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Abdelgawwad AMA, Monari A, Tuñón I, Francés-Monerris A. Spatial and Temporal Resolution of the Oxygen-Independent Photoinduced DNA Interstrand Cross-Linking by a Nitroimidazole Derivative. J Chem Inf Model 2022; 62:3239-3252. [PMID: 35771238 PMCID: PMC9277591 DOI: 10.1021/acs.jcim.2c00460] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
DNA damage is ubiquitous in nature and is at the basis of emergent treatments such as photodynamic therapy, which is based on the activation of highly oxidative reactive oxygen species by photosensitizing O2. However, hypoxia observed in solid tumors imposes the necessity to devise oxygen-independent modes of action able to induce DNA damage under a low oxygen concentration. The complexity of these DNA damage mechanisms in realistic environments grows exponentially when taking into account light absorption and subsequent excited-state population, photochemical and (photo)-redox reactions, the multiple species involved in different electronic states, noncovalent interactions, multiple reaction steps, and the large number of DNA reactive sites. This work tackles all the intricate reactivity of a photosensitizer based on a nitroimidazole derivative reacting toward DNA in solution under UV light exposition. This is performed through a combination of ground- and excited-state quantum chemistry, classical molecular dynamics, and hybrid QM/MM simulations to rationalize in detail the formation of DNA interstrand cross-links (ICLs) exerted by the noncanonical noncovalent photosensitizer. Unprecedented spatial and temporal resolution of these phenomena is achieved, revealing that the ICL is sequence-specific and that the fastest reactions take place at AT, GC, and GT steps involving either the opposite nucleobases or adjacent Watson-Crick base pairs. The N7 and O6 positions of guanine, the N7 and N3 sites of adenine, the N4 position of cytosine, and the O2 atom of thymine are deemed as the most nucleophile sites and are positively identified to participate in the ICL productions. This work provides a multiscale computational protocol to study DNA reactivity with noncovalent photosensitizers, and contributes to the understanding of therapies based on photoinduced DNA damage at molecular and electronic levels. In addition, we believe the depth understanding of these processes should assist the design of new photosensitizers considering their molecular size, electronic properties, and the observed regioselectivity toward nucleic acids.
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Affiliation(s)
| | - Antonio Monari
- Université Paris Cité, CNRS, ITODYS, F-75006 Paris, France.,Université de Lorraine and CNRS, UMR 7019 LPCT, F-5400 Nancy, France
| | - Iñaki Tuñón
- Departament de Química Física, Universitat de València, 46100 Burjassot, Spain
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Bignon E, Gillet N, Jiang T, Morell C, Dumont E. A Dynamic View of the Interaction of Histone Tails with Clustered Abasic Sites in a Nucleosome Core Particle. J Phys Chem Lett 2021; 12:6014-6019. [PMID: 34165307 DOI: 10.1021/acs.jpclett.1c01058] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
Apurinic/apyrimidinic sites are the most common forms of DNA damage under physiological conditions, yet their structural and dynamical behavior within nucleosome core particles has just begun to be investigated and is dramatically different from that of abasic sites in B-DNA. Clusters of two or more abasic sites are repaired even less efficiently and hence constitute hot spots of high mutagenicity notably due to enhanced double-strand break formation. On the basis of an X-ray structure of a 146 bp DNA wrapped onto a histone core, we investigate the structural behavior of two bistranded abasic sites positioned at mutational hot spots during microsecond-range molecular dynamics simulations. Our simulations allow us to probe interactions of histone tails at clustered abasic site locations, with a definitive assignment of the key residues involved in the NCP-catalyzed formation of DNA-protein cross-linking in line with recent experimental findings, and pave the way for a systematic assessment of the response of histone tails to DNA lesions.
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Affiliation(s)
- Emmanuelle Bignon
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, F69342 Lyon, France
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280 CNRS, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Natacha Gillet
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, F69342 Lyon, France
| | - Tao Jiang
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, F69342 Lyon, France
| | - Christophe Morell
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280 CNRS, Université Claude Bernard Lyon 1, 5 rue de la Doua, 69100 Villeurbanne, France
| | - Elise Dumont
- Univ Lyon, ENS de Lyon, CNRS UMR 5182, Laboratoire de Chimie, F69342 Lyon, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
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Bignon E, Gillet N, Chan CH, Jiang T, Monari A, Dumont E. Recognition of a tandem lesion by DNA bacterial formamidopyrimidine glycosylases explored combining molecular dynamics and machine learning. Comput Struct Biotechnol J 2021; 19:2861-2869. [PMID: 34093997 PMCID: PMC8141532 DOI: 10.1016/j.csbj.2021.04.055] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Revised: 04/19/2021] [Accepted: 04/20/2021] [Indexed: 11/30/2022] Open
Abstract
The combination of several closely spaced DNA lesions, which can be induced by a single radical hit, constitutes a hallmark in the DNA damage landscape and radiation chemistry. The occurrence of such a tandem base lesion gives rise to a strong coupling with the double helix degrees of freedom and induces important structural deformations, in contrast to DNA strands containing a single oxidized nucleobase. Although such complex lesions are known to be refractory to repair by DNA glycosylases, there is still a lack of structural evidence to rationalize these phenomena. In this contribution, we explore, by numerical modeling and molecular simulations, the behavior of the bacterial glycosylase responsible for base excision repair (MutM), specialized in excising oxidatively-damaged defects such as 7,8-dihydro-8-oxoguanine (8-oxoG). The difference in lesion recognition between a simple damage and a tandem lesion featuring an additional abasic site is assessed at atomistic resolution owing to microsecond molecular dynamics simulations and machine learning postprocessing, allowing to extensively pinpoint crucial differences in the interaction patterns of the damaged bases. Our results reveal substantial changes in the interaction network surrounding the 8-oxoG upon addition of an adjacent abasic site, leading to the perturbation of the intercalation triad which is crucial for lesion recognition and processing. The recognition process might also be impacted by a more constrained MutM-DNA binding upon tandem damage, as shown by the machine learning post-processing. This work advocates for the use of such high throughput numerical simulations for exploring the complex combinatorial chemistry of tandem DNA lesions repair and more generally local multiple damaged sites of the utmost significance in radiation chemistry.
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Affiliation(s)
- Emmanuelle Bignon
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Natacha Gillet
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Chen-Hui Chan
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Tao Jiang
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019, 54000 Nancy, France
| | - Elise Dumont
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342 Lyon, France
- Institut Universitaire de France, 5 rue Descartes, 75005 Paris, France
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Kellum AH, Qiu DY, Voehler MW, Martin W, Gates KS, Stone MP. Structure of a Stable Interstrand DNA Cross-Link Involving a β- N-Glycosyl Linkage Between an N6-dA Amino Group and an Abasic Site. Biochemistry 2020; 60:41-52. [PMID: 33382597 DOI: 10.1021/acs.biochem.0c00596] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Abasic (AP) sites are one of the most common forms of DNA damage. The deoxyribose ring of AP sites undergoes anomerization between α and β configurations, via an electrophilic aldehyde intermediate. In sequences where an adenine residue is located on the opposing strand and offset 1 nt to the 3' side of the AP site, the nucleophilic N6-dA amino group can react with the AP aldehyde residue to form an interstrand cross-link (ICL). Here, we present an experimentally determined structure of the dA-AP ICL by NMR spectroscopy. The ICL was constructed in the oligodeoxynucleotide 5'-d(T1A2T3G4T5C6T7A8A9G10T11T12C13A14T15C16T17A18)-3':5'-d(T19A20G21A22T23G24A25A26C27X28T29A30G31A32C33A34T35A36)-3' (X=AP site), with the dA-AP ICL forming between A8 and X28. The NMR spectra indicated an ordered structure for the cross-linked DNA duplex and afforded detailed spectroscopic resonance assignments. Structural refinement, using molecular dynamics calculations restrained by NOE data (rMD), revealed the structure of the ICL. In the dA-AP ICL, the 2'-deoxyribosyl ring of the AP site was ring-closed and in the β configuration. Juxtapositioning the N6-dA amino group and the aldehydic C1 of the AP site within bonding distance while simultaneously maintaining two flanking unpaired A9 and T29 bases stacked within the DNA is accomplished by the unwinding of the DNA at the ICL. The structural data is discussed in the context of recent studies describing the replication-dependent unhooking of the dA-AP ICL by the base excision repair glycosylase NEIL3.
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Affiliation(s)
- Andrew H Kellum
- Department of Chemistry, Vanderbilt University Center for Structural Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - David Y Qiu
- Department of Chemistry, Vanderbilt University Center for Structural Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - Markus W Voehler
- Department of Chemistry, Vanderbilt University Center for Structural Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
| | - William Martin
- Department of Biochemistry, Vanderbilt University, Nashville, Tennessee 37232, United States
| | - Kent S Gates
- Departments of Chemistry and Biochemistry, University of Missouri, Columbia, Missouri 65221, United States
| | - Michael P Stone
- Department of Chemistry, Vanderbilt University Center for Structural Biology, and the Vanderbilt-Ingram Cancer Center, Vanderbilt University, Nashville, Tennessee 37235, United States
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Bignon E, Claerbout VEP, Jiang T, Morell C, Gillet N, Dumont E. Nucleosomal embedding reshapes the dynamics of abasic sites. Sci Rep 2020; 10:17314. [PMID: 33057206 PMCID: PMC7560594 DOI: 10.1038/s41598-020-73997-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 07/31/2020] [Indexed: 12/16/2022] Open
Abstract
Apurinic/apyrimidinic (AP) sites are the most common DNA lesions, which benefit from a most efficient repair by the base excision pathway. The impact of losing a nucleobase on the conformation and dynamics of B-DNA is well characterized. Yet AP sites seem to present an entirely different chemistry in nucleosomal DNA, with lifetimes reduced up to 100-fold, and the much increased formation of covalent DNA-protein cross-links leading to strand breaks, refractory to repair. We report microsecond range, all-atom molecular dynamics simulations that capture the conformational dynamics of AP sites and their tetrahydrofuran analogs at two symmetrical positions within a nucleosome core particle, starting from a recent crystal structure. Different behaviours between the deoxyribo-based and tetrahydrofuran-type abasic sites are evidenced. The two solvent-exposed lesion sites present contrasted extrahelicities, revealing the crucial role of the position of a defect around the histone core. Our all-atom simulations also identify and quantify the frequency of several spontaneous, non-covalent interactions between AP and positively-charged residues from the histones H2A and H2B tails that prefigure DNA-protein cross-links. Such an in silico mapping of DNA-protein cross-links gives important insights for further experimental studies involving mutagenesis and truncation of histone tails to unravel mechanisms of DPCs formation.
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Affiliation(s)
- Emmanuelle Bignon
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France. .,Institut des Sciences Analytiques, UMR 5280, Université de Lyon 1 (UCBL) CNRS, Lyon, France.
| | - Victor E P Claerbout
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Tao Jiang
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Christophe Morell
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon 1 (UCBL) CNRS, Lyon, France
| | - Natacha Gillet
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France
| | - Elise Dumont
- Univ. Lyon, ENS de Lyon, CNRS UMR 5182, Université Claude Bernard Lyon 1, Laboratoire de Chimie, F69342, Lyon, France. .,Institut Universitaire de France, 5 rue Descartes, 75005, Paris, France.
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Liebl K, Zacharias M. Unwinding Induced Melting of Double-Stranded DNA Studied by Free Energy Simulations. J Phys Chem B 2017; 121:11019-11030. [PMID: 29064703 DOI: 10.1021/acs.jpcb.7b07701] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
DNA unwinding plays a major role in many biological processes, such as replication, transcription, and repair. It can lead to local melting and strand separation and can serve as a key mechanism to promote access to the separate strands of a double-stranded DNA. While DNA unwinding has been investigated extensively by DNA cyclization and single-molecule studies on a length-scale of kilo base pairs, it is neither fully understood at the base pair level nor at the level of molecular interactions. By employing a torque acting on the termini of DNA oligonucleotides during molecular dynamics free energy simulations, we locally unwind the central part of a DNA beyond an elastic (harmonic) regime. The simulations reproduce experimental results on the twist elasticity in the harmonic regime (characterized by a mostly quadratic free energy change with respect to changes in twist) and a deformation up to 7° was found as a limit of the harmonic response. Beyond this limit the free energy increase per twist change dropped dramatically coupled to local base pair disruptions and significant deformation of the nucleic acid backbone structure. Restriction of the DNA bending flexibility resulted in a stiffer harmonic response and an earlier onset of the anharmonic response. Whereas local melting with a complete disruption of base pairing and flipping of nucleotides was observed in case of an AT rich central segment strong backbone changes and changes in the stacking arrangements were observed in case of a GC rich segment. Unrestrained MD simulations starting from locally melted DNA reformed regular B-DNA after 50-300 ns simulation time. The simulations may have important implications for understanding DNA recognition processes coupled with significant structural alterations.
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Affiliation(s)
- Korbinian Liebl
- Physik-Department T38, Technische Universität München , James-Franck-Str. 1, 85748 Garching, Germany
| | - Martin Zacharias
- Physik-Department T38, Technische Universität München , James-Franck-Str. 1, 85748 Garching, Germany
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