Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 510
Aptamer sequence: GGGAGACAAGAATAAACGCTCAATTTAACGTATTTATTCAAGCTCGTATTCGACAGGAGGCTCACAACAGGC
Target unique ID: Q9Y251
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_501 | 3.0 M NaSCN selection | Protein | HPSE_HUMAN | 13 nM | 100 mM NaCl, 20 mM KCl, 5 mM MgCl2 | 22719856 |
Structure information of aptamer
| Aptamer Sequence: | GGGAGACAAGAATAAACGCTCAATTTAACGTATTTATTCAAGCTCGTATTCGACAGGAGGCTCACAACAGGC |
| 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_501 | Description | 3.0 M NaSCN selection |
| Aptamer chemistry | DNA | Length | 72 nt |
| GC content | 43.1% | Molecular weight | 22,240.32 Da |
| Molarity of 1 μg/μl solution | 44.96 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted therapy |
| Sequence | GGGAGACAAGAATAAACGCTCAATTTAACGTATTTATTCAAGCTCGTATTCGACAGGAGGCTCACAACAGGC | ||
| Applications | Inhibit heparanase | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | Q9Y251 | Protein name | Heparanase (EC 3.2.1.166) (Endo-glucoronidase) (Heparanase-1) (Hpa1) [Cleaved into: Heparanase 8 kDa subunit; Heparanase 50 kDa subunit] |
| Gene name(s) | HPSE HEP HPA HPA1 HPR1 HPSE1 HSE1 | Organism | Heparanase (EC 3.2.1.166) (Endo-glucoronidase) (Heparanase-1) (Hpa1) [Cleaved into: Heparanase 8 kDa subunit; Heparanase 50 kDa subunit] |
| Status | reviewed in uniprot database | Length | 543 |
| Mass | 61,149 | Activity regulation | Inhibited by EDTA, laminarin sulfate and, to a lower extent, by heparin and sulfamin and activated by calcium and magnesium |
| Involvement in disease | N/A | Catalytic activity | Reaction=endohydrolysis of (1->4)-beta-D-glycosidic bonds of heparan sulfate chains in heparan sulfate proteoglycan |
| PDB ID(s) | 5E8M;5E97;5E98;5E9B;5E9C;5L9Y;5L9Z;5LA4;5LA7;6ZDM;7RG8; |
 |
Function | Endoglycosidase that cleaves heparan sulfate proteoglycans (HSPGs) into heparan sulfate side chains and core proteoglycans. |
Activity data
 |
Interaction ID | 510 |
| Target type | Protein | |
| Target unique ID | Q9Y251 | |
| Activity | 13 nM | |
| Binding Conditions/Buffer | 100 mM NaCl, 20 mM KCl, 5 mM MgCl2 |
|
| Assay | OC MZ-6 cells cultured in medium supplemented with anti-heparanase antibody, 1.5 M short, 1.5 M long and 3.0 M aptamers |
|
| PubMed ID | 22719856 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_502 | DNA | GGGAGACAAGAATAAACGCTCAAATGGACTTTTGAATGTGGCAACAAATTCGACAGGAGGCTCACAACAGGC | |
| Apta_790 | DNA | GGGAGACAAGAATAAACGCTCAAGAAGTGAAAATGACAGAACACAACATTCGACAGGAGGCTCACAACAGGC | |
| Apta_490 | DNA | GGGAGACAAGAATAAACGCTCAAGGGCGTGGTGGGTGGGGTACTAATAATGTGCGTTTGTTCGACAGGAGGCTCACAACAGGC | |
| Apta_422 | DNA | GGGAGCTCAGAATAAACGCTCAATTCGGGAATGATTATCAAATTTATGCCCTCTGATTTCGACATGAGGCCCGGATC | |
| Apta_272 | RNA | GGGAGACAAGAAUAAACGCUCAACACAGAACGCGGUCCCCACACAGGACAGGAGCCAGCCCCGGUUCGACAGGAGGCUCACAACAGGC | |
| Apta_433 | RNA | GGGAGACAAGAAUAAACGCUCAACGUUCAGUAUAACAGUCCGAGUCUAACACACAAUGGGACACUGAAUUCGACAGGAGGCUCACAACAGGC | |
| Apta_432 | RNA | GGGAGACAAGAAUAAACGCUCAAGGCAUUUCUGCUAGUCUGGUUGUAAGAUAUUCAACACGUGAGUUUCGACAGGAGGCUCACAACAGGC | |
| Apta_137 | RNA | GGGAGACAAGAAUAAACGCUCAAGUGACGUCCUGAUCGAUUGUGCAUUCGGUGUGACGAUCUUUCGACAGGAGGCUCACAACAGGC | |
| Apta_903 | DNA | ATACGGGAGCCAACACCAGACGGTAAATAAAGTCAGTATCGATACTCTATTCGAGAGCAGGTGTGACGGAT | |
| Apta_904 | DNA | ATACGGGAGCCAACACCAGACGGTAAATAAAGTCAGTATCGAGTACTCTATTCGAGAGCAGGTGTGACGGAT | |
| Apta_1108 | DNA | GTGCTTAGGTGCAGAACGCACACACGCTCGGTATGACGTGTTCGCTACGGTATAATTGCAGGCGCGAGCACAACAG | |
| Apta_171 | RNA | GGGAGCUCAGAAUAAACGCUCAACCAGUCUUGUGGCUUUGAAAGAGAGGAGUGUUCGACAUGAGGCCCGGAUCCGGC | |
| Apta_1068 | DNA | CGGGACAAGACAACGAACGAACAGGAAGAGAACCGGAATGCAGACGTCAGGG | |
| Apta_1220 | DNA | TGGCGACAAGAAGACGTACAAACACGCACCAGGCCGGAGTGGAGTATTCTGAGGTCGG | |
| Apta_1118 | DNA | GGGAATGGATCCACATCTACGAATTCATCAGGGCTAAAGAGTGCAGAGTTACTTAGTTCACTGCAGACTTGACGAAGCTT | |
| Apta_723 | RNA | GGGAGCUCAGAAUAAACGCUCAAAUCCGUGGACAGGGCGUAAGCGCCUUCGACAUGAGACACGGAUCCUGCGACGAAUUCAGC | |
| Apta_854 | RNA | GGGAGCUCAGAAUAAACGCUCAAGGGUAGGGAUCGUUACCCCGACAUUUUAAUGGGCCGAUGUUUCGACAUGAGGCCCGGAUCCGGC | |
| Apta_972 | DNA | TGACAGTACGTACTGAACTAATTTATAAGTAATTTGCTATGGTGGTATCC | |
| Apta_975 | DNA | AGACATAGTACATAACCGATCAATGAACATTTAATTAAATGGTGGTATCC | |
| Apta_1025 | DNA | GAAGAGTAGATGAAACGTTTTTTCGCCCGATAAAAGGGACGTGCGTCAGACA |
DEV TOOL
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