Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 88
Aptamer sequence: UACCGACUAGCAAAACCUGCUGGCGACGUUUAGAU
Target unique ID: P00749
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_87 upanap-84 Protein UROK_HUMAN 61.8 nM HBS, 2 mM MgCl2, 0.1% BSA, and 0.025% Tween20 20962041
Structure information of aptamer
Aptamer Sequence: UACCGACUAGCAAAACCUGCUGGCGACGUUUAGAU
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_87 Description upanap-84
Aptamer chemistry RNA Length 35 nt
GC content 48.6% Molecular weight 11,427.64 Da
Molarity of 1 μg/μl solution 87.51 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence UACCGACUAGCAAAACCUGCUGGCGACGUUUAGAU
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 88
Target type Protein
Target unique ID P00749
Activity 61.8 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_85 RNA UGCGACUGUUAUAACCUAACAGCGACGUAAAGAUA 62.86%
Apta_86 RNA GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU 62.86%
Apta_96 RNA UCGCUAAUUAUAGGCGGAGUGCGACGUUAUAAAUA 54.29%
Apta_647 RNA GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC 52.63%
Apta_848 RNA CACCACGAUCACGGUUUCCCUCGCAGGUAAGGUGUAGA 52.63%
Apta_647 RNA GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC 52.63%
Apta_293 RNA CGGCCACAGAAUGAAAAACCUCAUCGAUGUUGCAUAGUUG 52.50%
Apta_374 RNA GUCCCGUGCGCAAAAGUUCUUAGCGCUAGCAGUCCUAGUUGC 52.38%
Apta_152 RNA UUACCACGCGCUCUUAACUGCUAGCGCCAUGGC 51.43%
Apta_379 RNA UACGACACGAUUGGGACGUGUCUAUGGGAC 51.43%
Apta_1 RNA ACGAAGCUUGAUCCCGUUUGCCGGUCGAUCGCUUCGA 51.35%
Apta_154 RNA ACACGCGAGAUAGAGCGAGGCCUCCAAAAAUGGCCACGCCAGGAAGCAAGU 49.02%
Apta_381 RNA AUUCUGUUGGCGAACUGUACGCAAGUACUGGAUGACAGCCUAUCUAU 48.94%
Apta_849 RNA UCCCGAUUACUGUACAUACCUUAGCCCAUAGCUGGCUGC 48.72%
Apta_94 RNA AUGACAGGAUGCAGAGCUCCACUGUCUAGUGUUUA 48.57%
Apta_95 RNA CCGCGACAGUCGUAAGUUUUGACUGACUGAACGUU 48.57%
Apta_588 RNA CCGGUGCGCAUAACCACCUCAGUGCGAGCAAGGAA 48.57%
Apta_630 DNA GACCAGGGCAAACGGTAGGGAGTGGTC 48.57%
Apta_855 RNA UCACUGUUAUCCGAUAGCAGCGCGGGAUGA 48.57%
Apta_1292 RNA GGCACGUGUAUUACCCUAGUGGUCGACGUGCC 48.57%

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AptaDB is an online database we developed to integrate comprehensive information about aptamer.
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