Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 709
Aptamer sequence: CACGCAACAACACAACATGCCCAGCGCCTGGAACATATCCTATGAGTTAGTCCGCCCACA
Target unique ID: 445434
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_664 RC6 Molecule Microcystin-LR 61 nM 50 mM Tris, pH 7.5, 150 mM NaCl, and 2 mM MgCl2 22958101
Structure information of aptamer
Aptamer Sequence: CACGCAACAACACAACATGCCCAGCGCCTGGAACATATCCTATGAGTTAGTCCGCCCACA
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_664 Description RC6
Aptamer chemistry DNA Length 60 nt
GC content 53.3% Molecular weight 18,280.76 Da
Molarity of 1 μg/μl solution 54.70 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Aptasensor
Sequence CACGCAACAACACAACATGCCCAGCGCCTGGAACATATCCTATGAGTTAGTCCGCCCACA
Applications Application in microcystin detection
Target information
Type Detail Type Detail
PubChem ID 445434 Molecular name Microcystin-LR
Molecular formula C49H74N10O12 Molecular weight 995.2
IUPAC name (5R,8S,11R,12S,15S,18S,19S,22R)-15-[3-(diaminomethylideneamino)propyl]-18-[(1E,3E,5S,6S)-6-methoxy-3,5-dimethyl-7-phenylhepta-1,3-dienyl]-1,5,12,19-tetramethyl-2-methylidene-8-(2-methylpropyl)-3,6,9,13,16,20,25-heptaoxo-1,4,7,10,14,17,21-heptazacyclopentacosane-11,22-dicarboxylic acid InChIKey ZYZCGGRZINLQBL-GWRQVWKTSA-N
LogP 0.618 Topological polar surface area 343.14
Hydrogen bond acceptor 11 Hydrogen bond donor 10

Synonym(s):
Microcystin-LR; Microcystin LR; 101043-37-2; Cyanoginosin LR; Toxin-LR; Microcystis aeruginosa toxin; Toxin I (Microcystis aeruginosa); UNII-EQ8332842Y; Cyanoginosin LA, 5-L-arginine-; CHEBI:6925; CHEMBL444092; MCYST-LR; C49H74N10O12; EQ8332842Y; Cyanoginosin-LR; (5R,8S,11R,12S,15S,18S,19S,22R)-15-[3-(diaminomethylideneamino)propyl]-18-[(1E,3E,5S,6S)-6-methoxy-3,5-dimethyl-7-phenylhepta-1,3-dienyl]-1,5,12,19-tetramethyl-2-methylidene-8-(2-methylpropyl)-3,6,9,13,16,20,25-heptaoxo-1,4,7,10,14,17,21-heptazacyclopentacosane-11,22-dicarboxylic acid; Akerstox; toxin I, cyanobacterium; Microcystin-a; 1,7-anhydro[D-alanyl-L-leucyl-(3S)-3-methyl-D-beta-aspartyl-L-arginyl-(2S,3S,4E,6E,8S,9S)-3-amino-4,5,6,7-tetradehydro-9-methoxy-2,6,8-trimethyl-10-phenyldecanoyl-D-gamma-glutamyl-2,3-didehydro-N-methylalanine]; cyclo[2,3-didehydro-N-methylalanyl-D-alanyl-L-leucyl-erythro-3-methyl-D-beta-aspartyl-L-arginyl-(2S,3S,4E,6E,8S,9S)-3-amino-4,5,6,7-tetradehydro-9-methoxy-2,6,8-trimethyl-10-phenyldecanoyl-D-gamma-glutamyl]; cyclo[D-alanyl-L-leucyl-(3S)-3-methyl-D-beta-aspartyl-L-arginyl-(2S,3S,4E,6E,8S,9S)-3-amino-4,5,6,7-tetradehydro-9-methoxy-2,6,8-trimethyl-10-phenyldecanoyl-D-gamma-glutamyl-2,3-didehydro-N-methylalanyl]; 5-L-Argininecyanoginosin LA; 5-L-Arginine-microcystin LA; cyclo(Ala-Leu-MAsp-Arg-Adda-isoGlu-Mdha); HSDB 7751; Toxin T 17 (Microcystis aeruginosa); BRN 4779759; Toxin, blue green alga, Microcystis aeruginosa; GTPL4735; SCHEMBL21245230; HY-P0072; 1859AH; 2545AH; BDBM50061067; NSC733608; ZINC169715525; CS-5404; NSC 733608; NSC-733608; M2912; C05371; Q6839436; Microcystin-LR solution, 10 mug/mL in methanol, analytical standard; 15-(3-Guanidino-propyl)-8-isobutyl-18-((1E,3E)-6-methoxy-3,5-dimethyl-7-phenyl-hepta-1,3-dienyl)-1,5,12,19-tetramethyl-2-methylene-3,6,9,13,16,20,25-heptaoxo-1,4,7,10,14,17,21heptaaza-cyclopentacosane-11,22-dicarboxylic acid; 15-(3-Guanidino-propyl)-8-isobutyl-18-(6-methoxy-3,5-dimethyl-7-phenyl-hepta-1,3-dienyl)-1,5,12,19-tetramethyl-2-methylene-3,6,9,13,16,20,25-heptaoxo-1,4,7,10,14,17,21heptaaza-cyclopentacosane-11,22-dicarboxylic acid; 8-[3-amino(imino)methylaminopropyl]-15-isobutyl-5-[6-methoxy-3,5-dimethyl-7-phenyl-(1E,3E)-1,3-heptadienyl]-4,11,18,22-tetramethyl-21-methylene-3,7,10,14,17,20,23-heptaoxo-2,6,9,13,16,19,22-heptaazacyclopentacosane-1,12-dicarboxylic acid

Activity data
Interaction ID 707
Target type Molecule
Target unique ID 6437382
Activity 43 nM
Binding Conditions/Buffer

50 mM Tris, pH 7.5, 150 mM NaCl, and 2 mM MgCl2
Assay

Determination of the dissociation constants (KD) for aptamers. On the basis of the fluorescence recovered, saturation curves were obtained and the dissociation constants were calculated by nonlinear regression analysis
PubMed ID 22958101
Interaction ID 709
Target type Molecule
Target unique ID 445434
Activity 61 nM
Binding Conditions/Buffer

50 mM Tris, pH 7.5, 150 mM NaCl, and 2 mM MgCl2
Assay

Determination of the dissociation constants (KD) for aptamers. On the basis of the fluorescence recovered, saturation curves were obtained and the dissociation constants were calculated by nonlinear regression analysis
PubMed ID 22958101
Interaction ID 716
Target type Molecule
Target unique ID 6437088
Activity 28 nM
Binding Conditions/Buffer

50 mM Tris, pH 7.5, 150 mM NaCl, and 2 mM MgCl2
Assay

Determination of the dissociation constants (KD) for aptamers. On the basis of the fluorescence recovered, saturation curves were obtained and the dissociation constants were calculated by nonlinear regression analysis
PubMed ID 22958101
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_1232 DNA GGCCACACAAACAACATGACAACACGTCTCACATAACGCCCACGTGCTGCCGCCTCATCG 58.33%
Apta_663 DNA CACGCACAGAAGACACCTACAGGGCCAGATCACAATCGGTTAGTGAACTCGTACGGCGCG 56.67%
Apta_1265 DNA CACGCACACAACAGCCAATAATGTATAACGCTGTCCACTGTGTGGTGTCCCCCGCGTCG 56.67%
Apta_472 DNA CCCCCACATTCAAATGGCCCCCCTACTCAATTACTGCACA 55.00%
Apta_1069 DNA CCGGAGAAAAAAAACTTGATGAGCCAGGAAAACGAGGGTTGGAACGCGACTG 55.00%
Apta_1172 DNA GACGCCACTGACTACCCCAGTATCTCTTCAACGCGTATTGAAGTCAGTCGGTCGTCA 55.00%
Apta_1173 DNA TTGACTTGCCACTGACTACCCCAGTATCTCTTCAACGCTATGGTGCATGTACTACGTATTGAAGTCAGTCGGTCGTCATC 55.00%
Apta_1008 DNA ATAGGAGTCGACCGACCAGACCATTCCCACGCCAAGACCAATTTTCCCTGTGCGTCTACATCTAGACTC 53.62%
Apta_421 DNA ATCTACGAATTCATCAGGGCTAAAGAGTGCAGAGTTACTTAGCCCGTGA 53.33%
Apta_636 DNA TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAGCCCCCCA 53.33%
Apta_728 DNA CGACCCGGCACAAACCCAGAACCATATACACGATCATTAGTCTCCTGGGCCG 53.33%
Apta_834 DNA CGCAATACCAAAGTGGCGAGAGCGCTGTCTTGAGTGAGTGGTTGG 53.33%
Apta_1227 DNA CACACCAAACACACAAGTGGACCCTGACGCATGGATAGGGTGACGGTATACGCGGGCATG 53.33%
Apta_527 DNA ATACGGGAGCCAACACCAACAACCTAGATGTTCTGATAACACGAATCGCTTCGAAGAGCAGGTGTGACGGAT 52.78%
Apta_1105 DNA TACGACTCACTATAGGGATCCAATGGCACAGCGCCTGGAACGTACTCTGTACCTGGAATTCCCTTTAGTGAGGGTT 52.63%
Apta_618 DNA GCGGCAAATCAGCATACGAGTGTACAGGGACGGGACGGGTGGGTAAAAGGTGTCGCCTCAG 52.46%
Apta_792 DNA ATACCAGCTTATTCAATTCCCAAATTGCCACCACTTACAGCATGATAACATACTACATCTTTTCATCAAGATAGTAAGTGCAATCT 52.33%
Apta_931 DNA ATACGACTCACTATTAGGGACCACATAAACATGCATCGCTCAATAACGGGATATTGTTGTGCTAGACTACTGACTACAA 51.90%
Apta_591 DNA CTCTCGGGACGACGGCTGGCACGTTTGGTTCAAGAATGTGGGTGTCGTCCC 51.67%
Apta_635 DNA TAGCCGGATCGCGCTGGCCAGATGATATAAAGGGTCAACCCCCCA 51.67%

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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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