Quantitative analysis of DNA–porphyrin interactions

The binding of manganese(III)‐tetra(4‐N‐methylpyridyl)porphyrin (MnTMpyP) with synthetic poly(dA‐dT) 2 , poly(dI‐dC) 2 , and poly(dG‐dC) 2 DNAs as well as calf thymus (CT) DNA has been quantitatively studied in detail using induced CD (circular dichroism) spectroscopy in the Soret absorption band. The CD spectra, which changed greatly depending on the porphyrin to DNA base‐pair molar ratio ( r ), were normalized with respect to DNA concentration and deconvoluted. Three independent component binding modes (named mode 1, 2, and 3 in the order of increasing r values) were identified, which successfully simulated the observed CD spectra with negligibly small residuals for a wide range of r values. In the case of poly(dA‐dT) 2 , poly (dI‐dC) 2 , and CT DNA, all the three modes appeared, whereas in the case of poly(dG‐dC) 2 DNA, only modes 1 and 3 appeared in the r range studied. The r dependence of each binding mode, i.e., its relative affinity toward DNA, has been revealed by this analysis. Mode 1, which appeared as a single binding mode at very low r values ( r ≤ ca. 0.05), was inhibited by the addition of methyl green, a drug that preferentially binds to the major groove of poly (dA‐dT) 2 DNA. Berenil, a known minor groove binder to poly(dA‐dT) 2 or poly(dI‐dC) 2 DNA, inhibited modes 2 and 3. From these inhibition experiments as well as comparison of the component spectra for DNAs of different sequence, a binding site on DNA was proposed for each component binding mode. The number of DNA base pairs covered by a single molecule of porphyrin was estimated. © 2005 Wiley Periodicals, Inc. Biopolymers 81: 376–391, 2006 This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at biopolymers@wiley.com