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Study of interactions between DNA/RNA nucleotides and PHENPOD by surface enhanced Raman spectroscopy

PHENPOD is a multifunctional molecule consisted of 1, 10-phenanthroline as linkage for two aza-crowns containing pyridine. Surface-enhanced Raman scattering (SERS) was used to study interactions between PHENPOD and DNA/RNA mononucleotides (AMP, GMP, CMP, UMP), single-stranded RNA polynucleotides (poly A, poly G, poly C, poly U) and double-stranded DNA/RNA polynucleotides (poly dAdT-poly dAdT, poly dGdC-poly dGdC, poly rA-poly rU). New bands observed in the SERS spectra of PHENPOD with mononucleotides and single-stranded polynucleotides originated mainly from nucleic bases, indicating interactions between the PHENPOD molecules and the nucleotides. However, mixtures of PHENPOD and nucleotides containing guanine produced very weak bands arising from vibrational modes of the purine base, if compared to the spectra of the polyamine molecules with other nucleobases. SERS measurements with double-stranded polynucleotides indicated selective binding of the PHENPOD molecules with the DNA polynucleotides. Adding poly dAdT-poly dAdT into the PHENPOD solution, an intensity of the polyamine bands decreased and new bands appeared, belonging to adenine stretching modes. It can be assumed that the PHENPOD molecules interacted with the minor and major groove of the adenine-thymine polynucleotide, while the phenanthroline moiety intercalated between the base pairs. On the other hand, in the spectra of mixtures of PHENPOD with poly dGdC-poly dGdC new bands were not obtained, and the intensity of the polyamine bands slightly increased, implying the lack of interactions between the polyamine molecules and the guanine-cytosine polynucleotide. In the spectrum of the PHENPOD molecules with the double-stranded RNA polynucleotide no significant changes were observed, as well.

surface-enhanced Raman spectroscopy; nucleotides; intercalation; groove binding

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