Recognition of Anionic Porphyrins by DNA Aptamers

Abstract

DNA sequences were isolated by in vitro selection for binding to N-methylmesoporphyrin IX (NMM), a molecule that behaves as a stable transition-state analogue for porphyrin chelatases. Clones approximately 280 and approximately 120 nucleotides long were obtained, which bound to NMM with sub-micromolar affinity but bound mesoporphyrin IX (MPIX), as well as various metalloderivatives of MPIX, with lower affinity. Footprinting experiments with dimethyl sulfate, DNase I, and bound hemin molecules activated by superoxide identified a series of short guanine-rich motifs to be the binding sites for the various porphyrins. One clone, PS2, examined in depth, gave a methylation footprint with bound NMM but not with bound MPIX nor with a number of metalloporphyrins. The binding domain PS2, synthesized as a short oligonucleotide, itself showed high-affinity binding to NMM. The binding sequences from different clones were loosely homologous, and the footprinting data were consistent with their folding to form one or more guanine quartets in the presence of NMM. Ultraviolet--visible absorption and circular dichroism spectroscopy of the DNA--NMM complexes indicates, however, that the interaction is not primarily intercalative in nature. The preferential binding of NMM by these aptamers raises the possibility of their being able to catalyze the chelation of metal ions by the porphyrin MPIX.

Anion Recognition in Water: Recent Advances from a Supramolecular and Macromolecular Perspective

“…An aptamer for AMP has been coupled to fluorescent nanoparticles, thereby providing a highly selective sensor for that target 77. Besides this, aptamers have been reported for biologically relevant anionic porphyrins,78 again highlighting the possibilities for further exploitation in aqueous anion‐recognition chemistry. Very recently, DNA‐like oligomers with synthetic units replacing nucleobases were reported for pattern‐based detection of anion pollutants in water 79.…”

Inhibiting Plasmodium falciparum growth and heme detoxification pathway using heme-binding DNA aptamers

“…Therefore, the initial objective was to examine whether hemebinding aptamers could first, bind heme at this pH, and second, inhibit hemozoin formation. For this proof-of-concept study, we elected to use several previously reported heme-binding DNA aptamers (27,28) (Table 1), which were all discovered using SELEX carried out at pH 7-8.…”

In vivo veritas: Using yeast to probe the biological functions of G-quadruplexes

“…Nonetheless, there is evidence that they can discriminate to some extent among different quadruplex folds [21,32,33]. Affinity chromatography using the selective quadruplex ligand N-methyl mesoporphyrin (NMM) coupled to acrylic beads has been used successfully to select quadruplexes from complex mixtures of nucleic acids [19,34], and so use of this ligand and probably others should be possible. Another approach would be to use well-defined quadruplex binding domains of proteins, but again, knowledge of the specificity of these domains is at an early stage.…”