Intercalative and nonintercalative binding of large cationic porphyrin ligands to calf thymus DNA

Abstract

The large meso-substituted porphine, meso-tetra(4-N-methylpyridyl)porphine has been identified as a DNA-interactive ligand with a capacity for intercalation (1,2). Subsequently, the 2-N-methyl, 3-N-methyl and N-trimethylanilinium analogues of this porphyrin intercalator have been obtained for physico-chemical analyses (absorption spectroscopy, viscometry, circular dichroism, unwinding of supercoiled DNA). In this paper we discuss the factors affecting the character of porphyrin binding (intercalative, as is the case for the 4-N-methyl and 3-N-methyl porphines, versus non-intercalative, as is the case for the 2-N-methyl and N-trimethylanilinium porphines) and the impact that porphyrins' binding has upon the structure of DNA. The molecular conformation of the porphyrin ligand varies slightly within this series so that the ability of a given porphyrin to intercalate may be correlated with the arrangement of charged groups, the planarity of the porphine ring and the effective width of the individual molecules. The results from these studies indicate that sequence selective binding occurs within a small aperture of solution conditions.

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

“…Instrument calibration of wavelength and intensity (⌬⑀) was ascertained by using 1 mM aqueous solutions of K 3 Table I are the optical, MCD, and CD data measured in the Soret region of each PdP(4)/B-DNA system. Representative spectra are shown in the figures.…”

“…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.…”

Solution Properties and Photonuclease Activity of Cationic Bis-porphyrins Linked with a Series of Aliphatic Diamines.

“…8,[41][42][43][44] Therefore, the characterization in the solution state of these cationic bis-porphyrins was first done by visible spectrometry. The value of the e ).…”

“…[3][4][5] For the binding, three major modes have been proposed: intercalation, outside binding in the groove, and outside binding with self-stacking along the DNA surface. 6) These binding modes have been suggested using the physicochemical method of viscometry 7,8) and spectroscopic techniques such as UV-visible absorption, [6][7][8] circular dichroism (CD), [6][7][8][9] fluorescence, 10,11) and NMR spectroscopy. 12,13) For the photonuclease activity, cationic TMPyP is more efficient in strand scission of plasmid DNA than an anionic porphyrin like hematoporphyrin derivative (HPD).…”

Synthesis and DNA‐Recognition and ‐Cleavage Properties of Multiply Charged Porphyrin Esters

“…In contrast, porphyrins 3 and 6 showed positive CD maxima centered at 428 nm and 410 nm, respectively, indicating outside groove binding [20]. Both the negative maximum at 405 nm and the positive one at 445 nm of porphyrins 4 and 5 suggest that these two compounds bind to CT-DNA by means of outside stacking [20].…”