Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 753
Aptamer sequence: GGGCGAAUUCCCGAGGACCAAAUAGUACCACCCGGGAAAACAGCUAAUGCCGAAACGGAGAUUUUUUCUGCAGAAGCU
Target unique ID: 135440064
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_690 R10-B35 Molecule 8-Hydroxy-2'-deoxyguanosine 5 μM 20 mM NH4CH3CO2 (pH 6.0), 300 mM NaCl, and 5 mM MgCl2 9751715
Structure information of aptamer
Aptamer Sequence: GGGCGAAUUCCCGAGGACCAAAUAGUACCACCCGGGAAAACAGCUAAUGCCGAAACGGAGAUUUUUUCUGCAGAAGCU
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_690 Description R10-B35
Aptamer chemistry RNA Length 78 nt
GC content 50.0% Molecular weight 25,157.07 Da
Molarity of 1 μg/μl solution 39.75 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Aptasensor
Sequence GGGCGAAUUCCCGAGGACCAAAUAGUACCACCCGGGAAAACAGCUAAUGCCGAAACGGAGAUUUUUUCUGCAGAAGCU
Applications Binding to 8-oxodG
Target information
Type Detail Type Detail
PubChem ID 135440064 Molecular name 8-Hydroxy-2-deoxyguanosine
Molecular formula C10H13N5O5 Molecular weight 283.24
IUPAC name 2-amino-9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-1,7-dihydropurine-6,8-dione InChIKey HCAJQHYUCKICQH-VPENINKCSA-N
LogP -2.364 Topological polar surface area 159.25
Hydrogen bond acceptor 8 Hydrogen bond donor 5

Synonym(s):
88847-89-6; 8-Hydroxy-2'-deoxyguanosine; 8-Oxo-dG; 8-Oxo-2'-deoxyguanosine; 8-Hydroxydeoxyguanosine; 8-Oxo-7,8-dihydro-2'-deoxyguanosine; 8-OHdG; 8-Oxo-7-hydrodeoxyguanosine; 8-Oxo-2'-deoxyguanine; 2'-deoxy-8-oxoguanosine; Guanosine, 2'-deoxy-7,8-dihydro-8-oxo-; 2-Amino-9-((2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-3H-purine-6,8(7H,9H)-dione; 7,8-Dihydro-2'-deoxy-8-oxoguanosine; 8-hydroxy-deoxyguanosine; CHEBI:40304; 8-oxo-2'-dG; UNII-4RGB38T3IB; CID 5287560; 4RGB38T3IB; 2-amino-9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-3,7-dihydropurine-6,8-dione; 8HG; 8-oxodG; 8-oxo-7,8-dihydrodeoxyguanosine; 7,8-dihydro-8-oxo-2'-deoxyguanosine; 2'-deoxy-8-hydroxyguanosine; CCRIS 8239; 7,8-Dihydro-8-oxodeoxyguanosine; oh8dG; 2'-deoxy-7,8-dihydro-8-oxoguanosine; 8 Oxo dG; 8-Hydroxydesoxyguanosin; 2a5b; 8-hydroxydeoxy-guanosine; 8 OHdG; Guanosine, 7,8-dihydro-2'-deoxy-8-oxo-; Epitope ID:151526; 8-hydroxy-2'deoxyguanosine; 8-hydroxy-2-deoxyguanosine; SCHEMBL114652; CHEMBL1230628; DTXSID60904338; HMS3649O10; 1510AH; MFCD00210311; ZINC16051666; 8-Oxo-2'-deoxyguanosine (8-Oxo-dG); CS-W012256; DB02502; HY-W011540; AC-32342; AS-74648; A848840; Q270154; SR-01000946628; SR-01000946628-1; 8-Hydroxy-2 inverted exclamation marka-deoxyguanosine; 8-Hydroxy-2''-Deoxyguanosine; 8-Hydroxydeoxyguanosine; 2-Amino-9-(2-deoxyribofuranosyl)-3,7-dihydropurine-6,8-dione; 2-amino-8-hydroxy-9-((2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl)-1H-purin-6(9H)-one; 2-amino-8-hydroxy-9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-6,9-dihydro-1H-purin-6-one; 2-amino-8-hydroxy-9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)tetrahydrofuran-2-yl]-1H-purin-6-one; 2-amino-9-[(2R,4S,5R)-4-hydroxy-5-(hydroxymethyl)oxolan-2-yl]-6,7,8,9-tetrahydro-3H-purine-6,8-dione; 8-Hydroxydeoxyguanosine?2-amino-8-hydroxy-9-((2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-purin-6(9H)-one; 8-Hydroxydeoxyguanosine2-amino-8-hydroxy-9-((2S,4R,5S)-4-hydroxy-5-(hydroxymethyl)-tetrahydrofuran-2-yl)-1H-purin-6(9H)-one

Activity data
Interaction ID 753
Target type Molecule
Target unique ID 135440064
Activity 5 μM
Binding Conditions/Buffer

20 mM NH4CH3CO2 (pH 6.0), 300 mM NaCl, and 5 mM MgCl2
Assay

Affinity and specificity of RNA R10-B35 to 8-oxodG
PubMed ID 9751715
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_1289 RNA GGGAGAGGAUACUACACGUGGAAAAACCAACAAAUUGGGAAAAAUGUUAAGGGUCCACUUCAUGCCAUUGCAUGUAGCAGAAGCUUCCG 53.93%
Apta_563 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGAAAGCCAAAGCCGUAGCGCAGAUGAUCUCGCCAUCAGUACCGAAACGGUAGCGAGAGCUC 52.04%
Apta_522 RNA GGGCGACCCUGAUGAGCACACGAGGGGGAAACCCCGGACAAUCAGACACGGUGUUCGAAACGGUGAAAGCCGUAGGUUGCCCUUU 51.76%
Apta_156 RNA GGGAGAAUUCCGACCAGAAGGGUUAGCAGUCGGCAUGCGGUACAGACAGACCUUUCCUCUCUCCUUCCUCUUCU 51.28%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 51.14%
Apta_382 RNA GGCGUGACCUGAUGAGUCACGCAGACGCUAGCGAAUUGGUUCCUCGAAAGGGGAAAGCGUUAUUAAGAAACCAAAAUGUGUUACGAAACGUUCCC 50.53%
Apta_724 RNA GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC 50.53%
Apta_155 RNA GACCCAGGGCCGGGACGCAAAGCAGCCAAAACAGACGGCCCCAGUCAGGGAGUU 50.00%
Apta_394 RNA GGGCGAAUUCAACUGCCAUCUAGGCAGUAACCAGGAGUUAGUAGGACAAGUUUCGUCC 50.00%
Apta_561 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUGUGGAAACAGACGUGGCACAUGACUACGUCGAAACGGUAGCGAGAGCUC 50.00%
Apta_566 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCCUGCGAUGCAGAAAGGUGCUGACGACACAUCGAAACGGUAGCGAGAGCUC 50.00%
Apta_612 RNA GGGCGACCCUGAUGAGCCUUAGGAUAUGCUUCGGCAGAAGGACGUCGAAACGGUGAAAGCCGUAGGUUGCCC 50.00%
Apta_1113 DNA CCGCCCAAATCCCTAAGAGCACAAACACCAAACACAACCACCCCAACCAGACACACTACACACGCA 50.00%
Apta_720 RNA GGGAGAAUUCCGACCAGAAGCUUAGUAUAGCGAGGUUUAGCUACACUCGUGCUGAUCGUUUGGUACGGGACCUGCGUGUAGCCCAUAUGUGCGUCUACAUGGAUCCUCA 49.54%
Apta_1225 RNA GGAGGCGCCAACUGAAUGAAAGAGGUAACGAAAGAUGAUUGUGCCUGCUUCGGCAGUACAACUUCUCGGAUAAAUGAUUAUCCGUAACUAGUCGCGUCAC 49.00%
Apta_710 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACGAAACGGUAGCGAGAGCUC 48.94%
Apta_433 RNA GGGAGACAAGAAUAAACGCUCAACGUUCAGUAUAACAGUCCGAGUCUAACACACAAUGGGACACUGAAUUCGACAGGAGGCUCACAACAGGC 48.91%
Apta_157 RNA GGGUUCACUGCAGACUUGACGAAGCUUACAAACAAGAGCAAAAAGGGAGUUGACGUAGACUGUGCGGAAUGGAUCCACAUCUACGAAUUC 48.89%
Apta_272 RNA GGGAGACAAGAAUAAACGCUCAACACAGAACGCGGUCCCCACACAGGACAGGAGCCAGCCCCGGUUCGACAGGAGGCUCACAACAGGC 48.86%
Apta_5 RNA GGGAGAGCCAUACCUGACAAAGACGCUAGCGAAUUGGUUCCUCACUCAAAAGUAGGGGAAAGCGUUAUUAAGAAACCAAAAUUUGACAGGUUACGCAUCCUGCAUCCUCCAGGUUACGCAUCC 48.78%

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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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