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. 1999 Dec;73(12):10113–10121. doi: 10.1128/jvi.73.12.10113-10121.1999

TABLE 1.

Oligonucleotide primers used in this study

Primer namea Genomic location (nucleotides) Nucleotide sequenceb (5′ to 3′)
Strand-specific and competitive template primers
 T7.5UTR.1 1–20 TAATACGACTCACTATAGGGTTAAAACAGCCTGTGGGTTG
 T7.3UTR.7359 7341–7359 TAATACGACTCACTATAGGGGCACCGTTATCTAGTTCGG
 2C.4365*4774 4365–4387* CATACAGTTCAAGTCCAAATGCC*
4774–4798 ATCGAGGTTATCTCCATGTACAGCC
 3UTR.7359 7341–7359 GCACCGTTATCTAGTTCGG
REF primers (sense/antisense pairs)
 5UTR.1 1–20 TTAAAACAGCCTGTGGGTTG
 5UTR.603 584–603 TCAATTGTCACCATAAGCAG
 5UTR.450 450–474 CCGGCCCCTGAATGCGGCTAATCCT
 1C.2154 2134–2154 TGCGCCTGGTGGTGAGTATGC
 1C.2093 2093–2120 TGTTCTGTGGGTCTGCAATGGCCACAG
 2B.4022 3994–4022 GCCATTGGAATCCCATAATATTGGGACAC
 2A.3307 3307–3338 GGGGCTGTCTACGTAGGCAACTACAGAGTGGT
 2B.4417 4393–4417 CGTGCAAGAGACAGCATACAGGTTC
 2C.4365 4365–4387 CATACAGTTCAAGTCCAAATGCC
 3C.5552 5524–5552 CCATCCTTGTCCACCAACTCTTTAGCGTC
 3C.5479 5479–5507 CCTGGGCCAACCATCCTGATGAATGACCA
 3D.6693 6669–6693 GTTGGTTTCCTTGTGCGAGTATCCG
 3D.6693.82T-C 6669–6693 GTTGGTTTCCTCGTGCGAGTATCCGc
 3D.6255 6255–6279 CCCGTATGTCGCATTAGGTATCAAG
 Tag.3DT.C 7389–poly(A) CGATCTGAGTCATGTCACTGTTTTTTTTTTTTTTC
a

With the exception of Tag.3DT.C, virus-specific primer names include the viral gene designation and the number of the first nucleotide on the 5′ end of the primer. In primer 2C.4365*4774, the location of a deletion that was engineered into the primer is indicated (*). 

b

Primers 5UTR, 5UTR.603, 5UTR.450, 1C.2154, 2B.4022, and 2B.4417 were based on the published sequence of pNI4. All remaining primer sequences were based on sequence information obtained from CVB1T (unpublished data). The Tag sequence in primer Tag.3DT.C is a nonviral sequence appended to the 5′ end to facilitate amplification of the 3′ end of the virus and is italicized. T7 promoter sequences in T7.5UTR.1 and T7.3UTR.7359 are underlined. 

c

This primer has the same sequence as 3D.6669-93 but with a T-to-C transition at nucleotide 6682 (shown in boldtype).