Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_377 | G9-Ⅰ | Protein | POLG_HCV77 | 11.6 nM | 50 mM Tris/HCl (pH 7.8), 30 mM NaCl, 5 mM CaCl2 and 10 mM dithiothreitol | 10848986 |
Structure information of aptamer
| Aptamer Sequence: | CUUCGGGAUUUGAGGGUAGAAUGGGACUA |
| 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_377 | Description | G9-Ⅰ |
| Aptamer chemistry | RNA | Length | 29 nt |
| GC content | 48.3% | Molecular weight | 9,404.61 Da |
| Molarity of 1 μg/μl solution | 106.33 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted binding |
| Sequence | CUUCGGGAUUUGAGGGUAGAAUGGGACUA | ||
| Applications | Selected aptamers have potential as anti-HCV compounds | ||
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 | 383 |
| Target type | Protein | |
| Target unique ID | P27958 | |
| Activity | 11.6 nM | |
| Binding Conditions/Buffer | 50 mM Tris/HCl (pH 7.8), 30 mM NaCl, 5 mM CaCl2 and 10 mM dithiothreitol |
|
| Assay | Binding curves of selected RNA aptamers and DNS3. Data points were obtained by filter binding assay (50 mL reaction) as described in Materials and methods (G9-I, circle; G9-II, cross; and G9-III, square). The concentration of labeled aptamers was 5 nm |
|
| PubMed ID | 10848986 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_93 | RNA | CUCCGCUAUCUAACGUAUGAUAGAAUGGAUGACUA | |
| Apta_924 | RNA | GCCUUUUCGGGAUACGCGGAGGGUGGGCAA | |
| Apta_925 | RNA | GCUCGGCCAGGUCGCGGGUGGAUGUGAGGG | |
| Apta_237 | RNA | UUCAACGCUGUGAAGGGCUUAUACGAGCGGAUUACCC | |
| Apta_212 | RNA | AGGAAGGCUUUAGGUCUGAGAUCUCGGAAU | |
| Apta_218 | RNA | AGCCGCGAGGGGAGGGAUAGGGUAGGGCGCGGCU | |
| Apta_379 | RNA | UACGACACGAUUGGGACGUGUCUAUGGGAC | |
| Apta_633 | RNA | GGCAUCGGAAAGUGGGUUGAUGUAAGUAACAGGCGAUGCC | |
| Apta_381 | RNA | AUUCUGUUGGCGAACUGUACGCAAGUACUGGAUGACAGCCUAUCUAU | |
| Apta_51 | RNA | GCCUUAGUAACGUGCUUUGAUGUCGAUUCGACAGGAGGC | |
| Apta_95 | RNA | CCGCGACAGUCGUAAGUUUUGACUGACUGAACGUU | |
| Apta_230 | RNA | GGGAGGACGAUGCGGGCGUGAAUGGUGUUGUGAGG | |
| Apta_231 | RNA | GGGAGGACGAUGCGGGUGUGGGGCG | |
| Apta_373 | RNA | CCAUACGGGAGAGAAACU | |
| Apta_136 | RNA | CGUGUCGUCCUGGUACGAUUUGGUAUAUAACCGUGGCUUUUCGACA | |
| Apta_242 | RNA | GCUUCCAGGAAGAGAAGUGUCAUGUGAUCAGUCCUGGUGGGUGG | |
| Apta_402 | RNA | GCCUGUAAGGUGGUCGGUGUGGCGAGUGUGUUAGGAGAGAUUGC | |
| Apta_606 | RNA | CGGUUGGAUGGGUGUUGGUGGUUUGUUGAGUCCAGGCGGC | |
| Apta_98 | RNA | CGAUGCGGUCUCAUGCGUCGAGUGUGAGUUUACCUUCG | |
| Apta_647 | RNA | GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC |
DEV TOOL
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