Quantitative analysis of DNA–porphyrin interactions

Abstract

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 < or = 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.

DNA binding and nuclease activity of cationic iron(IV) and manganese(III) corrole complexes

“…S8, supporting information). This is in agreement with an outside groove binding between 2b and CT‐DNA, similar to the corresponding manganese porphyrin Mn III TMPyP . Moreover, sharp changes in ellipticity without changing shape on increasing the R [ 2b ]/[DNA] ratio indicate a homogeneous binding mode.…”

“…A negative ICD band is a signal of intercalate binding, a positive ICD band is characteristic of external (groove) binding, and a conserved ICD band is characteristic of outside binding mode . Outside binding with self‐stacking or difunctional binding (both of intercalation and outside groove binding) can induce a bisignate CD band …”

Lighting up left-handed Z-DNA: photoluminescent carbon dots induce DNA B to Z transition and perform DNA logic operations

“…Our results clearly indicated that SC-dots could influence the interactions between DNA and MG, a proven DNA major groove binder (29,45,46). Figure 4B showed CD spectral changes in the presence of SC-dots.…”

Vibrational and electronic circular dichroism study of the interactions of cationic porphyrins with (dG‐dC)10and (dA‐dT)10

“…# 2007 ple by Pasternack 3 and recently in this journal. 4 It has been shown that in addition to classical intercalation, there are another three modifications: (a) hemi-intercalation, intercalation in one strand of the nucleotide, 5 (b) semi-intercalation, the interacting molecule is wedged between base-pairs and causes their opening, and (c) quasi-intercalation, the interacting molecule pushes one base-pair toward the major groove and interacts with the neighbouring base-pairs. 6 Spectroscopic methods, especially electronic circular dichroism (ECD), play a dominant role in the investigations of DNA-porphyrin interactions.…”