Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 323
Aptamer sequence: GGUUACCAGCCUUCACUGCUCCCGGACGCGUCUGUAUCCGCUACCCGCCGCACCACGGUCGGUCACAC
Target unique ID: P14780
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_314 F3 Protein MMP9_HUMAN 8.1 nM 50 mM Tris HCl, pH 7.4, 50 mM NaCl, 100 mM KCl, 5 mM CaCl2, 1 mM Magnesium Acetate 23043415
Structure information of aptamer
Aptamer Sequence: GGUUACCAGCCUUCACUGCUCCCGGACGCGUCUGUAUCCGCUACCCGCCGCACCACGGUCGGUCACAC
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_314 Description F3
Aptamer chemistry RNA Length 68 nt
GC content 66.2% Molecular weight 21,823.74 Da
Molarity of 1 μg/μl solution 45.82 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence GGUUACCAGCCUUCACUGCUCCCGGACGCGUCUGUAUCCGCUACCCGCCGCACCACGGUCGGUCACAC
Applications Used for ex vivo imaging slices of human brain tumors
Target information
Type Detail Type Detail
Uniprot ID P14780 Protein name Matrix metalloproteinase-9 (MMP-9) (EC 3.4.24.35) (92 kDa gelatinase) (92 kDa type IV collagenase) (Gelatinase B) (GELB) [Cleaved into: 67 kDa matrix metalloproteinase-9; 82 kDa matrix metalloproteinase-9]
Gene name(s) MMP9 CLG4B Organism Matrix metalloproteinase-9 (MMP-9) (EC 3.4.24.35) (92 kDa gelatinase) (92 kDa type IV collagenase) (Gelatinase B) (GELB) [Cleaved into: 67 kDa matrix metalloproteinase-9; 82 kDa matrix metalloproteinase-9]
Status reviewed in uniprot database Length 707
Mass 78,458 Activity regulation Inhibited by histatin-3 1/24 (histatin-5)
Involvement in disease Intervertebral disc disease (IDD) Catalytic activity Reaction=Cleavage of gelatin types I and V and collagen types IV and V
PDB ID(s)
1GKC;1GKD;1ITV;1L6J;2OVX;2OVZ;2OW0;2OW1;2OW2;4H1Q;4H2E;4H3X;4H82;4HMA;4JIJ;4JQG;4WZV;4XCT;5CUH;5I12;5TH6;5TH9;5UE3;5UE4;6ESM;
Function Matrix metalloproteinase that plays an essential role in local proteolysis of the extracellular matrix and in leukocyte migration.
Activity data

No relevant experimental diagram

 Interaction ID 323
Target type Protein
Target unique ID P14780
Activity 8.1 nM
Binding Conditions/Buffer

50 mM Tris HCl, pH 7.4, 50 mM NaCl, 100 mM KCl, 5 mM CaCl2, 1 mM Magnesium Acetate
Assay

N/A
PubMed ID 23043415
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_766 RNA GGUUACCAGCCUUCACUGCGGACGGACAGAGAGUGCAACCUGCCGUGCCGCACCACGGUCGGUCACAC 79.41%
Apta_936 RNA GGAGCUCAGCCUUCACUGCGAUCACCGUGUCGGUGGCUAGUCGAUGUAUCCCGAUCACCAUUGGGGGCAAGUUUAGACAGGCACCACGGUCGGAUCCAC 59.60%
Apta_710 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACGAAACGGUAGCGAGAGCUC 55.32%
Apta_131 RNA GGGAGGACGAUGCGGUCCUGUCGUCUGUUCGUCCCCAGACGACUCGCCCGA 54.41%
Apta_315 RNA GGGAGGACGAUGCGGUCGUAUUAUCCGCUGCACGCCAGACGACUCGCCCGA 54.41%
Apta_170 RNA GGGAGACAAGACUAGACGCUCAAUGUGGGCCACGCCCGAUUUUACGCUUUUACCCGCACGCGAUUGGUUUGUUUCCC 53.25%
Apta_376 RNA GGGAGCUCAGCCUUCACUGCACUCCGGCUGGUGGACGCGGUACGAGCAAUUUGUACCGGAUGGAUGUUCGGGCAGCGGUGUGGCAGGGAUGAGCGGCACCACGGUCGGAUCCAC 52.63%
Apta_396 RNA GGGAGGACGAUGCGGCAGUCUGCAUCGUAGGAAUCGCCACCGUAUACUUUCCCACCAGACGACUCGCUGAGGAUCCGAGA 52.50%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 52.27%
Apta_561 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUGUGGAAACAGACGUGGCACAUGACUACGUCGAAACGGUAGCGAGAGCUC 52.22%
Apta_566 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCCUGCGAUGCAGAAAGGUGCUGACGACACAUCGAAACGGUAGCGAGAGCUC 52.22%
Apta_383 RNA GGCGUGACCUGAUGAGUCACGCUAAGGAGGAUUUCCGAAAGCGGCUACGGUCCGCCAGUGUUACGAAACGUUCCC 52.00%
Apta_276 RNA GGACCGAGAAGUUACCCUGUAAUCUUAGGAUGAAUCGCAUGCUCUAGCGACCUUUUCGGCUUCGGCGUACGCACAUCGCAGCAAC 51.76%
Apta_413 RNA GUGAGACCAGCCGAGUGGUGUCUGGCUAUUCACUGGAGCGUGGGUGGAACCCCUGCGCACUCGUUUGGCUGUCCGGGCCUUCGGGCCGGGAUUAUCUCU 51.52%
Apta_134 RNA GGGAGGACGAUGCGGGCCGUUGUUGUGUGCCGCCCCAGACGACUCGCCCGA 51.47%
Apta_301 RNA AUACCAGCUUAUUCAAUUGCCUGAAAAGUUGAACUCCAAAUACGCGCUGAGAUAGUAAGUGCAAUCU 51.47%
Apta_300 RNA AUACCAGCUUAUUCAAUUGCCUGAAACUGCUGCAUCGUCUCCCACGUAUUACACAUGAAGAUAGUAAGUGCAAUCU 51.32%
Apta_398 RNA GGGAGGACGAUGCGGCUUUAAUCCUCGCACUCAGCGCGCAUCACCCUUGACAUCACAGACGACUCGCUGAGGAUCCGAGA 51.25%
Apta_414 RNA GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA 51.25%
Apta_137 RNA GGGAGACAAGAAUAAACGCUCAAGUGACGUCCUGAUCGAUUGUGCAUUCGGUGUGACGAUCUUUCGACAGGAGGCUCACAACAGGC 51.16%

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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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