Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 711
Aptamer sequence: CACGCACAGAAGACACCTACAGGGCCAGATCACAATCGGTTAGTGAACTCGTACGGCGCG
Target unique ID: 445434
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_663 RC4 Molecule Microcystin-LR 76 nM 50 mM Tris, pH 7.5, 150 mM NaCl, and 2 mM MgCl2 22958101
Structure information of aptamer
Aptamer Sequence: CACGCACAGAAGACACCTACAGGGCCAGATCACAATCGGTTAGTGAACTCGTACGGCGCG
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_663 Description RC4
Aptamer chemistry DNA Length 60 nt
GC content 56.7% Molecular weight 18,481.87 Da
Molarity of 1 μg/μl solution 54.11 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Aptasensor
Sequence CACGCACAGAAGACACCTACAGGGCCAGATCACAATCGGTTAGTGAACTCGTACGGCGCG
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 706
Target type Molecule
Target unique ID 6437382
Activity 106 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 711
Target type Molecule
Target unique ID 445434
Activity 76 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 715
Target type Molecule
Target unique ID 6437088
Activity 222 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_728 DNA CGACCCGGCACAAACCCAGAACCATATACACGATCATTAGTCTCCTGGGCCG 61.67%
Apta_992 DNA TCACTGACAGTAGGCCCATACGCACATTCAACAATCGGTAGTCCATACAACCGCGCCCCGTG 58.06%
Apta_664 DNA CACGCAACAACACAACATGCCCAGCGCCTGGAACATATCCTATGAGTTAGTCCGCCCACA 56.67%
Apta_868 DNA CCCAGAAACAGCACCCTTACATCGACTGGACCTTCCGCG 56.67%
Apta_1068 DNA CGGGACAAGACAACGAACGAACAGGAAGAGAACCGGAATGCAGACGTCAGGG 56.67%
Apta_1069 DNA CCGGAGAAAAAAAACTTGATGAGCCAGGAAAACGAGGGTTGGAACGCGACTG 56.67%
Apta_1172 DNA GACGCCACTGACTACCCCAGTATCTCTTCAACGCGTATTGAAGTCAGTCGGTCGTCA 56.67%
Apta_232 DNA AGCAGCACAGAGGTCAGATGCTATGAGCAGATCCGATAGAAAGTTAATGCCCTAGAACATCCTATGCGTGCTACCGTGAA 55.00%
Apta_639 DNA CTAAGCACAGGGAAACCAGCTAATGAGTTAGGCCTGTCCCCCACG 55.00%
Apta_1047 DNA TAGTCCCAAGGCACATAAGGGCCGGAGGTCTAGCGTCAGGGATACAGAGA 55.00%
Apta_1218 DNA CGACACCACACAGCAGTAAGCACTACAACATAGTGGTCTAGACTATCTCGGGCCGGTG 55.00%
Apta_1227 DNA CACACCAAACACACAAGTGGACCCTGACGCATGGATAGGGTGACGGTATACGCGGGCATG 55.00%
Apta_527 DNA ATACGGGAGCCAACACCAACAACCTAGATGTTCTGATAACACGAATCGCTTCGAAGAGCAGGTGTGACGGAT 54.17%
Apta_4 DNA CCTGCCTTTGGAACCGACCGCCAGGCCGAGGAAAGGCACCGACAGC 53.33%
Apta_79 DNA ATCTCGAGTCATAGGGGGCGCGAACATACGCGGTTGGTGTGGTTGGCTGACTCGT 53.33%
Apta_449 DNA CGCACTATGTTTTACGAGCCGTTTCCTCGGCAGATAGTAAGTGCG 53.33%
Apta_592 DNA CTCTCGGGACGACCACTACGCATAGTTTCTATCGCCAGGAAGGGTCGTCCC 53.33%
Apta_684 DNA GGCGGACCAAGGGGACACCACAGATGAATGTACAGTACCATGTTACTGCGCCCGTAGGTG 53.33%
Apta_697 DNA CTCTCGGGACGACGGACGCTAATCTTACAAGGGCGTAGTGTATGTCGTCCC 53.33%
Apta_875 DNA GCCGCGACCATACAACGCAAACAACACGCCTGTACGCTTG 53.33%

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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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