Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 387
Aptamer sequence: AUUCUGUUGGCGAACUGUACGCAAGUACUGGAUGACAGCCUAUCUAU
Target unique ID: P27958
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_381 | 10G-1 | Protein | POLG_HCV77 | 650 nM | 50 mM Tris/HCl (pH 7.7), 30 mM NaCl, 5 mM CaCl2, 10 mM dithiothreitol and 1% BSA Elution Buffer (200 uL of 0.4 M sodium acetate, 5 mM EDTA, and 7 M urea (pH 5.5)) | 9310370 |
Structure information of aptamer
| Aptamer Sequence: | AUUCUGUUGGCGAACUGUACGCAAGUACUGGAUGACAGCCUAUCUAU |
| 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_381 | Description | 10G-1 |
| Aptamer chemistry | RNA | Length | 47 nt |
| GC content | 44.7% | Molecular weight | 15,023.91 Da |
| Molarity of 1 μg/μl solution | 66.56 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted binding |
| Sequence | AUUCUGUUGGCGAACUGUACGCAAGUACUGGAUGACAGCCUAUCUAU | ||
| Applications | The NS3-binding region in 10G-1 can serve as a basis for designing more potential inhibitors of the NS3 protein | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P27958 | Protein name | Genome polyprotein [Cleaved into: Core protein precursor (Capsid protein C) (p23); Mature core protein (p21); Envelope glycoprotein E1 (gp32) (gp35); Envelope glycoprotein E2 (NS1) (gp68) (gp70); Viroporin p7; Protease NS2 (p23) (EC 3.4.22.-) (Non-structural protein 2) (NS2); Serine protease/helicase NS3 (EC 3.4.21.98) (EC 3.6.1.15) (EC 3.6.4.13) (Hepacivirin) (NS3 helicase) (NS3 protease) (NS3P) (Viroporin p70); Non-structural protein 4A (NS4A) (p8); Non-structural protein 4B (NS4B) (p27); Non-structural protein 5A (NS5A) (p56/58); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5B) (p68)] |
| Gene name(s) | N/A | Organism | Genome polyprotein [Cleaved into: Core protein precursor (Capsid protein C) (p23); Mature core protein (p21); Envelope glycoprotein E1 (gp32) (gp35); Envelope glycoprotein E2 (NS1) (gp68) (gp70); Viroporin p7; Protease NS2 (p23) (EC 3.4.22.-) (Non-structural protein 2) (NS2); Serine protease/helicase NS3 (EC 3.4.21.98) (EC 3.6.1.15) (EC 3.6.4.13) (Hepacivirin) (NS3 helicase) (NS3 protease) (NS3P) (Viroporin p70); Non-structural protein 4A (NS4A) (p8); Non-structural protein 4B (NS4B) (p27); Non-structural protein 5A (NS5A) (p56/58); RNA-directed RNA polymerase (EC 2.7.7.48) (NS5B) (p68)] |
| Status | reviewed in uniprot database | Length | 3011 |
| Mass | 327,146 | Activity regulation | Inhibited by the antiviral drug hexamethylene amiloride (By similarity) |
| Involvement in disease | N/A | Catalytic activity | Reaction=Hydrolysis of four peptide bonds in the viral precursor polyprotein, commonly with Asp or Glu in the P6 position, Cys or Thr in P1 and Ser or Ala in P1 |
| PDB ID(s) | 1A1R;1A1V;1CWX;1HEI;1JR6;1N1L;1ONB;1R7C;1R7D;1R7E;1R7F;1R7G;1RGQ;2A4R;2F9V;2HD0;2JXF;2KDR;2N1P;2O8M;2OBO;2OBQ;2OC0;2OC1;2OC7;2OC8;2OIN;2P59;2QV1;2XI2;2XI3;2XNI;3RC4;3RC5;4CL1;4JZN;4JZO;4MWF;4N0Y;4Q0X;4XVJ;4Z0X;5EOC;5ERW;5FGB;5FGC;5JZI;5YXN;5YXU;6BQJ;6BQK;6BZU;6BZV;6BZW;6BZY;6UYD;6WO5;6WOQ; |
 |
Function | Packages viral RNA to form a viral nucleocapsid, and promotes virion budding (Probable). |
Activity data
 |
Interaction ID | 387 |
| Target type | Protein | |
| Target unique ID | P27958 | |
| Activity | 650 nM | |
| Binding Conditions/Buffer | 50 mM Tris/HCl (pH 7.7), 30 mM NaCl, 5 mM CaCl2, 10 mM dithiothreitol and 1% BSA Elution Buffer (200 uL of 0.4 M sodium acetate, 5 mM EDTA, and 7 M urea (pH 5.5)) |
|
| Assay | The binding of 10G-1 to NS3. Labeled 10G-1 was mixed with different amounts of NS3 and the RNA . protein complexes were separated on filters. The radioactivity retained on the filter was divided by the total number of counts in the reaction mixture. This ratio was plotted against the concentration of NS3 in the mixture |
|
| PubMed ID | 9310370 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_270 | RNA | CUGUCGAACAUGCUGAGGGUAACGUACUGGCAAGCUCACCUCAGCGUAGCUAa | |
| Apta_93 | RNA | CUCCGCUAUCUAACGUAUGAUAGAAUGGAUGACUA | |
| Apta_520 | RNA | GGGAGAUCUACGGAUCUCAGGGCUCUUACGGGAGCUACAUGGAAGGAGUCCAUGUGU | |
| Apta_92 | RNA | ACAACUUAAUGCGACGUUGGUAAAGCAUAUCAAAC | |
| Apta_95 | RNA | CCGCGACAGUCGUAAGUUUUGACUGACUGAACGUU | |
| Apta_97 | RNA | UUGUCGUCUUCUCCAGUUAGUCAACGAACUUGUGU | |
| Apta_374 | RNA | GUCCCGUGCGCAAAAGUUCUUAGCGCUAGCAGUCCUAGUUGC | |
| Apta_521 | RNA | GGGUUGGGAAGAAACUGUGGCACUUCGGUGCCAGCAACCC | |
| Apta_575 | RNA | AGAGCUUGACGGUCCCGAGAGUCGAGCCCAAGCUGACACUGGACCUUUGCGGACCACGUGUUGAUCGUCG | |
| Apta_599 | RNA | GUCUCUGUGUGCGCCAGAGAACACUGGGGCAGAUAUGGGCCAGCACAGAAUGAGGCCC | |
| Apta_599 | RNA | GUCUCUGUGUGCGCCAGAGAACACUGGGGCAGAUAUGGGCCAGCACAGAAUGAGGCCC | |
| Apta_153 | RNA | CCACAGUUCAGAGGCACCGCGAACAAAACGCAAGACAGAGUGCCGACAAGAAC | |
| Apta_271 | RNA | CUGUCGAGCAUGCUCAGGGUAACGUAUAGUCAAGACACCUCAAGUGUAACU | |
| Apta_1143 | RNA | ACGAGUUGUCGCAUGUGCGGUUCAGUCUGGUCCUUCAGCACCGUACAACAA | |
| Apta_87 | RNA | UACCGACUAGCAAAACCUGCUGGCGACGUUUAGAU | |
| Apta_96 | RNA | UCGCUAAUUAUAGGCGGAGUGCGACGUUAUAAAUA | |
| Apta_237 | RNA | UUCAACGCUGUGAAGGGCUUAUACGAGCGGAUUACCC | |
| Apta_370 | RNA | GGGAGGACGCGUCGCCGUAAUGGAUGUUUUGCUCCCUG | |
| Apta_377 | RNA | CUUCGGGAUUUGAGGGUAGAAUGGGACUA | |
| Apta_634 | RNA | GGUCUUACGUCGUUCGCGACUAUUGGGAGACC |
DEV TOOL
 |
 |
 |
 |