I am planning to make some mutant p53 cell lines using the CRISPR system and homologous directed repair to introduce the mutant gene. What is the best way to determine if the mutant is homozygous or heterozygous?
PCR might not discriminate if the alteration is point mutation. Isolate DNA from those cells and amplify the mutant region using PCR primers that are common to both mutant and WT p53 and sequence it. The mutant nucleotides will be half the size in intensity (peak height) and will have twin color, if it is heterozygous. If it is homozygous, the peak will be of single color for that nucleotide and will be of equal height as of adjacent nucleotides. See attached figure below.
PCR. Using primers for wt p53 and primers for the mutant one. Two different bands mean heterozygus, one band means homozygous (wt or mutant depending on the weight).
PCR might not discriminate if the alteration is point mutation. Isolate DNA from those cells and amplify the mutant region using PCR primers that are common to both mutant and WT p53 and sequence it. The mutant nucleotides will be half the size in intensity (peak height) and will have twin color, if it is heterozygous. If it is homozygous, the peak will be of single color for that nucleotide and will be of equal height as of adjacent nucleotides. See attached figure below.
In my opinion sequencing is the best option. Alternatively, if by any chance your mutation creates/destroys a restriction site you can use that as a marker (you can do PCR and then digest the amplicons).
I would also agree that sequencing is probably the method for determining whether you have a homozygous or heterozygous mutation. It would be helpful if you have a wild type non-mutant sample for comparison. A homozygous mutation would be better identified when compared to a homozygous wild type base. Heterozygous mutations are simply identified because of the double peak as Goodwin shows in the figure.
If you know the target locus for the existed mutation and the mutation create some kind of SNP (single nucleotide polymorphism because of point mutation), then you can develop specific SNAP primer for the mutated site. One pair of the primers (forward and reverse) for the reference sequence (wt) and the other pairs (forward and reverse) for the alternate sequence. If PCR product using reference primers and alternate primers are both positive, you have heterozygous genotype, if positive for reference and negative for alternate, your is homozygous for reference allele, and if negative for reference and positive for alternate, yours is homozygous for alternate allele, respectively. This SNAP can be used to investigate sequence variation at single site, when you know the sequences of the surrounding the point mutation.
1) Sequencing. It is the gold standard but you have to do PCR, digest with ExoI and Sap, PCR again with only one primer and Sanger's terminators method, precipitation with PEG, glycogen an sodium acetate and finally capillary electrophoresis.
2) Restriction Fragment Length Polymorphism (RFLP). If mutation creates/destroys a restriction site, after the first PCR you can digest with the restriction enzyme and then perform an agarose gel electrophoresis.
3) Amplification Refractory Mutation System PCR (ARMS). You can design three different primers: the first forward primer one has the last 3' base complementary to wild type base; the second forward primer has the same sequence of the first one but has the last 3' base complementary to mutation base; the third is the reverse primer. You can set up a two-tubes PCR for each sample: if you have amplification only in the first tube it is homozygous wild type; only in the second it is homozygous mutant; in both it is heterozygous.
4) Oligonucleotide Ligation Assay (OLA-PCR). After the first round of PCR, you have again 3 oligonucleotides quite similar to the primers used in the ARMS: there is a common primer that has a fluorophore at 5' and the 3' end is one base before the mutation site; then there are two interrogation primers designed on the same strand of the common primer: the first one has the first 5' base complementary to the wild type; the second one has the first 5' base complementary to mutation and it is 2 bases longer at 3'. Then there is a second round of "PCR" using the first PCR yield as template, the three oligonucleotides and the enzyme Taq Ligase. Fragments are separated by capillary electrophoresis.
5) Primer Extension or SNAPshot: again you have the PCR yield as template and then a mini-sequencing PCR is performed: there is only one primer designed with the last 3' base just before the mutation site; then only dideoxynucleotides are used and so only one base wil be added to the primers. Again fragments are runned on Capillary electrophoresis
6) fast denaturation of PCR yield and slow reanniling: in this way Homoduplex-Heteroduplex chains will be formed. These products will be separated by DHPLC.
7) TaqMan or FRET PCR and analysis of melting curves
You can try T7E1 assay for a preliminary test. Theoretically, if the mutation is homozygous, no band would be cut out. If the mutation is heterozygous, bands would be cut out.