Oligonucleotide primers used to amplify bisulfite-treated DNAa
| Amplified DNA | Primer pairb | Product size (bp) |
|---|---|---|
| 5′ LAT promoter | ULAT1 (5′ GGTTGGTTAAAAAAGGGAGGG 3′), ULAT2 (5′ CTAAAAACTTATATATAAAATCCC 3′) | 320 |
| 3′ LAT promoter | LAT1 (5′ AAAATTATATTATTTATTTAYGTGGTGTTG 3′), AT2 (5′ AACAAACRAACRAAACATTCCRAC 3′) | 271 |
| “a” sequence | Aseq1 (5′ GTGTAGAGGTGAGTAGTGTTTGTTTG 3′), Aseq2 (5′ CTCTATTAATTTCACCTATAACAACC 3′) | 125 |
| ICP4 promoter | ICP4w1 (5′ GGTTTGTTTTTGGYGGTTTYGYGTYGG 3′), ICP4w2 (5′ CCCRAACCCCRCCCCCTACCC 3′) | 360 |
↵a Primers were designed to be complementary to DNA in which all Cs have been converted to U by the bisulfite reaction. In order to prevent bias against DNA that might contain methylated Cs (and therefore be protected from the bisulfite reaction), primer-landing sites containing CpGs were avoided in the design of the primers.
↵b Y can be any C or T nucleotide, and R can be any A or G nucleotide.