TABLE 1.
Profiles of oligonucleotides for methylation assays
| Oligoduplex | Sequencea | Length (nt) | Tm (°C)b | GC (%) | Use |
|---|---|---|---|---|---|
| 1 | 5′-GGACGCTTCACCGGATGTACAGGCATGCGACGACCCCTAG-3′ | 40 | 90.2 | 62.5 | Specific methylation by M.PabI |
| 3′-CCTGCGAAGTGGCCTACATGTCCGTACGCTGCTGGGGATC-5′ | |||||
| 2 | 5′-GGACGCTTCACCGGATGCTAAGGCATGCGACGACCCCTAG-3′ | 40 | 90.2 | 62.5 | Nonspecific methylation by M.PabI |
| 3′-CCTGCGAAGTGGCCTACGATTCCGTACGCTGCTGGGGATC-5′ | |||||
| 3 | 5′-GTGAAATGGATCCAAACTG-3′ | 19 | 63.2 | 42.1 | Specific methylation by M.BamHI |
| 3′-CACTTTACCTAGGTTTGAC-5′ | |||||
| 4 | 5′-GTGAAATAGCTAAACTG-3′ | 17 | 56.3 | 35.3 | Specific methylation by M.AluI |
| 3′-CACTTTATCGATTTGAC-5′ | |||||
| 5 | 5′-GTGAAATGAATTCAACCTG-3′ | 19 | 61.1 | 36.8 | Specific methylation by M.EcoRI |
| 3′-CACTTTACTTAAGTTGGAC-5′ |
a
Underlining indicates a recognition sequence of each methyltransferase.
b
Midpoint temperatures (Tm) were calculated as 81.5 + 0.41(GC%) − 675/N, where N stands for total number of bases (4).