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 × 10<sup>−5</sup> mol
dm<sup>−3</sup>, at which they are optimally oriented towards the nanoparticles,
with the phenanthridine plane placed perpendicularly to the silver surface. A band
at 228 cm<sup>−1</sup>, 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<sup>−1</sup>) as well as diminution of the CN stretching band at 1421
cm<sup>−1</sup> 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.
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