Table 1. HCV poly-U/UC RNA constructs developed for RIG-I binding and activation studies.
| RNA constructa | 5′ armb | U-core | 3′ arm |
| Con1 pU/UC | 5′GGCCAUCCUGUUUUUUUCCC(U11)C | U34 | CUCCUUUUUUUUUCCUCUUUUUUUCCUUUUCUUUCCUUU |
| JFH1 pU/UC | 5′ACUGUUCC | U43 | C(U14)CCCUCUUUCUUCCCUUCUCAUCUUAUUCUACUUUCUUUCUU |
| pU/UC C26 | 5′GGCCAUCCUGUUUUUUUCCC(U11)C | U34 | CUCCUUUUUUUUUCCUCUUUUUUUCCUUUUCUUUCCUUU(C26) |
| pU/UC 3′C26 | 5′GGCCAUCCUGUUUUUUUCCC(U11)C | U34 | CUCCUUUUUUUUUCCCCCCCCCCCCCCCCCCCCCCCCCC |
| pU/UC C67U | 5′GGCCAUCCUGUUUUUUUCCC(U11)C | U34 | UUCCUUUUUUUUUCCUCUUUUUUUCCUUUUCUUUCCUUU |
| poly-U 107 | 5′UUUUUUUUUUUUUUUUUUUU(U11)U | U34 | UUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUUU |
| Δcore | 5′GGCCAUCCUGUUUUUUUCCC(U11)C | --- | CUCCUUUUUUUUUCCUCUUUUUUUCCUUUUCUUUCCUUU |
| U8core | 5′GGCCAUCCUGUUUUUUUCCC(U11)C | U8 | CUCCUUUUUUUUUCCUCUUUUUUUCCUUUUCUUUCCUUU(C26) |
| U17core | 5′GGCCAUCCUGUUUUUUUCCC(U11)C | U17 | CUCCUUUUUUUUUCCUCUUUUUUUCCUUUUCUUUCCUUU(C17) |
| pU/UC 62 | 5′GGCCAUCCUG---------------- | U34 | CUCCUUUUUUUUUCCUCU--------------------- |
| 5′C | 5′CCCCCCCCCC---------------- | U34 | CUCCUUUUUUUUUCCUCU--------------------- |
| 3′C | 5′GGCCAUCCUG---------------- | U34 | CCCCCCCCCCCCCCCCCC--------------------- |
| poly-U 62 | 5′UUUUUUUUUU---------------- | U34 | UUUUUUUUUUUUUUUUUU--------------------- |
| poly-U 62-C | 5′UUUUUUUUUU---------------- | U34 | CUUUUUUUUUUUUUUUUU--------------------- |
| U/C1 | 5′UUCCUUCCUU---------------- | U34 | CUCCUUUUUUUUUCCUCU--------------------- |
| U/C2 | 5′UUUUUUUUUG---------------- | U34 | CUCCUUUUUUUUUCCUCU--------------------- |
| U/C3 | 5′UUUUUUUUUG---------------- | U34 | CUUUUUUUUUUUUCCUUU--------------------- |
| U/C4 | 5′GGUUUUCCUU---------------- | U34 | CUUUUUUUUUUUUUUUUU--------------------- |
| U/C5 | 5′GGCCAUCCUG---------------- | U10 | C(U10)C(U10)CUCUCCUUUUUUUUUCCUCU------- |
| U/C6 | 5′GGCCAUCCUG---------------- | U15 | C(U15)CUUCUCCUUUUUUUUUCCUCU------------ |
| U/C7 | 5′GGCCAUCCUG---------------- | U10 | CCC(U10)CCC(U8)CUCCUUUUUUUUUCCUCU------ |
| U/C8 | 5′GGCCAUCCUG---------------- | U18 | CCCCCC(U10)CUCCUUUUUUUUUCCUCU---------- |
a
The X-region RNA construct has the sequence 5′-GGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGCCGCUUGACUGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGAUCAAGU-3′. The X-region-U34 RNA construct has the sequence 5′-GGGUGGCUCCAUCUUAGCCCUAGUCACGGCUAGCUGUGAAAGGUCCGUGAGC(U34)CGCUUGACUGCAGAGAGUGCUGAUACUGGCCUCUCUGCAGAUCAAGU-3′.
b
All RNAs include a 5′-ppp and three guanine nucleotides at the 5′ end of the RNA. Dashes indicate nucleotide deletions, and underlined nucleotides show changes from the HCV Con1 poly-U/UC sequence. Long homo-polymeric nucleotide sequences are indicated in parentheses with the nucleotide designation followed by the number of nucleotides in the sequence.