Structure effects on the reactivity of two new cyanine/DNA systems

Cyanines are a class of fluorescent molecules that play an important role in the biochemical field. Due to the high affinity towards double strands of nucleic acids, they are used to selectively stain these bio-substrates and can play a role in DNA fragments sequencing, and in conformational studies of biomolecules based on FRET. New cyanines are tested with the aim to optimise their properties, both in terms of selectivity and in photo-physical behaviour. Two different cyanine/DNA systems have been analysed by spectrophotometric and spectrofluorometric titrations under different (salt content and temperature) conditions. The molecular structure of the two cyanines used, Cy-Ph and Cy-dPh, differ for the presence, in Cy-dPh, of an additional phenyl ring that enhances the possible aromatic extension of the system. The results obtained show that both dyes bind DNA with high affinity, intercalating between the polynucleotide base-pairs. For both systems the binding features strongly depend on the salt content of the medium, enlightening the importance of dye/DNA electrostatic attraction in the binding process. The higher aromatic extension of Cy-dPh plays an important role. The binding constant are significantly higher for the Cy-dPh/DNA system with respect to the Cy-Ph/DNA system. The thermodynamic parameters of binding (DH and DS) are also higher for the Cy-dPh/DNA system. Interestingly, when these values are reported in a Chaires plot [2], the values for the latter system approach to the higher-energy cluster of bis-intercalators. The possible ability of Cy-dPh to bis-intercalate into DNA would agree with some deviations occurring in the binding isotherms under high DNA loading conditions. This aspects will be further analysed by means of mechanistic studies based on fast reaction techniques.