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
GeneRuler™ High Range DNA Ladder MBI Fermentas
GeneRuler™ 1kb DNA Ladder Mix MBI Fermentas
GeneRuler™ 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

All oligonucleotides were purchased from Invitrogen (Karlsruhe) and adjusted to a standard concentration of 100 pmol/µl.

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

Name application reference
Lambda cI mut cI deleted W. Reiser, ZMBH
Lambda cI857 heat inducible MBI Fermentas

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

Luria Broth (LB) 10 g/l tryptone
5 g/l yeast extract
10 g/l NaCl
Luria Broth (LB) plus 10 g/l tryptone
5 g/l yeast extract
20 g/l NaCl
TB 10 g/l bacto tryptone
5 g/l NaCl
Standard I 15.6 g/l peptone P
2.8 g/l yeast extract
5.6 g/l NaCl
1 g/l D-glucose
Minimal medium 9.8 % M63 salts
0.2 % glycerol
0.1 g/l Thiamine
1 mM MgSO4
0.8 % amino acid mix
M9 20 % M9 salts
2 mM MgSO4
0.4 % glucose
0.1 mM CaCl2


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.

Methods

Preparing chemically competent cells

First, a 20 ml over night culture was inoculated in antibiotic free LB medium from a fresh single colony and transferred into 400 ml antibiotic free LB medium the next day. This culture was incubated at 37 °C while shacking until an OD600 of 0.5 – 0.6 was achieved. The culture was than cooled down on ice, centrifuged (8 min, 4 °C, 3500 rpm), the supernatant discarded and the pellet resuspended in 10 ml 100 mM CaCl2. After addition of further 190 ml 100 mM CaCl2 the suspension was incubated on ice for 30 min. The suspension was than again centrifuged (8 min, 4 °C, 3500 rpm), the supernatant discarded, the pellet resuspended in 20 ml 82.5 mM CaCl2 with 17.5 % glycerol and aliquoted. The aliquots were flash frozen in liquid nitrogen and than stored at -80 °C until usage.

Transformation of bacteria

For enrichment of vectors, E .coli TOP10 and DH5α were used. For the transformation 100 µl of the competent cells were thawed on ice and 50 – 200 ng DNA solution added (depending on the concentration of the DNA solution). After a 20 minute incubation on ice, cells were made permeable for the DNA by heat shocking for 45 seconds at 42 °C and a further 2 minute incubation on ice. The samples were than rescued by adding 250µl preheated antibiotic free LB-medium and incubated for one hour at 37 °C while shacking for induction of the antibiotic resistance. The selection for plasmid containing and therefore antibiotic resistant bacteria was conducted by plating them on antibiotic containing LB-agar plates.

Isolation of plasmid DNA by alkaline lysis (mini and maxiprep)

For analysis of ligations and transformations QIAprep Spin Kits (Qiagen, Hilden) were used following the manufacturer instructions. For miniprep a single colony was picked from a LB-agar plate or glycerol stock was used to inoculate 5 ml LB-medium with appropriate antibiotic for selection (100 µg/µl ampicillin, 50 µg/µl kanamycin, 35 µg/µl chloramphenicol). Bacteria were grown over night at 37 °C while shaking (200 rpm). By using 4 ml over night culture with this kit the yield was around 6-10 µg. For maxipreps the Qiagen CompactPrep Plasmid Maxi Kit was used following the instructions given by the instruction manual. In this case 250 ml LB-medium were inoculated and used for preparation of plasmid DNA. The routinely yield was 300-400 µg plasmid DNA. Purity and amount of DNA was analysed using a NanoDrop.

DNA amplification using polymerase chain reaction (PCR)

By using PCR smallest amount of DNA can be detected and amplified. The principle of PCR is the selective amplification of any region of the DNA. Nevertheless, the sequence at both ends must be known for the binding of two complementary primers. The DNA region of interest is than amplified exponentially while the reproduction of the DNA takes place in three temperature stpes: denaturation of parental DNA at high temperature (95-98 °C), hybridisation of primers (58-65 °C) and DNA elongation (72 °C). For the amplification a heat-stable DNA polymerase I with a 3’-5’ exonuclease activity (proof reading) is used such as Pfu (from Pyrococcus furiosus) and Phusion (a Pyrocuccus-like enzyme) or the non proof reading enzyme Taq (from Thermus aquaticus). Phsuion polymerase was used in a 2x master mix adding only primers (20pmol each) and DNA template (~10ng) or alternatively colonies from agar plates (1-5 colonies) in a final volume of 50 µl. For taq and Pfu polymerase following reaction batch was commonly used:


1 µl template (10 ng) / colonies
2 µl primer 1 (10 pmol/µl)
2 µl primer 2 (10 pmol/µl)
1 µl polymerase (2,5 Units)
1 µl dNTP mix (10 mM)
5 µl 10x buffer
38 µl dH2O

The PCR procedure was as follows:

Initiale denaturation 95- 98 °C, 3-5 min 1 cycle
denaturation 95-98 °C, 15 sec - 1 min
annealing 58-65 °C, 15 sec - 1 min 25-28 cycles
elongation 72 °C, 15 sec - 3 min
termination 72 °C, 5 – 10 min 1 cycle
4 °C forever

For site directed mutagenesis PCR Pfu turbo polymerase (Stratagene) was used in the same reaction batch described above. The temperature program was as follows:

initiale denaturation 95 °C, 30 sec 1 cycle
denaturation 95 °C, 30 sec
annealing 55 °C, 1 min 16 cycles
elongation 68 °C, 2 min per kb of plasmid
termination 68 °C, 10 min 1 cycle
4 °C forever

For point mutagenesis primers with around 33 bases were used having the base to be altered in the middle. The melting temperature of these primers was always over 78 °C. If this melting temperature could not be achieved using 15 unchanged nucleotides at both sites the flanking arms were enlarged properly. After the PCR reaction 10 units of DpnI was added directly to the PCR tube, mixed and incubated for 1-5 h at 37 °C. DpnI digests the parental methylated plasmid DNA leaving only the mutated one. After purification using QIAquick PCR Purification Kit the plasmid was transformed as described above.

Purification of DNA from PCR reactions

PCR products were purified by the QIAquick PCR Purification Kit from Qiagen following the instructions of the Qiagen Handbook. To check the purity and amount of extracted DNA an aliquot was analysed using a NanoDrop.

Enzymatic hydrolysis of DNA by restriction enzymes

The restriction digest of DNA was used for analysis of purified DNA form mini or maxiprep or for isolation of specific DNA fragments for further cloning. Analytical digestions were routinely conducted in 20 µl volume. In all digestions a minimum of 2 Units restriction enzyme(s) was used per microgram DNA. Optimised buffer conditions were secured by using NEB buffer system. The final reaction volume was achieved by adding H2O dest. and the sample was incubated at optimal temperature for the restriction enzyme(s) (normally 37 °C). Preparative digestions were conducted in a volume of 50 µl. For analysis and preparation DNA loading dye was added to the samples and they were loaded on a agarose gel or alternatively purified by QIAquick PCR Purification Kit from Qiagen.

Agarose gel electrophoresis for separating DNA

In the agarose gel electrophoresis a mixture of DNA fragments with different sizes are separated in an electrical field by their size. This is achieved by moving the negatively charged DNA through an agarose matrix while shorter fragments will run faster. The size of the pores can be controlled by agarose concentration. The higher the agarose concentration the smaller the pores are and the smaller fragments can be separated. Agarose concentrations between 0.7 and 1.5 % agarose in 0.5x TE buffer were used. The agarose was dissolved completely by heating up and 0.1 µg/ml ethidium bromide was added. The DNA fragments were separated using a constant voltage between 80 and 130 V. Under UV light (λ = 254 nm) DNA is visible through the unspecific intercalated ethidium bromide and can be documented or cut out and extracted from the gel.

Isolation of DNA fragments from an agarose gel

Plasmid DNA and DNA fragments were extracted using the Gel Extraction Kit from Qiagen following the manufacture instructions. To check the purity and amount of extracted DNA an aliquot was analysed using a NanoDrop.

Ligation of dsDNA fragments

T4 DNA ligase was used to form covalent phosphodiesterbonds between doublestranded DNA fragments having blunt or compatible sticky ends. For the ligation the restricted vector -DNA and the insert were mixed 1:3 or 1:5 in a total ligationvolume of 20 µl. This mixture was incubated in ligation buffer using 5 Weiss units T4 DNA ligase over night at 16 °C or at room temperature for 20 minutes and afterwards used to transform chemical competent cells.

Lysing of bacteria by ultrasonication

For the lysis of bacteria an ultrasonic tip was used. The 10-15 ml of bacteria over night cultures were sonicated with an ultrasonic tip three time for 15 seconds. After sonication cell extract was observed under microscope.

Glycerol stock

To store bacteria for long term glycerol stocks were used. Therefore 1 ml of an over night culture were added to 150 µl of 80 % Glycerol into a cryo tube, vortexed and incubated at room temperature for 30 min. Afterwards the glycerole stock was stored at -80 °C.

Preparation of plating bacteria for bacteriophage experiments

A overnight culture of the appropriate E. coli strain was grown in LB medium containing 10 mM MgSO4 and 0.2 % maltose at 30 °C to reduce the amount of cell debris in the medium. The added maltose leads to a substantial induction of the maltose operon including the lamb gene, which encodes the cell surface receptor to which bacteriophage λ binds. After harvesting the cells they were resuspended in 10 mM MgSO4 and diluted to a final concentration of 2.0 OD600. The suspension of plating bacteria was stored at 4 °C for up to 1 week.

Bacteriophage λ plaque assay

Tenfold serial dilutions of the bacteriophage stocks were prepared, 100 µl of it mixed with the same amount of plating bacteria, incubated for 20 minutes at 37 °C to allow the bacteriophage particles to adsorb to the bacteria, this mixture added to 3 ml molten top agar which was kept liquid at 48 °C and the entire contend poured onto a agar plate. After harden of the top agar the inverted plates were incubated at 37 °C over night. On the next day plaques could be counted.

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