Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_505 | Yellow | Protein | HPSE_HUMAN | N/A | 50% DMEM, 50% Ham's F-12 Cell culture medium supplemented with: 50 mg/ml ascorbic acid, 250 ng/ml amphotericin B, 5mg/ml insulin (bovine pancreas), 0.4 ng/ml hydrocortisone and 10% heat-inactivated fetal bovine serum | 25295847 |
Structure information of aptamer
| Aptamer Sequence: | CTAAAGTGCCTCACGCTGTTAACTC |
| 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_505 | Description | Yellow |
| Aptamer chemistry | DNA | Length | 25 nt |
| GC content | 48.0% | Molecular weight | 7,576.91 Da |
| Molarity of 1 μg/μl solution | 131.98 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted therapy |
| Sequence | CTAAAGTGCCTCACGCTGTTAACTC | ||
| Applications | Inhibit the enzymatic action of 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
|
No relevant experimental diagram |
Interaction ID | 514 |
| Target type | Protein | |
| Target unique ID | Q9Y251 | |
| Activity | N/A | |
| Binding Conditions/Buffer | 50% DMEM, 50% Ham's F-12 Cell culture medium supplemented with: 50 mg/ml ascorbic acid, 250 ng/ml amphotericin B, 5mg/ml insulin (bovine pancreas), 0.4 ng/ml hydrocortisone and 10% heat-inactivated fetal bovine serum |
|
| Assay | N/A |
|
| PubMed ID | 25295847 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_196 | DNA | AGGAAGGCTTTAGGTCTGAGATCTC | |
| Apta_204 | DNA | CCAAGGCTTTAGGTCTGAGATCTCCC | |
| Apta_205 | DNA | TTAAGGCTTTAGGTCTGAGATCTCTT | |
| Apta_60 | DNA | GGAATGAGTGCCCTGCAAGCGAGGGCTAGC | |
| Apta_387 | DNA | CTTTAATGCCCTTCACTAGGTCTAAGCTACTACTTACCCG | |
| Apta_207 | DNA | AGGAAGGCTTTAGGTGGAAT | |
| Apta_325 | DNA | TACTGCATGCACACCACTTCAACTA | |
| Apta_325 | DNA | TACTGCATGCACACCACTTCAACTA | |
| Apta_538 | DNA | GTGTTGTCTCTCTGTGTCTC | |
| Apta_1160 | DNA | TTCAGTATCCCACGGGTGGAATCA | |
| Apta_602 | DNA | GGGCGAGAACAGTGTCCCAGTCGCTAGTTTTCTCTGCCC | |
| Apta_203 | DNA | GGAAGGCTTTAGGTCTGAGATCTCGG | |
| Apta_249 | DNA | CCCTGTTCCCCCTCCGCCGCTTGACTCTCC | |
| Apta_541 | DNA | CACGTGTTGTCTCTCTGTGTCTCGTG | |
| Apta_542 | DNA | GCACGTGTTGTCTCTCTGTGTCTCGTGC | |
| Apta_543 | DNA | GGCACGTGTTGTCTCTCTGTGTCTCGTGCC | |
| Apta_677 | DNA | CCAAATGCGACGGGGCCTGTTTTAATGGGG | |
| Apta_946 | DNA | TACCGGGTAATATGCACACATGCTGATAGCAAGCAATGCA | |
| Apta_1022 | DNA | CTCCTTCAACGAAGTGGGTTCCTTCAACGAAGTGGGTCTC | |
| Apta_1198 | DNA | CTTTTAAGAACCGGACGAACTAGAATATTATATTTT |
DEV TOOL
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