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

Abstract

We report our detailed electronic MCD, CD, and optical spectroscopic measurements and analysis of the porphyrin Soret (B0) region of four‐coordinate 5,10,15,20‐tetrakis(4‐N‐methylpyridyl)porphyrinatopalladium(II), PdP(4), and its bound states with B‐DNA duplexes poly(A‐T)2, poly(G‐C)2, and calf thymus DNA (CT DNA). For system PdP(4)/poly(A‐T)2 it was possible to conclude that the porphyrin is bound edge‐on in the major groove, specifically at the 5′AT3′ site. For this orientation the porphyrin's electric dipole transition moments (edtm), μx (most perturbed direction) and μy (least perturbed direction), have tilt angles α ∼ 90° and ∼ 45°, respectively, relative to the helix axis. It was further concluded from the small shifts of B0 optical and MCD band intensities and wavelengths and from the net MCD (+) A‐term sign retention upon binding that the porphyrin's frontier pπ MOs (1a1u 3a2u 4eg) are only weakly perturbed by the heterocyclic bases of poly(A‐T)2, and therefore that the LUMO (4eg) splitting is less than the |1a1u−3a2u| energy separation, ΔHOMO, that is, ΔLUMO < ΔHOMO for the bound state in PdP(4)/poly(A‐T)2. For intercalation systems PdP(4)/poly(G‐C)2 and /CT DNA, with PdP(4) centered in the intercalation “pocket” and having two of its 4‐N‐methylpyridyls extending into each of the major and minor grooves, the edtms μx and μy were determined to be oriented perpendicular (γ ∼ 0°) and parallel (γ ∼ 90°) to the hydrogen bonds of the base pairs, respectively. Intercalation is characterized by a much stronger binding interaction, viz., the B0 optical band and net MCD extrema wavelength shifts are relatively large, and the net MCD (+) A‐term of PdP(4) is substantially quenched as it becomes the (−) pseudo‐A‐term of intercalated PdP(4)/poly(G‐C)2. This A‐term sign reversal informs that the porphyrin MOs are so strongly perturbed by the GC base pairs that ΔLUMO > ΔHOMO, which gives rise to a (−) pseudo‐A‐term. Also, the findings demonstrate (1) the potential of PdP(4) as a sensitive, discriminating analytical probe of DNA sequences and (2) the diagnostic capability of the composite of five spectra [net MCD, CD, and optical of free and bound PdP(4)] in differentiating the site and sequence selectivity and preferred binding mode of this porphyrin. © 1999 John Wiley & Sons, Inc. Biospectroscopy 5: 179–188, 1999

Electronic and vibrational circular dichroism spectroscopic study of non-covalent interactions of meso-5,10,15,20-tetrakis(1-methylpyridinium-4-yl)porphyrin with (dG-dC)10 and (dA-dT)10

“…The distinctive changes in UV-ECD support our observations in the Soret spectral region that TMPyP interacts with (dA-dT) 10 by at least two binding modes: in addition to external binding mode to the phosphate backbone, which does not change the oligonucleotide structure significantly, another binding mode took place (for example an edge-on minor groove or a major groove binding took place as was suggested in [18]) which disturbs the arrangement of oligonucleotide bases [6]. Indeed, at the ratio 6/1, the UV-ECD spectrum reflects the transition state between B-and modified Z-forms of the (dA-dT) 10 [17].…”

Binding of nickel(II) tetrakis(dimethylpyrazolium-4-yl)porphyrin to poly(dG-dC)2 and poly(dA-dT)2

“…The MCD signals of NiPzP changed from a genuine (+) A-term to a (-) pseudo-A-term upon interaction with poly(dG-dC) 2 . Such change was also observed for binding of Pd(II)TMPyP to poly(dG-dC) 2 [26]. The negative band appeared at 405 nm (∆ε/M = -10.3 T -1 ; Table 2); however, the positive band at longer wavelength could not be observed clearly.…”

“…It has also been shown that the binding mode of porphyrins to the nucleic acid duplex, e.g. intercalative or outside binding mode, can also be tuned by varying the metal center and the thickness of the complex molecule based on the presence or absence of axial ligands [13,[23][24][25][26][27]. Thus, the thin square planar copper(II) derivatives of H 2 TMPyP and H 2 PzP are capable of intercalation, because these metalloporphyrins are not ligated at their vacant axial site by aquo ligands and can intercalate into the pocket between two adjacent, closely spaced (3.4 Å) base pairs of B-DNA.…”

B-DNA Binding with Cobalt(III) and Vanadyl(2+) Derivatives of Tetracationic 5,10,15,20-Tetrakis(4-N-methylpyridyl)porphine: Combined CD, Optical, and Electronic MCD Spectra

“…It is of advantage to next examine the CD and reported FLD r data and relate them to our MCD conclusions. First, the large amplitude of the (+) CD band (λ 0 CD = 444 nm, Δε 0 = +32 cm -1 M -1 ) is definitive for groove binding, which is in contrast to much weaker CD bands observed in cases of weak “nonspecific” outside binding (wnob), e.g., Δε ∼ 1.5 cm -1 M -1 in PdP(2) /poly(G-C) 2 . Second, the (+) CD sign would tentatively be assignable to edge-on minor groove binding (AT-rich segments 14 ) with one drug edtm, μ e D (either μ ex D or μ ey D of the porphyrin's orthogonal edtm pair), having orientation angles α/β/β‘ = ∼45°/0°/90° .…”