Computing the electronic circular dichroism spectrum of DNA quadruple helices of different topology: A critical test for a generalized excitonic model based on a fragment diabatization

Unraveling the complexity: Advanced methods in analyzing DNA, RNA, and protein interactions

Exploring the intricate interplay within and between nucleic acids, as well as their interactions with proteins, holds pivotal significance in unraveling the molecular complexities steering cancer initiation and progression. To investigate these interactions, a diverse array of highly specific and sensitive molecular techniques has been developed. The selection of a particular technique depends on the specific nature of the interactions. Typically, researchers employ an amalgamation of these different techniques to obtain a comprehensive and holistic understanding of inter- and intramolecular interactions involving DNA-DNA, RNA-RNA, DNA-RNA, or protein-DNA/RNA. Examining nucleic acid conformation reveals alternative secondary structures beyond conventional ones that have implications for cancer pathways. Mutational hotspots in cancer often lie within sequences prone to adopting these alternative structures, highlighting the importance of investigating intra-genomic and intra-transcriptomic interactions, especially in the context of mutations, to deepen our understanding of oncology. Beyond these intramolecular interactions, the interplay between DNA and RNA leads to formations like DNA:RNA hybrids (known as R-loops) or even DNA:DNA:RNA triplex structures, both influencing biological processes that ultimately impact cancer. Protein-nucleic acid interactions are intrinsic cellular phenomena crucial in both normal and pathological conditions. In particular, genetic mutations or single amino acid variations can alter a protein's structure, function, and binding affinity, thus influencing cancer progression. It is thus, imperative to understand the differences between wild-type (WT) and mutated (MT) genes, transcripts, and proteins. The review aims to summarize the frequently employed methods and techniques for investigating interactions involving nucleic acids and proteins, highlighting recent advancements and diverse adaptations of each technique.

Processes triggered in guanine quadruplexes by direct absorption of UV radiation: From fundamental studies toward optoelectronic biosensors

Guanine quadruplexes (GQs) are four-stranded DNA/RNA structures exhibiting an important polymorphism. During the past two decades, their study by time-resolved spectroscopy, from femtoseconds to milliseconds, associated to computational methods, shed light on the primary processes occurring when they absorb UV radiation. Quite recently, their utilization in label-free and dye-free biosensors was explored by a few groups. In view of such developments, this review discusses the outcomes of the fundamental studies that could contribute to the design of future optoelectronic biosensors using fluorescence or charge carriers stemming directly from GQs, without mediation of other molecules, as it is the currently the case. It explains how the excited state relaxation influences both the fluorescence intensity and the efficiency of low-energy photoionization, occurring via a complex mechanism. The corresponding quantum yields, determined with excitation at 266/267 nm, fall in the range of (3.0-9.5) × 10-4 and (3.2-9.2) × 10-3 , respectively. These values, significantly higher than the corresponding values found for duplexes, depend strongly on certain structural factors (molecularity, metal cations, peripheral bases, number of tetrads …) which intervene in the relaxation process. Accordingly, these features can be tuned to optimize the desired signal.

Analysis of Site Energies and Excitonic Couplings: The Role of Symmetry and Polarization

An excitonic coupling model is developed based on an equation-of-motion coupled cluster combined with the fragment molecular orbital method. The effects of polarization and excitonic coupling on the splitting of quasi-degenerate levels in systems containing multiple chromophores are elucidated on dimers of formaldehyde, water, formic acid, hydrogen fluoride, and carbon monoxide. It is shown that the level structure is mainly determined by the mutual polarization of chromophores and to a lesser extent by the excitonic coupling. The role of symmetry in excitonic coupling in dimers is discussed. The excitonic coupling between all residues in the photoactive yellow protein (PDB: 2PHY) is analyzed.

The van der Waals interaction and absorption and electron circular dichroism spectra of two-dimensional bilayer stacked structures

van der Waals (vdW) heterojunctions based on two-dimensional (2D) materials, graphene and transition metal dichalcogenides (TMDs), are a research hotspot for future optoelectronic and exciton devices. Bond-free vdW interactions are key to 2D material heterojunction device reliability and stability. However, most of the current research on 2D stacked materials heterostructures mainly focuses on optical properties and electronic structure. Furthermore, vdW interaction in 2D heterostructures is studied and understood on the basis of qualitative description and energy ranges from the literature. There are few studies on the nature of vdW interaction based on practical calculations of the quantitative strength and microscopic mechanism of vdW interaction between 2D stacked materials. Therefore, this paper explores the vdW interaction between 2D material stacked bilayer structures, including bilayer graphene, graphene/MoS2 and graphene/WS2 heterostructures, focusing on quantitative analysis of the energy components of the vdW interaction. We first visually observed the weak interactions in the three stacked bilayer structures through noncovalent interaction (NCI) analysis, and found that the interactions are concentrated in the binding region between the two-layer structures. We mainly decomposed the weak interaction energy in the three 2D material bilayer heterostructures through energy decomposition analysis based on the force field (EDA-FF) method and obtained the energy values and proportions of the three components-electrostatic energy, exchange repulsion energy and dispersion energy of the total binding energy between the 2D stacked bilayer structures. The vdW interaction energy is the sum of the exchange repulsion energy and dispersion energy, and the dispersion energy of the vdW interaction accounts for more than 60% of the binding energy of the weak interaction between the 2D bilayer stacked structures. The vdW strengths in the bilayer structures are on the order of 177.07, 123.85, and 133.93 kJ/mol, approxmately 1-2 orders of magnitude larger than the classically defined vdW energies of 0.1-10 kJ/mol. Furthermore, we calculate the density of states of the three 2D stacked structures, and further obtained HOMO-LOMO information; to further understand the electronic structures of the graphene/MoS2 and graphene/WS2 heterostructures, we calculated their optical absorption spectra and electron circular dichroism (ECD) spectra. According to the calculation results, the two heterostructures have strong absorption peaks in the visible region, and the charge transfer forms at the strong absorption peak can be determined according to the charge transfer diagram. The ECD spectra indicate that the configurations of the graphene/MoS2 and graphene/WS2 heterostructures have large chirality. Our work contributes to a deeper understanding of the nature of the weak interactions and optical properties in 2D stacked materials, which plays a fundamental role in promoting the construction of stable 2D heterostructure configurations and the development of multifunctional 2D devices. The research is conducive to further promoting the basic research and practical development of strong optoelectronic and excitonic 2D heterojunctions devices.

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

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.