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MG aptamer
Timeline
The 2.8 A crystal structure of the aptamer bound to tetramethylrosamine, a high-affinity MG analog was determined[2]
A detailed picture of ligand structure and dynamics in RNA aptamer-malachite green complexes was developed[3]
The dynamical nature of the malachite green molecule inside the RNA ligand-binding site was examined using molecular dynamics[4]
The solution structure of an RNA aptamer that binds triphenyl dyes in complex with malachite green was present and compared with a previously determined crystal structure of a complex formed with tetramethylrosamine[5]
A new probe contains a fragment of malachite green aptamer was developed for fluorescent detection of nucleic acids for real-time in vivo[6]
A generation of tandem repeats of a malachite green RNA aptamer using rolling circle transcription was demonstrate[7]
Take malachite green aptamer as an example, inclusion of the aptamer in a carrier may facilitate production of large quantities of RNA aptamers, and may open an approach to screening aptamer libraries in vivo[8]
The binding of malachite green aptamer to its original selection target and three related molecules was determined by isothermal titration calorimetry, equilibrium dialysis, and fluorescence titration[9]
Isothermal titration calorimetry was used rationally to compare the thermodynamics of binding of malachite green and TMR to the malachite green aptamer[10]
Competitive binding studies using isothermal titration calorimetry and stopped flow kinetics was conducted with the aim of understanding the adaptive nature of RNA aptamer-malachite green interaction[11]
DNA aptamers for malachite green were isolated by modified in vitro selection method which is based on the target-induced release of aptamers as the separation technique[12]
A simple way was developed to stabilize the apparent of malachite green-aptamer binding over 24 h, which may be beneficial in stabilizing other triphenylmethane or carbocation ligand-aptamer interactions[13]
A facile colorimetric aptasensor based on unmodified gold nanoparticles for rapid, highly sensitive and selective detection of malachite green[14]
An RNA scaffolds containing multiple tandem repeats of malachite green aptamer to increase the brightness of the aptamer-fluorogen system was constructed and tested[15]
An innovative levo (L)-malachite green aptamer with excellent stability is designed for effective monitoring of the content of malachite green in aquaculture[16]
A low background and label-free aptamer-based biosensor for miRNA assay by RNA-regulated fluorescence of malachite green was reported[17]
Description
Dilara Grate and Charles Wilson reported and characterized MG-binding RNA motifs obtained by SELEX in a work published in 1999. Later, Jeremy Flinders et al. resolved the structure of the MG-RNA complex by NMR spectroscopy in a work they published in 2004[1,5].SELEX
MG-specific RNA aptamers were selected and amplified from a pool containing approximately 5×1015 different random sequence molecules. MG agarose affinity chromatography was used as a basis for enrichment. The fraction of MG agarose-binding RNAs appeared to plateau after eight cycles. Final pool was dominated by 30–40 major species and sequences for 14 unique clones were obtained and their ability to bind MG agarose determined[1].
Detailed information are accessible on SELEX page.
Structure
2D representation
Here we used Ribodraw to complete the figure, through the 3D structure information[5].
5'-GGUACCCGACUGGCGAGAGCCAGGUAACGAAUGGUACC-3'
3D visualisation
Jeremy Flinders et al. resolved the structure of the MG-RNA complex by NMR spectroscopy and X-ray crystallography in a work they published in 2004. The PDB ID of this structure is 1Q8N[5].Additional available structures that have been solved and detailed information are accessible on Structures page.
(Clicking the "Settings/Controls info" to turn Spin off)
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Binding pocket
Left: Surface representation of the binding pocket of the aptamer generated from PDB ID: 1Q8N by NMR and X-ray crystallography. Malachite green (MG) (shown in sticks) is labeled in yellow. Right: The hydrogen bonds of binding sites of the aptamer bound with MG or other nucleotides surround small molecules.
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Ligand information
SELEX ligand
The RNA concentration dependence of the shift in maximum wavelength indicates the apparent Kd of this RNA aptamer. This affinity for soluble MG closely matches that measured for agarose-immobilized ligand by an equilibrium matrix binding assay[1].
Structure ligand
MG (Malachite green) is an organic compound that is used as a dyestuff and controversially as an antimicrobial in aquaculture. Malachite green is traditionally used as a dye for materials such as silk, leather, and paper. Despite its name the dye is not prepared from the mineral malachite. The name just comes from the similarity of color.-----From Wikipedia
| PubChem CID | Molecular Formula | MW | CAS | Solubility | Drugbank ID |
|---|---|---|---|---|---|
| 11294 | C23H25N2 | 364.9 g/mol | 569-64-2 | 100 mg/mL in DMSO; 3.85 mg/mL in H2O | DB03895 |
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Similar compound
We screened the compounds with great similarity to TO1 by using the ZINC database and showed some of the compounds' structure diagrams. For some CAS numbers not available, we will supplement them with Pubchem CID.
| Zinc_id | Named | CAS | Pubchem CID | Structure |
|---|---|---|---|---|
| ZINC13763987 | Crystal Violet | 548-62-9;7438-46-2 | 3468 |  |
| ZINC5140632 | Tetramethylrhodamine | 62669-71-0 | 65220 |  |
| ZINC3953819 | Brilliant Green | 10309-95-2 | 11295 |  |
| ZINC8577555 | Rosamine | NA | 2762681 |  |
| ZINC4521863 | Rhodamine I | 115532-52-0 | 2762683 |  |
| ZINC4521864 | Rhodamine II | 115532-49-5 | 5009757 |  |
| ZINC59301830 | [4-[[4-(diethylamino)phenyl]-phenylmethylidene]cyclohexa-2,5-dien-1-ylidene]-dimethylazanium | NA | 10504023 |  |
| ZINC504413298 | [4-[[4-(dimethylamino)phenyl]-phenylmethylidene]cyclohexylidene]-dimethylazanium | NA | 125339933 |  |
| ZINC4558687 | [4-[(2-chlorophenyl)-[4-(dimethylamino)phenyl]methylidene]cyclohexa-2,5-dien-1-ylidene]-dimethylazanium | NA | 107405 |  |
References
[1] Laser-mediated, site-specific inactivation of RNA transcripts.Grate, D., & Wilson, C.
Proceedings of the National Academy of Sciences of the United States of America, 96(11), 6131–6136. (1999)
[2] 2.8 A crystal structure of the malachite green aptamer.
Baugh, C., Grate, D., & Wilson, C.
Journal of molecular biology, 301(1), 117–128. (2000)
[3] Binding to an RNA aptamer changes the charge distribution and conformation of malachite green.
Nguyen, D. H., DeFina, S. C., Fink, W. H., & Dieckmann, T.
Journal of the American Chemical Society, 124(50), 15081–15084. (2002)
[4] Dynamics studies of a malachite green−RNA complex revealing the origin of the red-shift and energetic contributions of stacking interactions.
Nguyen, D. H., Dieckmann, T., Colvin, M. E., & Fink, W. H.
The Journal of Physical Chemistry B, 108(4), 1279-1286. (2003)
[5] Recognition of planar and nonplanar Ligands in the malachite green±RNA aptamer complex.
Flinders, J., DeFina, S. C., Brackett, D. M., Baugh, C., Wilson, C., & Dieckmann, T.
Chembiochem : a European journal of chemical biology, 5(1), 62–72. (2004)
[6] Binary malachite green aptamer for fluorescent detection of nucleic acids.
Kolpashchikov D. M.
Journal of the American Chemical Society, 127(36), 12442–12443. (2005)
[7] Fluorescence generation from tandem repeats of a malachite green RNA aptamer using rolling circle transcription.
Furukawa, K., Abe, H., Abe, N., Harada, M., Tsuneda, S., & Ito, Y.
Bioorganic & medicinal chemistry letters, 18(16), 4562–4565. (2008)
[8] Engineered 5S ribosomal RNAs displaying aptamers recognizing vascular endothelial growth factor and malachite green.
Zhang, X., Potty, A. S., Jackson, G. W., Stepanov, V., Tang, A., Liu, Y., Kourentzi, K., Strych, U., Fox, G. E., & Willson, R. C.
Journal of molecular recognition: JMR, 22(2), 154–161. (2009)
[9] Entropy and Mg2+ control ligand affinity and specificity in the malachite green binding RNA aptamer.
Bernard Da Costa, J., & Dieckmann, T.
Molecular bioSystems, 7(7), 2156–2163. (2011)
[10] Thermodynamics of ligand binding to a heterogeneous RNA population in the malachite green aptamer.
Sokoloski, J. E., Dombrowski, S. E., & Bevilacqua, P. C.
Biochemistry, 51(1), 565–572. (2012)
[11] Thermodynamics and kinetics of adaptive binding in the malachite green RNA aptamer.
Da Costa, J. B., Andreiev, A. I., & Dieckmann, T.
Biochemistry, 52(38), 6575–6583. (2013)
[12] Selection and characterization of malachite green aptamers for the development of light-up probes.
Wang, H., Wang, J., Sun, N., Cheng, H., Chen, H., & Pei, R.
ChemistrySelect, 1(8), 1571-1574. (2016)
[13] Organic additives stabilize RNA aptamer binding of malachite green.
Zhou, Y., Chi, H., Wu, Y., Marks, R. S., & Steele, T. W. J.
Talanta, 160, 172–182. (2016)
[14] Colorimetric aptasensor for detection of malachite green in fish sample based on RNA and gold nanoparticles.
Jia, J., Yan, S., Lai, X., Xu, Y., Liu, T., & Xiang, Y.
Food Analytical Methods, 11, 1668-1676. (2018)
[15] Labeling RNAs in live cells using malachite green aptamer scaffolds as fluorescent probes.
Yerramilli, V. S., & Kim, K. H.
ACS synthetic biology, 7(3), 758–766. (2018)
[16] Exploiting the application of l-aptamer with excellent stability: an efficient sensing platform for malachite green in fish samples.
Luo, X., Chen, Z., Li, H., Li, W., Cui, L., & Huang, J.
The Analyst, 144(14), 4204–4209. (2019)
[17] A label-free aptamer-based biosensor for microRNA detection by the RNA-regulated fluorescence of malachite green.
Wang, H., Wang, H., Zhang, M., Jia, Y., & Li, Z.
RSC advances, 9(56), 32906–32910. (2019)
[18] A self-assembling split aptamer multiplex assay for SARS-COVID19 and miniaturization of a malachite green DNA-based aptamer.
R O'Steen, M., & M Kolpashchikov, D.
Sensors and actuators reports, 4, 100125. (2022)