Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 89
Aptamer sequence: AAUAACCUUAAUGCGACGUUGGUUUGUCAACAACG
Target unique ID: P00749
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_88 upanap-21(6) Protein UROK_HUMAN 4.6 nM HBS, 2 mM MgCl2, 0.1% BSA, and 0.025% Tween20 20962041
Structure information of aptamer
Aptamer Sequence: AAUAACCUUAAUGCGACGUUGGUUUGUCAACAACG
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_88 Description upanap-21(6)
Aptamer chemistry RNA Length 35 nt
GC content 40.0% Molecular weight 11,413.61 Da
Molarity of 1 μg/μl solution 87.61 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence AAUAACCUUAAUGCGACGUUGGUUUGUCAACAACG
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 89
Target type Protein
Target unique ID P00749
Activity 4.6 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
91.43%
Apta_90 RNA ACAACCUAAAUGCGACGUUGGGUCAAAAACGUGAA 68.57%
Apta_92 RNA ACAACUUAAUGCGACGUUGGUAAAGCAUAUCAAAC 68.57%
Apta_91 RNA GAUAACCUCGAUGCGACGUUCGGCCUCAAAAUCAA 65.71%
Apta_1141 RNA ACGAGUCUGGUCCUUCCUUUGACGACUAUUGUUUGGUAUCGAUCAACAACAA 55.77%
Apta_709 RNA AGUGAUACCAGCAUCGUCUUGAUGCCCUUGGCAGCACU 52.63%
Apta_1 RNA ACGAAGCUUGAUCCCGUUUGCCGGUCGAUCGCUUCGA 51.35%
Apta_98 RNA CGAUGCGGUCUCAUGCGUCGAGUGUGAGUUUACCUUCG 50.00%
Apta_269 RNA AACGCUCAACGUCAGAAGGCAACGUAUAGGCAAGCACACUUCGACAUGAGGC 50.00%
Apta_424 RNA UGCUAGUAUAUCGCACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG 49.02%
Apta_425 RNA UGCCGCCAUAUCACACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG 49.02%
Apta_426 RNA UGCCGCUAUAAUGCACGGAUUUAAUCGCCGUAGAAAAGCAUGUCAAAGCCG 49.02%
Apta_1142 RNA ACGAGUCACACGUUGAUGACUGGAUGGUAGUUAAAGAGGGUGGGGCAACAA 49.02%
Apta_1143 RNA ACGAGUUGUCGCAUGUGCGGUUCAGUCUGGUCCUUCAGCACCGUACAACAA 49.02%
Apta_1144 RNA ACGAGUCUGGUCCUUCCUCCCUAAUUGCUGUUGAGGUAUCGGCUACAACAA 49.02%
Apta_859 RNA GGGAGUCUGAAGUCGGACUUGUUAUCAAUUCACUUCAGACU 48.78%
Apta_379 RNA UACGACACGAUUGGGACGUGUCUAUGGGAC 48.57%
Apta_1249 RNA AAUCGGCCCAAUUUUACCUUCGGACUUCAGUAUCUAGUGUGGCUUUAAAUCAUAGC 48.21%
Apta_1166 RNA GAUGUAACUGAAUGAAAUGGUGAAGGACGGGUCCAGUAGGCUGC 47.73%
Apta_51 RNA GCCUUAGUAACGUGCUUUGAUGUCGAUUCGACAGGAGGC 46.15%

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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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