Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 592
Aptamer sequence: GGAUGUCCAGUCGCUUGCAAUGCCCUUUUAGACCCUGAUGAGGAUCAUCGGACUUUGUCCUGUGGAGUAAGAUCGCGAAACGGUGAAAGCCGUAGGUCU
Target unique ID: 2519
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_559 S2.caf.D11 Molecule Caffeine 1 mM 500 mM NaCl, 10 mM MgCl2, 1 mM EDTA, 10 mM sodium phosphate, 90 mM HEPES (pH 7.5) 15026535
Structure information of aptamer
Aptamer Sequence: GGAUGUCCAGUCGCUUGCAAUGCCCUUUUAGACCCUGAUGAGGAUCAUCGGACUUUGUCCUGUGGAGUAAGAUCGCGAAACGGUGAAAGCCGUAGGUCU
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_559 Description S2.caf.D11
Aptamer chemistry RNA Length 99 nt
GC content 51.5% Molecular weight 31,865.83 Da
Molarity of 1 μg/μl solution 31.38 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Aptasensor
Sequence GGAUGUCCAGUCGCUUGCAAUGCCCUUUUAGACCCUGAUGAGGAUCAUCGGACUUUGUCCUGUGGAGUAAGAUCGCGAAACGGUGAAAGCCGUAGGUCU
Applications Detect caffeine or aspartame
Target information
Type Detail Type Detail
PubChem ID 2519 Molecular name Caffeine
Molecular formula C8H10N4O2 Molecular weight 194.19
IUPAC name 1,3,7-trimethylpurine-2,6-dione InChIKey RYYVLZVUVIJVGH-UHFFFAOYSA-N
LogP -1.029 Topological polar surface area 61.82
Hydrogen bond acceptor 6 Hydrogen bond donor 0

Synonym(s):
caffeine; 58-08-2; 1,3,7-Trimethylxanthine; Guaranine; Thein; Methyltheobromine; Cafeina; Theine; Koffein; Mateina; Alert-pep; Caffein; Cafipel; Coffeine; Refresh'n; Caffedrine; Stim; Cafamil; Cafecon; Caffine; Dexitac; Nodaca; Anhydrous caffeine; No-Doz; Eldiatric C; 7-Methyltheophylline; Hycomine; Organex; Vivarin; Nix Nap; Methyltheobromide; Coffein; Phensal; 3,7-Dihydro-1,3,7-trimethyl-1H-purine-2,6-dione; Caffeine, synthetic; Quick-Pep; Coffeinum; Tirend; 1,3,7-Trimethyl-2,6-dioxopurine; 1,3,7-Trimethylpurine-2,6-dione; Theophylline, 7-methyl; DHCplus; Tri-Aqua; 1H-Purine-2,6-dione, 3,7-dihydro-1,3,7-trimethyl-; Kofein; Miudol; Caffeine, anhydrous; Theobromine, 1-methyl-; Propoxyphene Compound 65; 1,3,7-Trimethyl-3,7-dihydro-1H-purine-2,6-dione; Kofein [Czech]; Coffein [German]; Koffein [German]; 1-methyltheobromine; Caffeine (natural); Xanthine, 1,3,7-trimethyl; Caffeina [Italian]; Theophylline Me; Methylxanthine theophylline; Theobromine Me; NCI-C02733; SK-65 Compound; Anacin; Anacin Maximum Strength; P-A-C Analgesic Tablets; C8H10N4O2; HSDB 36; FEMA No. 2224; BRN 0017705; 1,3,7-trimethyl-2,3,6,7-tetrahydro-1H-purine-2,6-dione; NSC 5036; A.S.A. and Codeine Compound; UNII-3G6A5W338E; 1,3,7-trimethyl-1H-purine-2,6(3H,7H)-dione; AI3-20154; CHEMBL113; CFF; CHEBI:27732; 3G6A5W338E; NSC-5036; MFCD00005758; caffenium; SK 65 Compound; Caffeina; DSSTox_CID_232; Caffeine [BAN:JAN]; CAFFEINE-D3; DSSTox_RID_75448; DSSTox_GSID_20232; cafeine; peyona; teina; CAS-58-08-2; Caffeine (USP); SMR000326667; CCRIS 1314; SR-01000075187; Anhydrous caffeine (TN); EINECS 200-362-1; Monomethyl derivative of Theophylline; Caffeine [USP:BAN:JAN]; Anhydrous caffeine (JP15); Caffeine hydrous; 1gfz; Caffeine, BioXtra; TNP00310; Monohydrate Caffeine; Respia (TN); 1-methyl-Theobromine; 7-methyl Theophylline; Cafergot (Salt/Mix); 1,7-Trimethylxanthine; Spectrum_001301; 1l5q; 1l7x; 2a3b; 3g6m; 3,7-dihydro-1,3,7-trimethyl-1H-purine; Xanthine,3,7-trimethyl; Theine, methyltheobromine; Spectrum2_001261; Spectrum3_000321; Spectrum4_001782; Spectrum5_000423; Lopac-C-0750; bmse000206; MolMap_000054; Probes1_000150; Probes2_000128; C 0750; EC 200-362-1; SCHEMBL5671; Anhydrous caffeine (JP17); NCIOpen2_008255; BIDD:PXR0172; Lopac0_000228; 1, 3, 7-Trimethylxanthine; BSPBio_001921; GTPL407; KBioGR_002325; KBioSS_001781; 1,3,7-trimethyl-1,3,7-trihydropurine-2,6-dione; 5-26-13-00558 (Beilstein Handbook Reference); MLS001055341; MLS001056714; MLS001066409; BIDD:ER0554; BIDD:GT0632; DivK1c_000730; SPECTRUM1500155; CU-01000012617-3; SPBio_001222; Caffeine melting point standard; MEGxp0_001350; ZINC1084; 1,3,7-trimethyl-2,6-dioxo-1,2,3,6-tetrahydropurine; component of Dilone (Salt/Mix); DTXSID0020232; 1,7-Trimethyl-2,6-dioxopurine; ACon1_000085; BDBM10849; HMS502E12; KBio1_000730; KBio2_001781; KBio2_004349; KBio2_006917; KBio3_001141; Caffeine 1.0 mg/ml in Methanol; NSC5036; Caffeine, powder, ReagentPlus(R); component of Percodan (Salt/Mix); NINDS_000730; Bio1_000473; Bio1_000962; Bio1_001451; HMS1920I09; HMS2091O11; HMS2232M13; HMS3260N17; HMS3372J18; HMS3435F10; HMS3715D13; Pharmakon1600-01500155; NoDoz Caplets and Chewable Tablets; Caffeine 10 microg/mL in Methanol; CS-M0795; Tox21_201685; Tox21_300010; Tox21_500228; BBL016491; caffeine (1,3,7-trimethylxanthine); Caffeine 100 microg/mL in Methanol; CCG-38825; NSC755917; PDSP1_001016; PDSP1_001235; PDSP2_001000; PDSP2_001219; STK177283; Propoxyphene Compound 65 (Salt/Mix); AKOS000121334; 5-26-13-00558 (Beilstein); ACN-034787; Bayer Select Headache Pain (Salt/Mix); Caffeine, anhydrous, 99%, FCC, FG; DB00201; LP00228; MCULE-3362813910; NSC-755917; SDCCGMLS-0064595.P001; SDCCGMLS-0064595.P002; SDCCGSBI-0050216.P005; IDI1_000730; 3,3,7-trimethyl-1H-purine-2,6-dione; NCGC00015208-01; NCGC00015208-02; NCGC00015208-03; NCGC00015208-04; NCGC00015208-05; NCGC00015208-06; NCGC00015208-07; NCGC00015208-08; NCGC00015208-10; NCGC00015208-11; NCGC00015208-12; NCGC00015208-13; NCGC00015208-14; NCGC00015208-15; NCGC00015208-16; NCGC00015208-17; NCGC00015208-18; NCGC00015208-20; NCGC00015208-29; NCGC00090699-01; NCGC00090699-02; NCGC00090699-03; NCGC00090699-04; NCGC00090699-05; NCGC00090699-06; NCGC00090699-07; NCGC00090699-08; NCGC00090699-09; NCGC00168808-01; NCGC00168808-02; NCGC00254057-01; NCGC00259234-01; NCGC00260913-01; AC-12774; AS-15340; Caffeine, SAJ special grade, >=98.5%; component of P-A-C Compound (Salt/Mix); O926; component of A.S.A. Compound (Salt/Mix); SBI-0050216.P004; DB-023002; WLN: T56 BN DN FNVNVJ B1 F1 H1; EU-0100228; FT-0664195; N1379; N2379; 3378-EP2269610A2; 3378-EP2275420A1; 3378-EP2277848A1; 3378-EP2277867A2; 3378-EP2280003A2; 3378-EP2284160A1; 3378-EP2289510A1; 3378-EP2295409A1; 3378-EP2295434A2; 3378-EP2301937A1; 3378-EP2305219A1; 3378-EP2305662A1; 3378-EP2305671A1; 3378-EP2305677A1; 3378-EP2305682A1; 3378-EP2305695A2; 3378-EP2305696A2; 3378-EP2305697A2; 3378-EP2305698A2; 3378-EP2308562A2; 3378-EP2308840A1; 3378-EP2308867A2; 3378-EP2308870A2; 3378-EP2308879A1; 3378-EP2311801A1; 3378-EP2311802A1; 3378-EP2311803A1; 3378-EP2311806A2; 3378-EP2311808A1; 3378-EP2311829A1; 3378-EP2311842A2; 3378-EP2314588A1; 3378-EP2314590A1; 3378-EP2314593A1; 3378-EP2316457A1; 3378-EP2316458A1; 3378-EP2316825A1; 3378-EP2316826A1; 3378-EP2316827A1; 3378-EP2316828A1; 3378-EP2371814A1; BIM-0050216.0001; C07481; D00528; Q60235; 1,3,7-trimethyl-3,7-dihydropurine-2,6-dione; 1H-Purine-2, 3,7-dihydro-1,3,7-trimethyl-; AB00051930-09; AB00051930_10; Caffeine, purum, anhydrous, >=99.0% (HPLC); 3,7-dihydro-1,3,7-trimethyl-1H-purine (9CI); Caffeine, anhydrous, tested according to Ph.Eur.; L000155; 3,7-Dihydro-1,3,7-trimethyl-1H-purin-2,6-dion; Caffeine, Sigma Reference Standard, vial of 250 mg; SR-01000075187-1; SR-01000075187-4; SR-01000075187-7; SR-01000075187-8; BRD-K02404261-001-02-7; BRD-K02404261-001-03-5; BRD-K02404261-001-07-6; Caffeine, certified reference material, TraceCERT(R); Caffeine, meets USP testing specifications, anhydrous; Melting point standard 235-237C, analytical standard; 1,3,7-Trimethyl-3,7-dihydro-1H-purine-2,6-dione #; Caffeine, British Pharmacopoeia (BP) Reference Standard; Caffeine, European Pharmacopoeia (EP) Reference Standard; F3371-0262; Z112207564; Caffeine 2000 microg/mL in Water:Methanol (81:19 g/g); 07E4FB58-FD79-4175-8E3D-05BF96954522; 3,7-Dihydro-1,3,7-trimethyl-1H-purin-2,6-dion (coffein); Caffeine solution, analytical standard, 1.0 mg/mL in methanol; Caffeine, United States Pharmacopeia (USP) Reference Standard; Caffeine, Pharmaceutical Secondary Standard; Certified Reference Material; Caffeine for system suitability, European Pharmacopoeia (EP) Reference Standard; Caffeine melting point standard, United States Pharmacopeia (USP) Reference Standard; Caffeine solution, 1.0 mg/mL in methanol, ampule of 1 mL, certified reference material; 114303-55-8; Caffeine Melting Point Standard, Pharmaceutical Secondary Standard; Certified Reference Material; Caffeine, PharmaGrade, EP, Manufactured under appropriate GMP controls for pharma or biopharmaceutical production; Mettler-Toledo Calibration substance ME 18872, Caffeine, analytical standard, for the calibration of the thermosystem 900, traceable to primary standards (LGC)

Activity data
Interaction ID 592
Target type Molecule
Target unique ID 2519
Activity 1 mM
Binding Conditions/Buffer

500 mM NaCl, 10 mM MgCl2, 1 mM EDTA, 10 mM sodium phosphate, 90 mM HEPES (pH 7.5)

Assay

Measurement of fluorescence at 535 nm versus time at various concentrations of caffeine (S2.caf.D11)

PubMed ID 15026535
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_551 RNA GGAUGUCCAGUCGCUUGCAAUGCCCUUUUAGACCCUGAUGAGCGGUGCUAGUUAGUUGCAGUUUCGGUUGUUACGCGAAACGGUGAAAGCCGUAGGUCU
80.81%
Apta_613 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGCAUGAUGCAGAAGGACGUCGAAACGGUAGCGAGAGCUC 60.61%
Apta_612 RNA GGGCGACCCUGAUGAGCCUUAGGAUAUGCUUCGGCAGAAGGACGUCGAAACGGUGAAAGCCGUAGGUUGCCC 58.59%
Apta_561 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUGUGGAAACAGACGUGGCACAUGACUACGUCGAAACGGUAGCGAGAGCUC 56.57%
Apta_562 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUUAGGGCCAAGUGUGGUGAAAGACACACUCGAAACGGUAGCGAGAGCUC 56.57%
Apta_566 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCCUGCGAUGCAGAAAGGUGCUGACGACACAUCGAAACGGUAGCGAGAGCUC 55.56%
Apta_874 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGCCUUAGGAUAUGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACAGAAGGACGUCGAAACGGUAGCGAGAGCUC 55.56%
Apta_1056 RNA GUCAUGUUGUGUUGUGGUCCAUCCUUUUCUACGCCAGUCGAGUCUGUAGCGUGGGAGUAAACUGAACGGUCAGACAGGA 55.56%
Apta_893 RNA ACCGAGUCCAGAAGCUUGUAGUACUUAUGUCCCAUCGAACGCAGUGUAUCUUGCACCGACUCUCUGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC 55.14%
Apta_894 RNA ACCGAGUCCAGAAGCUUGUAGUACUGACCCUUCCCGACGCACGGACCAGUGAUGCCAACCCACCCGCCUAGAUGGAGUUGAAUUCUCCCUAUAGUGAGUCGUAUUAC 55.14%
Apta_710 RNA GGAUAAUAGCCGUAGGUUGCGAAAGCGACCCUGAUGAGUCUGGAUACCAUGCAUGAUGCACCUUGGCAGUCUUACGAAACGGUAGCGAGAGCUC 54.55%
Apta_294 RNA AUACCAGCUUAUUCAAUUGCCUGAUUAGCGGUAUCACGAUUACUUACCUUCGUUGCUGAGAUAGUAAGUGCAAUCU 53.54%
Apta_299 RNA AUACCAGCUUAUUCAAUUGCCUGAAGACUGGAUAUACUCUUAAGCAUUUCUAUAAUCGAGAUAGUAAGUGCAAUCU 53.54%
Apta_399 RNA GGGAGGACGAUGCGGCAAACCAGCUAUUUCCUGAGGUACCCCGGCUCUCCAUGGCAGACGACUCGCUGAGGAUCCGAGA 52.53%
Apta_414 RNA GGGAGGACGAUGCGGCCGAUUAGAACUGGGCUGAGGCGUUCUGCAUUUCGGUGAUCAGACGACUCGCUGAGGAUCCGAGA 52.53%
Apta_499 RNA GGACGCGUGGUACCAGGCCGAUCUAUGGACGCUAUAGGCACACCGGAUACUUUAACGAUUGGCUAAGCUUCCGCGGGGAUC 52.53%
Apta_696 RNA GAGUGCGCCCAUUGAUAAGAGCGUAGGUUCAACGGAGUCGUAGUCGUUCUCAAGUUGACGGUGCAUUAGAGUCCU 52.53%
Apta_295 RNA AUACCAGCUUAUUCAAUUGCCUGAAAAGCUAUCGCCCAAUUCGCAGUGAUAUCCUUUAAGAUAGUAAGUGCAAUCU 51.52%
Apta_298 RNA AUACCAGCUUAUUCAAUUGCCUGAAAACUGGUGUACCUCUUUGCCCUAUCUUAUCUGGAGAUAGUAAGUGCAAUCU 51.52%
Apta_380 RNA GGGAUGCUUCGGCAUCCCCGAAGCCGCUAUGGACCAGUGGCGCGGCUUCGGCCCGACGGAGUGGUACCGCUUCGGCGGUACGUAAGCUUGGG 51.52%