CHAPTER II MATERIALS AND METHODS 2.1 Chemicals and ...

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Table 2.2: Sequences of oligonucleotide and their specific assay.
2.4 Non-denaturing gel electrophoresis
Non-denaturing gel electrophoresis was employed to separate DNA samples in
their native states. In this study, various forms of DNA structures such as duplex,
single strand, and G-quadruplexes were separated from each other when they
migrated through polyacrylamide gel. To maintain the native forms of DNA sample,
the electrophoresis was run at 4 o C and electrophoresis buffer and gel were
supplemented with KCl.
Polyacrylamide gel was prepared by mixing 40% acrylamide/bis-
acrylamide (19:1) with 5X TBE buffer, 4M KCl, and the distilled water to the desired
percentage of gel and the final concentration of 50 mM KCl in the gel. For 80 ml gel,
the gel polymerization was started by adding 1000 µl of 10% ammonium persulfate
and 35 µl of TEMED (N, N, N' , N' -tetramethylethylenediamine) before pouring to
the gel mold.
Sequences Assay
VT-66 5’- GCCTGTCCCC GCCCCCCGGG GCGGGCCGGG
GGCGGGGTCC
CTTCCCGAGC CATGCGCCAC CTCCTT -3’
P16 5’- FAM-AAGGAGGTGGCGCATG -3’
DNA polymerase
stop assay
32G4 5’- FAM-AGTATAGGGG CGGGCCGGGG GCGGGGTTAG TA -3’ Duplex/Quadruplex
32C4 5’- TACTAACCCCGCCCCCGGCCCGCCCCTATACT -3’
competition assay