Binding of a Phenanthridine-Biguanide Derivative with DNA/RNA Polynucleotides Studied by Surface-Enhanced Raman Spectroscopy (SERS)

Abstract

Surface-enhanced Raman spectroscopy (SERS) in the near-infrared region has been applied to study interactions between a phenanthridine-biguanide derivative (PB) and polynucleotides. The PB molecules scatter radiation in the silver citrate colloid most intensively at concentration of 2.5 6 10−5 mol dm−3, at which they are optimally oriented towards the nanoparticles, with the phenanthridine plane placed perpendicularly to the silver surface. A band at 228 cm−1, attributed to the Ag–N stretching mode, implies that chemical mechanism, along with the electromagnetic mechanism, contributes to the total enhancement of the scattered radiation. A decrease in intensity and shifts of the biguanide-related bands in the SERS spectra of the mixtures of PB with DNA indicate binding of the small molecules with the nucleic acid. Studies with double-stranded DNA analogues reveal that the molecules of PB intercalate into the G–C base pairs by the phenanthridine system and bind within the minor groove of the A–T sequences through the biguanide substituent. Intensity decrease in the SERS spectrum of the PB/RNA mixture confirms insertion of the molecules between A–U base pairs, whereas an upward shift of the amino groups bending mode (1078 cm−1) as well as diminution of the CN stretching band at 1421 cm−1 imply hydrogen bonding of the biguanide moiety with the nucleobases. SERS spectra of the mixtures containing the single-stranded polynucleotides show that the polynucleotide secondary structure does not affect binding of PB with the polynucleotides but that affinity towards the polynucleotides depends solely on the molecular structure of the nucleic bases.