Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 86
Aptamer sequence: UGCGACUGUUAUAACCUAACAGCGACGUAAAGAUA
Target unique ID: P00749
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_85 upanap-12 Protein UROK_HUMAN 5 nM HBS, 2 mM MgCl2, 0.1% BSA, and 0.025% Tween20 20962041
Structure information of aptamer
Aptamer Sequence: UGCGACUGUUAUAACCUAACAGCGACGUAAAGAUA
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_85 Description upanap-12
Aptamer chemistry RNA Length 35 nt
GC content 40.0% Molecular weight 11,459.69 Da
Molarity of 1 μg/μl solution 87.26 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence UGCGACUGUUAUAACCUAACAGCGACGUAAAGAUA
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 86
Target type Protein
Target unique ID P00749
Activity 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_87 RNA UACCGACUAGCAAAACCUGCUGGCGACGUUUAGAU 62.86%
Apta_96 RNA UCGCUAAUUAUAGGCGGAGUGCGACGUUAUAAAUA 62.86%
Apta_855 RNA UCACUGUUAUCCGAUAGCAGCGCGGGAUGA 62.86%
Apta_86 RNA GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU 57.14%
Apta_271 RNA CUGUCGAGCAUGCUCAGGGUAACGUAUAGUCAAGACACCUCAAGUGUAACU 54.90%
Apta_716 RNA GGCGCUUCAUGCCGAAAGGCCCGUUGUAACGUC 54.29%
Apta_1292 RNA GGCACGUGUAUUACCCUAGUGGUCGACGUGCC 54.29%
Apta_1122 RNA ACAACCCGGAACAACGUCUAACAGUGUACCAUAACCCGGCAUUCA 53.33%
Apta_270 RNA CUGUCGAACAUGCUGAGGGUAACGUACUGGCAAGCUCACCUCAGCGUAGCUAa 52.83%
Apta_293 RNA CGGCCACAGAAUGAAAAACCUCAUCGAUGUUGCAUAGUUG 52.50%
Apta_93 RNA CUCCGCUAUCUAACGUAUGAUAGAAUGGAUGACUA 51.43%
Apta_95 RNA CCGCGACAGUCGUAAGUUUUGACUGACUGAACGUU 51.43%
Apta_588 RNA CCGGUGCGCAUAACCACCUCAGUGCGAGCAAGGAA 51.43%
Apta_715 RNA GGCGCUGCACGCCGAAAGGCCCGUUGAAACGUC 51.43%
Apta_1140 RNA UAGUGUGAGAGCCGUGAGUGAAAGGCCGCGACAAAGAUCGGA 50.00%
Apta_424 RNA UGCUAGUAUAUCGCACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG 49.02%
Apta_425 RNA UGCCGCCAUAUCACACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG 49.02%
Apta_426 RNA UGCCGCUAUAAUGCACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG 49.02%
Apta_326 DNA GCAACAGGGTATCCAAAGGATCAAA 48.57%
Apta_342 RNA GCGACUGGUUACCCGGUCG 48.57%

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AptaDB is an online database we developed to integrate comprehensive information about aptamer.
The detail of this database is described here:

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