Orientation and linear dichroism characteristics of porphyrin-DNA complexes

Abstract

The linear dichroism spectra of complexes of tetrakis(N-methyl-4-pyridinio)prophine (H2TMpyP) and its zinc(II) derivative (ZnTMpyP) with DNA oriented in a flow gradient have been investigated. The dichroism of H2TMpyP determined within the Soret band and the Qy band system is consistent with an intercalative conformation in which the plane of the porphyrin ring system is nearly parallel to the planes of the DNA bases. In the case of ZnTMpyP on the other hand, the porphyrin ring system is inclined at angles of 62-67 degrees with respect to the axis of the DNA helix. The pyridyl groups in both cases are characterized by a low degree of orientation with respect to the axis of the helix. In contrast to H2TMpyP which does not significantly affect the degree of alignment of the DNA in the flow gradient, the binding of ZnTMpyP causes a significant decrease (about 50% for a base pair/ZnTMpyP ratio of 20) in the intrinsic dichroism at 260 nm due to the oriented DNA bases; the binding of ZnTMpyP to DNA either gives rise to regions of higher flexibility or causes bends or kinks at the binding sites. Increasing the ionic strength has little influence on the linear dichroism of the ZnTMpyP-DNA complexes, but the number of molecules bound at intercalation sites diminishes in the case of the H2TMpyP-DNA complexes; the accompanying changes in the linear dichroism characteristics suggest that external H2TMpyP complexes are formed at the expense of intercalation complexes.(ABSTRACT TRUNCATED AT 250 WORDS)

Circular dichroism and the interactions of water soluble porphyrins with DNA—A minireview

“…10 At fixed concentration of porphyrin and DNA, H 2 T4 tends to intercalate at low NaCl concentration (providing a negative induced CD feature at 446 nm), but as salt is added, external binding becomes relatively more favorable with the appearance of a positive induced CD feature at shorter wavelength. Linear flow dichroism studies helped confirm that the binding mode of H 2 T4 to natural DNA is sensitive to salt concentration, 11 and recent fluorescence titration results are also consistent with this interpretation of the CD data. 12 As shown in Figure 2A, the titration of H 2 T4/poly(dG-dC) 2 with NaCl can be fit with a simple model in which the porphyrin is either intercalated or free in solution.…”

Analysing DNA complexes by circular and linear dichroism

“…Whereas the free porphyrin ligands tend to be intercalated in DNA as judged by LD, metallo-porphyrins with axial (chloride) ligands are oriented at angles that indicate groove- binding [Geacintov et al, 1987;Sehlstedt et al, 1994 (b)]. The CD is consistent with LD: as expected intercalators possess weak induced CD and groove-binders produce strongly positive LD signals.…”

5,10,15,20-Tetrakis(4-N-methylpyridyl)porphyrinatopalladium(II) as a differentiation probe for sensing binding modes with B-DNA duplexes: Electronic MCD and CD spectra

“…Several new conclusions are drawn regarding the (1) analytically and structurally interesting site/sequence specificity of the binding, (2) electronic excited state properties of free and bound PdP(4), (3) perturbation effects of intercalation and external binding on the porphyrin frontier (,*) MOs, and (4) orientation of bound PdP(4) in each of the three B-DNA systems. Our findings are based on a detailed analysis of MCD, CD, and optical (UV-visible) spectra measured in the analytically sensitive porphyrin Soret (B 0 ) band region (⑀ max ϳ 10 5 cm Ϫ1 M Ϫ1 ), in addition to insight gained from previous experimental (e.g., viscosity, [1][2][3][4][5][6] unwinding of supercoiled DNA, 3,6,7 footprinting, 8,9 optical, 1,3,10,11 CD, 1,3,7,10,12 flow linear dichroism (FLD), 4,5,13,14 NMR, 2,4,5,15,16 resonance Raman (RR), [17][18][19][20][21] laser-induced dichroism (LID), 22 and photoluminescence 23 ) and computational 24,25 work on these and similarly bound porphyrin systems. Use is also made of matrix method CD (mm-CD) sector rules, 26,27 based on the nondegenerate electric dipole transition moment (edtm) coupling ( e D Ϫ e DNA ) model, for interpreting the signs of DNA-induced CD bands in drugs that are achiral in the unbound state with transition energies below those of the DNA bases.…”