Electronic states of DNA and M-DNA studied by optical absorption

To unveil the electronic states of divalent metal ion incorporated M-DNAs, where M is Mg, Mn, Ni, Co, or Fe, optical absorption spectra have been studied in aqueous solutions of single-stranded (SS) 30mer DNA of poly(dA) (adenine), poly(dG) (guanine), poly(dT) (thymine), poly(dC) (cytosine), salmon-sperm DNA (B-DNA), and M-DNA. The absorption spectrum of the double-stranded (DS) B-DNA can be reproduced with the sum of the four absorption spectra of the SS oligo-DNAs in the ratio corresponding to the composition of B-DNA. This observation suggests that the interactions between complementary strands of DS DNA are negligibly weaker than the bandwidths of the optical spectra. In the metal-incorporated M-DNAs, except for Fe-DNA, the absorption spectra show no significant qualitative change from that of B-DNA. Quantitatively, however, the absorption intensity decreases by $\approx$15% uniquely in a DS poly(dA)-poly(dT) solution with adding ${\text{MCl}}_2$, while nothing happens quantitatively and qualitatively in any SS oligo-DNA and DS poly(dG)-poly(dC) solutions, suggesting some suppression of the electronic excitation only in the Adenine-M-Thymine complex. In contrast, remarkable differences have been observed in Fe-DNA, prepared with ${\text{FeCl}}_2$ and B-DNA. New absorption bands appear in the intragap energy of Fe-DNA, in addition to the suppression of the interband absorption peak of DNA at 4.8 eV. The intragap absorption is attributed to the appearance of Fe${}^{3+}$ species with the same spectral feature as that of ${\text{FeCl}}_3$, that is, purely ionic Fe${}^{3+}$ species. This observation suggests that ${\text{FeCl}}_2+\mathrm{B}$-DNA forms Fe-DNA with hydrated Fe${}^{3+}$ ions with ionic bonds. Thus, it is concluded that the charge transfer from Fe${}^{2+}$ to DNA has occurred in Fe-DNA and that the transferred charges are expected to be located in the nearby bases.

Figure 1

Schematic structures of (a) B-DNA and (b) M-DNA in B-form, where the ovals represent the bases. Each divalent metal ion M is inserted between the bases of a base pair as described in the legend of Fig. 2 [18].

Figure 2

Model structure of metal ion incorporated base pair, Adenine-M-Thymine (A-M-T) [20]. Hydrogen atoms have remained, but two hydrogen bonds are disconnected by the insertion of a large hydrated metal ion. Counter anions are located on the two DNA backbones, which are linear polymer chains with alternatively connected PO${}_4^{-}$ anion and deoxyribose sugar.

Figure 3

Absorption spectrum in an aqueous solution of B-DNA. The small bars in the bottom represent the HOMO-LUMO gaps for the four bases, cytosine (C), guanine (G), adenine (A), and thymine (T), from the left to the right, calculated by Iguchi with the Hückel approximation [32].

Figure 4

Absorption spectra in aqueous solutions of the four 30mer SS oligo-DNAs, poly(dG), poly(dA), poly(dC), and poly(dT). The bars in the bottom of each panel represent the Hückel estimation [32]. The leftmost bar represents the energy difference between LUMO and HOMO. The second bar represents the difference of LUMO and 2nd HOMO for poly(dG) and poly(dA), and 2nd LUMO and HOMO for poly(dC). The third bar shows that of LUMO and 3rd HOMO for poly(dG) and 2nd LUMO and HOMO for poly(dA). The forth bar for poly(dA) corresponds to the difference of LUMO and 3rd HOMO.

Figure 5

Absorption spectra in aqueous solutions of DS poly(dG-dC) (left) and DS poly(dA-dT) (center) are shown together with the sum of the corresponding spectra of SS oligo-DNAs in Fig. 4 by the dotted curves. The spectrum of B-DNA (right) is compared with the sum of the spectra of the DS poly(dG-dC) (left) and the DS poly(dA-dT) (center) with the ratio of 0.37:0.63 by the dotted curve, which is in good agreement with the experimentally observed ratio of 0.4 (GC):0.6 (AT) in the salmon-sperm DNA [33].

Figure 6

Absorption spectra in aqueous solutions of Mg-DNA, Mn-DNA, and Ni-DNA, together with that of B-DNA. The peak intensity is normalized to compare the spectral shape. Co-DNA and Zn-DNA show almost the same spectra as these. However, Fe-DNA behaves differently as discussed in Sec. 3c. Omerzu $et$ $al.$ reported red shifts of the peak position up to 0.1 eV in Zn-DNA [19]. Such a large shift is not found in the present study including Zn-DNA.

Figure 7

Absorption spectra in an aqueous solution of B-DNA (dashed curve) and Mn-DNA + unreacted MnCl${}_2$ (solid curve) prepared by in situ adding of MnCl${}_2$ into the B-DNA.

Figure 8

Absorption spectra in aqueous solutions of DS poly(dA-dT) (dashed curve) and DS poly(dA-dT) after in situ MnCl${}_2$ addition (solid curve). A definite suppression of the absorption area by 15% below 5.5 eV was observed.

Figure 9

Absorption spectra in aqueous solution of FeCl${}_3$, FeCl${}_2$, and FeO(OH). The absorption intensity of FeCl${}_3$ is stronger than the others more than 10 times. Although the valence of Fe is +3 in both of FeCl${}_3$ and FeO(OH), the spectra differ qualitatively from each other, so that we can easily discriminate them.

Figure 10

Time evolution of Fe${}^{3+}$ concentration per base pair (bp) in aqueous solutions of FeCl${}_2$, DS poly(dG-dC) + FeCl${}_2$, and DS poly(dA-dT) + FeCl${}_2$. FeCl${}_2$ is principally transformed to FeO(OH) at elevated temperatures, but does not at room temperature for 30 min. The incremental spectra of DS oligo-DNAs with FeCl${}_2$ are well reproduced by the spectrum of FeCl${}_3$, suggesting the electronic states of Fe-oligo-DNA is of ionic in character.

Figure 11

Absorption spectra in aqueous solution of Fe-DNA prepared with the dialysis method from B-DNA and FeCl${}_2$ (solid curve). Dashed curve represents the spectra of B-DNA. Dotted curve represents the difference between the spectra of Fe-DNA and Fe${}^{3+}$Cl${}_3^{3-}$, which demonstrates the suppression of the inter-$\pi$-band absorption, as also found in Mn-DNA.

Figure 12

Absorption spectra in aqueous solutions of DS Fe-poly(dG-dC) and DS Fe-poly(dA-dT), which are measured at 30 min after adding FeCl${}_2$ into DS poly(dG-dC) and DS poly(dA-dT), shown by solid curves. Dashed curves represent the spectra before adding FeCl${}_2$. Dotted curves represent the difference spectra between the solid curve and the spectra of unreacted FeCl${}_2$, and FeCl${}_3$ as a reference spectrum for Fe${}^{3+}$ in Fe-DNA, which is suppressed by $\approx 30$%. In Fe-poly(dG-dC), the dashed curve overlaps entirely with the dotted curve.

Figure 13

Schematic description of the promotion energy from HOMO of Fe${}^{3+}$ to LUMO of DNA bases.