Edited by: John D. Wade, Florey Institute of Neuroscience and Mental Health, Australia
Reviewed by: Robert Vianello, Rudjer Boskovic Institute, Croatia; Giampaolo Barone, University of Palermo, Italy
*Correspondence: Elise Dumont, Laboratoire de Chimie, UMR 5182 Centre National de la Recherche Scientifique, École Normale Supérieure de Lyon, 46, Allée d'Italie, 69364 Lyon 07, France
Antonio Monari, Faculté de Sciences et Techniques, Boulevard des Aiguillettes, Vandoeuvre-les-Nancy, 54506 Nancy, France
This article was submitted to Chemical Biology, a section of the journal Frontiers in Chemistry
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DNA is constantly exposed to damaging threats coming from oxidative stress, i.e., from the presence of free radicals and reactive oxygen species. Sensitization from exogenous and endogenous compounds that strongly enhance the frequency of light-induced lesions also plays an important role. The experimental determination of DNA lesions, though a difficult subject, is somehow well established and allows to elucidate even extremely rare DNA lesions. In parallel, molecular modeling has become fundamental to clearly understand the fine mechanisms related to DNA defects induction. Indeed, it offers an unprecedented possibility to get access to an atomistic or even electronic resolution. Ab initio molecular dynamics may also describe the time-evolution of the molecular system and its reactivity. Yet the modeling of DNA (photo-)reactions does necessitate elaborate multi-scale methodologies to tackle a damage induction reactivity that takes place in a complex environment. The double-stranded DNA environment is first characterized by a very high flexibility, but also a strongly inhomogeneous electrostatic embedding. Additionally, one aims at capturing more subtle effects, such as the sequence selectivity which is of critical important for DNA damage. The structure and dynamics of the DNA/sensitizers complexes, as well as the photo-induced electron- and energy-transfer phenomena taking place upon sensitization, should be carefully modeled. Finally the factors inducing different repair ratios for different lesions should also be rationalized. In this review we will critically analyze the different computational strategies used to model DNA lesions. A clear picture of the complex interplay between reactivity and structural factors will be sketched. The use of proper multi-scale modeling leads to the in-depth comprehension of DNA lesions mechanisms and also to the rational design of new chemo-therapeutic agents.
DNA stability is essential to maintain cellular integrity of living organisms and avoid genetic mutations. Threats to DNA stability can be triggered by oxidative stress induced by the presence of metabolic reactive radical and oxygen species (ROS) or by photoreactivity. Oxidative and light-induced stress can have a very strong influence on the biological processes governed by DNA, as well as in the indirect activation or transduction of signal cascades, that may result in different malignant outcomes for the life of the involved cells (Salmon et al.,
In contrast to photochemical degradation mechanisms, oxidative stress sources can also derive from endogenous processes and mechanism. Inflammatory conditions are a known source of ROS (Kamp et al.,
DNA is also constantly exposed to light, and hence efficient dissipative channels exist to hamper potentially dangerous photochemical pathways. Nevertheless, inherently stable DNA photoproducts have been reported and their photochemistry has been deeply analyzed (Sinha and Hader,
The cells response to the oxidative and photochemical stress normally results in an acceleration of protective mechanisms aimed to expel the stress enhancing factors. In the case of DNA lesions the activation of “repair” proteins, that may vary greatly in terms of specificity and efficiency, is invoked. The latter enzymes usually excise the damaged DNA area (Sancar and Sancar,
Apoptosis induction favored by the controlled production of DNA lesions has a very important therapeutic significance. Indeed, the formation of irreversible DNA lesions, and the interference with the replication process, has been and is currently exploited in the development of chemotherapeutic agents. For instance, we may cite the renown case of the cisplatin (Florea and Büsselberg,
From an experimental point of view, one relies on the use of techniques able to identify and possibly quantify the different lesions formed in DNA. Combination of mass-spectrometry with gas-phase chromatography is usually used to provide such informations both for isolated and cellular DNA (Frelon et al.,
As this brief survey evidences, the induction of DNA lesions triggered by different sources of stress involves a very complex interplay between different phenomena taking place at molecular level, and having more general and systemic consequences. On the other hand, it is precisely that complexity that strongly suggests a multidisciplinary approach to tackle this non trivial problem, in particular combining adequate spectroscopic techniques with state-of-the-art molecular multiscale modeling. Molecular modeling is invaluable in providing atomistic or even electronic scale description of the involved phenomena. For instance, molecular dynamics techniques allow to assess for the structural deformation of lesioned DNA and its time evolution, as well as to infer the existence of different stable interaction modes with smaller sensitizers. The ground- and excited- state behavior and the reactivity, for instance in terms of free energy profiles along reaction coordinates, are described by using hybrid quantum mechanics/ molecular mechanics (QM/MM) methods allowing to take into account the role of the environment (Senn and Thiel,
In the present review we will present some examples of the molecular modeling of DNA under external stress, both concerning ground-state and photochemical pathways, underlying the fundamental questions that may be answered by a proper simulation and modeling.
DNA oxidative stress is dominated by a combinatorial radical chemistry, in biological media hydroxyl (HO•) and peroxyl (HOO•) radical being by far the principal players. However, other non-radical reactive chemical moieties can play a role and have a strong biological influence: 1O2, H2O2, alkylating agents, low-energy electrons, and each of them has been tackled by simulation means.
We will hereby focus on radical induced ground-state reactivity, and mostly on the hydroxyl radical HO•, as its study exemplifies the methods employed in DNA damage molecular modeling. The hydroxyl radical is prone to abstract an hydrogen, with subsequent production of one water molecule and an highly reactive radical specie embedded in the biological macromolecule (see Figure
It has been shown that for a given double-strand DNA fragment (ds-DNA), an hydrogen uptake can occur at many positions, on the nucleobase (Cadet et al.,
Modeling has been early invoked to provide a rationale, and ultimately predict, the preferential hydrogen abstraction sites: indeed, because of its general high reactivity, the hydroxyl radical selectivity is governed by the accessibility to the solvent. The latter is an information reliably estimated by bioinformatics approaches such as the computation of Solvent Accessible Surface Area (SASA). Tullius et al. have exploited this approach to rationalize the HO•-induced DNA strand breaking (Balasubramanian et al.,
The hydrogen abstraction is the key limiting step of the whole damage process (Regulus et al.,
For instance, DFT confirms that hydrogen abstraction for pyrimidine nucleobases, i.e., cytosine and thymine, occurs preferentially on C5 positions and on the corresponding methyl group (C5 m), not only because of solvent accessibility but also due to electronic favors (Ji et al.,
It is remarkable that a sound agreement can be achieved between experiment and theory even when calculations on model, isolated moieties are performed (Bera and Schaefer,
However, QM/MM-MD simulatons, e.g., in a Car-Parrinello framework, have nowadays been successfully performed both for reactivity in DNA double strands and in solvated nucleoside (Abolfath et al.,
When coming to DNA reactivity and damage generations, experiments are performed on isolated nucleobases, small DNA fragments (trinucleotides), longer oligonucleotides or even larger ds-DNA structures. It is now well recognized that reactivity in model systems can largely differ due to the geometrical constraint imposed within a ds-DNA and the strongly heterogenous environment. Providing a most direct comparison between reaction profiles for isolated moieties vs. nucleobases embedded in a complex macromolecular environment allows to pinpoint the structural and electrostatic factors that can dramatically tune or reserve the intrinsic reactivity of nucleobases. Many elementary lesions in DNA subunits have been first targeted based on QM studies on isolated fragments (Duncan Lyngdoh and Schaefer,
Predictions of the reactivity order between different nucleobases can indeed be assessed on model π-stacked systems (thymine propensity to form lower triplet states or dimerize (Durbeej and Eriksson,
Cluster models where a reaction profile is obtained employing hybrid QM/MM (Barnett et al.,
Structural and dynamic changes of an oxidized abasic site in ds-DNA have been studied by molecular dynamics to unravel representative conformation(s) of the double-helix and infer the role played by structural modifications on the DNA chemical reactivity (Chen et al.,
Indeed, MD simulations provide a starting point for tackling the reactivity, within the framework of hybrid QM/MM-MD simulations. A decade ago Parrinello and coworkers rationalized the role of the B-DNA (Gervasio et al.,
QM/MM-MD simulations of DNA reactivity are becoming more and more popular, with several choices concerning the biais techniques (metadynamics Gervasio et al.,
The next subsection is devoted to theoretical studies focusing on reactions implying two nucleobases, where the distortion of the DNA structure is even larger and hence a proper dynamic description of the reaction becomes crucial.
After the initial radical hit, modified nucleobases (X), such as oxidized AP, see Figure
Formation of ICLs obeys a multistep pathway that can be studied based on model systems (Labet et al.,
The formation of ICLs can be formally written as X → B, where X denotes the modified (oxidized) nucleobase and B one of the four canonical nucleobases (Figure The reactivity to situate the barrier to covalently bind two nucleobases together. This can rely on DFT calculations performed on dinucleoside monophosphate, in gas-phase or with implicit solvation. Alternatively the reactivity can be treated within a B-DNA fragment, to account notably for the helical embedding. The barrier to overcome to bridge up two nucleobases together is strongly dependent on DNA conformation and on the nucleobases themselves. However this dependence is non trivial, and attacks corresponding to strand offset have also been reported. The structural consequences of the formation of such bonds, and in particular the free-energy necessary to induce the helical deformation. In this case molecular modeling can palliate the lack of experimental structures. In particular modeling provides starting conformations of the reactant, but perhaps more importantly, provides a computationally efficient way to build up in silico the structures of a given modified oligonucleotide.
The latter point is fundamental in the absence of NMR or X-ray structure even for the most commonly formed intra- and inter-strand oxidatively-generated lesions. Also, from a modeling perspective, the typical timescale for the reorganization of a 12 base-pair oligonucleotide bearing a central defect, poses a central challenge since it spans tens of nanoseconds, to be compared to the current limitations of 10–100 ps for QM/MM-MD schemes. The identification of suitable reaction coordinates and collective variables describing the process will allow the use of rare-event accelerating methods such as meta-dynamics, however the problem is still far from being trivial. Their inherent complexity also explains why the modeling of this class of lesions is much less developed, despite their strong biological significance.
One important breakthrough in the study of intrastrand-cross links has been recently performed using Car-Parrinello QM/MM molecular dynamics (Garrec et al.,
All in all it clearly appears that the modeling of ground-state DNA reactivity is an extremely complicated problem requiring the correct equilibrium between a proper description of the electronic factors and a suitable sampling of the conformational space of a very flexible macromolecule. To tackle the latter problems some techniques developed in particular in the field of the enzymatic catalysis (Garcia-Mesenguer et al.,
DNA is constituted by π-stacked nucleobases that can be regarded as chromophores and whose absorbance is mostly confined in the UVB regions of the spectrum. The absorption region capable of producing DNA lesions can be enlarged for instance by photosensitization, i.e., by the interaction with endogenous or exogenous compounds (Epe,
Even if UVB wavelengths are normally filtered by the ozone layer, and efficient deactivation pathways of the nucleobases excited states exist, DNA lesions resulting from direct photoactivation are usually reported and are considered as extremely dangerous for their potential carcinogenicity.
The photochemical pathways leading to the formation of the cyclobutane thymine dimer (
Recently, more complex photochemical mechanisms have been taken into account (Esposito et al.,
The same group (Vayá et al.,
Barbatti and Lischka have reported a systematic study of the deactivation pathways for the four DNA nucleobases (adenine, thymine, guanine and cytosine) as well as for uracil (Barbatti et al.,
Robb group (Groenhof et al.,
Novel strategies to prove the photostability of DNA nucleobases start emerging, notably very recently Garavelli's group reported the modeling of near UV 2D-electronic spectroscopy as a tool to characterize the double excited, multi excimer and charge-transfer states that may be responsible of the ultrafast deactivation dynamics. These advancements could pave the way toward a better interplay between theory and modeling to give an atomistic level description of the different dynamic phenomena (Nenov et al.,
Although, extremely efficient DNA relaxation pathways may lead to a drawback evidenced by the works of Gonzalez's group that have underlined a femtosecond intersystem crossing taking place in the case of cytosine (Richter et al.,
In DNA photosensitization the absorption of light and the subsequent photochemical pathways are mediated by an interacting chromophore. By definition in the case of sensitization the chromophore needs to be recovered inaltered at the end of the process, acting in an almost catalytical way. This excludes covalent interactions with DNA that characterize the action of important antitumoral drugs such as the cisplatin.
The study of DNA photosensitization is complicated by the fact that one should be able to achieve a good knoweldge of different phenomena. First of all, a clear picture of the structure of the DNA/sensitizers aggregate is compulsory. Usually three main modes of interaction have been characterized for canonical B-DNA (Zeglis et al.,
Moreover the three interaction modes can most often coexist, with a population ratio strongly dependent on the environmental factors such as the DNA sequence or the salt concentration. As a consequence, X-Ray resolved structures are quite rare, and structural determination becomes crucial, requiring a proper modeling that may confirm more indirect experimental observation such as the ones based on circular dichroism.
On that context we should cite the extensive molecular simulations performed by the Lavery group using molecular dynamics and different sampling techniques such as metadynamics and umbrella sampling (Wilhelm et al.,
Also the interaction between simple organic molecules and DNA should be described most carefully, which necessitates the resort to molecular dynamic simulations to sample the relevant possible conformations. A particularly striking case is the one of benzophenone, a paradigmatic sensitizers (Cuquerella et al.,
Photosensitization involving the excitation of the chromophore, and the subsequent excited-state interactions with the nearby nucleobases, the influence of the environment on excited state properties is crucial and should be thoughtfully taken into account. Indeed the optical properties of many chromophores can be modulated by the environment, one of the most well known cases being the light-switch effects (Friedman et al.,
More recently a refined explanation for the light-switch effect was offered coupling a multiscale modeling to describe the interactions with the surroundings together with TDDFT and high level ab-initio calculations. Firstly the intercalation interaction mode and the main features of the absorption spectrum of [Ru(dppz)(bipy)2]2+ interacting with DNA were modeled, also taking into account polarizable embedding and validating the computational protocol (Very et al.,
Usually photosensitization can be classified considering the physical phenomenon producing the lesion with DNA. Type I photosensitization is due to a charge transfer usually toward guanine, type II sensitization on the other hand is based on an energy-transfer between the sensitizer (triplet) excited state and molecular oxygen giving raise to 1O2 and the subsequent oxidative events. Finally, one should also take into account triplet photosensitization characterized by an energy-transfer between the photosensitizers and DNA bases, usually thymine; thymine dimers are the most common final products of triplet sensitization. Since the physical processes underlining these photosensitization pathways are different, modeling strategies should be tailored to provide a satisfactory description.
Concerning type I photosensitization some evidences of important electron transfer between nearby guanine and different ruthenium complexes have been reported already at Franck-Condon level using QM/MM performed with an extended QM partition and TDDFT calculations (Chantzis et al.,
Also in the case of type II sensitization the role of the environment may be far from innocent. For instance in the case of a DNA interacting drug known as palmatine the production of 1O2 as well as fluorescence is triggered only by interaction with DNA (Hirakawa et al.,
The role of the environment in tuning type II photosensitization, and in particularly in driving the population of the triplet manifold was recently pointed out by Nogueira et al. in the case of the interaction between DNA and phenothiazinium dyes (Nogueira et al.,
Triplet photosensitization is also an experimentally-known component of DNA damage that can be timely tackled by modeling. Since it involves the preliminary population of the photosensitizer triplet state manifold, one may ask if the macromolecular environment keeps the road to photosensitization open, or if it hinders its development. Acetophenone is a known triplet photosensitizer (Epe,
But in order to be efficient in terms of triplet-photosensitization, the population of the triplet manifold should be rapidly followed by energy transfer to the nearby thymine. This aspect has been recently deeply analyzed for the case of benzophenone (Dumont et al.,
Obviously a deeper characterization of energy- and electron-transfer processes will necessitate to take into account non-adiabatic and state-hopping dynamics. Furthermore, since the triplet manifolds are involved in most of the cases the spin-orbit coupling should not be neglected. This aspect coupled with the necessity to take into account the environment and many interacting chromophores and the relative long time scale of the full sensitization process will necessitate a considerable computational effort that can be achieved only through a proper methodological development. Still significant progresses have been made allowing to get a clearer vision of a fundamental and rather complicated process whose biological relevance cannot be underestimated.
Even if the canonical B-DNA form is by far the most common one, particular DNA sequences may adopt the so-called non-canonical conformations. The biological relevance of such structures is now clearly evidenced. On that context particular significance has to be attributed to the guanine-quadruplex (G4), that are present in guanine-rich sequences such as the telomeres (Neidle and Parkinson,
The relative peculiar structure of G4 has necessitated an important computational effort to rationalize their structure and their stability (Ilchenko and Dubey,
A rather serious complication in the study of G4 is connected to the polymorphism observed for such structures (Ilchenko and Dubey,
In parallel, the necessity to correctly represent the polymorphism of the G4 non-canonical structures has pushed toward the validation of force-fields, which are usually parameterized to reproduce the behavior of canonical B-DNA (Grunenberg et al.,
However, the combination of well parameterized force fields and of QM and QM/MM techniques allows to correctly reproduce the interaction of sensitizers with G4. The most common G4 sensitizers are rather extended and planar π-conjugated cations (Ilchenko and Dubey,
It is evident that despite some difficulty the sensitization of non-canonical DNA structure, both at the ground and for the excited-state, is no more considered as an exotic novelty. On the contrary it is displaying all its potentiality in the rational design of novel therapeutic strategies. Molecular modeling is playing an active role on the field and will certainly drive not only the comprehension of the mechanisms leading to a selective sensitization, but also the prediction of entirely novel sensitizers.
The impressive progresses of modeling and simulation techniques have now made possible tackling problems as complex as the generation of oxidatively-induced DNA lesions and the interaction of DNA with potential drugs. However, this domain should still be considered very challenging also from a computational chemistry point of view. Indeed, many different factors should be taken into account and treated on the same footing to have a proper, and biologically relevant, description of the various phenomena comming into play.
Particular attention should be taken for instance to model the conformational degrees of freedom of the very flexible DNA macromolecule, this of course calls for adequate and long-scale molecular dynamics trajectory. Techniques allowing a good estimate of the free-energy, especially but not exclusively, in the case of sensitization binding energies are also of paramount importance. This aspect will of course require the development of efficient force fields as well as of proper sampling techniques.
The study of the electron density reorganization taking place on the ground- or on the excited states is also fundamental to go beyond the simple structural description and propose hints on the reactivity or the photochemistry of DNA alone or in presence of sensitizers. The envisaged QM or QM/MM techniques should conjugate the precision of the description with the efficiency necessary to make possible the sampling of important region of the configuration space, and hence having access to good statistical properties. This is especially true since in many case energy- or electron-transfer phenomena have to be taken into due accounts, i.e., one has to deal with some of the most challenging situations for QM methods.
We believe that from a methodological point of view the development of novel multiscale techniques in particular for what concerns excited state non-adiabatic dynamics as well as ab-initio QM/MM dynamics will allow the treatment of more and more complex scenarios, coupling a good accuracy with good statistics. On that context the development of proper sampling techniques allowing the definition of good and physical relevant reaction coordinates taking into account all the relevant collective variables will certainly be one of the most important challenges of the next years.
Nowadays, the atomistic scale description of DNA related phenomena offered by multiscale modeling allows to rationalize and properly describe phenomena as diverse as the behavior of DNA under oxidative stress or the environment controlled behavior of phototherapy drugs. The selectivity of potential drug candidates toward different DNA configurations as well as the differential dynamical behavior of different DNA sequences are now accessible at least at a semi-quantitative level.
Modern day molecular modeling is therefore able to provide a molecular and electronic description of the factor governing DNA chemistry under external perturbation, therefore molecular modeling can nowadays be considered as a fundamental tool to provide unprecedented insights in chemical biology. Conversely, the knowledge of the mechanism of DNA lesions induction are also paving the way to the rational design of novel therapeutic agents. Therefore we may safely say that the communication between the
Both authors contributed equally to the present review.
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
This work has been performed in the framework of the COST Action “Biomimetic Radical Chemistry” whose support is gratefully acknowledged. AM thanks CNRS for the funding of the “chaire d'excellence” program. The authors thanks Dr. Raymond Grüber for useful discussion and for providing some of the figures.