engleski

Spectrometric sensing of the ds-DNA/RNA structures by small molecule reporters

Small molecules targeting DNA and RNA have attracted significant scientific interest not only because of their biomedicinal applications, but also due to widespread use of spectrophotometric markers in the related scientific research – for instance, fluorescent techniques significantly developed during the last two decades and now represent about 60% of the detection enabling technologies used in molecular biology and medicine. Small molecules targeting double stranded (ds)-DNA/RNA often rely on the one dominant non-covalent binding mode for their interaction (e.g., intercalation, minor or major groove binding, external electrostatic binding). However, the combination of different binding modes with additional steric and structural features controlling three-dimensional recognition were intensively explored within the last decades. Our research1 was particularly focused on small organic molecules binding via non-covalent interactions (logKs > 5 M-1) to the most of naturally occurring ds-DNA and ds-RNA secondary structures and yielding different signals for each of the most common secondary structures (e.g. Scheme 1 ; A-DNA/RNA, B-DNA, subtypes of DNA characterized by narrower minor groove, etc.) by sensitive and biologically applicable methods (UV/Vis, CD, fluorescence, SERS). The development of such singlemolecule sensors, able to report simultaneously the presence of several different secondary structures of DNA / RNA varieties by different spectroscopic signals could replace the necessary application of several dyes, each one specific for one DNA or RNA target. Here presented results1 suggest that such multipurpose signalling selectivity can be achieved by fine tuning of small molecule structure in respect to the slightly different binding sites of various polynucleotides.

DNA/RNA recognition; small molecules; supramolecular chemistry

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