Site-directed mutagenesis introduces site-specific mutations into double-stranded plasmid DNA in vitro. Mutagenesis was achieved with the QuikChange Multi Site-Directed Mutagenesis Kit (Agilent). The individually designed mutagenic oligonucleotide forward primer included one or several central mismatch base(s) with 12-20 complementary nucleotides on each adjacent site. The melting temperature Tm of the primer was calculated with the following formula, with a target melting temperature of
≥75 °C:
𝑇𝑇𝑚𝑚= 81.5 + 0.41 × (%𝐺𝐺𝐺𝐺)−675
𝑁𝑁 −% 𝑚𝑚𝑚𝑚𝑚𝑚𝑚𝑚𝑚𝑚𝑚𝑚𝑚𝑚ℎ
% GC: GC-content of primer in a whole number
% mismatch: mismatch between template and primer in percent, as a whole number N: primer length in bases
In the first step, the mutant strand was synthesized and linearly amplified by the thermostable, high fidelity Pfu polymerase during multiple rounds of denaturing, annealing, and elongation.
Reagents
Thermal Cycling Conditions
Cycles Temperature Time
1 95 °C 1 min
30 95 °C 1 min
55 °C 1 min
65 °C 2 min / kb of plasmid length
8 °C ∞
10× QuikChange Multi reaction buffer 2.5 µl
dsDNA template 100 ng
mutagenic forward primer 100 ng each
dNTP mix 1 µl
QuikChange Multi enzyme blend 1 µl
dH2O X µl to final volume of 25 µl
37 Following the generation and amplification of the mutant strand, 1 µl DPN I enzyme was added. DPN I (from diplococcus pneumoniae) is a methylation dependent restriction enzyme that degrades the template DNA, which is methylated by E. coli bacteria. The mutant strand on the other hand, which is synthesized in vitro, is not methylated and therefore not degraded. The reaction mixture was incubated for 1 h at 37 °C. The DPN I-treated DNA was now ready for transformation into XL10-Gold ultracompetent cells (3.1.3).
3.1.2 DNA Insertion, Phosphorylation, and Ligation
Insertion of new bases into a double-stranded DNA plasmid was achieved by a site-directed mutagenesis procedure (QuikChange site-directed Mutagenesis Kit). The mutagenic primers included around 20 bases on the 3' end, which were complementary to the DNA template, whereas the non-complementary bases designated for insertion were added upstream on the 5' end of the primer. The insertion was split between the forward and reverse primer. Primers were designed in a non-overlapping fashion and in back-to-back orientation. In the first step, the mutant strands were synthesized and exponentially amplified during multiple rounds of denaturing, annealing, and elongation.
Reagents
10× reaction buffer 5 µl
dsDNA template 50 ng
oligonucleotide primer for 0.3 µl (100 µmol/l) oligonucleotide primer rev 0.3 µl (100 µmol/l)
dNTP mix 1 µl
DMSO 2 µl
PfuTurbo DNA polymerase (2.5 U/μl) 1 µl
dH2O X µl to final volume of 50 µl
Thermal Cycling Conditions
Cycles Temperature Time
1 95 °C 1 min
18 95 °C 45 sec
55 °C 1 min
65 °C 21 min
8 °C ∞
Following the thermal cycling, 1 µl DPN I was added to the samples to digest the template DNA (1 h, 37 °C).
Methods
38 Phosphorylation and Ligation:
The in vitro synthesized DNA strands are linear and not phosphorylated at the 5'-OH ends. The 5'-OH ends were phosphorylated by a polynucleotide kinase (PNK).
Alternatively, it would also be possible to order primers with a 5' phosphate group.
A T4 DNA ligase was added to create circular plasmids by joining of the new 5' phosphate group with the 3'-OH group. PEG was added for increased efficiency of the ligation reaction. The reaction was incubated for 1 h at room temperature.
Reagents
polymerase product (linear plasmid) 6 µl polynucleotide kinase (PNK) 2 µl
T4 DNA ligase buffer 2 µl
T4 DNA ligase 2 µl
PEG 4000 Solution (50 %) 2 µl
dH2O 6 µl
The circular plasmids were now ready for transformation into XL1-Blue competent cells.
3.1.3 Transformation of Plasmid DNA into Bacteria
Transformation introduces foreign DNA into bacteria, a process during which competent bacterial cells take up and replicate DNA.
For the purpose of amplification, plasmids were transformed into XL1-Blue competent E. coli. The XL1-Blue cells were prepared according to the Mix & Go E. coli Transformation Kit and Buffer Set. Aliquots were stored at -80 °C. For transformation, 100 µl XL1-Blue competent E. coli were thawed on ice, mixed with 10 ng of the respective plasmid, and incubated for 20 min on ice.
Plasmids synthesized with the QuikChange Multi Site-Directed Mutagenesis Kit (Agilent) were transformed into XL10-Gold ultracompetent cells. For this, 45 µl XL10-Gold cells were thawed on ice and supplemented with 2 µl β-mercaptoethanol. Following 10 min of incubation, 1.5 µl of the DPN-I digested DNA was added and the mixture was incubated for 30 min on ice. Next, the tubes were heat-pulsed in a 42 °C water bath for 30 sec. Prior to plating, the bacteria were incubated in 500 µl NZY+ medium for 1 h at 37 °C, 220 rpm.
3.1.4 Growth and Selection of Recombinant Bacteria
For selection of successfully transformed bacteria, plasmids contained an antibiotic resistance gene. Following transformation, 100 µl of the bacteria were plated on LB agar plates, which contained 100 µg/ml Ampicillin. The plates were incubated for 16 h at 37 °C.
Since all recombinant plasmids carried the Ampicillin resistance gene, only successfully transformed bacteria could grow colonies.
39 3.1.5 Isolation of Plasmids from Bacteria
Following transformation of plasmids into competent bacteria and plating of the bacteria on LB-Ampicillin agar plates, single colonies were picked to inoculate either 3 ml (for "miniprep") or 100 ml (for "maxiprep") LB medium. The LB medium contained 100 µl of an Ampicillin stock solution. This only allowed the growth of successfully transformed bacteria. The inoculated medium was incubated for 16 h at 37 °C and 300 rpm.
The plasmid DNA was isolated from the bacteria using the centrifugation protocol of the E.Z.N.A.® Plasmid DNA Mini I Kit (for "miniprep") or the vacuum protocol of the E.Z.N.A.® FastFilter Plasmid DNA Maxi Kit (for "maxiprep").
The DNA was eluted in 50 µl (for "miniprep") or 1.2 ml dH2O (for "maxiprep").
3.1.6 Nucleid Acid Quantification
DNA concentration of plasmids was assessed by light absorbance at a wavelength of 260 nm in a Nanodrop spectrophotometer. According to the Beer-Lambert law, light absorbance is directly proportional to the concentration of a substance:
𝐴𝐴=ε× B × C or 𝐺𝐺= 𝐴𝐴
ε× B
where A is light absorbance, ε the wavelength-dependent molar extinction coefficient, B is the path length, and C is the concentration of e.g. DNA. At a wavelength of 260 nm, the molar extinction coefficient of double-stranded DNA is 50 µ𝑔𝑔×𝑐𝑐𝑚𝑚1 𝑚𝑚𝑚𝑚 .
The quotient of absorbance at 260 nm and 280 nm assesses for contamination by proteins, RNA, and phenol. Ratios around 1.8 were considered as "pure" for DNA.
3.1.7 DNA Sequencing
The recombinant DNA plasmids were sequenced by the Sanger method in the SEQLAB Laboratories (Göttingen). Samples were prepared by mixing 1200 ng of the respective plasmid, 30 pmol sequencing primer, and X µl dH2O to a final volume of 15
3.2 Cell Biological and Virological Methods