Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 96
Aptamer sequence: CCGCGACAGUCGUAAGUUUUGACUGACUGAACGUU
Target unique ID: P00749
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_95 upanap-24 Protein UROK_HUMAN 51.2 nM HBS, 2 mM MgCl2, 0.1% BSA, and 0.025% Tween20 20962041
Structure information of aptamer
Aptamer Sequence: CCGCGACAGUCGUAAGUUUUGACUGACUGAACGUU
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_95 Description upanap-24
Aptamer chemistry RNA Length 35 nt
GC content 48.6% Molecular weight 11,421.58 Da
Molarity of 1 μg/μl solution 87.55 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence CCGCGACAGUCGUAAGUUUUGACUGACUGAACGUU
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 96
Target type Protein
Target unique ID P00749
Activity 51.2 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_658 RNA CUGCGAUCAGGGGUAAAUUUCCGCGCAGGCUCCACGCCGC 57.50%
Apta_271 RNA CUGUCGAGCAUGCUCAGGGUAACGUAUAGUCAAGACACCUCAAGUGUAACU 54.90%
Apta_270 RNA CUGUCGAACAUGCUGAGGGUAACGUACUGGCAAGCUCACCUCAGCGUAGCUAa 52.83%
Apta_85 RNA UGCGACUGUUAUAACCUAACAGCGACGUAAAGAUA 51.43%
Apta_93 RNA CUCCGCUAUCUAACGUAUGAUAGAAUGGAUGACUA 51.43%
Apta_212 RNA AGGAAGGCUUUAGGUCUGAGAUCUCGGAAU 51.43%
Apta_715 RNA GGCGCUGCACGCCGAAAGGCCCGUUGAAACGUC 51.43%
Apta_716 RNA GGCGCUUCAUGCCGAAAGGCCCGUUGUAACGUC 51.43%
Apta_381 RNA AUUCUGUUGGCGAACUGUACGCAAGUACUGGAUGACAGCCUAUCUAU 51.06%
Apta_293 RNA CGGCCACAGAAUGAAAAACCUCAUCGAUGUUGCAUAGUUG 50.00%
Apta_365 RNA GGACCUAUGCAGUAGCCAGUGUGGACUGGGCUGCCCCCCC 50.00%
Apta_603 RNA CUUGUCUGAACAAUUUCGUCUGCCUUUGCGUUCCGACGGC 50.00%
Apta_243 RNA GCUUGAAGCUAGCAGUAAGACUAGCGCUACGGAUGGGUGUGCG 48.84%
Apta_859 RNA GGGAGUCUGAAGUCGGACUUGUUAUCAAUUCACUUCAGACU 48.78%
Apta_86 RNA GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU 48.57%
Apta_87 RNA UACCGACUAGCAAAACCUGCUGGCGACGUUUAGAU 48.57%
Apta_97 RNA UUGUCGUCUUCUCCAGUUAGUCAACGAACUUGUGU 48.57%
Apta_377 RNA CUUCGGGAUUUGAGGGUAGAAUGGGACUA 48.57%
Apta_379 RNA UACGACACGAUUGGGACGUGUCUAUGGGAC 48.57%
Apta_714 RNA GGCGGUUCCUGCCGAAAGGCUCGUGGCAACGUC 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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