Sequence composition and target localization within the human CD40 mRNA of the siRNAs (siRNA-1 through siRNA-8) designed to screen for effective CD40 gene silencing
siRNA anti-hCD40 . | hDC40 mRNA targeted region* . | Sequence . |
|---|---|---|
| siRNA-1 | 173-193 | 5′-UGCCUUCCUUGCGGUGAAAUU-3′ |
| 3′-UUACGGAAGGAACGCCACUUU-5′ | ||
| siRNA-2 | 192-212 | 5′-GCGAAUUCCUAGACACCUGUU-3′ |
| 3′-UUCGCUUAAGGAUCUGUGGAC-5′ | ||
| siRNA-3 | 479-499 | 5′-UGUCACCCUUGGACAAGCUUU-3′ |
| 3′-UUACAGUGGGAACCUGUUCGU-5′ | ||
| siRNA-4 | 709-729 | 5′-UUUUCCCGACGAUCUUCCUUU-3′ |
| 3′-UUAAAAGGGCUGCUAGAAGGA-5′ | ||
| siRNA-5 | 62-82 | 5′-CCACCCACUGCAUGCAGAGUU-3′ |
| 3′-UUGGUGGGUGACGUACGUCUC-3′ | ||
| siRNA-6 | 137-157 | 5′-CUGGUGAGUGACUGCACAGUU-3′ |
| 3′-UUGACCACUCACUGACGUGUC-5′ | ||
| siRNA-7 | 214-234 | 5′-CAGAGAGACACACUGCCACUU-3′ |
| 3′-UUGUCUCUCUGUGUGACGGUG-5′ | ||
| siRNA-8 | 242-262 | 5′-UACUGCGACCCCAACCUAGUU-3′ |
| 3′-UUAUGACGCUGGGGUUGGAUC-5′ | ||
| msiRNA-2 | 192-212 | 5′-GCGAAUUCGAUCUCACCUGUU-3′ |
| 3′-UUCGCUUAAGCUAGAGUGGAC-5′ | ||
| siRNA-C | - | 5′-ACUACAAGACUCGUGACCAUU-3′ |
| 3′-UUUGAUGUUCUGAGCACUGGU-5′ |
siRNA anti-hCD40 . | hDC40 mRNA targeted region* . | Sequence . |
|---|---|---|
| siRNA-1 | 173-193 | 5′-UGCCUUCCUUGCGGUGAAAUU-3′ |
| 3′-UUACGGAAGGAACGCCACUUU-5′ | ||
| siRNA-2 | 192-212 | 5′-GCGAAUUCCUAGACACCUGUU-3′ |
| 3′-UUCGCUUAAGGAUCUGUGGAC-5′ | ||
| siRNA-3 | 479-499 | 5′-UGUCACCCUUGGACAAGCUUU-3′ |
| 3′-UUACAGUGGGAACCUGUUCGU-5′ | ||
| siRNA-4 | 709-729 | 5′-UUUUCCCGACGAUCUUCCUUU-3′ |
| 3′-UUAAAAGGGCUGCUAGAAGGA-5′ | ||
| siRNA-5 | 62-82 | 5′-CCACCCACUGCAUGCAGAGUU-3′ |
| 3′-UUGGUGGGUGACGUACGUCUC-3′ | ||
| siRNA-6 | 137-157 | 5′-CUGGUGAGUGACUGCACAGUU-3′ |
| 3′-UUGACCACUCACUGACGUGUC-5′ | ||
| siRNA-7 | 214-234 | 5′-CAGAGAGACACACUGCCACUU-3′ |
| 3′-UUGUCUCUCUGUGUGACGGUG-5′ | ||
| siRNA-8 | 242-262 | 5′-UACUGCGACCCCAACCUAGUU-3′ |
| 3′-UUAUGACGCUGGGGUUGGAUC-5′ | ||
| msiRNA-2 | 192-212 | 5′-GCGAAUUCGAUCUCACCUGUU-3′ |
| 3′-UUCGCUUAAGCUAGAGUGGAC-5′ | ||
| siRNA-C | - | 5′-ACUACAAGACUCGUGACCAUU-3′ |
| 3′-UUUGAUGUUCUGAGCACUGGU-5′ |
Selected sequences were of the type AA(N19)UU (N, any nucleotide) and were submitted to a basic local alignment search tool (BLAST)15 search against the human genome sequence to ensure gene specificity. The siRNA-C, with a scrambled sequence, was used as control for the initial screening on ECV-304 cells. The mismatched siRNA-2 (msiRNA-2), whose sequence was identical to that siRNA-2 except for the underlined 5-nt mismatch mutated by transversion, was used as control in the endothelial cell assays. The 21 nucleotide RNA sequences displayed in each row are arranged by complementary homology yielding the corresponding siRNA duplexes, with 2 unpaired uridine nucleotides at the 3′ end of each strand.
indicates absence of homology with respect to the hCD40 mRNA sequence
Numbers indicate the position of the targeted region within the hCD40 mRNA sequence from ATG initiation codon