Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 87
Aptamer sequence: GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU
Target unique ID: P00749
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_86 upanap-79 Protein UROK_HUMAN 7.3 nM HBS, 2 mM MgCl2, 0.1% BSA, and 0.025% Tween20 20962041
Structure information of aptamer
Aptamer Sequence: GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU
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_86 Description upanap-79
Aptamer chemistry RNA Length 35 nt
GC content 51.4% Molecular weight 11,472.73 Da
Molarity of 1 μg/μl solution 87.16 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU
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 87
Target type Protein
Target unique ID P00749
Activity 7.3 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_85 RNA UGCGACUGUUAUAACCUAACAGCGACGUAAAGAUA 57.14%
Apta_91 RNA GAUAACCUCGAUGCGACGUUCGGCCUCAAAAUCAA 57.14%
Apta_647 RNA GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC 55.26%
Apta_647 RNA GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC 55.26%
Apta_293 RNA CGGCCACAGAAUGAAAAACCUCAUCGAUGUUGCAUAGUUG 55.00%
Apta_659 RNA CAGAGGGAGUACUGAUCAACCCGAGCCUUCCGUCCCUGAG 55.00%
Apta_560 RNA GGAAGAGAUGGCGACUAAAACGACUUGUCGC 54.29%
Apta_274 DNA GATACTGAGCATCGTACATGATCCCGCAACGGGCAGTATT 52.50%
Apta_848 RNA CACCACGAUCACGGUUUCCCUCGCAGGUAAGGUGUAGA 50.00%
Apta_447 RNA ACGCUCAACGAGCCAGGAACAUCGACGUCAGCAAACGCGAGCGCAACCAGUAACACC 49.12%
Apta_520 RNA GGGAGAUCUACGGAUCUCAGGGCUCUUACGGGAGCUACAUGGAAGGAGUCCAUGUGU 49.12%
Apta_154 RNA ACACGCGAGAUAGAGCGAGGCCUCCAAAAAUGGCCACGCCAGGAAGCAAGU 49.02%
Apta_315 RNA GGGAGGACGAUGCGGUCGUAUUAUCCGCUGCACGCCAGACGACUCGCCCGA 49.02%
Apta_60 DNA GGAATGAGTGCCCTGCAAGCGAGGGCTAGC 48.57%
Apta_95 RNA CCGCGACAGUCGUAAGUUUUGACUGACUGAACGUU 48.57%
Apta_322 DNA GAAGTGAAAATGACAGAACACAACA 48.57%
Apta_322 DNA GAAGTGAAAATGACAGAACACAACA 48.57%
Apta_358 DNA GGGAATCGCCACCCGACGCAGGGTTTCCC 48.57%
Apta_372 RNA GACCAUACGGGAGAGAAACU 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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