Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 590
Aptamer sequence: GGAACACUAUCCGAUGGCACCGACCAUAGGCUCGGGUUGCCAGAGGUUCCACACUUUCAUCGAAAAGCCUAUGCUAGGCAAUGACAUGGACUCCUUGGUCAUUAGGAUCG
Target unique ID: 171548
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_557 N Molecule Biotin 5.7 μM 0.1 M KCl, 5 mM MgCl2, and 10 mM Na-HEPES (pH 7.4) 9772167
Structure information of aptamer
Aptamer Sequence: GGAACACUAUCCGAUGGCACCGACCAUAGGCUCGGGUUGCCAGAGGUUCCACACUUUCAUCGAAAAGCCUAUGCUAGGCAAUGACAUGGACUCCUUGGUCAUUAGGAUCG
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_557 Description N
Aptamer chemistry RNA Length 110 nt
GC content 51.8% Molecular weight 35,325.97 Da
Molarity of 1 μg/μl solution 28.31 μM Number of G-quadruplexes 2
G-Score 19 Function Aptasensor
Sequence GGAACACUAUCCGAUGGCACCGACCAUAGGCUCGGGUUGCCAGAGGUUCCACACUUUCAUCGAAAAGCCUAUGCUAGGCAAUGACAUGGACUCCUUGGUCAUUAGGAUCG
Applications Detection of biotin
Target information
Type Detail Type Detail
PubChem ID 171548 Molecular name Biotin
Molecular formula C10H16N2O3S Molecular weight 244.31
IUPAC name 5-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoic acid InChIKey YBJHBAHKTGYVGT-ZKWXMUAHSA-N
LogP 0.797 Topological polar surface area 78.43
Hydrogen bond acceptor 3 Hydrogen bond donor 3

Synonym(s):
biotin; d-biotin; 58-85-5; vitamin H; Vitamin B7; coenzyme R; Bioepiderm; Bios II; Factor S; D(+)-Biotin; Biodermatin; Medebiotin; (+)-Biotin; D-(+)-Biotin; Biotinum; Biotine; Meribin; Factor S (vitamin); Lutavit H2; Biotina; 3H-Biotin; NSC 63865; CCRIS 3932; HSDB 346; Injacom H; 5-((3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoic acid; cis-Hexahydro-2-oxo-1H-thieno(3,4)imidazole-4-valeric acid; cis-Tetrahydro-2-oxothieno(3,4-d)imidazoline-4-valeric acid; 1swk; 1swn; 1swr; MFCD00005541; Rovimix H 2; D-Biotin Factor S; UNII-6SO6U10H04; 5-[(3aS,4S,6aR)-2-oxo-hexahydro-1H-thieno[3,4-d]imidazolidin-4-yl]pentanoic acid; AI3-51198; 5-[(3aS,4S,6aR)-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid; 5-[(3aS,4S,6aR)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoic acid; cis-(+)-Tetrahydro-2-oxothieno[3,4]imidazoline-4-valeric acid; (+)-cis-Hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-valeric acid; 1H-Thieno(3,4-d)imidazole-4-pentanoic acid, hexahydro-2-oxo-, (3aS-(3aalpha,4beta,6aalpha))-; 2'-Keto-3,4-imidazolido-2-tetrahydrothiophene-N-valeric acid; CHEBI:15956; 6SO6U10H04; (3aS,4S,6aR)-Hexahydro-2-oxo-1H-thieno(3,4-d)imidazole-4-valeric acid; 1H-thieno[3,4-d]imidazole-4-pentanoic acid, hexahydro-2-oxo-, (3aS,4S,6aR)-; Hexahydro-2-oxo-1H-thieno(3,4-d)imidazole-4-pentanoic acid, (3aS-(3aalpha,4beta,6aalpha))-; beta-Biotin; 5-(2-Oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoic acid; DSSTox_CID_2679; Vitamin Bw; (3aS,4S,6aR)-Hexahydro-2-oxo-1H-thieno[3,4-d]imidazole-4-valeric acid; (3aS-(3aalpha,4b,6aalpha))-Hexahydro-2-oxo-1H-thieno(3,4-d)imidaz- ole-4-pentanoic acid; DSSTox_RID_76688; DSSTox_GSID_22679; 22377-59-9; medobiotin; Deacura; Gabunat; Hexahydro-2-oxo-1H-thieno(3,4-d)imidazole-4-pentanoic acid; Rombellin; Biokur; Biotine [INN-French]; Biotinum [INN-Latin]; Biotina [INN-Spanish]; Biotin Gelfert; Biotin Hermes; Biotine Roche; Gelfert, Biotin; Biotin ratiopharm; Biotin-ratiopharm; Hermes, Biotin; Roche, Biotine; 1H-Thieno(3,4-d)imidazole-4-pentanoic acid, hexahydro-2-oxo-, (3aS,4S,6aR)-; 5-((3AS,4S,6aR)-rel-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoic acid; BTN; SMR000112255; D(+)Biotin; EINECS 200-399-3; Biotin [USP:INN:JAN]; hexahydro-2-oxo-1H-thieno[3,4-d]imidazole-4-pentanoic acid; d-biotine; delta-Biotin; Vitamin-h; NSC-63865; L-Biotin; 1avd; 1ndj; 1stp; 1swg; 1swp; 2avi; 4bcs; 4ggz; 4jnj; Bioepiderm (TN); CAS-58-85-5; Bios H; NCGC00094984-04; 1H-Thieno[3,4-d]imidazole-4-pentanoic acid, hexahydro-2-oxo-, [3as-(3aalpha,4beta,6aalpha)]-; Biotin111In; delta-(+)-Biotin; Biotin (8CI); delta-biotin factor s; 1df8; 1n9m; 2gh7; 3t2w; 4bj8; Prestwick0_000418; Prestwick1_000418; Prestwick2_000418; Prestwick3_000418; cid_253; BDBM12; Biotin Silver Nanoparticles; bmse000227; CHEMBL857; Probes2_000006; SCHEMBL8763; BSPBio_000376; Biotin (JP17/USP/INN); MLS001066402; MLS001074888; MLS001331736; MLS001333089; D-Biotin, analytical standard; SPBio_002315; BPBio1_000414; cid_171548; GTPL4787; DTXSID7022679; AMF0005; 1n43; 2f01; Biotin, >=99.0% (T); HMS1569C18; HMS2096C18; HMS2271O06; HMS3713C18; HY-B0511; Tox21_113050; Tox21_302161; AC8089; BBL028095; Biotin, tested according to Ph.Eur.; s3130; STK801941; ZINC35024346; AKOS001287669; Tox21_113050_1; CCG-220418; DB00121; MCULE-7440963355; MD-1003; 1H-Thieno(3,4-d)imidazole-4-pentanoic acid, hexahydro-2-oxo-, (3aS-(3aalpha,4b,6aalpha))-; D-Biotin 10 microg/mL in Acetonitrile; Biotin, meets USP testing specifications; Biotin, SAJ special grade, >=98.0%; NCGC00179580-01; NCGC00179580-02; NCGC00179580-04; NCGC00255377-01; 22879-79-4; 56846-45-8; AC-19998; BP-20441; AB0068872; Biotin, >=99% (TLC), lyophilized powder; Biotin, Vetec(TM) reagent grade, >=99%; AB00374191; B0463; Biotin Impurity D - mixture of diastereomers; 58B855; C00120; D00029; M02926; AB00374191-08; AB00374191_11; A929752; Biotin, plant cell culture tested, >=99% (TLC); Q181354; SR-01000765521; Biotin, certified reference material, TraceCERT(R); Q-200929; SR-01000765521-2; BRD-K89210380-001-03-8; BRD-K89210380-001-13-7; 6AE43AA3-BC3D-4C49-9DB9-5913A2401EB6; Biotin, European Pharmacopoeia (EP) Reference Standard; F2173-0855; Hexahydro-2-oxo-1H-thieno(3,4-d)imidazole-4-pentanoate; Z210803762; Biotin, United States Pharmacopeia (USP) Reference Standard; cis-(+)-Tetrahydro-2-oxothieno[3,4]imidazoline-4-valerate; (+)-cis-Hexahydro-2-oxo-1H-thieno[3,4]imidazole-4-valerate; 5-(2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl)pentanoate; Daunorubicin hydrochloride, Antibiotic for Culture Media Use Only; (3aS,4S,6aR)-Hexahydro-2-oxo-1H-thieno[3,4-d]imidazole-4-valerate; Biotin, Pharmaceutical Secondary Standard; Certified Reference Material; 1H-Thieno[3,4-d]imidazole-4-pentanoic acid, hexahydro-2-oxo-, (3aS,4S,6aR)- (9CI); 5-((3aR,6S,6aS)-2-Oxo-hexahydro-thieno[3,4-d]imidazol-6-yl)-pentanoic acid; 5-[(3aR,6S,6aS)-2-oxo-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-6-yl]pentanoic acid; Biotin for system suitability, European Pharmacopoeia (EP) Reference Standard; hexahydro-2-oxo-[3aS-(3aa,4b,6aa)]-1H-Thieno[3,4-d]imidazole-4-pentanoate; hexahydro-2-oxo-[3aS-(3aa,4b,6aa)]-1H-Thieno[3,4-d]imidazole-4-pentanoic acid; hexahydro-2-oxo-[3as-(3alpha,4beta,6alpha)]-1H-Thieno[3,4-d]imidazole-4-pentanoate; hexahydro-2-oxo-[3as-(3alpha,4beta,6alpha)]-1H-Thieno[3,4-d]imidazole-4-pentanoic acid; BIOTIN, PharmaGrade, USP, meets FCC testing specifications, Manufactured under appropriate GMP controls for pharma or biopharmaceutical production.; Biotin, powder, BioReagent, suitable for cell culture, suitable for insect cell culture, suitable for plant cell culture, >=99%

Activity data
Interaction ID 590
Target type Molecule
Target unique ID 171548
Activity 5.7 μM
Binding Conditions/Buffer

0.1 M KCl, 5 mM MgCl2, and 10 mM Na-HEPES (pH 7.4)
Assay

Saturation curve for the binding of the biotin aptamer to immobilized ligand as described in the Materials and Methods
PubMed ID 9772167
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_724 RNA GGGAGAGGAUACUACUGUCAUACGUUAGGCUGUAGGCGAGGUGAAAUGAGCGGUAAUAGCCUCAGCGUAGCAUAUGCAUGAAUUCGAAGCUUCGC 54.55%
Apta_59 RNA GGACCUCGGCGAAAGCUAACGUCUCAUGGCUAAAUUGCCAUGUUGCUACAAAUGAUAUGACUAGAGAGGUUAGGUGCCUCGUGAUGUCCAGUCGC 53.64%
Apta_224 RNA GGGGCCACCAACGACAUUGAACCACGUAGGCUCGUUUCUGAGCCGAUCUCGAUGUUGAUAUAAAUAGUGCCCAUGGAUC 52.73%
Apta_705 RNA CCGUAAUACGACUCACUAUAGGGGAGCUCGGUACCGAAUUCAAGGUACUCUGUGCUUGUCGAUGUGUAUUGAUGGCACUUUCGAGUCAACGAGUUGACAGAACAAGUAGUCAAGCUUUGCAGAGAGGAUCCUU 52.63%
Apta_225 RNA GGGGCCACCAACGACAUUUAUCGAAUUGAUAACCUUACGCGAGAGCGUAGUUCGUUGAUAUAAAUAGUGCCCAUGGAUC 51.82%
Apta_400 RNA GGGAGGACGAUGCGGAUACCAGCGAAUAACUCGCUGAGGAACCCGACUCACAAACAGACGACUCGCUGAGGAUCCGAGA 51.82%
Apta_414 RNA GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA 51.82%
Apta_429 RNA GCAUGCAGUGUCUAUUCUCGAGUAGCGAUCGUUGAAGGGGUAUAAGGUUGGCAGAUCGCUAGCAUGCAACUGACUCGGAUAAGCA 51.82%
Apta_624 RNA GGGAAUGGAUCCACAUCUACGAAUUCGAAUUGCCGUAAUUUCCCGUGGAGCGAUGCUUCACUGCAGACUUGACGAAGCUU 51.82%
Apta_854 RNA GGGAGCUCAGAAUAAACGCUCAAGGGUAGGGAUCGUUACCCCGACAUUUUAAUGGGCCGAUGUUUCGACAUGAGGCCCGGAUCCGGC 51.82%
Apta_936 RNA GGAGCUCAGCCUUCACUGCGAUCACCGUGUCGGUGGCUAGUCGAUGUAUCCCGAUCACCAUUGGGGGCAAGUUUAGACAGGCACCACGGUCGGAUCCAC 51.82%
Apta_352 RNA GGGAGGACGAUGCGGUGGUCUCCCAAUUCUAAACUUUCUCCAUCGUAUCUGGGCAGACGACUCGCCCGA 50.91%
Apta_353 RNA GAAUUCCGCGUGUGCCAGCGAAAGUUGCGUAUGGGUCACAUCGCAGGCACAUGUCAUCUGGGCGGUCCGUUCGGGAUCC 50.91%
Apta_399 RNA GGGAGGACGAUGCGGCAAACCAGCUAUUUCCUGAGGUACCCCGGCUCUCCAUGGCAGACGACUCGCUGAGGAUCCGAGA 50.91%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 50.91%
Apta_5 RNA GGGAGAGCCAUACCUGACAAAGACGCUAGCGAAUUGGUUCCUCACUCAAAAGUAGGGGAAAGCGUUAUUAAGAAACCAAAAUUUGACAGGUUACGCAUCCUGCAUCCUCCAGGUUACGCAUCC 50.41%
Apta_415 RNA GGGAGGACGAUGCGGAAACUCAUCGGUAGCCUUCCUGCGGUCAGUCUAUUAGGACCAGACGACUCGCUGAGGAUCCGAGA 50.00%
Apta_427 RNA GAAGCUUUCACACAACAAGGCCCGGGACUGUAUUAGGGAAAUUAGAGUACAGACAGUCGCCGUGGGUCGAAUUCCGCUCA 50.00%
Apta_499 RNA GGACGCGUGGUACCAGGCCGAUCUAUGGACGCUAUAGGCACACCGGAUACUUUAACGAUUGGCUAAGCUUCCGCGGGGAUC 50.00%
Apta_547 RNA GGGAGAAGGCGGCGCGUAGGCGAGCUUUAGGCCCGACAUUCCCCUAAAAAAGCUUGUUCUAUUCGUGGACGAUGCGCAC 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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