TABLE 1.
Names, annealing sites, and sequences of primers used in this study
| Primer type and namea | Genomic locationb strand | Nucleotide sequence (5′ to 3′)c |
|---|---|---|
| CVB3-specific primers | ||
| 3END | 7399-7377, − | CGCACCGAATGCGGAGAATTTAC |
| 5PUFF | 1235-1254, + | ATGCAGTACCACTACTTAGG |
| 998 | 1021-998, − | CGTTATGGTGGAGTTACCTAATGT |
| E1 | 644-627, − | CACCGGATGGCCAATCCA |
| E2 | 450-464, + | TCCGGCCCCTGAATG |
| E3 | 563-537, − | ACACGGACACCCAAAGTAGTCGGTTCC |
| E3REV | 537-562, + | GGAACCGACTACTTTGGGTGTCCGTG |
| E7 | 139-118, − | TGACTGTTGATCGGTGTGTGTT |
| E8 | 63-82, + | ACGGTACCTTTGTGCGCCTG |
| ID9 | 3201-3220, + | CTAGACTCTGCCAATACGAG |
| KS1 | 692-668, − | GCTAAGTGGTATAAACCCAACAAAG |
| KS2 | 303-325, + | CCCCAGTGTAGATCAGGTCGATG |
| PE62 | 82-63, − | CAGGCGCACAAAGTACCGT |
| PE108 | 128-109, − | CGGTGTGTGTTACTTCTAAG |
| PE127 | 403-383, − | GAGCGTCCCATGGGTTTCCCC |
| PE128 | 484-464, − | TCCGCAGTTAGGATTAGCCGC |
| PE129 | 261-241, − | AGGTTTTTCGAAGTAGTTGGC |
| PE130 | 578-558, − | TAGGAATAAAATGAAACACGG |
| PE162 | 182-163, − | GGTAACAGAAGTGCTTGATC |
| PE227 | 244-228, − | TGGGCCGGATAACGAACG |
| PE351 | 371-352, − | GCCAACGCAGCCACCGCCAC |
| PE627 | 647-628, − | AGTCACCGGATGGCCAATCC |
| RN | 5528-5509, − | CACCAACCTCTTGATCATTC |
| S | 1-20, + | TTAAAACAGCCTGTGGGTTG |
| S1 | 1-28, + | TTAAAACAGCCTGTGGGTTGATCCCACC |
| S2 | 21-49, + | ATCCCACCCACAGGGCCCATTGGGCGCTA |
| S3 | 33-61, + | GGGCCCATTGGGCGCTAGCACTCTGGTAT |
| S4 | 45-74, + | CGCTAGCACTCTGGTATCACGGTACCTTTG |
| Primers for cloning | ||
| DC-TAIL | AATCGATCTGTCGACCCCCCCCCC | |
| 5CMV | GGGAATATTCTGCTTCGCGATGTACGGGCCAGAT | |
| 3CMV | AAAGCGGCCGCCGCGGAATTTCGATAAGCCAGTAAGCAGTG | |
| 28RIBOZ1 | 1-20, + | ATGAGGCCGAAAGGCCGAAAACCCGGTATCCCGGGTTCTTAAAACAGCCTGTGGGTTG |
| 28RIBOZ2 | GACACTGATCCGCGGGTGTTTTAACTGATGAGGCCGAAAGGCCGAAAACCCGGTATC | |
| 28RIBOZPCR | CCACTAGTTCTAGACACTGATCCGCGGG | |
| S2TD8 | 8-36, + | ATAACCGCGGAGCCTGTGGGTTGATCCCACCCATAGGGC |
| S2TD13 | 13-41, + | ATAACCGCGGTGGGTTGATCCCACCCATAGGCGGCCATT |
| S2TD18 | 18-45, + | ATAACCGCGGTTGATCCCACCCATAGGGCCCATTGGGC |
| S2TD31 | 31-57, + | ATAACCGCGGTAGGGCCCATTGGGCGCTAGCACTCTG |
| S2TD50 | 50-76, + | ATAACCGCGGCACTCTGGTATCACGGTACCTTTGTG |
| TD8RIBOZ1 | 8-23, + | ATGAGGCCGAAAGGCCGAAAACCCGGTATCCCGGGTTCAGCCTGTGGGTTGATCCACCC |
| TD8RIBOZ2 | GACACTGATCCGCGGGCACAGGCTCTGATGAGGCCGAAAGGCCGAAAACCCGGTATC | |
| TD50RIBOZ1 | 50-69, + | ATGAGGCCGAAAGGCCGAAAACCCGGTATCCCGGGTTCGCACTCTGGTATCACGGTAC |
| TD50RIBOZ2 | GACACTGATCCGCGGGCAGAGTGCCTGATGAGGCCGAAAGGCCGAAAACCCGGTATC | |
| Primers for amplification of GADPH | ||
| 5-GAPDH | AGGTGAAGGTCGGAGTCAACG | |
| 3-GAPDH | GGTGAAGACGCCAGTGGACTC |
a
With the exception of DC-Tail, 5CMV, 3CMV, 28RIBOZPCR, and 5- and 3-GADPH, sequences of primers are based on the CVB3/28 genome (GenBank accession no. AY752944).
b
Nucleotide position numbering is as for CVB3/28 (Genbank accession no. AY752944). Positive is same sense as genomic RNA, negative is antisense to genomic RNA.
c
Underlined sequences are not genomic cDNA.