Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 290
Aptamer sequence: CCGTAATACGACTCACTATAGGGGAGCTCGGTACCGAATTCATGTTGGTAGTTGGCTTGTGTTCGTGTGTTAAGCTTTCAGAGAGGATCCTT
Target unique ID: P0C6X7
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_281 | NG8 | Protein | R1AB_SARS | 5.4 nM | Buffer A: 50 mM Tris-HCl pH 6.8, 150 mM KCl, 20 mM imidazole, 0.05% Tween-20, 0.1% Triton X-100; Buffer B (Elution Buffer): 30 mL; 50 mM Tris-HCl pH 6.8, 150 mM KCl, 500 mM | 19031435 |
Structure information of aptamer
| Aptamer Sequence: | CCGTAATACGACTCACTATAGGGGAGCTCGGTACCGAATTCATGTTGGTAGTTGGCTTGTGTTCGTGTGTTAAGCTTTCAGAGAGGATCCTT |
| The optimal secondary structure in dot-bracket notation: | .(((...))).(((.((....(((((((.((((((((((.((.((((.....)))).)).))))).))))).))))))))).)))....... |
| The centroid secondary structure in dot-bracket notation: | .....................(((((((.((((((((((.((.((((.....)))).)).))))).))))).)))))))............. |
The MFE structure
The Centroid structure
The mountain plot representation
Aptamer information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Aptamer ID | Apta_281 | Description | NG8 |
| Aptamer chemistry | DNA | Length | 92 nt |
| GC content | 46.7% | Molecular weight | 28,730.15 Da |
| Molarity of 1 μg/μl solution | 34.81 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted therapy |
| Sequence | CCGTAATACGACTCACTATAGGGGAGCTCGGTACCGAATTCATGTTGGTAGTTGGCTTGTGTTCGTGTGTTAAGCTTTCAGAGAGGATCCTT | ||
| Applications | Inhibit SARS-CoV replication | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P0C6X7 | Protein name | Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor nsp1 (Leader protein) (Non-structural protein 1) (nsp1); Non-structural protein 2 (nsp2) (p65 homolog); Papain-like protease nsp3 (PL-PRO) (EC 3.4.19.12) (EC 3.4.22.-) (Non-structural protein 3) (nsp3) (PL2-PRO); Non-structural protein 4 (nsp4); 3C-like proteinase nsp5 (3CL-PRO) (3CLp) (EC 3.4.22.69) (Main protease) (Mpro) (Non-structural protein 5) (nsp5) (SARS coronavirus main proteinase); Non-structural protein 6 (nsp6); Non-structural protein 7 (nsp7); Non-structural protein 8 (nsp8); Non-structural protein 9 (nsp9); Non-structural protein 10 (nsp10) (Growth factor-like peptide) (GFL); RNA-directed RNA polymerase nsp12 (Pol) (RdRp) (EC 2.7.7.48) (Non-structural protein 12) (nsp12); Helicase nsp13 (Hel) (EC 3.6.4.12) (EC 3.6.4.13) (Non-structural protein 13) (nsp13); Proofreading exoribonuclease nsp14 (ExoN) (EC 2.1.1.-) (EC 3.1.13.-) (Guanine-N7 methyltransferase) (Non-structural protein 14) (nsp14); Uridylate-specific endoribonuclease nsp15 (EC 4.6.1.-) (NendoU) (Non-structural protein 15) (nsp15); 2'-O-methyltransferase nsp16 (EC 2.1.1.57) (Non-structural protein 16) (nsp16)] |
| Gene name(s) | rep 1a-1b | Organism | Replicase polyprotein 1ab (pp1ab) (ORF1ab polyprotein) [Cleaved into: Host translation inhibitor nsp1 (Leader protein) (Non-structural protein 1) (nsp1); Non-structural protein 2 (nsp2) (p65 homolog); Papain-like protease nsp3 (PL-PRO) (EC 3.4.19.12) (EC 3.4.22.-) (Non-structural protein 3) (nsp3) (PL2-PRO); Non-structural protein 4 (nsp4); 3C-like proteinase nsp5 (3CL-PRO) (3CLp) (EC 3.4.22.69) (Main protease) (Mpro) (Non-structural protein 5) (nsp5) (SARS coronavirus main proteinase); Non-structural protein 6 (nsp6); Non-structural protein 7 (nsp7); Non-structural protein 8 (nsp8); Non-structural protein 9 (nsp9); Non-structural protein 10 (nsp10) (Growth factor-like peptide) (GFL); RNA-directed RNA polymerase nsp12 (Pol) (RdRp) (EC 2.7.7.48) (Non-structural protein 12) (nsp12); Helicase nsp13 (Hel) (EC 3.6.4.12) (EC 3.6.4.13) (Non-structural protein 13) (nsp13); Proofreading exoribonuclease nsp14 (ExoN) (EC 2.1.1.-) (EC 3.1.13.-) (Guanine-N7 methyltransferase) (Non-structural protein 14) (nsp14); Uridylate-specific endoribonuclease nsp15 (EC 4.6.1.-) (NendoU) (Non-structural protein 15) (nsp15); 2'-O-methyltransferase nsp16 (EC 2.1.1.57) (Non-structural protein 16) (nsp16)] |
| Status | reviewed in uniprot database | Length | 7073 |
| Mass | 790,248 | Activity regulation | Inhibited by Remdesivir (GS-5734) |
| Involvement in disease | N/A | Catalytic activity | Reaction=a ribonucleoside 5'-triphosphate + RNA(n) = diphosphate + RNA(n+1) |
| PDB ID(s) | 1Q2W;1QZ8;1UJ1;1UK2;1UK3;1UK4;1UW7;1WOF;1YSY;1Z1I;1Z1J;2A5A;2A5I;2A5K;2ACF;2AHM;2ALV;2AMD;2AMQ;2BX3;2BX4;2C3S;2D2D;2DUC;2FAV;2FE8;2FYG;2G9T;2GA6;2GDT;2GRI;2GT7;2GT8;2GTB;2GX4;2GZ7;2GZ8;2GZ9;2H2Z;2H85;2HOB;2HSX;2IDY;2JZD;2JZE;2JZF;2K7X;2K87;2OP9;2OZK;2PWX;2Q6G;2QC2;2QCY;2QIQ;2RHB;2RNK;2V6N;2VJ1;2XYQ;2XYR;2XYV;2Z3C;2Z3D;2Z3E;2Z94;2Z9G;2Z9J;2Z9K;2Z9L;3D62;3E9S;3EBN;3R24;4TWW;4TWY;4WY3;4ZUH;5B6O;5C5N;5C5O;5C8S;5C8T;5C8U;5E6J;5F22;5N19;5N5O;5NFY;6JYT;6LNQ;6NUR;6NUS;6W79;6WCO;7LCP;7LCQ; |
 |
Function | Multifunctional protein involved in the transcription and replication of viral RNAs. |
Activity data
 |
Interaction ID | 290 |
| Target type | Protein | |
| Target unique ID | P0C6X7 | |
| Activity | 5.4 nM | |
| Binding Conditions/Buffer | Buffer A: 50 mM Tris-HCl pH 6.8, 150 mM KCl, 20 mM imidazole, 0.05% Tween-20, 0.1% Triton X-100; Buffer B (Elution Buffer): 30 mL; 50 mM Tris-HCl pH 6.8, 150 mM KCl, 500 mM |
|
| Assay | Effect of modified aptamers on the ATPase activity of SCV helicase |
|
| PubMed ID | 19031435 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_1101 | DNA | CCGTAATACGACTCACTATAGGTATGTGACGCGCGTCAATCGCTGTCCTACCAAGCTTTGCAGAGAGGATCCTT | |
| Apta_1114 | DNA | TAATACGACTCACTATAGGGAGACCCAAGCCGATTTATTTTGTGCAGCTTTTGTTCCCTTTAGTGAGGGTTAATT | |
| Apta_953 | DNA | TCACCTCATACGACTCACTATAGCGGATCCGAGCCGGGGTGTTCTGTTGGCGGGGGCGGTGGGCGGGCTGGCTCGAACAAGCTTGC | |
| Apta_1102 | DNA | TACGACTCACTATAGGGATCCGTGACTGTACGGGCTCAGTCGTTACTTGAGAGTTGAATTCCCTTTAGTGAGGGTT | |
| Apta_140 | DNA | GGCAGGAAGACAAACACGATGGGGGGGTATGATTTGATGTGGTTGTTGCATGATCGTGGTCTGTGGTGCTGT | |
| Apta_950 | DNA | CACCTAATACGACTCACTATAGCGGATCCGAAGGGGGCGCGAGGTGTAAGGGTGTGGGGTGGTGGGTGGGCCTGGCTCGAACAAGCTTGC | |
| Apta_1103 | DNA | TACGACTCACTATAGGGATCCACCTATGGCAGATTGAGCCCAAGGGCTGTGCAGCGAATTCCCTTTAGTGAGGGTT | |
| Apta_550 | DNA | GGTAATACGACTCACTATAGGGAGATACCAGCTTATTCAATTTTACAGAACAACCAACGTCGCTCCGGGTACTTCTTCATCGAGATAGTAAGTGCAATCT | |
| Apta_887 | DNA | ACGCTCGGATGCCACTACAGGGGGGTGGTCCTGAGGGTGGTGTGGTTGGTTTGGTTTCCTCATGGACGTGCTGGTGAC | |
| Apta_1104 | DNA | TACGACTCACTATAGGGATCCCCCCGAGTGAAGAGCAGGACAGCGGGACAGCGTCGAATTCCCTTTAGTGAGGGTT | |
| Apta_1105 | DNA | TACGACTCACTATAGGGATCCAATGGCACAGCGCCTGGAACGTACTCTGTACCTGGAATTCCCTTTAGTGAGGGTT | |
| Apta_1106 | DNA | TACGACTCACTATAGGGATCCTTCGCATCCGGCACGATGGCTAGGACACCCCGATGAATTCCCTTTAGTGAGGGTT | |
| Apta_78 | DNA | ATCTCGACTAGTCATAGGGGGCGCGAACATACGCGGTTGGTGTGGTTGGCTGACAATACTCGT | |
| Apta_932 | DNA | ATACGACTCACTATTAGGGATGTCCACCATATAGATCGATTTAAGTCCCTCGTTATTAATGCTAGACTACTGACTACAA | |
| Apta_951 | DNA | CACCTAATACGACTCACTATAGCGGATCCGAGGGGGTAGCGGGTGGGCCGGTGGATGCGGGGCGCCGGCGCCTGGCTCGAACAAGCTTGC | |
| Apta_1119 | DNA | GGGAATGGATCCACATCTACGAATTCGGTTGTGAAGATTGGGAGCGTCGTGGCTACTTCACTGCAGACTTGACGAAGCTT | |
| Apta_704 | DNA | GTACGAATTCACGAGGTTGCCAGCGGGGCCAGCCACTTCTGTCAGTGAATTCCTGCTCGTATATCTACTCGCCCGCCTGCGAGCATGGAGTCGGATCCTCTA | |
| Apta_127 | DNA | GGTATTGAGGGTCGCATCCACTGGTCGTTGTTGTCTGTTGTCTGTTATGTTGTTTCGTGATGGCTCTAACTCTCCTCT | |
| Apta_128 | DNA | GGTATTGAGGGTCGCATCCCGTAGTGTGTTCTTATTCGTGTCTGTGTGTGTTCTGTCGGATGGCTCTAACTCTCCTCT | |
| Apta_247 | DNA | GGCTTTACACTTTATGCTTCCGTACCAGAACATATCGAGTGATCCTGGGAGGATAACAATTTCACACAGGAAACAG |
DEV TOOL
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