Aptamer-target interaction descriptor
Aptamer-target interaction information
Interaction ID: 1225
Aptamer sequence: GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC
Target unique ID: 11294
Aptamer ID Aptamer descriptor Target chemistry Target name Affinity Binding Conditions/Buffer PubMed ID
Apta_647 MG4 Molecule Malachite green 0.117 μM 20 mM NaCl, 12 mM MgCl2, 4 mM spermidine, 20 mM DTT, 2 mM NTPs and 80 mM Tris-HCl pH 7.9 14640641
Structure information of aptamer
Aptamer Sequence: GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC
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_647 Description MG4
Aptamer chemistry RNA Length 38 nt
GC content 60.5% Molecular weight 12,300.41 Da
Molarity of 1 μg/μl solution 81.30 μM Number of G-quadruplexes No QGRS found
G-Score N/A Function Live-cell imaging
Sequence GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC
Applications Binding to MG
Target information
Type Detail Type Detail
PubChem ID 11294 Molecular name Malachite green
Molecular formula C23H25ClN2 Molecular weight 364.9
IUPAC name [4-[[4-(dimethylamino)phenyl]-phenylmethylidene]cyclohexa-2,5-dien-1-ylidene]-dimethylazanium;chloride InChIKey FDZZZRQASAIRJF-UHFFFAOYSA-M
LogP 1.398 Topological polar surface area 6.25
Hydrogen bond acceptor 1 Hydrogen bond donor 0

Synonym(s):
MALACHITE GREEN; 569-64-2; Basic Green 4; China Green; Malachite green chloride; Victoria Green B; Grenoble Green; Diamond Green B; Solid Green O; Basic green; Victoria Green; Benzal Green; Burma Green B; Light Green N; Diamond Green Bx; Victoria Green S; Fast Green O; Green MX; Solid Green Crystals O; Calcozine Green V; Malachite Green A; Malachite Green B; C.I. Basic Green 4; Victoria Green WB; Malachite Green AN; Malachite Green CP; Malachite Green WS; Oji Malachite Green; Tertrophene Green M; Victoria Green WPB; CI Basic Green 4; Malachite Green J3E; Astra Malachite Green; Diamond Green B extra; Malachite Green Powder; Mitsui Malachite Green; Diamond Green P Extra; Malachite green chloride salt; Malachite Lake Green A; Diabasic Malachite Green; Malachite Green Crystals; Acryl Brilliant Green B; Astra Malachite Green B; Hidaco Malachite Green LC; Hidaco Malachite Green SC; Astra Malachite Green BXX; Hidaco Malachite Green Base; New Victoria Green Extra I; New Victoria Green Extra O; Malachite Green (Indicator); New Victoria Green Extra II; ADC Malachite Green Crystals; Malachite Green Crystals BPC; Tokyo Aniline Malachite Green; Bronze Green Toner A-8002; C.I. 42000; Aizen Malachite Green Crystals; China Green (Biological Stain); Light Green N (Biological Stain); Malachite green hydrochloride; Lincoln Green Toner B 15-2900; UNII-12058M7ORO; CI 42000; Tetramethyl diapara-amido-triphenyl carbinol; MAGENTAGREENCRYSTALS; Malachite Green Hydrochloride (Biological stain); Ammonium, (4-(p-(dimethylamino)-alpha-phenylbenzylidene)-2,5-cyclohexadien-1-ylidene)-dimethyl-, chloride; CHEBI:72449; 12058M7ORO; (4-(4-Dimethylaminobenzhydriylidene)cyclohexa-2,5-dienylidene)dimethylammonium chloride; (4-(alpha-(4-Dimethylamino)phenyl)benzylidene)cyclohexa-2,5-dien-1-ylidene dimethylammonium chloride; Green Malaquite; Viride Malachitum; 14426-28-9; Methanaminium,N-[4-[[4-(dimethylamino)phenyl]phenylmethylene]-2,5-cyclohexadien-1-ylidene]-N-methyl-, chloride; N-(4-((4-(Dimethylamino)phenyl)(phenyl)methylene)cyclohexa-2,5-dien-1-ylidene)-N-methylmethanaminium chloride; Aizen Malachite Green; Basonyl Green 830; Basacryl Green X-BF; Caswell No. 534C; Malachite Green J 3E; Malachit-grun [German]; Victoria Green (VAN); Atlantic Malachite Green; Malachit-grun; 2437-29-8; Basonyl Green NB 832; Zelen malachitova; Zelen malachitova [Czech]; Zelen zasadita 4 [Czech]; Zelen zasadita 4; Fast Green 0; CCRIS 1219; HSDB 1406; EINECS 209-322-8; NSC 47726; EPA Pesticide Chemical Code 039504; malachite-green; AI3-18509; Sentry AQ maracide W/biospheres; Methanaminium, N-(4-((4-(dimethylamino)phenyl)phenylmethylene)-2,5-cyclohexadien-1-ylidene)-N-methyl-, chloride (1:1); Methanaminium, N-[4-[[4-(dimethylamino)phenyl]phenylmethylene]-2,5-cyclohexadien-1-ylidene]-N-methyl-, chloride (1:1); N-{4-[[4-(dimethylamino)phenyl](phenyl)methylene]cyclohexa-2,5-dien-1-ylidene}-N-methylmethanaminium chloride; MFCD00011751; MALACHITEGREEN; DSSTox_CID_5512; DSSTox_GSID_25512; SCHEMBL28216; CHEMBL186357; DTXSID1025512; C.I. Basic Green 4 (8CI); BRILLIANT GREEN HYDROCHLORIDE; NSC47726; Tox21_303977; NSC-47726; AKOS000282983; Malachite Green solution, for microscopy; NCGC00357201-01; (4-(alpha-(4-(Dimethylamino)phenyl)benzylidene)cyclohexa-2,5-dien-1-ylidene)dimethylammonium chloride; [4-[[4-(dimethylamino)phenyl]-phenylmethylidene]cyclohexa-2,5-dien-1-ylidene]-dimethylazanium;chloride; AC-19099; AS-13876; CAS-569-64-2; Methanaminium, N-(4-((4-(dimethylamino)phenyl)phenylmethylene)-2,5-cyclohexadien-1-ylidene)-N-methyl-, chloride; T296; FT-0628106; Malachite Green chloride, analytical standard; C18367; A918855; Q408815; J-006507; Q-200675; WLN: L6Y DYJ AUYR&R DN1&1& DUK1&1 &Q &G; Ammonium,5-cyclohexadien-1-ylidene]-dimethyl-, chloride; 4-{[4-(dimethylamino)phenyl](phenyl)methylene}-N,N-dimethylcyclohexa-2,5-dien-1-iminium chloride; N-(4-((4-(dimethylamino)phenyl)(phenyl)methylene)cyclohexa-2,5-dienylidene)-N-methylmethanaminium chloride; N-[4-[[4-Dimethylamino)phenyl]phenylmethylene]-2,5-cyclohexadien-1-ylidene]-N-methylmethanaminium chloride

Activity data
Interaction ID 690
Target type Molecule
Target unique ID 11294
Activity 1 μM
Binding Conditions/Buffer

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

Addition of the minimal aptamer RNA induces a shift in the UV absorption maximum of MG from 616 nm to 630 nm. The concentration dependence of the RNA-induced shift suggests a KD 1 mM
PubMed ID 10339553
Interaction ID 1225
Target type Molecule
Target unique ID 11294
Activity 0.117 μM
Binding Conditions/Buffer

20 mM NaCl, 12 mM MgCl2, 4 mM spermidine, 20 mM DTT, 2 mM NTPs and 80 mM Tris-HCl pH 7.9
Assay

Addition of the minimal aptamer RNA induces a shift in the UV absorption maximum of MG from 616 nm to 630 nm. The concentration dependence of the RNA-induced shift suggests a KD 1 mM
PubMed ID 14640641
Similar aptamers
Aptamer ID Aptamer chemistry Sequence Similarity
Apta_647 RNA GGAUCCCGACUGGCGAGAGCCAGGUAACGAAUGGAUCC
100.00%
Apta_560 RNA GGAAGAGAUGGCGACUAAAACGACUUGUCGC 57.89%
Apta_668 RNA GGAACCCAACUAGGCGUUUGAGGGGAUUCGGCCACGGUAACAACCCCUC 57.14%
Apta_86 RNA GAAACGACUCGACAACCUCGAGCGACGUGAAUCAU 55.26%
Apta_717 RNA GGCGCAGCCCGCCGAAAGGCACGUGGAACCGUC 55.26%
Apta_633 RNA GGCAUCGGAAAGUGGGUUGAUGUAAGUAACAGGCGAUGCC 55.00%
Apta_1288 RNA GGCGCACUGGCGCUGCGCCUUCGGGCGCCAAUCGUAGCGUGUCGGCGCC 53.06%
Apta_87 RNA UACCGACUAGCAAAACCUGCUGGCGACGUUUAGAU 52.63%
Apta_371 RNA GGCAGACCAUACGGGAGAGAAACUUGCC 52.63%
Apta_713 RNA GGCGGUGCUGGCCGAAAGGCGCUUGGAAACGUC 52.63%
Apta_715 RNA GGCGCUGCACGCCGAAAGGCCCGUUGAAACGUC 52.63%
Apta_365 RNA GGACCUAUGCAGUAGCCAGUGUGGACUGGGCUGCCCCCCC 52.50%
Apta_394 RNA GGGCGAAUUCAACUGCCAUCUAGGCAGUAACCAGGAGUUAGUAGGACAAGUUUCGUCC 51.72%
Apta_243 RNA GCUUGAAGCUAGCAGUAAGACUAGCGCUACGGAUGGGUGUGCG 51.16%
Apta_32 DNA CGGTAAACTGCGTCCGAAGGGGCTGCAGTGACCCGAATGGGTCCG 51.11%
Apta_63 DNA GACCCGTGGTAGGGTAGGATGGGGTGGTC 50.00%
Apta_138 RNA GGAGGUGCUCCGAAAGGAACUCC 50.00%
Apta_218 RNA AGCCGCGAGGGGAGGGAUAGGGUAGGGCGCGGCU 50.00%
Apta_374 RNA GUCCCGUGCGCAAAAGUUCUUAGCGCUAGCAGUCCUAGUUGC 50.00%
Apta_378 RNA UGCUCUUAGAAUGGGACUAAGACACGGGAC 50.00%

ABOUT

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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