. 2006 Sep 13;80(22):11343–11354. doi: 10.1128/JVI.02072-05

TABLE 1.

Oligonucleotides used for PCR-based mutagenesis

Oligonucleotide no.	Position (nt) (sense)^f	Sequence (5′ to 3′)	Construct
1	8717-8739 (+)^a^,^d	`G CAC GAT GCA TCT GGC AAA AGG G`
2	9588-9617 (−)^a^,^d^,^e	`TGC ACT AGT AGT ACT TGA TCT GCA GAG AGG`
3	9348-9380 (+)^a^,^c	`GC ATC TAT CTA GCC CCC AAC CGA TGA ACG GGG`	pMT(L588A)
4	9348-9380 (−)^a^,^c	`CCC CGT TCA TCG GTT GGG GGC TAG ATA GAT GCC`	pMT(L588A)
5	9348-9380 (+)^a^,^c	`GGC ATC TAT CTA CTC GCC AAC CGA TGA ACG GGG`	pMT(P589A)
6	9348-9380 (−)^a^,^c	`CCC CGT TCA TCG GTT GGC GGC TAG ATA GAT GCC`	pMT(P589A)
7	9351-9383 (+)^a^,^c	`ATC TAT CTA CTC CCC AAC GCA TGA ACG GGG AGC`	pMT(R591A)
8	9348-9380 (−)^a^,^c	`GCT CCC CGT TCA TGC GTT GGG GAG TAG ATA GAT`	pMT(R591A)
9	9363-9380 (+)^a^,^b	`GCCAAGCTTC GCC GCA GTG GCT GGA GTT GTC CCC AAC CGA TGA ACG GGG`	pMT(3A-I)
10	9294-9314 (−)^a^,^b^,^d	`GCCAAGCTTGT CAC CGC TTG TAG AAT TGT CAT GGA CCA GCG GGG TCG GGC ACG`	pMT(3A-I)
11	5297-5328 (+)^b	`CTA CAA GCG GTG ACA ACC TTC GCC GCA GTG GC`	pMT(3A-I/S68T)
12	5297-5328 (−)^b	`GC CAC TGC GGC GAA GGT TGT CAC CGC TTG TAG`	pMT(3A-I/S68T)
13	5288-5308 (+)^b	`CGC GCG ATG ACA ATT CTA CAA GCG GTG`	pMT(3A-II)
14	9294-9308 (−)^a^,^b	`G AAT TGT CAT CGC GCG GGG TCG GGC ACG`	pMT(3A-II)
15	9372-9390 (+)^a^,^b	`TAT GTC ATG TAT AAA TGA ACGGGGAGCTAAACAC`	pMT(3A-II)
16	5321-5353 (−)^b	`CA TTT ATA CAT GAC ATA GAC AAC TCC AGC CAC TGC`	pMT(3A-II)
17	5297-5327 (+)^b^,^c	`CTA CAA GCG GTG AAA AAG TTC GCC GCA GTG G`	pMT(3A/TT-KK)
18	5297-5331 (−)^b^,^c	`CC AGC CAC TGC GGC GAA CTT TTT CAC CGC TTG TAG`	pMT(3A/TT-KK)
19	7602-7621 (+)^a^,^d	`GGCGGATCC ATG TCT TAT TCC TGG ACA GG`
20	9348-9371 (−)^a^,^d	`GGCTCTAGA CTA TCA TCG GTT GGG GAG TAG ATA GAT`	pcDNA(NS5B/WT)
21	9282-9308 (−)^a^,^d	`GGCTCTAGA CTA TCA GCG GGG TCG GGC ACG AGA CAG GCT GTG`	pcDNA(NS5B/CΔ21)
22	5328-5353 (−)^b^,^d	`GGCTCTAGA CTA TCA TTT ATA CAT GAC ATA GAC AAC TCC AGC`	pcDNA(NS5B/3A-II)
23	5321-5353 (−)^b^,^d	`GGCTCTAGA CTA TCA TTT ATA CAT GAC AAC TCC AGC CAC TGC`	pcDNA(NS5B/3A-III)
24	5321-5338 (−)^b^,^d	`GGCTCTAGA CTA TCA TCG GTT GGG GAC AAC TCC AGC CAC TGC`	pcDNA(NS5B/3A-IV)
25	9348-9371 (−)^a^,^d	`GGCTCTAGA CTA TCA TGC GTT GGG GAG TAG ATA GAT`	pcDNA(NS5B/R591A)

Nucleotide positions refer to the HCV subtype 1b sequence (NCBI accession no. AJ238799).

Nucleotide sequences belonging to poliovirus 3A protein are underlined. Nucleotide positions of the poliovirus 3A sequence refer to the poliovirus 1 Mahoney sequence (NCBI accession no. NC002058).

The oligonucleotide contains nucleotide changes, which are in bold.

The oligonucleotide contains an enzyme recognition site, which is shown in italics.

Nucleotide positions after 9605 represent the nucleotide sequence of the vector (pBR322).

+, positive sense; −, negative sense.