Shedding Light on the Photophysics and Photochemistry of I-Motifs Using Quantum Mechanical Calculations

Abstract

I-motifs are non-canonical DNA structures formed by intercalated hemiprotonated (CH·C)+ pairs, i.e., formed by a cytosine (C) and a protonated cytosine (CH+), which are currently drawing great attention due to their biological relevance and promising nanotechnological properties. It is important to characterize the processes occurring in I-motifs following irradiation by UV light because they can lead to harmful consequences for genetic code and because optical spectroscopies are the most-used tools to characterize I-motifs. By using time-dependent DFT calculations, we here provide the first comprehensive picture of the photoactivated behavior of the (CH·C)+ core of I-motifs, from absorption to emission, while also considering the possible photochemical reactions. We reproduce and assign their spectral signatures, i.e., infrared, absorption, fluorescence and circular dichroism spectra, disentangling the underlying chemical-physical effects. We show that the main photophysical paths involve C and CH+ bases on adjacent steps and, using this basis, interpret the available time-resolved spectra. We propose that a photodimerization reaction can occur on an excited state with strong C→CH+ charge transfer character and examine some of the possible photoproducts. Based on the results reported, some future perspectives for the study of I-motifs are discussed.

Keywords: TD-DFT; non-canonical DNA structure; protonated cytosine.

Figure 1

Schematic drawing of (a) an I motif structure; blue and yellow triangles represent CH${}^{+}$ and C bases, respectively; (b) (CH·C)${}^{+}$ dimer; (c) dC${}_2$ 4 model; (d) C2-4 models, with C2, C2-2, C2-3. Color code: C (grey), H (white), O (red), N (light blue), P (yellow).

Figure 2

Computed IR spectra for C2-4 (black line) and dC2-4 (black dashed lines). PCM/M052X/6-31G(d) calculations. The experimental spectrum measured for (dC)${}_{30}$ at pH 5.5 [55] is also reported (dotted magenta line).

Figure 3

Absorption (top) and ECD (bottom) spectra computed for the different I-motif models. TD-PCM/M052X/6-31G(d) transition shifted by −0.6 eV and broadened with a Gaussian with HWHM = 0.2 eV. The intensities of absorption spectra are normalized with respect to the number of C2 pairs. $\Delta ϵ$ expressed in 10${}^{-40}$ esu${}^2$ cm${}^2$. The experimental spectrum (in mdeg) measured for (dC)${}_{30}$ at pH 5.5 [55] is also reported (dotted magenta line).

Figure 4

Schematic description of three excited states representative of the main excited states families in dC2-4. The excited state can be represented by an electron transferred from the NTO on the left (HOLE) to that on the right (PARTICLE).

Figure 5

Schematic drawing of the most relevant minima and pseudo-minima obtained by optimizing the lowest energy excited states in C2-2. The description of the character of the excited states in terms of the involved NTO is shown on the left. (a) CH${}^{+}$-$\pi {\pi }_{CT}^{*}$-min, (b) C-CH${}^{+}$-CT-min, (c) CH${}^{+}\pi {\pi }^{*}$-min*, (d) C$\pi {\pi }^{*}$-min.

Figure 6

Schematic drawing of the possible decay paths occurring in the core of I-motifs. CH${}^{+}$ bases are represented as triangles, C bases as rectangles. The intensity of the color inside the bases is proportional to its participation in the excited state. The fluorescence spectrum of (dC)${}_{20}$ at acid pH [58] is sketched in gray.

Figure 7

Computed difference IR spectra with respect to the ground electronic state for C2-4 associated with CH${}^{+}$-$\pi {\pi }_{CT}^{*}$-min (black line) and C-CH${}^{+}$-CT-min (red line). In the inset, we show the experimental DIR spectra measured for dC${}_{30}$ at pH 5.5, after 16 ps (blue line) and 150 ps (magenta line). IR frequencies scaled by 0.955. MC/TD-M052X/6-31G(d) calculations.

Figure 8

Schematic description of the minimum energy path associated with the formation of C2-4-dim on the PE of C-CH${}^{+}$-CT. The structures of C-CH${}^{+}$-CT-min and C2-4-dim are also shown. The dashed lines refer to the energy barrier predicted for the same path for dC2-4.

Figure 9

ECD spectra computed for C2-4 (black continuous lines) and dC2-4 (red continuous lines) compared with those computed for C2-4-dim (dashed black lines) and dC2-4-dim (dashed red lines). TD-PCM/M052X/6-31G(d) transition shifted by −0.6 eV and broadened with a Gaussian with HWHM = 0.2 eV. $\Delta ϵ$ expressed in 10${}^{-40}$ esu${}^2$ cm${}^2$.