Surface-enhanced Raman scattering study of the binding modes of a dibenzotetraaza[14]annulene derivative with DNA/RNA polynucleotides

Binding modes of a dibenzotetraaza[14]annulene (DBTAA) derivative with synthetic nucleic acids were studied using surface-enhanced Raman spectroscopy (SERS). Changes in SERS intensity and appearance of new bands in spectra were attributed to different complexes formed between the DBTAA molecules and DNA/RNA polynucleotides. A decrease in intensity pointed to intercalation as the dominant binding mode of the annulene derivative with poly dGdC-poly dGdC and poly rA-poly rU, whereas new bands in the spectra at 735 cm−1 and 1345 cm−1 revealed binding within the minor groove of poly dAdT-poly dAdT. When all the dominant binding sites were occupied, SERS spectra implied that small molecules bind on the outside of the DNA analogues, while exist mainly as free molecules in equimolar ratio with the synthetic RNA polynucleotide, thereby indicating higher affinity for DNA than for RNA

Cationic side-chains control DNA/RNA binding properties and antiproliferative activity of dicationic dibenzotetraaza[14]annulene derivatives

Studied dicationic dibenzotetraaza[14]annulene derivatives intercalate into synthetic double stranded DNA and RNA, while their positively charged side-chains additionally interact within the minor groove of polynucleotides, contributing to the overall affinity of compounds and controlling pronounced A-T(U) over G-C sequence preference as well as stronger thermal stabilization of ds-DNA than ds-RNA. Furthermore, all compounds showed moderate to high antiproliferative activity against five human tumour cell lines, whereby clear correlation between structure of the side-chain and cytotoxic activity was observed