Abstract
The interactions of two different porphyrins, without axial ligands—5,10,15,20‐tetrakis(1‐methylpyridinium‐4‐yl)porphyrin‐Cu(II) tetrachloride (Cu(II)TMPyP) and with bulky meso substituents—5,10,15,20‐tetrakis(N,N,N‐trimethylanilinium‐4‐yl)porphyrin tetrachloride (TMAP), with (dG‐dC)~10~ and (dA‐dT)~10~ were studied by combination of vibrational circular dichroism (VCD) and electronic circular dichroism (ECD) spectroscopy at different [oligonucleotide]/[porphyrin] ratios, where [oligonucleotide] and [porphyrin] are the concentrations of oligonucleotide per base‐pair and porphyrin, respectively. The combination of VCD and ECD spectroscopy enables us to identify the types of interactions, and to specify the sites of interactions: The intercalative binding mode of Cu(II)TMPyP with (dG‐dC)~10~, which has been well described, was characterized by a new VCD “marker” and it was shown that the interaction of Cu(II)TMPyP with (dA‐dT)~10~ via external binding to the phosphate backbone and major groove binding caused transition from the B to the non‐B conformer. TMAP interacted with the major groove of (dG‐dC)~10~, was semi‐intercalated into (dA‐dT)~10~, and caused significant variation in the structure of both oligonucleotides at the higher concentration of porphyrin. The spectroscopic techniques used in this study revealed that porphyrin binding with AT sequences caused substantial variation of the DNA structure. It was shown that VCD spectroscopy is an effective tool for the conformational studies of nucleic acid–porphyrin complexes in solution. © 2007 Wiley Periodicals, Inc. Biopolymers 85:349–358, 2007.
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