The interaction of poly(diallyldimethyl ammonium chloride) (PDDA) with DNA has been studied by spectroscopic analysis of different kinds of nucleic acid probes, microscopic IR- and CD-spectroscopy. The two spectroscopic changes of ethidium bromide (EB) on its binding to DNA, namely red-shift of its maximum absorption wavelength (νmax) and enhancement of fluorescence intensity are utilized to study the interaction of PDDA with DNA. Reversion of νmaxand decrease in fluorescence of DNA-EB system on addition of PDDA show the dissociation of DNA/EB complex and the formation of the DNA/PDDA complex. At the same time, the binding constant of EB and the number of binding sites per nucleotide decrease with increase in the concentrations of PDDA, indicating non-competitive inhibition of EB binding to DNA in the presence of PDDA. From the Scatchard analysis, we obtain the association constant of PDDA to DNA is 4.7 × 104M-1. Contrary to EB, the binding of PDDA with DNA can greatly enhance the fluorescence intensity of groove-binding probes, Hoechst 33258 and DAPI, which can also be used to investigate the formation of the DNA/PDDA complex. The fluorescence analysis shows that the interaction of DNA with PDDA may have effect on the conformation of secondary structure of DNA. IR-spectra show that PDDA interacts with DNA through both the phosphate groups and the bases of DNA and the formation of DNA/PDDA complex causes the change of the conformation of the DNA secondary structure, which is further proved by CD-spectra. © 2003 Elsevier B.V. All rights reserved.
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