Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 803
Aptamer sequence: GGCACGUGUAUUACCCUAGUGGUCGACGUGCC
Target unique ID: 1188
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_1292 XBA Molecule Xanthine 3.3 μM 20 mM Tris-HCl (pH 7.5), 0.3 M NaCl and 5 mM MgCl2 9512549
Structure information of aptamer
Aptamer Sequence: GGCACGUGUAUUACCCUAGUGGUCGACGUGCC
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_1292 Description XBA
Aptamer chemistry RNA Length 32 nt
GC content 59.4% Molecular weight 10,232.08 Da
Molarity of 1 μg/μl solution 97.73 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Targeted binding
Sequence GGCACGUGUAUUACCCUAGUGGUCGACGUGCC
Applications Binding to xanthine
Target information
Type Detail Type Detail
PubChem ID 1188 Molecular name Xanthine
Molecular formula C5H4N4O2 Molecular weight 152.11
IUPAC name 3,7-dihydropurine-2,6-dione InChIKey LRFVTYWOQMYALW-UHFFFAOYSA-N
LogP -1.061 Topological polar surface area 94.4
Hydrogen bond acceptor 3 Hydrogen bond donor 3

Synonym(s):
xanthine; 69-89-6; 2,6-Dihydroxypurine; Isoxanthine; Xanthin; 2,6-dioxopurine; Pseudoxanthine; 1H-Purine-2,6(3H,7H)-dione; Xanthic oxide; 1H-Purine-2,6-diol; 9H-Purine-2,6-diol; Purine-2,6-diol; 3,7-Dihydro-1H-purine-2,6-dione; 1H-Purine-2,6-dione, 3,7-dihydro-; 2,6(1,3)-Purinedion; 3,7-dihydropurine-2,6-dione; Purine-2(3H),6(1H)-dione; USAF CB-17; 9H-xanthine; XAN; 2,6-Dioxo-1,2,3,6-tetrahydropurine; 3,9-dihydro-1H-purine-2,6-dione; 9H-Purine-2,6-(1H,3H)-dione; 7H-purine-2,6-diol; 1H-Purine-2,6-dione, 3,9-dihydro-; Purine-2,6-(1H,3H)-dione; UNII-1AVZ07U9S7; NSC 14664; EPA Pesticide Chemical Code 116900; CHEBI:17712; AI3-52268; MFCD00078453; Xanthine (VAN) (8CI); CID 5280342; CHEMBL1424; 1AVZ07U9S7; Purine-2,6(1H,3H)-dione; xanthine (2,6-dihydroxypurine); 9H-Purine-2,6(1H,3H)-dione; 1H-purine-2,6(3H,9H)-dione; CCRIS 994; EINECS 200-718-6; Dioxopurine; Dioxypurin; 7H-xanthine; 3H-Purine-2,6-diol (9CI); 7H-Purine-2,6-diol (9CI); 2-Oxohypoxanthine; 2,6-dioxypurine; Xanthine,(S); 2,6-Dihydroxypurin; Xanthine, 98%; Purine-2,3H)-dione; Xanthine, >=99%; 2uz9; Xanthine-13C-15N2; 2H-Purin-2-one, 1,3-dihydro-6-hydroxy-; 2H-Purin-2-one, 3,9-dihydro-6-hydroxy-; 6H-Purin-6-one, 1,9-dihydro-2-hydroxy-; bmse000127; MolMap_000070; Xanthine, p.a., 99%; 9H-Purine-2,3H)-dione; Cambridge id 5126190; SCHEMBL4965; 2,2,3,6-tetrahydropurine; Oprea1_474175; 2H-Purin-2-one, 3,7-dihydro-6-hydroxy- (9CI); Xanthine, BioUltra, >=99%; 3,9-dihydropurine-2,6-dione; AMY239; GTPL4557; DTXSID4035120; 3,7-dihydro-purine-2,6-dione; 3,9-Dihydro-purine-2,6-dione; BDBM82009; CHEBI:48517; LRFVTYWOQMYALW-UHFFFAOYSA-; HMS1659G11; HMS3604G12; BCP15189; CAS_1188; NSC_1188; NSC14664; 1H-purine-2,6(3H, 7H)-dione; BBL028159; BDBM50227193; NSC-14664; STL064827; STL453051; ZINC13517187; AKOS000498219; AKOS005208756; AKOS015896921; AC-8422; AM83905; CCG-266216; CS-W018105; DB02134; FS-3231; HY-W017389; MCULE-6687728468; SDCCGMLS-0065805.P001; 2,6-Dioxo-1,2,3, 6-tetrahydropurine; NCGC00164338-01; 173793-02-7; 173793-03-8; 173793-05-0; 173793-06-1; 173793-08-3; 51953-16-3; 51953-25-4; 51953-27-6; K177; SY030113; AB0014073; DB-015929; 2,3,6,7-tetrahydro-1H-purine-2,6-dione; FT-0631300; S3693; 7117-EP2269989A1; 7117-EP2272832A1; 7117-EP2272835A1; 7117-EP2272844A1; 7117-EP2272848A1; 7117-EP2292227A2; 7117-EP2295406A1; 7117-EP2295434A2; 7117-EP2295435A1; 7117-EP2298312A1; 7117-EP2298769A1; 7117-EP2298772A1; 7117-EP2301937A1; 7117-EP2305684A1; 7117-EP2308562A2; 7117-EP2308839A1; 7117-EP2308878A2; 7117-EP2311806A2; 7117-EP2311832A1; 7117-EP2311833A1; 7117-EP2316974A1; C00385; D71218; Q50980; X-0950; AB00171825-02; 108079-EP2287164A1; 108079-EP2298769A1; A836687; 6H-Purin-6-one, 1,7-dihydro-2-hydroxy- (9CI); Z57825360; 92AB342E-6550-4B2B-AD76-E75AC1C2EB45; Xanthine, >=99.5% (HPLC), purified by recrystallization; 1262670-81-4

Activity data

No relevant experimental diagram

 Interaction ID 803
Target type Molecule
Target unique ID 1188
Activity 3.3 μM
Binding Conditions/Buffer

20 mM Tris-HCl (pH 7.5), 0.3 M NaCl and 5 mM MgCl2
Assay

N/A
PubMed ID 9512549

No relevant experimental diagram

 Interaction ID 1000
Target type Molecule
Target unique ID 135398634
Activity 1.3 μM
Binding Conditions/Buffer

20 mM Tris-HCl (pH 7.5), 0.3 M NaCl and 5 mM MgCl2
Assay

N/A
PubMed ID 9512549
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_1167 RNA GGCGCGAGGAAGGAGGUCUGAGGAGGUCACUGCGCC 58.33%
Apta_367 RNA CGAGCGUAGAAUGUCUUCCCACUAGACGUCGUUCGGCCCC 57.50%
Apta_371 RNA GGCAGACCAUACGGGAGAGAAACUUGCC 56.25%
Apta_633 RNA GGCAUCGGAAAGUGGGUUGAUGUAAGUAACAGGCGAUGCC 55.00%
Apta_85 RNA UGCGACUGUUAUAACCUAACAGCGACGUAAAGAUA 54.29%
Apta_138 RNA GGAGGUGCUCCGAAAGGAACUCC 53.12%
Apta_634 RNA GGUCUUACGUCGUUCGCGACUAUUGGGAGACC 53.12%
Apta_955 RNA ACGUAUCCCUUUUCGCGUA 53.12%
Apta_956 RNA ACGUUUCCCUUUUCGCGUA 53.12%
Apta_315 RNA GGGAGGACGAUGCGGUCGUAUUAUCCGCUGCACGCCAGACGACUCGCCCGA 52.94%
Apta_313 RNA UGCCCUGCCCUCACCCGUUAGCCUGAGCGCCCCGCA 52.78%
Apta_365 RNA GGACCUAUGCAGUAGCCAGUGUGGACUGGGCUGCCCCCCC 52.50%
Apta_658 RNA CUGCGAUCAGGGGUAAAUUUCCGCGCAGGCUCCACGCCGC 52.50%
Apta_152 RNA UUACCACGCGCUCUUAACUGCUAGCGCCAUGGC 51.52%
Apta_289 RNA GGGGGCUUAUCAUUCCAUUUAGUGUUAUGAUAACC 51.43%
Apta_1 RNA ACGAAGCUUGAUCCCGUUUGCCGGUCGAUCGCUUCGA 51.35%
Apta_51 RNA GCCUUAGUAACGUGCUUUGAUGUCGAUUCGACAGGAGGC 51.28%
Apta_1121 RNA GACAGCGUGCCUAGAAGUCCAAGCUUAAAUAACCACGCUCGACAAGC 51.06%
Apta_132 RNA GGGAGGACGAUGCGGCGUUUCCUCUGGUUCGUCCCCAGACGACUCGCCCGA 50.98%
Apta_133 RNA GGGAGGACGAUGCGGUGAGUCGUUCCCUUCGUCCCCAGACGACUCGCCCGA 50.98%

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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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