Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_504 | Pink | 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: | TTGCTCCTTATAGAGCCGTCCGAGC |
| 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_504 | Description | Pink |
| Aptamer chemistry | DNA | Length | 25 nt |
| GC content | 56.0% | Molecular weight | 7,608.91 Da |
| Molarity of 1 μg/μl solution | 131.42 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted therapy |
| Sequence | TTGCTCCTTATAGAGCCGTCCGAGC | ||
| 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 | 513 |
| 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_227 | DNA | ACGCGCCTATGGTGCATCGCATGCCGACC | |
| Apta_126 | DNA | TCCTCATATAGAGTGCGGGGCGTGT | |
| Apta_1084 | DNA | TTCCCTCCTCTGTTGTTCCCCCCTCCTCTC | |
| Apta_406 | DNA | AAAGCCCACTGCATAGAGGCCGCTCAACATGCGAGCCGGT | |
| Apta_199 | DNA | TAGGTCTGAGATCTCGGAAT | |
| Apta_346 | DNA | GTACGTTCAGGAGCAGTGCGA | |
| Apta_1020 | DNA | CTGCTTTGGTAGGGCAG | |
| Apta_701 | DNA | GTACTGGCGTTCGGGGGGTACCGCTGC | |
| Apta_463 | DNA | GTTCTCATGCACACTTATAGCGGGGGGATCCAGTACT | |
| Apta_145 | DNA | GGTGCGGTTCGTGCGGTTGTAGTACTCGTGGCCGATAGA | |
| Apta_222 | DNA | AGCGACTGACGATCTTGAGTAAACCGCTCATCCACGTAGT | |
| Apta_240 | DNA | TTTTTAATTAAAGCTCGCCATCAAATAGCTTT | |
| Apta_631 | DNA | GGGATCGAAACGTAGCGCCTTCGATCCC | |
| Apta_912 | DNA | TAGTATGGACTTGTCTTCTTGTCAGAGTCTGGCAGCACGT | |
| Apta_917 | DNA | TCGATTTCCTTAGTTGTCTTCCTTAGTGAG | |
| Apta_937 | DNA | TTGCCCACAGATCTGTGGAAGCCGAACCGCGTGCTAGTCGTG | |
| Apta_1036 | DNA | ATACCAGTCTATTCAATTGGGCCCGTCCGTATGGTGGG | |
| Apta_1097 | DNA | AGGCCCTACACGCCTTTTAGCGAGGGCGTTCCGTGGAGGA | |
| Apta_498 | DNA | GAACTCATTGGCTGGAGGCGGCAGTACCGCTTGAGTT | |
| Apta_364 | DNA | TATGGTATGCTGTGTGGTATGGGGTGGCGTGCTCT |
DEV TOOL
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