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Binding modes of a DBTAA derivative with DNA/RNA polynucleotides revealed by SERS

Owing to their structural resemblance to porphyrins, widely known for their diversity of interactions with DNA, dibenzotetraaza(14)annulenes (DBTAA) have attracted much attention as molecules having potential nucleic acid binding ability. The molecular structure of newly synthesized derivatives suggests that the planar DBTAA core can easily intercalate between the base pairs, while long and flexible substituents at meso positions of the macrocycle can facilitate groove binding. Binding modes of the DBTAA derivative with synthetic DNA and RNA 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 polynucleotides. Intercalation was revealed as the dominant binding mode of the annulene derivative with poly dGdC-poly dGdC and poly rA-poly rU, whereas binding within the minor groove of poly dAdT-poly dAdT was also considered. When all the dominant binding sites were occupied, SERS spectra indicated that the small molecules bind on the outside of the DNA analogues, while exist mainly as free molecules in equimolar ratio with the synthetic RNA polynucleotide, implying higher affinity for DNA than for RNA.

surface-enhanced Raman spectroscopy; annulene; polynucleotide; binding

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