TABLE 1.
Primers used for PCR and hybridizationa
| Name | Location | Sequence |
|---|---|---|
| miRNA probe oligonucleotides | ||
| BART3-3p | 139145L | ACACCTGGTGACTAGTGGTGCG |
| BART4 | 139249L | AGCACACCAGCAGCATCAGGTC |
| BART1-3p | 139409L | AGACATAGTGGATAGCGGTGCTA |
| BART5 | 139698L | CGATGGGCAGCTATATTCACCTT |
| BART6 | 140093L | TCTAAGGCTAGTCCGATCCCCG |
| BART18 | 145984L | CTGTATAGGAAGTGCGAACTTG |
| BART7 | 146496L | CCCTGGACACTGGACTATGAT |
| BART8 | 146793L | CTGTACAATCTAGGAAACCGT |
| BART9 | 147018L | CTACGGGACCCATGAAGTGTTA |
| BART10 | 147378L | ACAGCCAACTCCATGGTTATGT |
| BART12 | 147958L | AAACCACACCAAACACCACAGGA |
| BART13 | 149585L | TCAGCCGTCCCTGGCAAGTTAC |
| BART14 | 148765L | TGTAAATCGGCAGCGTAGGGTA |
| Promoter usage | ||
| P2 (DH) | 138203R | CACAGCAGCACAATAGAAGCAC |
| P2 | 138081R | CTCGATCCGAGAGACCGACT |
| P1 | 138356R | GCCATTTTTCAAGCTGCTAAACC |
| BART RT primers | ||
| 1R | 138356R | Same as P1 |
| 1aL | 139513L | CGGCACAGATTAGAAGATGA |
| 1bR | 140641R | CTACCTGCCCCTCTAATCTG |
| 1bL | 140625L | TTCTAGAAACACGTGTCCCG |
| 2R | 146302R | GCTGATAAGTGCTGCGTCCACT |
| 2L | 146268L | CGTCCAAATTCAGCTCA |
| 3L | 149659L | ATTCCCGGGGAAGGTGTGTC |
| BamHI A sequencing primers | ||
| 138356R | Same as P1 | |
| 138895R | CGGAATATGCAAGTGCATCTT | |
| 139001R | CTATAGGTCCTACCGGAGCT | |
| 139566R | TTTCCTTGATAGAGACACAA | |
| 139711L | TCCAGCGATACGTCGATGGG | |
| 140216L | TAGTGAGCCAGGCTTTCTAT | |
| 140764L | TGGGTCCTGAGACCCAAAGGGACAG | |
| 145931R | ATTGTTGCCGTTGAAAGACG | |
| 146161R | TTTTTTGCAAATTGGCCTTA | |
| 146302R | Same as 2R | |
| 146552L | CGTACTGGCCACACTAAACA | |
| 147281R | AGACAGGCGGCGCATTGGAA | |
| 147378L | ACAGCCAACTCCATGGTTATGT | |
| 148881L | AGCAGTCGCATGGCGGGAGTAT | |
| 149659L | Same as 3L | |
| Other oligonucleotides for probes | ||
| U6 | ATATGGAACGCTTCACGAATT | |
| Ex3 | 149659L | ATTCCCGGGGAAGGTGTGTC |
| Ex1 | 138419L | TCCATGTTGCTGAGGAGCTT |
| Primers for 5′ RACE | ||
| a | 146420L | CATGGTCCAAGTAGGTCACC |
| b | 146394L | CTACTGCCTTATGCAGCCCACCAA |
| dT-adapter | GACTCGAGTCGACATCGAT(17) | |
| Adapter | GACTCGAGTCGACATCG | |
| Primers for cloning pre-miRNAs | ||
| BART3 | 139076R-E | ATCACGAGGAATTCCCTTTGGTGGAAC |
| 139154L-H3 | ATCACGAGAAGCTTCCTCCGGTGACAC | |
| BART1 | 139340R-E | ATCACGAGGAATTCCCCGTGGGGGGTCTTAG |
| 139417L-H3 | ATCACGAGAAGCTTCCCGGGCGAGACATAG | |
| BART6 | 140016R-E | ATCACGAGGAATTCTGACCTTGTTGGTAC |
| 140107L-H3 | ATCACGAGAAGCTTTGGCCTTGAGTTAC | |
| BART18 | 145942R-E | ATCACGAGGAATTCTGAAAGACGGGTG |
| 146040L-H3 | ATCACGAGAAGCTTCGACATTATCGAG | |
| BART7 | 146425R-E | ATCACGAGGAATTCTCCAGTGTCCTGATC |
| 146510L-H3 | ATCACGAGAAGCTTTCCGAGTGCACTGTC | |
| BART14 | 148731R-E | ATCACGAGGAATTCCAGGGGTGGCCGGTAC |
| 148815L-H3 | ATCACGAGAAGCTTCAGGTCGCGCGTCCAG | |
| Primers for cloning introns | ||
| 1-1a | 138501R-E | ATCACGAGGAATTCGGATCAGGGTATGTAAAC |
| 138931L-H3 | ATCACGAGAAGCTTGCCCCTACTGGTTAGAAAG | |
| 1a-1b | 140198R-E | ATCACGAGGAATTCTAGAAAGCCTGGCTCACTAT |
| 140527L-H3 | ATCACGAGAAGCTTCACTGCCATAAGTCCTCATG | |
| 1b-2 | 145320R-E | ATCACGAGGAATTCAGTATCCAGTTCTAGAAG |
| 146000L-H3 | ATCACGAGAAGCTTATACAAGGCTTTAACACT | |
| 2-3 | 148819R-E | ATCACGAGGAATTCCTCTTCGGAAACGCCAAC |
| 149550L-H3 | ATCACGAGAAGCTTGTGGGCATGACCCTATTG | |
| Primers for cloning exons | ||
| 1 | 138361R-E | ATCACGAGGAATTCTTTTCAAGCTGCTAAACCAC |
| 138479L-H3 | ATCACGAGAAGCTTTCACATGAAGAGGCTAGTGC | |
| 1a | 139454R-E | ATCACGAGGAATTCCCCACCGAACCAGGCATGAT |
| 139535L-H3 | ATCACGAGAAGCTTGGTGGTCATGTTTCCCTCCA | |
| 1b | 140565R-E | ATCACGAGGAATTCTTCTATCAGAATAACAGGGG |
| 140664L-H3 | ATCACGAGAAGCTTCATACAGATTAGAGGGGCAG | |
| 2 | 146233R-E | ATCACGAGGAATTCATGCCGTTGAACGTGTCACT |
| 146310L-H3 | ATCACGAGAAGCTTCTTATCAGCGCTGGAGGCAC | |
| 3a | 149591R-E | ATCACGAGGAATTCTCCACGGAGACTCGGACGTA |
| 149696L-H3 | ATCACGAGAAGCTTCGCCCCCATTTCTAAAGTCA | |
| 3b | 149914R-E | ATCACGGAGAATTCTATGAACAGGCTGCGCGGAT |
| 150050L-H3 | ATCACGAGAAGCTTACGGCAGCCGCTACTTTACG | |
| 4 | 150261R-E | ATCACGAGGAATTCTCCTGAACGACGAG |
| 150340L-H3 | ATCACGAGAAGCTTTCGACGAGCTCCG | |
| 5a | 155278R-E | ATCACGAGGAATTCCAGCAGGATGCGC |
| 155335L-H3 | ATCACGAGAAGCTTATCCTGCGTCCTC | |
| 5b | 156528R-E | ATCACGAGGAATTCGGCATGTTGCTGAGCGAGCT |
| 156709L-H3 | ATCACGAGAAGCTTGCAGCCTGGTCTCTGGTTTC | |
| 6 | 156865R-E | ATCACGAGGAATTCTGGAAGTTGTACTC |
| 156913L-H3 | ATCACGAGAAGCTTCCTCCAACGTCTTTG | |
| 7a | 158629R-E | ATCACGAGGAATTCTCCGTGTGATTCTCCCGCGT |
| 158726L-H3 | ATCACGAGAAGCTTCCTTTCCGAGTCTGCGAGCT | |
| 7b | 159800R-E | ATCACGAGGAATTCTGCGCCGTGAAGG |
| 160192L-H3 | ATCACGAGAAGCTTCAGAGGAGGGCGC | |
| Primers for cloning BART cDNAs | ||
| 138353R | GTTGCCATTTTTCAAGCTGCTAAACCACGAGTGG | |
| 160086L | CTCTCGGAGCTCCTCTATTGGAACTCTGGC |
a
Primers are numbered at the 5′ end according to the EBV genome sequence AJ507799 and extend in the direction indicated (R, rightward; L, leftward). The EBV-specific nucleotides are shown in boldface in the primers containing restriction sites.