Aptamer-target interaction descriptor
Aptamer-target interaction information
| Aptamer ID | Aptamer descriptor | Target chemistry | Target name | Affinity | Binding Conditions/Buffer | PubMed ID |
|---|---|---|---|---|---|---|
| Apta_91 | upanap-25 | Protein | UROK_HUMAN | 5.5 nM | HBS, 2 mM MgCl2, 0.1% BSA, and 0.025% Tween20 | 20962041 |
Structure information of aptamer
| Aptamer Sequence: | GAUAACCUCGAUGCGACGUUCGGCCUCAAAAUCAA |
| 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_91 | Description | upanap-25 |
| Aptamer chemistry | RNA | Length | 35 nt |
| GC content | 48.6% | Molecular weight | 11,410.66 Da |
| Molarity of 1 μg/μl solution | 87.64 μM | Number of G-quadruplexes | No QGRS found |
| G-Score | N/A | Function | Targeted binding |
| Sequence | GAUAACCUCGAUGCGACGUUCGGCCUCAAAAUCAA | ||
| Applications | RNA aptamers specifically targeting human uPA and blocking the interaction to its receptor at low nanomolar concentrations | ||
Target information
| Type | Detail | Type | Detail |
|---|---|---|---|
| Uniprot ID | P00749 | Protein name | Urokinase-type plasminogen activator (U-plasminogen activator) (uPA) (EC 3.4.21.73) [Cleaved into: Urokinase-type plasminogen activator long chain A; Urokinase-type plasminogen activator short chain A; Urokinase-type plasminogen activator chain B] |
| Gene name(s) | PLAU | Organism | Urokinase-type plasminogen activator (U-plasminogen activator) (uPA) (EC 3.4.21.73) [Cleaved into: Urokinase-type plasminogen activator long chain A; Urokinase-type plasminogen activator short chain A; Urokinase-type plasminogen activator chain B] |
| Status | reviewed in uniprot database | Length | 431 |
| Mass | 48,523 | Activity regulation | Inhibited by SERPINA5 |
| Involvement in disease | Quebec platelet disorder (QPD) | Catalytic activity | Reaction=Specific cleavage of Arg-|-Val bond in plasminogen to form plasmin |
| PDB ID(s) | 1C5W;1C5X;1C5Y;1C5Z;1EJN;1F5K;1F5L;1F92;1FV9;1GI7;1GI8;1GI9;1GJ7;1GJ8;1GJ9;1GJA;1GJB;1GJC;1GJD;1KDU;1LMW;1O3P;1O5A;1O5B;1O5C;1OWD;1OWE;1OWH;1OWI;1OWJ;1OWK;1SC8;1SQA;1SQO;1SQT;1U6Q;1URK;1VJ9;1VJA;1W0Z;1W10;1W11;1W12;1W13;1W14;2FD6;2I9A;2I9B;2NWN;2O8T;2O8U;2O8W;2R2W;2VIN;2VIO;2VIP;2VIQ;2VIV;2VIW;2VNT;3BT1;3BT2;3IG6;3KGP;3KHV;3KID;3M61;3MHW;3MWI;3OX7;3OY5;3OY6;3PB1;3QN7;3U73;4DVA;4DW2;4FU7;4FU8;4FU9;4FUB;4FUC;4FUD;4FUE;4FUF;4FUG;4FUH;4FUI;4FUJ;4GLY;4H42;4JK5;4JK6;4K24;4MNV;4MNW;4MNX;4MNY;4OS1;4OS2;4OS4;4OS5;4OS6;4OS7;4X0W;4X1N;4X1P;4X1Q;4X1R;4X1S;4XSK;4ZHL;4ZHM;4ZKN;4ZKO;4ZKR;4ZKS;5HGG;5WXF;5WXO;5WXP;5WXQ;5WXR;5WXS;5WXT;5XG4;5YC6;5YC7;5Z1C;5ZA7;5ZA8;5ZA9;5ZAE;5ZAF;5ZAG;5ZAH;5ZAJ;5ZC5;6AG2;6AG3;6AG7;6AG9;6JYP;6JYQ;6L04;6L05;6NMB;6XVD;7DZD; |
 |
Function | Specifically cleaves the zymogen plasminogen to form the active enzyme plasmin. |
Activity data
|
No relevant experimental diagram |
Interaction ID | 92 |
| Target type | Protein | |
| Target unique ID | P00749 | |
| Activity | 5.5 nM | |
| Binding Conditions/Buffer | HBS, 2 mM MgCl2, 0.1% BSA, and 0.025% Tween20 |
|
| Assay | N/A |
|
| PubMed ID | 20962041 |
Similar aptamers
| Aptamer ID | Aptamer chemistry | Sequence | Similarity |
|---|---|---|---|
| Apta_89 | RNA | AAUAACCUUAAUGCGACGUUGGUUCGUCAACAUGG | |
| Apta_90 | RNA | ACAACCUAAAUGCGACGUUGGGUCAAAAACGUGAA | |
| Apta_88 | RNA | AAUAACCUUAAUGCGACGUUGGUUUGUCAACAACG | |
| Apta_92 | RNA | ACAACUUAAUGCGACGUUGGUAAAGCAUAUCAAAC | |
| Apta_86 | RNA | GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU | |
| Apta_1141 | RNA | ACGAGUCUGGUCCUUCCUUUGACGACUAUUGUUUGGUAUCGAUCAACAACAA | |
| Apta_96 | RNA | UCGCUAAUUAUAGGCGGAGUGCGACGUUAUAAAUA | |
| Apta_131 | RNA | GGGAGGACGAUGCGGUCCUGUCGUCUGUUCGUCCCCAGACGACUCGCCCGA | |
| Apta_269 | RNA | AACGCUCAACGUCAGAAGGCAACGUAUAGGCAAGCACACUUCGACAUGAGGC | |
| Apta_967 | DNA | GGGTAGCAGCCCCGCGGAGGGTCGGCTATAAGAACCAAGA | |
| Apta_1140 | RNA | UAGUGUGAGAGCCGUGAGUGAAAGGCCGCGACAAAGAUCGGA | |
| Apta_1211 | RNA | ACUAGCCUCAUCAGCUCAUGUGCCCCUCCGCCUGGAUCAC | |
| Apta_133 | RNA | GGGAGGACGAUGCGGUGAGUCGUUCCCUUCGUCCCCAGACGACUCGCCCGA | |
| Apta_135 | RNA | GGGAGGACGAUGCGGAUUCUGGUUACUGGCCGCCCCAGACGACUCGCCCGA | |
| Apta_1143 | RNA | ACGAGUUGUCGCAUGUGCGGUUCAGUCUGGUCCUUCAGCACCGUACAACAA | |
| Apta_668 | RNA | GGAACCCAACUAGGCGUUUGAGGGGAUUCGGCCACGGUAACAACCCCUC | |
| Apta_859 | RNA | GGGAGUCUGAAGUCGGACUUGUUAUCAAUUCACUUCAGACU | |
| Apta_1 | RNA | ACGAAGCUUGAUCCCGUUUGCCGGUCGAUCGCUUCGA | |
| Apta_94 | RNA | AUGACAGGAUGCAGAGCUCCACUGUCUAGUGUUUA | |
| Apta_379 | RNA | UACGACACGAUUGGGACGUGUCUAUGGGAC |
DEV TOOL
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