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Team:Heidelberg/Notebook/material
From 2008.igem.org
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.
