Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 758
Aptamer sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC
Target unique ID: 165580
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_548 LS13 Molecule Paromomycin 19.8 nM PBS with 10% (v/v) methanol 22793869
Structure information of aptamer
Aptamer Sequence: GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC
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_548 Description LS13
Aptamer chemistry RNA Length 79 nt
GC content 46.8% Molecular weight 25,394.90 Da
Molarity of 1 μg/μl solution 39.38 μM Number of G-quadruplexes 2
G-Score 17 Function Aptasensor
Sequence GGGAGAAGGCGGCGCGUAGGCGAGCUUUACCAGUUUUAUUUGUUUUAUUGUUAUAUGCUUAUUCGUGGACGAUGCGCAC
Applications Detection of antibiotics
Target information
Type Detail Type Detail
PubChem ID 165580 Molecular name Paromomycin
Molecular formula C23H45N5O14 Molecular weight 615.6
IUPAC name (2S,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(2R,3S,4R,5S)-5-[(1R,2R,3S,5R,6S)-3,5-diamino-2-[(2S,3R,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxyoxane-3,4-diol InChIKey UOZODPSAJZTQNH-LSWIJEOBSA-N
LogP -8.862 Topological polar surface area 347.32
Hydrogen bond acceptor 19 Hydrogen bond donor 13

Synonym(s):
paromomycin; Aminosidin; catenulin; AMINOSIDINE; Neomycin E; Hydroxymycin; 7542-37-2; Crestomycin; Paucimycin; Estomycin; Monomycin A; Zygomycin A1; Paromomycine; Paromomycin I; Paramomycin Sulfate; Humatin; Paromomicina; Paromomycinum; Paucimycinum; Antibiotic 503-3; Antibiotic SF 767B; UNII-61JJC8N5ZK; Gabbromycin; Paromomycin (INN); Paromomycin [INN]; R 400; (1R,2R,3S,4R,6S)-4,6-diamino-2-{[3-O-(2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl)-beta-D-ribofuranosyl]oxy}-3-hydroxycyclohexyl 2-amino-2-deoxy-alpha-D-glucopyranoside; 61JJC8N5ZK; Amminosidin; Gabromycin; Humycin; Aminosidine I; Quintomycin C; CHEBI:7934; Antibiotic 2230D; (2S,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(2R,3S,4R,5S)-5-[(1R,2R,3S,5R,6S)-3,5-diamino-2-[(2S,3R,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)oxan-2-yl]oxy-6-hydroxycyclohexyl]oxy-4-hydroxy-2-(hydroxymethyl)oxolan-3-yl]oxyoxane-3,4-diol; paramomycin sulphate; R-400; Hydroxymycin sulfate; 134235-09-9; Paramomycin; Monomycin; Paromomycin (TN); Paromomycin sulfate Rx346208; (2S,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-(((2R,3S,4R,5S)-5-(((1R,2R,3S,5R,6S)-3,5-diamino-2-(((2S,3R,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl)oxy)-6-hydroxycyclohexyl)oxy)-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl)oxy)tetrahydro-2H-pyran-3,4-diol; Aminosidine, sulfate; hATT & Paromomycin; Paromomycin [INN:BAN]; Paromomycine [INN-French]; Paromomycinum [INN-Latin]; Paromomicina [INN-Spanish]; (2S,3S,4R,5R,6R)-5-amino-2-(aminomethyl)-6-[(2R,3S,4R,5S)-5-[(1R,2R,3S,5R,6S)-3,5-diamino-2-[(2S,3R,4R,5S,6R)-3-amino-4,5-dihydroxy-6-(hydroxymethyl)tetrahydropyran-2-yl]oxy-6-hydroxy-cyclohexoxy]-4-hydroxy-2-(hydroxymethyl)tetrahydrofuran-3-yl]oxy-tetrahydropyran-3,4-diol; EINECS 231-423-0; BRN 0072285; Human .alpha.-1-antitrypsin & Paromomyin; SCHEMBL4072; 4-18-00-07534 (Beilstein Handbook Reference); CHEMBL370143; DTXSID8023424; ZINC60183170; AKOS030489917; DB01421; MCULE-1528618434; NCGC00166210-02; D-Streptamine, O-2-amino-2-deoxy-alpha-D-glucopyranosyl-(1-4)-O-(O-2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl-(1-3)-beta-D-ribofuranosyl-(1-5))-2-deoxy-; O-2-Amino-2-deoxy-.alpha.-D-glucopyranosyl-(1->4)-O-[O-2,6-diamino-2,6-dideoxy-.beta.-L-idopyranosyl-(1->3)-.beta.D-ribofuranosyl(1->5)]-2-deoxy-D-streptamine; C00832; D07467; 10845-EP2301536A1; 10845-EP2301538A1; 10845-EP2311455A1; 10845-EP2316452A1; AB00639998_04; Q415625; PAROMOMYCIN I; AMMINOSIDIN; CATENULIN; CRESTOMYCIN; MONOMYCIN A; NEOMYCIN E; (2R,3S,4R,5R,6S)-5-amino-6-{[(1R,2R,3S,4R,6S)-4,6-diamino-2-{[(2S,3R,4S,5R)-4-{[(2R,3R,4R,5S,6S)-3-amino-6-(aminomethyl)-4,5-dihydroxyoxan-2-yl]oxy}-3-hydroxy-5-(hydroxymethyl)oxolan-2-yl]oxy}-3-hydroxycyclohexyl]oxy}-2-(hydroxymethyl)oxane-3,4-diol; Streptamine, O-2,6-diamino-2,6-dideoxy-beta-L-idopyranosyl-(1-3)-O-beta-D-ribofuranosyl-(1-5)-O-(2-amino-2-deoxy-alpha-D-glucopyranosyl-(1-4))-2-deoxy-

Activity data
Interaction ID 581
Target type Molecule
Target unique ID 3081545
Activity 35.9 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 652
Target type Molecule
Target unique ID 3467
Activity 26.7 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 664
Target type Molecule
Target unique ID 6032
Activity 69.9 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 724
Target type Molecule
Target unique ID 8378
Activity 37 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 758
Target type Molecule
Target unique ID 165580
Activity 19.8 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 780
Target type Molecule
Target unique ID 19649
Activity 19.8 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Interaction ID 798
Target type Molecule
Target unique ID 36294
Activity 24.8 nM
Binding Conditions/Buffer

PBS with 10% (v/v) methanol
Assay

Promiscuity of aminoglycoside binding by GNP-Aptasensor
PubMed ID 22793869
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_547 RNA GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC 73.42%
Apta_43 RNA GGGAGAGCGGAAGCGUGCUGGGCCACCAUCCGUAACUAGCUAAUACUUGUUAUCUUUUUAUUUUCAUAACCCAGAGGUCGAUGGAUCCCCCC 59.78%
Apta_984 RNA GGGAGGACGAUGCGGCGUAUUGCGCGAGGAUUAUCCGCUCAUCGUUGUUGUUGUGCAGACGACUCGCCCGA 54.43%
Apta_724 RNA GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC 52.63%
Apta_720 RNA GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA 52.29%
Apta_1223 RNA GGAGGCGCCAACUGAAUGAAAGGUUACGCUUCAACGCCGUGCAGCUGCUUCGGCAGGCUUGUGAGUACAUGGCCCAUUGAUCCGUAACUAGUCGCGUCAC 52.00%
Apta_576 RNA GGCACCAAAGCUGAAGUAGCGGGAUAACUCAAAUUACUUUAGGUGUAUGAAGGUGAAACUAGCAAUGAA 51.90%
Apta_410 RNA GGGAGAGCGGAAGCGUGCUGGGCCUGUCGUUCGCUGUGUCUUGCUACGUUACGUUACACGGUUGGCAUAACCCAGAGGUCGAUGG 51.76%
Apta_414 RNA GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA 51.25%
Apta_500 RNA GGGAGAAAGGGAAGCUUGAGGUGCUAUGGAGUGGAGGAGUUGAAGGUGUCGGGGUUGGCAGAAGAAGGCGAGCGUACGGAUCCAUC 51.16%
Apta_1225 RNA GGAGGCGCCAACUGAAUGAAAGAGGUAACGAAAGAUGAUUGUGCCUGCUUCGGCAGUACAACUUCUCGGAUAAAUGAUUAUCCGUAACUAGUCGCGUCAC 51.00%
Apta_129 RNA GGGAGGACGAUGCGGACACCGUUAAUCUGAGGCCCUGUCCUAUUCCUUCACGCCUCAGA 50.63%
Apta_130 RNA GGGAGGACGAUGCGGUGGUAGCGCGAUAUAGCGCUGGUAGGGUUGCCGGUGAUCAGACGACUCGCCCGA 50.63%
Apta_352 RNA GGGAGGACGAUGCGGUGGUCUCCCAAUUCUAAACUUUCUCCAUCGUAUCUGGGCAGACGACUCGCCCGA 50.63%
Apta_1100 RNA GGGAGAAUUCCGACCAGAAGGGUUAGCGGUCGUCUUAAGUAGUUUUUGGUCCUUUCCUCUCUCCUUCCUCUUCU 50.63%
Apta_123 RNA GGGAGAAAGGGAAGCUUGAGCAGCAGGAGGGCCGGCGUUAGGGUUAGCGAGCCGAUUGAAAGAAGAAGGAACGAGCGUACGGAUCCGAUC 50.00%
Apta_137 RNA GGGAGACAAGAAUAAACGCUCAAGUGACGUCCUGAUCGAUUGUGCAUUCGGUGUGACGAUCUUUCGACAGGAGGCUCACAACAGGC 50.00%
Apta_432 RNA GGGAGACAAGAAUAAACGCUCAAGGCAUUUCUGCUAGUCUGGUUGUAAGAUAUUCAACACGUGAGUUUCGACAGGAGGCUCACAACAGGC 50.00%
Apta_562 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUUAGGGCCAAGUGUGGUGAAAGACACACUCGAAACGGUAGCGAGAGCUC 50.00%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 50.00%

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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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