier
CompactPrep Plasmid Maxi Kit Qiagen
HISpeed Plasmid Maxi Kit Qiagen
MaxPlax™ Lambda Packaging Extracts EPICENTRE Biotechnologies
QIAEX II Gel Extraction Kit Qiagen
QIAGEN Lambda Mini Kit Qiagen
QIAprep Spin Mini Kit Qiagen
QIAquick Gel Extraction Kit Qiagen
QIAquick PCR Purification Kit Qiagen

Marker

Marker supplier
GeneRulerTM High Range DNA Ladder MBI Fermentas
GeneRulerTM 1kb DNA Ladder Mix MBI Fermentas
GeneRulerTM 1kb Plus DNA Ladder Mix MBI Fermentas

Enzymes

Enzym supplier
Pfu DNA polymerase Stratagene
Pfu turbo DNA polymerase Stratagene
Phusion DNA polymerase Finnzymes
Taq DNA polymerase MBI Fermentas
T4 DNA ligase MBI Fermentas / New England Biolabs
AgeI New England Biolabs
BamHI New England Biolabs
BglI MBI Fermentas
BseJI MBI Fermentas
BspEI New England Biolabs
DpnI Roche Diagnostics / New England Biolabs
DraI New England Biolabs
EcoRI New England Biolabs
EcoRV New England Biolabs
HindIII New England Biolabs
KpnI New England Biolabs
NcoI New England Biolabs
NdeI New England Biolabs
NotI New England Biolabs
PstI New England Biolabs
SacI New England Biolabs
SalI MBI Fermentas
ScaI New England Biolabs
SfcI New England Biolabs
SmiI MBI Fermentas
SpeI New England Biolabs
SpeI New England Biolabs
XbaI New England Biolabs
XhoI MBI Fermentas
XmaI New England Biolabs

Plasmidvectors

Name application reference
BBa_B0015 terminator http://partsregistry.org
BBa_F1610 LuxI http://partsregistry.org
BBa_I15030 AI-1 amplifier http://partsregistry.org
BBa_I20260 GFP http://partsregistry.org
BBa_J01003 oriT http://partsregistry.org
BBa_J16002 cloning vector http://partsregistry.org
BBa_J23107 constitutive promotor http://partsregistry.org
BBa_T9002 AI-1 GFP receiver http://partsregistry.org
CheY-mCherry cloning vector V. Sourjik, ZMBH
ColE1 colicin E1 DSMZ
ColE9-J colicin E9 C. Kleanthous, University of York
pBad18 cloning vector V. Sourjik, ZMBH
pBad33 cloning vector V. Sourjik, ZMBH
pBluescript II SK (+) cloning vector V. Sourjik, ZMBH
pDest15 cloning vector DKFZ Library
pDK4 visualization V. Sourjik, ZMBH
pDK48 cloning vector V. Sourjik, ZMBH
pDK58 cloning vector V. Sourjik, ZMBH
pDK6 visualization V. Sourjik, ZMBH
pED374 oriT K. Derbyshire, Wadsworth
pES16 cloning vector V. Sourjik, ZMBH
pMMB863 oriT M. Bagdasarian, MSU
pQE-30 cloning vector Invitrogen
pSB1A2 cloning vector http://partsregistry.org
pSB2K3 cloning vector http://partsregistry.org
pTrc99a cloning vector V. Sourjik, ZMBH
pUB307 helper plasmid E. Lanka, BfR
RP4 helper plasmid M. Bagdasarian, MSU

Synthetic oligonucleotides

Name SEQUENCE (5´->3´)
Bam_fw GACAAGTGTTGGCCATGGAACAGG
Bam_rv GCCGTCTGTGATGGCTTCCATG
cI_mut_fw GCGTCTGGGTGGTGATGAGTTCACCTTCAAAAAACTG
cI_mut_rv CAGTTTTTTGAAGGTGAACTCATCACCACCCAGACGC
CmR_EcoRI_mut_fw GAATGCTCATCCGGAGTTCCGTATGGCAATG
CmR_EcoRI_mut_rev CATTGCCATACGGAACTCCGGATGAGCATTC
CmR_fw GCTAAAATGGAGAAAAAAATCACTGG
CmR_new_fw TACGAGGTACCTTTACAGCTAGCTCAGTCCTAGGTATTATGC
CmR_new_rev TATATAAGCTTTTACGCCCCGCCCTGCCACTCATCGCAGTACTGTTG
CmR_Prefix_fw GAATTCGCGGCCGCTTCTAGAGTTTACAGCTAGCTCAGTCCTAGG
CmR_rv AGGTTCTCCTTTATTAGCCGGATCCTCTAGATTACGCC
CmR_Suffix_rv CTGCAGCGGCCGCTACTAGTATATAAACGCAGAAAGGCCCACCC
colE1_kil_prot_rv_A_SpeI TATATACTAGTACTACTGAACCGCGATCCCCG
colE1_mut_EcoRI_fw GGTATTGCTATTGTTACAGGTATTCTATGCTCCTATATTGATAAG
colE1_mut_EcoRI_rv CTTATCAATATAGGAGCATAGAATACCTGTAACAATAGCAATACC
colE1_mut_PstI_1_fw GCAGTAAAAGTGAAAGTTCAGCAGCTATTCATGCAACTGC
colE1_mut_PstI_1_rv GCAGTTGCATGAATAGCTGCTGAACTTTCACTTTTACTGC
colE1_mut_PstI_2_fw GCTGCCCGGGCAAAAGCAGCAGCGGAAGCACAGG
colE1_mut_PstI_2_rv CCTGTGCTTCCGCTGCTGCTTTTGCCCGGGCAGC
colE1_mut_PstI_3_fw CATTAGAGAAGAAAGCAGCAGATGCAGGGGTGAG
colE1_mut_PstI_3_rv CTCACCCCTGCATCTGCTGCTTTCTTCTCTAATG
colE1_prot_fw_BamH1 TACGAGGATCCATGGAAACCGCGGTAGCG
colE1_prot_rv_HindIII TATATAAGCTTTTAAATCCCTAACACCTC
colE9_lysProt_rv_A_SpeI TATATACTAGTACTAGGTTTTCGGCTTAGAACCCC
colE9_mut_EcoRI_fw GTTGGGTGGACGATTCGAGAGTTCAATGGGGAAATAAAAATG
colE9_mut_EcoRI_rv CATTTTTATTTCCCCATTGAACTCTCGAATCGTCCACCCAAC
colE9_plasmid_rv_A_SpeI TATATACTAGTACACATGGAACTTTTGTGAC
colE9_prot_fw_BamH1 TACGAGGATCCATCGATTTGCCCATGACCC
colE9_prot_rv_XmaI TATATCCCGGGTTACTTACCTCGGTGAATATCG
DK13 TCACCCGCACGCGC
DK167 AGGATACTAGTAGGCCATTACTTT
DK9b CGATGCGGCCGCTCAAAATGTTTCCCAGTTTGG
F1610_fw_XbaI TACGATCTAGAAAAGAGGAGAAATACTAG
F1610_rv_HindIII TATATAAGCTTTATAAACGCAGAAAGGCCC
GAM_fw AGTGCTTTAGCGTTAACTTCCG
GAM_rv GGTTTTACCGCATACCAATAACG
GFP_CmR_fw CTCGTTGGTACCTCTAGATTTACAGCTAGCTCAGTCCTAGG
GFP_CmR_rv TATTCGACCGGTACTAGTTATAAACGCAGAAAGGCCCACC
GFP_new_fw TACGAGAGCTCTTTACAGCTAGCTCAGTCCTAGG
GFP_new_rv TATATACCGGTACTAGTTATAAACGCAGAAAGGCCCACC
Lambda_insert_fw TTGTAAAAACAGCCCTCCTC
Lambda_insert_rv GATATGACTATCAAGGCCGC
LuxP_mut_F CGTGAATTAGCAACAGAGTTCGGAAAGTTCTTCCC
LuxP_mut_R GGGAAGAACTTTCCGAACTCTGTTGCTAATTCACG
LuxP_prefix_F GAGGGAGAATTCGCGGCCGCTTCTAGATGAAGAAAGCGTTACTATTTTC
LuxP_sufffix_R GGAGAGCTGCAGCGGCCGCTACTAGTAATTATCTGAATATCTAAATGCG
LuxPc ATTACGCGGCCGCAGGAAACAGACCATGAAGAAAGCGTTACTATTTTCCC
LuxPd GTAATGTCGACTCAATTATCTGAATATC
LuxP-seq-FW CCCGTCCTGCCAGTGAGC
LuxQa ATCGACCATGGGCAATAAATTTCGCTTAGC
LuxQc GTAATGGATCCTTAGTGGAGGCTTGAGCC
LuxQTar_1a CACAAATCATTGCCAATGAACGTATGTTGCTTACTCCGCTGG
LuxQTar_1b CCAGCGGAGTAAGCAACATACGTTCATTGGCAATGATTTGTG
LuxQTar_2a CTTAGCGACCATGAGCCATGAGTTTGCCCAGTGGCAACTGGC
LuxQTar_2b GCCAGTTGCCACTGGGCAAACTCATGGCTCATGGTCGCTAAG
LuxS mutBbaIR CCACACCCACTTCTAGGATGTTCTTCGCGATTTGC
LuxS mutXbaIF GCAAATCGCGAAGAACATCCTAGAAGTGGGTGTGG
LuxS_mut_fw CATCCTTTCTGAGAAAGGCATTCATACATTAGAGC
LuxS_mut_rev GCTCTAATGTATGAATGCCTTTCTCAGAAAGGATG
LuxS_prefix_F GGAGAGGAATTCGCGGCCGCTTCTAGATGGGCAATGCACCAGCGGTTCG
luxS_suffix_R GAGGGACTGCAGCGGCCGCTACTAGTAGTCGATGCGTAGCTCTCTCAGC
LuxSa ATCAGTCCATGGGCAATGCACCAGCGGTTCG
LuxSb GTAATGGATCCTTAGTCGATGCGTAGC
mut_insert_fw CTGAGGGGACGGTACCTCTACATTTACAGCTAGCTCAG
mut_insert_rv CTGAGCTAGCTGTAAATGTAGAGGTACCGTCCCCTCAG
mut_insert2_fw GGCAGGCGGGGCGTAATCTATAGGATCCGGCTAATAAAGG
mut_insert2_rv CCTTTATTAGCCGGATCCTATAGATTACGCCCCGCCTGCC
mut_kpn1_pBlue CGAGGGGGGGCCCGGTTCCCAATTCGCCCTATAG
mut_kpn1_pBlue CTATAGGGCGAATTGGGAACCGGGCCCCCCCTCG
oriT_pre GAATTCGCGGCCGCTTCTAGAGGACAGGCTCATGCCGGCCGC
oriT_RP4_fw CTCGTTTCTAGAACTAGTGACAGGCTCATGCCGGCCGC
oriT_RP4_rv TATTCGGGTACCGTCCCCTCAGTTCAGTAATTTCCTGC
oriT_suf CTGCAGCGGCCGCTACTAGTAGTCCCCTCAGTTCAGTAATTTCCTGC
T9002_Lux_pR_rv_SpeI_BamHI_RBS TATATACTAGTGGATCCGGTTCTGTTTCCTCTCTAGTATTTATTCGAC
T9002_LuxpR_Not_Eco_Xba_G_fw TACGAGAATTCGCGGCCGCTTCTAGAGTCCCTATCAGTGATAGAGATTG
Term_new_fw TACGAAAGCTTCCAGGCATCAAATAAAACGAAAGG
Term_new_rv TATATGAGCTCTATAAACGCAGAAAGGCCCACCC
VF2 TGCCACCTGACGTCTAAGAA
VIC121 TTTATCGCAACTCTCTACTG
VIC122 CTGATTTAATCTGTATCAGG
VIC131 ATGTGTGGAATTGTGAGCGG
VIC132 CTGATTTAATCTGTATCAGG
VR ATTACCGCCTTTGAGTGAGC

Phages

Bacteria

E.coli strain usage reference
DH5a amplification of plasmids Invitrogen
HCB33 swarm assays V. Sourjik, ZMBH
MG1655 swarm assays V. Sourjik, ZMBH
TOP10 amplification of plasmids Invitrogen
UU1250 chemotaxis receptor knock out V. Sourjik, ZMBH

Bacteria Growth Media

E.coli strain usage reference
DH5a amplification of plasmids Invitrogen
HCB33 swarm assays V. Sourjik, ZMBH
MG1655 swarm assays V. Sourjik, ZMBH
TOP10 amplification of plasmids Invitrogen
UU1250 chemotaxis receptor knock out V. Sourjik, ZMBH


For cultivation of phages the media were supplied with 0.2 % maltose and 10 mM MgSO4. For preparation of agar plates 15 g/l agar, for preparation of top agar 7 g/l agar was added prior the autoclaving. For selection of resistant bacteria following antibiotics were added during cooling of at agar at about 50 °C:


Antibiotic concentration
Ampicillin 100 µg/ml
Chloramphenicol 35 µg/ml
Kanamycin 50 µg/ml

The same concentrations of antibiotics were used for selection of resistant in media.

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