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.

Triplet Excimer Formation in a DNA Duplex with Silver Ion-Mediated Base Pairs

“…T exc is suggested to be nonreactive because ground-state recovery is favored over CPD formation (Figure S6). Because previous calculations of a stacked cytosine dimer 31 and i-motif structures 75 without metal ions suggested the opposite, we studied how Ag + ion complexation affects the photoreactivity. We repeated all calculations starting from the T exc state, but with the Ag + ions removed.…”

Stabilization of G-Quadruplex Structures of the SARS-CoV-2 Genome by TMPyP4, BRACO19, and PhenDC3

“…DNA GQ structures are known to be fairly pH-insensitive [ 32 ]. Interestingly, the i-motif formed by the complementary strand of the GQ sequence is very pH-dependent and needs pH values lower than the physiological one [ 63 , 64 , 65 , 66 ]. Our RNA GQs were also found to be quite pH-insensitive, although a small destabilization trend was observed at higher pH values.…”