Team:Heidelberg LSL/Notebook materials
From 2012hs.igem.org
Kits for Purification of Plasmid-DNA and DNA fragments
DNA was extracted in small or medium scale using the Promega or Qiagen DNA preparation kits. For all DNA extractions before digestions/transformations, Promega Kits were applied. Only when performing sequencing, Qiagen kits were preferred.
Name | Product Description | Company |
small scale plasmid purification from E. coli Top10 cells before digestion or transformation into different E. coli strains | Promega | |
small scale plasmid purification from E. coli Top10 cells before sequencing | Qiagen | |
medium scale plasmid purification from E. coli Top10 cells before digestion or transformation into different E. coli strains | Promega | |
direct purification of DNA after restriction digests | Qiagen | |
Purification of DNA fragements from agarose gel | Qiagen |
LB growth media - components an recipe
LB media was prepared from 10 g/l tryptone, 5 g/l yeast extract and 5 g/l NaCl and autoclaved before usage. For preparing LB agar plates, 1.5 g of agar were added to the media. The media was furthermore substituted with 100 ug/ml ampicillin (for LB-amp) or 35 ug/ul chloramphenicol (for LB-cm).
Name | Usage | Company |
for preparing LB media | BD | |
for preparing LB media | BD | |
for preparing LB media | Sigma | |
for preparing agar plates | Sigma | |
usage: 100 ug/ml, selection of plasmid containing an amp resistance gene | Sigma | |
usage: 35 ug/ml, selection of plasmid containing an Cm resistance gene | Sigma | |
preparing agar plates | Sigma | |
dissolve in DMSO at 20 mg/ml. final concentration for blue-white screening: 100 ug/ml and for X-Gal assays in liquid LB culture: 200 ug/ml | Sigma |
E. coli Strains
E. coli Top10 were used for amplification of plasmid DNA and subsequent DNA substraction. Bl21(DE3) were used in all measurments/assays performed.
Strain | Genotype |
F- mcrA Δ(mrr-hsdRMS-mcrBC) φ80lacZΔM15 ΔlacX74 nupG recA1 araD139 Δ(ara-leu)7697 galE15 galK16 rpsL(StrR) endA1 λ- | |
F– ompT gal dcm lon hsdSB(rB- mB-) λ(DE3 [lacI lacUV5-T7 gene 1 ind1 sam7 nin5]) |
Enzymes
Name | Product Description | Company |
restriction enzyme, recognition sequence: GAATTC | Promega or NEB | |
restriction enzyme, recognition sequence: ACTAGT | Promega or NEB | |
restriction enzyme, recognition sequence: TCTAGA | Promega or NEB | |
restriction enyzme, recognition sequence: CTGCAG | Promega or NEB | |
Ligation of DNA fragments | Promega or Fermentas | |
Standard Taq PCR master mix for robust amplification of DNA-Fragments by PCR; used for colony-PCR screens | Fermentas |
Oligonucleotides
Oligos were annealed and subsequently cloned into EcoRI/XbaI predigested reporter backbones. Thereby short synthetic DNA-sequences (in this case for the promoters psulA, precA and precB) can be generated in a fast and easy manner.
Oligo Name | Oligo Sequence | sequence length |
psulA_fw | 5'-aattcgcggccgcttctagagGGGTTGATCTTTGTTGT CACTGGATGTACTGTACATCCATACAGTAACTCACc-3' | 74 |
psulA_rev | 5'-ctaggGTGAGTTACTGTATGGATGTACAGTACATCCAG TGACAACAAAGATCAACCCctctagaagcggccgcg-3' | 74 |
precB_fw | 5'aattcgcggccgcttctagagCCTGAAGGCTGGAAAGTGTGGGAGA ACGTCAGCGCGTTGCAGCAAACAATGCCCCTGATGAGTGAAAAGAc-3' | 92 |
precB_rev | 5'-ctaggTCTTTTCACTCATCAGGGGCATTGTTTGCTGCAACGCGCTG ACGTTCTCCCACACTTTCCAGCCTTCAGGctctagaagcggccgcg-3' | 92 |
precC_fw | 5'-aattcgcggccgcttctagagTTCACCCGGGGGCAGAGAAGGC GAGATGACCCGCCTGCATTGCCCGAATCGTCAGTAGTCAGGAGCCGCTc-3' | 92 |
precC_rev | 5'-ctaggAGCGGCTCCTGACTACTGACGATTCGGGCAATGCAGGCG GGTCATCTCGCCTTCTCTGCCCCCGGGTGAActctagaagcggccgcg-3' | 92 |
gel electrophoresis
For gel electrophoresis we used 1 % agarose dissolved in 1x TAE buffer. Gels were run at 110 V for 25-60 min.
Name | Usage | Company |
to be dissolved to 1 % in 1x TAE buffer | Sigma | |
for preparing LB media | BD | |
Tris-Acetate-EDTA buffer for gel electrophoresis | Sigma | |
dissolve to 1x in DNA samples before loading onto agarose gel | Promega | |
1kb DNA ladder | Promega | |
DNA ladder mix, 100 bp - 10 kb | Fermentas |
Measurements
The following materials and devices were used for our measurements and assays (DNA concentration, ONPG- and X-Gal assay)
Name | Usage | Company |
measurement of DNA concentration and purity | Thermo Scientific | |
light induction in UV-illumination chamber | BD, Sigma | |
light induction in UV-illumination chamber | BD, Sigma | |
visualization purposes | Sarstedt | |
Gel Documentation and UV-illumination of Bl21(DE3) E. coli transformed with radiation sensing constructs | Company Name | |
ONPG Assay | Company Name |