
10
For example, a typical gel for the analysis of five experimental DNA samples
includes a total of 21 lanes:
Lanes 1-3
Experimental sample 1 with U, M and W primers
Lanes 4-6
Experimental sample 2 with U, M and W primers
Lanes 7-9
Experimental sample 3 with U, M and W primers
Lanes 10-12
Experimental sample 4 with U, M and W primers
Lanes 13-15
Experimental sample 5 with U, M and W primers
Lane 16
Chemically modified control U DNA with U primers
Lane 17
Chemically modified control M DNA with M primers
Lane 18
Untreated control W DNA with W primers
Lanes 19-21
No DNA control with U, M, and W primers
Amplification Protocol
To prevent PCR contamination, read Sec. VI.
Appendix,
Laboratory Setup and
Precautions
before beginning.
STEP 1. Modification
Prior to performing PCR with the primer sets provided in CpG WIZ
Amplification Kits, one microgram of purified DNA must undergo bisulfite
modification with the reagents contained in CpGenome DNA Modification
Kit (S7820).
STEP 2. Amplification
"Hot start" PCR is recommended for this assay (refer to Sec. III.
Protocols,
Experimental Design
). This is accomplished by several mechanisms, including a
wax barrier or anti-Taq antibody. Refer to the instructions specified by the
manufacturer of the "hot start" PCR reagents, and modify the amplification
"master mix" and reaction conditions accordingly in steps b-f, below.
a. Determine the number of assays to be run in the experiment: run three
amplification reactions for each experimental DNA sample plus six control
reactions per each set of methylation assays (refer to Sec. III.
Protocols,
Experimental Design
).
b. Prepare three (3) "master mixes" which correspond to the 3 possible primer
sets U, M and W (primer cap colors-white, red and green) by mixing all the
reagents outlined below
except
for the template DNA.