Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 386
Aptamer sequence: GGGAUGCUUCGGCAUCCCCGAAGCCGCUAUGGACCAGUGGCGCGGCUUCGGCCCGACGGAGUGGUACCGCUUCGGCGGUACGUAAGCUUGGG
Target unique ID: P27958
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_380 | B.2 | Protein | POLG_HCV77 | 1.5 nM | 20 mM Tris-HCl (pH 7.0), 1 mM dithiothreitol (DTT), 0.25 U/ul RNasin, 100 ng/ul BSA, 250 mM NaCl, 0.03% n-octyl-B-D-glucopyranoside, 5 mM MgCl2, and 2.0% glycerol | 11907208 |
Structure information of aptamer
| Aptamer Sequence: | GGGAUGCUUCGGCAUCCCCGAAGCCGCUAUGGACCAGUGGCGCGGCUUCGGCCCGACGGAGUGGUACCGCUUCGGCGGUACGUAAGCUUGGG |
| 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_380 | Description | B.2 |
| Aptamer chemistry | RNA | Length | 92 nt |
| GC content | 67.4% | Molecular weight | 29,744.63 Da |
| Molarity of 1 μg/μl solution | 33.62 μM | Number of G-quadruplexes | 2 |
| G-Score | 19 | Function | Targeted binding |
| Sequence | GGGAUGCUUCGGCAUCCCCGAAGCCGCUAUGGACCAGUGGCGCGGCUUCGGCCCGACGGAGUGGUACCGCUUCGGCGGUACGUAAGCUUGGG | ||
| Applications | Binding to nonstructural 5B | ||
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 | 386 |
| Target type | Protein | |
| Target unique ID | P27958 | |
| Activity | 1.5 nM | |
| Binding Conditions/Buffer | 20 mM Tris-HCl (pH 7.0), 1 mM dithiothreitol (DTT), 0.25 U/ul RNasin, 100 ng/ul BSA, 250 mM NaCl, 0.03% n-octyl-B-D-glucopyranoside, 5 mM MgCl2, and 2.0% glycerol |
|
| Assay | Assays for the interaction of the B.2 aptamer and the NS5BC55 protein. Assays were performed as described in Materials and Methods with a constant amount of labeled B.2 RNA (0.12 nM) and increasing concentrations of purified protein between 0.19 and 48 nM |
|
| PubMed ID | 11907208 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_909 | RNA | GGGAAUUCGAGCUCGGUACCUUUACCGUAAGGCCUGUCUUCGUUUGACAGCGGCUUGUUGACCCUCCACUUUGUACCUGCUGCCAACUGCAGGCAUGCAAGCUUGG | |
| Apta_171 | RNA | GGGAGCUCAGAAUAAACGCUCAACCAGUCUUGUGGCUUUGAAAGAGAGGAGUGUUCGACAUGAGGCCCGGAUCCGGC | |
| Apta_623 | RNA | GGGAAUGGAUCCACAUCUACGAAUUCACCGCGGGGUUGCGGACCGGGAGCUCCAGCUUCACUGCAGACUUGACGAAGCUU | |
| Apta_376 | RNA | GGGAGCUCAGCCUUCACUGCACUCCGGCUGGUGGACGCGGUACGAGCAAUUUGUACCGGAUGGAUGUUCGGGCAGCGGUGUGGCAGGGAUGAGCGGCACCACGGUCGGAUCCAC | |
| Apta_337 | RNA | GGGAGGAUAUUUUCUCAGACCGUAAGUACCGAAUGUGCUUUUGGCCGAUUUUUGGCCCCUGCAGUUGCAGCAUCGUGAACUAGGAUCCGGG | |
| Apta_416 | RNA | GGACCUCGGCGAAAGCCGGUAACGCCACAAGUCGGAGGGUAAGAUCUGACAGGAACUGGGUGACGGAGGUUAGGUGC | |
| Apta_624 | RNA | GGGAAUGGAUCCACAUCUACGAAUUCGAAUUGCCGUAAUUUCCCGUGGAGCGAUGCUUCACUGCAGACUUGACGAAGCUU | |
| Apta_723 | RNA | GGGAGCUCAGAAUAAACGCUCAAAUCCGUGGACAGGGCGUAAGCGCCUUCGACAUGAGACACGGAUCCUGCGACGAAUUCAGC | |
| Apta_1168 | RNA | GCGACUACGGUGAGGGUCGGGUCCAGUAGCUUCGGCUACUGUUGAGUAGAGUGUGGGCUCCGUAGUCGC | |
| Apta_156 | RNA | GGGAGAAUUCCGACCAGAAGGGUUAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU | |
| Apta_256 | RNA | GGGCGCUAAGUCCUCGCUCAUGCGCGUCCCAUGGGGUAUAGAGGGGUCGAAGUGGACGCGCGACUCGGAUCCU | |
| Apta_414 | RNA | GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA | |
| Apta_612 | RNA | GGGCGACCCUGAUGAGCCUUAGGAUAUGCUUCGGCAGAAGGACGUCGAAACGGUGAAAGCCGUAGGUUGCCC | |
| Apta_718 | RNA | GGGUUGUGAGCUCCCGGCUCGCAUUGUGAGGUGGAGGGGGACGUGCUGCAGGUCGACGCAUGCGCCG | |
| Apta_1221 | RNA | GGAGGCGCCAACUGAAUGAACGAGUUGAAAUGCGGAUCAAGUUACUGCUUCGGCAGUACCUAGUGGGAAAAGUUCUUGGGUCCGUAACUAGUCGCGUCAC | |
| Apta_1222 | RNA | GGAGGCGCCAACUGAAUGAAACCGUGCUAAGGAGUUGGACUCCGCUGCUUCGGCAGAGCGAUAUAGUGCCAGCUGAUACAUCCGUAACUAGUCGCGUCAC | |
| Apta_494 | RNA | GGGAGAUACCAGCUUAUUCAAUUCUGGCAAUGGGCUAUCCCAAGUGCUAGGCUUCAGGGAGCGAGGACCAGACGACGUACCUAACCCUAAGGUGAGAUAGUAAGUGCAAUCU | |
| Apta_559 | RNA | GGAUGUCCAGUCGCUUGCAAUGCCCUUUUAGACCCUGAUGAGGAUCAUCGGACUUUGUCCUGUGGAGUAAGAUCGCGAAACGGUGAAAGCCGUAGGUCU | |
| Apta_305 | RNA | GGGAGGACGAUGCGGAUCGCCCUGAACCGGCCCAGCAGACUGCUGACGGCACGAUCCGCAUCGUCCUCCC | |
| Apta_383 | RNA | GGCGUGACCUGAUGAGUCACGCUAAGGAGGAUUUCCGAAAGCGGCUACGGUCCGCCAGUGUUACGAAACGUUCCC |
DEV TOOL
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