Malachite green aptamer

Kolpashchikov DM. Binary malachite green aptamer for fluorescent detection of nucleic acids. J. Am. Chem. Soc. 2005 127 12442-12443. 

Other detection methods involving gold surfaces include an electro-chemiluminescent method capable of detection at sub-nanomolar levels, a SERRS sensor that has 100 pM limits, and an electrochemical method in conjunction with assembly of carbon nanotubes reports fM detection. Magnetic nanoparticles have been used for detection of Hg(II) by NMR, and by flow cytometry. A malachite green aptamer has been used with detection by an increase in resonance scattering,as well as a hemolysin... 

The noncovalent specific labeling of NA probes based on the aptamer strategy has also been reported. The malachite green (37) aptamer, which was designed as a binary probe, assembles only in the presence of the target sequences and induces an increase in the intensity of the signal emitted by the F bound aptamer. 

As with DNA aptamers, there is a trend towards applying RNA aptamers to a particular application. Allosteric ribozyme sensors have been developed which are specific for caffeine and aspartame. " Using a fluorescence-based assay, caffeine or aspartame may be detected in solution over a 0.5 5mM concentration range. Aptamers designed to malachite green (151) or other triphenylmethane dyes have been developed that enhance the fluorescence of the dye up to 2300-fold. " A further fluorescence-based assay has been... 

The 2.8 A resolution crystal structure of an aptamer that binds to the chromo-phore malachite green shows the binding site as an asymmetric internal loop flanked by a pair of helices. There are several tiers of stacked nucleotides arranged in pairs, triples and a novel quadruple that encapsulates the ligand. 

Stead SL, Ashwin H, Johnston B, Tarbin JA, Sharman M, Kay J, Keely BJ, An RNA-aptamer-based assay for the detection and analysis of malachite green and leu-comalachite green residues in fish tissue. Anal. Chem. 2010 82(7) 2652-2660. 

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