Study of light-induced formation of photodimers in the i-motif nucleic acid structure by rapid-scan FTIR difference spectroscopy and hybrid hard- and soft-modelling

Benabou, Sanae; Ruckebusch, Cyril; Sliwa, Michel; Aviñó, Anna; Eritja, Ramón; Gargallo, Raimundo; Juan, Anna de

doi:10.1039/c8cp00850g

Cited by 3 publications

(11 citation statements)

References 55 publications

(74 reference statements)

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“…For example, their photoactivated behavior is still poorly understood, despite the fundamental role that optical spectroscopies have in their characterization 4,13,14 . Moreover, recent time‐resolved (TR) studies have highlighted the very rich photophysics and photochemistry of I‐motif structures 15,16 . In this respect, the oxidative processes of cytosine‐rich DNA region are particularly relevant, 17–19 since cytosine deamination, and the subsequent GC → AT transversion, can be carcinogenetic 20 …”

Section: Introductionmentioning

confidence: 99%

“…4,13,14 Moreover, recent time-resolved (TR) studies have highlighted the very rich photophysics and photochemistry of I-motif structures. 15,16 In this respect, the oxidative processes of cytosine-rich DNA region are particularly relevant, [17][18][19] since cytosine deamination, and the subsequent GC → AT transversion, can be carcinogenetic. 20 However, as shown by the studies on the photophysics and photochemistry of other DNA structures, 19,[21][22][23][24][25] the photoactivated dynamics of polynucleotides depends on the interplay of many different excited state processes, often involving more than one base.…”

Section: Introductionmentioning

confidence: 99%

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The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study

Martínez‐Fernández

Improta

2023

Photochem & Photobiology

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We here study the effect that a lowering of the pH has on the excited state processes of cytidine and a cytidine/cytidine pair in solution, by integrating time‐dependent density functional theory and CASSCF/CASPT2 calculations, and including solvent by a mixed discrete/continuum model. Our calculations reproduce the effect of protonation at N3 on the steady‐state infrared and absorption spectra of a protonated cytidine (CH+), and predict that an easily accessible non‐radiative deactivation route exists for the spectroscopic state, explaining its sub‐ps lifetime. Indeed, an extremely small energy barrier separates the minimum of the lowest energy bright state from a crossing region with the ground electronic state, reached by out‐of‐plane motion of the hydrogen substituents of the CC double bond, the so‐called ethylenic conical intersection typical of cytidine and other pyrimidine bases. This deactivation route is operative for the two bases forming an hemiprotonated cytidine base pair, [CH·C]+, the building blocks of I‐motif secondary structures, whereas interbase processes play a minor role. N3 protonation disfavors instead the nπ* transitions, associated with the long‐living components of cytidine photoactivated dynamics.

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Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study

Martínez‐Fernández

Improta

2023

Photochem & Photobiology

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“…No general picture is available for the excited state process occurring on I-motifs, although some interesting time-resolved (TR) studies have highlighted their very rich photophysics and photochemistry [ 39 , 55 , 56 , 57 , 58 , 59 ].…”

Section: Introductionmentioning

confidence: 99%

“…First, the absorption spectrum of I-motifs is significantly red-shifted with respect to that of duplexes [ 39 ], and they also absorb at frequencies greater than 300 nm, where protection from atmospheric ozone is smaller and the solar spectrum at Earth’s surface is more intense. Second, photochemical products [ 57 ] and excited states existing at the nanosecond time-scale have been shown to be present in I-motifs [ 55 , 56 ], increasing the possibility that ’secondary’ radical reactions occur. More generally, photoactivated cytosine oxidative processes have become particularly important [ 41 , 42 , 60 , 61 ], since cytosine deamination and, therefore, C→U mutation and GC→AT transversion can be carcinogenetic [ 62 ].…”

Section: Introductionmentioning

confidence: 99%

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

Improta

2023

IJMS

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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.

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“…In a recent work, the effect of UV light on these four sequences has been studied by means of rapid-scan infrared spectroscopy and multivariate data analysis (32). The cytosine-rich sequences were exposed to UV radiation in the scale of minutes, while IR spectra were recorded and changes were resolved in the scale of milliseconds.…”

Section: Introductionmentioning

confidence: 99%

Study of conformational transitions of i-motif DNA using time-resolved fluorescence and multivariate analysis methods

Benabou

Ruckebusch

Sliwa

et al. 2019

Nucleic Acids Research

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Recently, the presence of i-motif structures at C-rich sequences in human cells and their regulatory functions have been demonstrated. Despite numerous steady-state studies on i-motif at neutral and slightly acidic pH, the number and nature of conformation of this biological structure are still controversial. In this work, the fluorescence lifetime of labelled molecular beacon i-motif-forming DNA sequences at different pH values is studied. The influence of the nature of bases at the lateral loops and the presence of a Watson–Crick-stabilized hairpin are studied by means of time-correlated single-photon counting technique. This allows characterizing the existence of several conformers for which the fluorophore has lifetimes ranging from picosecond to nanosecond. The information on the existence of different i-motif structures at different pH values has been obtained by the combination of classical global decay fitting of fluorescence traces, which provides lifetimes associated with the events defined by the decay of each sequence and multivariate analysis, such as principal component analysis or multivariate curve resolution based on alternating least squares. Multivariate analysis, which is seldom used for this kind of data, was crucial to explore similarities and differences of behaviour amongst the different DNA sequences and to model the presence and identity of the conformations involved in the pH range of interest. The results point that, for i-motif, the intrachain contact formation and its dissociation show lifetimes ten times faster than for the open form of DNA sequences. They also highlight that the presence of more than one i-motif species for certain DNA sequences according to the length of the sequence and the composition of the bases in the lateral loop.

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Study of light-induced formation of photodimers in the i-motif nucleic acid structure by rapid-scan FTIR difference spectroscopy and hybrid hard- and soft-modelling

Cited by 3 publications

References 55 publications

The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study

The photophysics of protonated cytidine and hemiprotonated cytidine base pair: A computational study

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

Study of conformational transitions of i-motif DNA using time-resolved fluorescence and multivariate analysis methods

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