IAN G. GOODFELLOW; DAVID KERRIGAN; DAVID J. EVANS

TABLE 1.

Oligonucleotides used during this study

Name	Oligonucleotide sequence	Notes
^aThe poliovirus genome-sense strand only is shown. In the case of oligonucleotide pairs, designed for insertion into either the replicon-based cassette region or the 5′ NCR hypervariable region, the complementary oligonucleotide sequence is indicated for clarity.
^bThe double underlined C nucleotide is identical to the mut7 mutation defined in (Rieder et al. 2000).
^cThe double underline G nucleotide replaces a T, which would have introduced a termination codon to the sequence. The complementary base pairing is retained.
^dInsertions into the hypervariable region include the underlined initiation codon for the polyprotein. The double underlined nucleotides were exchanged from the native sequence to avoid introducing an initiation condon (see Fig. 1A).
^eT7 transcripts were generated from antisense templates containing a 3′ extension complementary to the T7 promoter oligonucleotide IG73. The sequence complementary to the template oligonucleotide is shown, excluding the T7 promoter region. See text and Figure 1 for a description of variations from the native sequence that are indicated with double underlining.
^fT7 promoter oligonucleotide. In certain cases an additional A nucleotide (complementary to a T included in the antisense partner oligonucleotide) was included at the 3′ end to increase T7 promoter activity and yield.
Cassette Vector oligonucleotides
WT	CGCGCCATTAATAATTACATACAGTTCAAGAGCAACACCGTATTGAGCCAGTATGTTTGTTAGTG	^a
SL3	CGCGCCATTAATAATTATATCCAATTTAAATCCAAACACCGTATCGAGCCAGTATGTTTGTTAGTG
Clal	CGCGCCATTAATAATTACATACAATCGATGAGCAAACACCGTAATCGATCAGTATGTTTGTTAGTG
Synth2	CGCGCCCGGGTAAGAGCAAACACCGTATTACCCGGG
Synth2^mut7	CGCGCCCGGGTAAGAGC $\text{[math]}$ AACACCGTATTACCCGGG	^b
Synth3	CGCGTCCGGGTAAGAGCAAACACCGTATTACCCGGG
Synth4	CGCGTTCGGGTAAGAGCAAACACCGTATTACCCGGG
Synth5	CGCGTTTGGGTAAGAGCAAACACCGTATTACCCGGG
Inv1	CGCGCGTG $\text{[math]}$ TTGTTTTACATACAGTTCAAGAGCAAACACCGTATTGAGCCAGTATGTAATAATTAC	^c
Inv3	CGCGCCATTAATAATTACATACACGAGTTGAGCAAACACCGTAAACTTGCAGTATGTTTGTTAGTG

Oligonucleotides for insertion into the 5′ NCR
WT^AUG	GATCATTAATAATTACA $\text{[math]}$ ACAGTTCAAGAGCAAACACCGTATTGAGCCAGTATGT $\text{[math]}$ TGTTAGTGATGGGAGCT	^d
Synth2	GATCCCGGGTAAGAGCAAACACCGTATTACCCGGGATGCGAGCT
Synth6	GATCCCGGTATCAAACACCGATACCGGGATGGGAGCT

Oligonucleotides used to generate T7 transcripts		^e
Synth2	CCCGGGTAAGAGCAAACACCGTATTACCCGGG
Synth2^mut7	CCCGGGTAAGAGC $\text{[math]}$ AACACCGTATTACCCGGG
Synth3	TCCGGGTAAGAGCAAACACCGTATTACCCGGG
Synth4	TTCGGGTAAGAGCAAACACCGTATTACCCGGG
Synth5	TTTGGGTAAGAGCAAACACCGTATTACCCGGG
C₂₈U	CATTAATAATTACATACAGTTCAAGAG $\text{[math]}$ AAACACCGTATTGAGCCAGTATGTTTGTTAGTG
Mut7 (A₂₉C)	CATTAATAATTACATACAGTTCAAGAGC $\text{[math]}$ AACACCGTATTGAGCCAGTATGTTTGTTAGTG
Mut6 (A₃₀C)	CATTAATAATTACATACAGTTCAAGAGCA $\text{[math]}$ ACACCGTATTGAGCCAGTATGTTTGTTAGTG
Mut2 (A₃₁G)	CATTAATAATTACATACAGTTCAAGAGCAA $\text{[math]}$ CACCGTATTGAGCCAGTATGTTTGTTAGTG
G₁₉A/C₂₂U	CATTAATAATTACATACA $\text{[math]}$ TT $\text{[math]}$ AAGAGCAAACACCGTATTGAGCCAGTATGTTTGTTAGTG
G₁₉A/C₂₂U/U₄₀C	CATTAATAATTACATACA $\text{[math]}$ TT $\text{[math]}$ AAGAGCAAACACCGTAT $\text{[math]}$ GAGCCAGTATGTTTGTTAGTG

Miscellaneous oligonucleotides
IG73	TAATACGACTCACTATAGGG (A)	^f

Structure and function analysis of the poliovirus cis-acting replication element (CRE)

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