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Balanikas E, Martinez-Fernandez L, Baldacchino G, Markovitsi D. Electron Holes in G-Quadruplexes: The Role of Adenine Ending Groups. Int J Mol Sci 2021; 22:ijms222413436. [PMID: 34948235 PMCID: PMC8704496 DOI: 10.3390/ijms222413436] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Revised: 11/30/2021] [Accepted: 12/01/2021] [Indexed: 11/16/2022] Open
Abstract
The study deals with four-stranded DNA structures (G-Quadruplexes), known to undergo ionization upon direct absorption of low-energy UV photons. Combining quantum chemistry calculations and time-resolved absorption spectroscopy with 266 nm excitation, it focuses on the electron holes generated in tetramolecular systems with adenine groups at the ends. Our computations show that the electron hole is placed in a single guanine site, whose location depends on the position of the adenines at the 3' or 5' ends. This position also affects significantly the electronic absorption spectrum of (G+)● radical cations. Their decay is highly anisotropic, composed of a fast process (<2 µs), followed by a slower one occurring in ~20 µs. On the one hand, they undergo deprotonation to (G-H2)● radicals and, on the other, they give rise to a reaction product absorbing in the 300-500 nm spectral domain.
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Affiliation(s)
- Evangelos Balanikas
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
| | - Lara Martinez-Fernandez
- Departamento de Química, Modúlo 13, Facultad de Ciencias and IADCHEM (Institute for Advanced Research in Chemistry), Campus de Excelencia UAM-CSIC, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
- Correspondence: (L.M.-F.); or (D.M.)
| | - Gérard Baldacchino
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
| | - Dimitra Markovitsi
- LIDYL, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France; (E.B.); (G.B.)
- Correspondence: (L.M.-F.); or (D.M.)
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Kim HW, Rhee YM, Shin SK. Charge-dipole interactions in G-quadruplex thrombin-binding aptamer. Phys Chem Chem Phys 2019; 20:21068-21074. [PMID: 30074033 DOI: 10.1039/c8cp03050b] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
DNAs form various structures through hydrogen-bonding, base-stacking and electrostatic interactions. Although these noncovalent interactions are known to be cooperative in stabilizing a G-quadruplex (G4) structure of DNA, we find from all-atom molecular dynamics simulations that the electrostatic charge-dipole interaction is competitive with both hydrogen-bonding and base-stacking interactions. For the thrombin-binding aptamer (TBA) forming a chair-type antiparallel G4 structure, we have examined effects of an intercalating metal ion [K+, Sr2+, Mn+: an ion having a charge of n+ (n = 1-4) with the ionic radius of K+] on structural properties and noncovalent interactions. When K+ in the TBA·K+ complex is replaced with Sr2+, guanine dipoles in the two G-tetrads are realigned toward the central metal ion, thereby distorting the planar G4 geometry. Replacing K+ with Sr2+ significantly enhances the charge-dipole interaction but substantially reduces the number of hydrogen bonds in the G-tetrads. In the case of TBA·Mn+ complexes, as the charge n increases, the charge-dipole interaction increases but both of the hydrogen-bonding and base-stacking interactions decrease. These results suggest that the charge-dipole interaction realigning guanine dipoles in the G-tetrads is not cooperative but competitive with both hydrogen-bonding and base-stacking interactions favoring the planar G-tetrad geometry. Obviously, the charge state of an intercalating metal ion is as important as the ionic radius in forming a stable G4 structure. Thus, a delicate balance between these competing noncovalent interactions makes the chair-type antiparallel G4 structure of TBA selective for intercalating metal ions.
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Affiliation(s)
- Hyun Woo Kim
- Center for Molecular Modeling and Simulation, Korea Research Institute of Chemical Technology, Daejeon 34114, Korea
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Livshits GI, Ghabboun J, Borovok N, Kotlyar AB, Porath D. Comparative electrostatic force microscopy of tetra- and intra-molecular G4-DNA. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:4981-4985. [PMID: 24899584 DOI: 10.1002/adma.201401010] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2014] [Revised: 04/05/2014] [Indexed: 06/03/2023]
Abstract
Two forms of G4-DNA, with parallel and pairwise anti-parallel strands, are studied using atomic force microscopy. The directionality of the strands affects the molecules' structural properties (different height and length) and their electrical polarizability. Parallel G4-DNA is twice as polarizable as anti-parallel G4-DNA, suggesting it is a better electrical wire for bio-nanoelectronics.
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Affiliation(s)
- Gideon I Livshits
- Institute of Chemistry and The Harvey M. Krueger Center for Nanoscience and Nanotechnology, The Hebrew University of Jerusalem, Edmond J. Safra Campus, 91904, Jerusalem, Israel
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Improta R. Quantum mechanical calculations unveil the structure and properties of the absorbing and emitting excited electronic states of guanine quadruplex. Chemistry 2014; 20:8106-15. [PMID: 24828154 DOI: 10.1002/chem.201400065] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Indexed: 12/20/2022]
Abstract
Herein, a full quantum mechanical study, in solution, of several models of guanine-quadruplex helices, both parallel and antiparallel, containing up to eight guanine residues, in their electronic excited state is reported. By exploiting TD-DFT calculations and including solvent effects by the polarizable continuum model, we provide the first atomistic description of the processes triggered by the absorption of UV light, reproducing and assigning the experimental optical and electronic circular dichroism spectra. The absorbing excited states are delocalized over multiple bases, whereas emission involves a stacked guanine dimer or a monomer. Several states, with a varying degree of localization and charge-transfer character, rule the photoexcited dynamics, which are deeply affected by the quadruplex topology. The lowest excited-state minimum for parallel quadruplex is an asymmetric excimer involving two stacked guanines, with a small charge transfer character, whereas for the anti-parallel structure, with the same topology of the thrombin binding aptamer, it is a fully symmetric excimer, characterized by a strong decrease of the stacking distance. A monomer-like decay path is the most relevant nonradiative decay pathway. Insights on the effect of the ions (K(+) or Na(+)) on the excited state decay are also provided.
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Affiliation(s)
- Roberto Improta
- Istituto Biostrutture e Bioimmagini, Consiglio Nazionale delle Ricerche, Via Mezzocannone 16, I-80134, Napoli (Italy).
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5
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Abstract
While the Watson-Crick base pairs are known to stabilize the DNA double helix and play a vital role in storage/replication of genetic information, their replacement with non-Watson-Crick base pairs has recently been shown to have interesting practical applications. Nowadays, theoretical calculations are routinely performed on very complex systems to gain a better understanding of how molecules interact with each other. We not only bring together some of the basic concepts of how mispaired or unnatural nucleobases interact with each other but also look at how such an understanding influences the prediction of novel properties and development of new materials. We highlight the recent developments in this field of research. In this Perspective, we discuss the success of DFT methods, particularly, dispersion-corrected DFT, for applications such as pH-controlled molecular switching, electric-field-induced stacking of disk-like molecules with guanine quartets, and optical birefringence of alkali-metal-coordinated guanine quartets. The synergy between theoretical models and real applications is highlighted.
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Affiliation(s)
- A K Jissy
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur 700032 West Bengal, India
| | - Ayan Datta
- Department of Spectroscopy, Indian Association for the Cultivation of Science, Jadavpur 700032 West Bengal, India
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Lech CJ, Phan AT, Michel-Beyerle ME, Voityuk AA. Electron-Hole Transfer in G-Quadruplexes with Different Tetrad Stacking Geometries: A Combined QM and MD Study. J Phys Chem B 2013; 117:9851-6. [DOI: 10.1021/jp404788t] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Christopher J. Lech
- Division of Physics and Applied Physics,
School of
Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Anh Tuân Phan
- Division of Physics and Applied Physics,
School of
Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Maria-Elisabeth Michel-Beyerle
- Division of Physics and Applied Physics,
School of
Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Alexander A. Voityuk
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
and Institute of Computational Chemistry, Universitat de Girona, 17071 Girona, Spain
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šponer J, Cang X, Cheatham TE. Molecular dynamics simulations of G-DNA and perspectives on the simulation of nucleic acid structures. Methods 2012; 57:25-39. [PMID: 22525788 PMCID: PMC3775459 DOI: 10.1016/j.ymeth.2012.04.005] [Citation(s) in RCA: 105] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Revised: 04/04/2012] [Accepted: 04/06/2012] [Indexed: 11/29/2022] Open
Abstract
The article reviews the application of biomolecular simulation methods to understand the structure, dynamics and interactions of nucleic acids with a focus on explicit solvent molecular dynamics simulations of guanine quadruplex (G-DNA and G-RNA) molecules. While primarily dealing with these exciting and highly relevant four-stranded systems, where recent and past simulations have provided several interesting results and novel insight into G-DNA structure, the review provides some general perspectives on the applicability of the simulation techniques to nucleic acids.
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Affiliation(s)
- Jiří šponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
- CEITEC – Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Xiaohui Cang
- Drug Discovery and Design Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, China
| | - Thomas E. Cheatham
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, 2000 East 30 South, University of Utah, Salt Lake City, UT 84112, United States
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Mondragón-Sánchez JA, Santamaria R, Garduño-Juárez R. Docking on the DNA G-quadruplex: A molecular electrostatic potential study. Biopolymers 2011; 95:641-50. [DOI: 10.1002/bip.21634] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2010] [Revised: 03/25/2010] [Accepted: 03/26/2010] [Indexed: 11/05/2022]
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Woiczikowski PB, Kubař T, Gutiérrez R, Cuniberti G, Elstner M. Structural stability versus conformational sampling in biomolecular systems: Why is the charge transfer efficiency in G4-DNA better than in double-stranded DNA? J Chem Phys 2010; 133:035103. [DOI: 10.1063/1.3460132] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
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10
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Mariani P, Spinozzi F, Federiconi F, Ortore MG, Amenitsch H, Spindler L, Drevensek-Olenik I. Guanosine quadruplexes in solution: a small-angle x-ray scattering analysis of temperature effects on self-assembling of deoxyguanosine monophosphate. J Nucleic Acids 2010; 2010. [PMID: 20725625 PMCID: PMC2915817 DOI: 10.4061/2010/472478] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 03/26/2010] [Indexed: 11/20/2022] Open
Abstract
We investigated quadruplex formation in aqueous solutions of 2′-deoxyriboguanosine 5′-monophosphate, d(pG), which takes place in the absence of the covalent axial backbone. A series of in-solution small angle X-ray scattering experiments on d(pG) have been performed as a function of temperature in the absence
of excess salt, at a concentration just above the critical one at which self-assembling occurs. A global fit
approach has been used to derive composition and size distribution of the scattering particles as a function
of temperature. The obtained results give thermodynamical justification for the observed phase-behavior,
indicating that octamer formation is essential for quadruplex elongation. Our investigation shows that d(pG)
quadruplexes are very suitable to assess the potential of G-quadruplex formation and to study the self-assembling thermodynamics.
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Affiliation(s)
- P Mariani
- Physical Science Section, Research Unit of Ancona, SAIFET Department, CNISM, Marche Polytechnic University, Via Brecce Bianche, 60131 Ancona, Italy
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11
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Woiczikowski PB, Kubar T, Gutiérrez R, Caetano RA, Cuniberti G, Elstner M. Combined density functional theory and Landauer approach for hole transfer in DNA along classical molecular dynamics trajectories. J Chem Phys 2009; 130:215104. [PMID: 19508103 DOI: 10.1063/1.3146905] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate in detail the charge transport characteristics of DNA wires with various sequences and lengths in the presence of solvent. Our approach combines large-scale quantum/classical molecular dynamics (MD) simulations with transport calculations based on Landauer theory. The quantum mechanical transmission function of the wire is calculated along MD trajectories and thus encodes the influence of dynamical disorder arising from the environment (water, backbone, counterions) and from the internal base dynamics. We show that the correlated fluctuations of the base pair dynamics are crucial in determining the transport properties of the wire and that the effect of fluctuations can be quite different for sequences with low and high static disorders (differences in base ionization potentials). As a result, in structures with high static disorder as is the case of the studied Dickerson dodecamer, the weight of high-transmissive structures increases due to dynamical fluctuations and so does the calculated average transmission. Our analysis further supports the basic intuition of charge-transfer active conformations as proposed by Barton et al. [J. Am. Chem. Soc. 126, 11471 (2004)]. However, not DNA conformations with good stacking contacts leading to large interbase hopping values are necessarily the most important, but rather those where the average fluctuation of ionization potentials along the base stack is small. The reason behind this is that the ensemble of conformations leads to average electronic couplings, which are large enough for sufficient transmission. On the other hand, the alignment of onsite energies is the critical parameter which gates the charge transport.
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Affiliation(s)
- P Benjamin Woiczikowski
- Department of Physical and Theoretical Chemistry, Technische Universitat Braunschweig, D-38106 Braunschweig, Germany
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12
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Grigorenko NA, Leumann CJ. Electron transfer through a stable phenanthrenyl pair in DNA. Chem Commun (Camb) 2008:5417-9. [DOI: 10.1039/b810751c] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Kunstelj K, Federiconi F, Spindler L, Drevensek-Olenik I. Self-organization of guanosine 5'-monophosphate on mica. Colloids Surf B Biointerfaces 2007; 59:120-7. [PMID: 17566718 DOI: 10.1016/j.colsurfb.2007.04.022] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2006] [Revised: 04/18/2007] [Accepted: 04/26/2007] [Indexed: 10/23/2022]
Abstract
Self-assembled aggregates of guanosine 5'-monophosphate (GMP) on the surface of muscovite mica were investigated by atomic force microscopy (AFM). Aqueous solutions of sodium, potassium and ammonium GMP salts were studied. For solution concentrations c < 0.005 wt% only small islands of deposited material are present on the surface. For c approximately 0.02 wt%, in addition to the islands and patches, also linear aggregates called G-wires are formed. The wire-like aggregates are on average 1.9 nm high and can be several micrometers long. They exhibit a profound directional growth along the six main crystallographic axes of the basal plane of mica. For c > 0.1 wt% flat terraces with the height of 2.5 nm appear. They are formed of G-wires lying with their long axis parallel to the substrate and stacking in a hexagonal arrangement. The morphology of the adsorbates is independent of the type of salt used to prepare the initial solution. This signifies that intrinsic potassium ions from the substrate play much more important role in the GMP adsorption than cations from the solution.
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Affiliation(s)
- Klemen Kunstelj
- Jozef Stefan Institute, Jamova 39, SI-1000 Ljubljana, Slovenia.
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Oliviero G, Amato J, Borbone N, Galeone A, Petraccone L, Varra M, Piccialli G, Mayol L. Synthesis and characterization of monomolecular DNA G-quadruplexes formed by tetra-end-linked oligonucleotides. Bioconjug Chem 2006; 17:889-98. [PMID: 16848394 DOI: 10.1021/bc060009b] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Guanine-rich DNA sequences are widely dispersed in the eukaryotic genome and are abundant in regions with relevant biological significance. They can form quadruplex structures stabilized by guanine quartets. These structures differ for number and strand polarity, loop composition, and conformation. We report here the syntheses and the structural studies of a set of interconnected d(TG(4)T) fragments which are tethered, with different orientations, to a tetra-end-linker in an attempt to force the formation of specific four-stranded DNA quadruplex structures. Two synthetic strategies have been used to obtain oligodeoxyribonucleotide (ODN) strands linked with their 3'- or 5'-ends to each of the four arms of the linker. The first approach allowed the synthesis of tetra-end-linked ODN (TEL-ODN) containing the four ODN strands with a parallel orientation, while the latter synthetic pathway led to the synthesis of TEL-ODNs each containing antiparallel ODN pairs. The influence of the linker at 3'- or 5'-ODN, on the quadruplex typology and stability, in the presence of sodium or potassium ions, has been investigated by circular dichroism (CD), CD thermal denaturation, (1)H NMR experiments at variable temperature, and molecular modeling. All synthesized TEL-ODNs formed parallel G-quadruplex structures. Particularly, the TEL-ODN containing all parallel ODN tracts formed very stable parallel G-quadruplex complexes, whereas the TEL-ODNs containing antiparallel ODN pairs led to relatively less stable parallel G-quadruplexes. The molecular modeling data suggested that the above antiparallel TEL-ODNs can adopt parallel G-quadruplex structures thanks to a considerable folding of the tetra-end-linker around the whole quadruplex scaffold.
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Affiliation(s)
- Giorgia Oliviero
- Dipartimento di Chimica delle Sostanze Naturali, Università degli Studi di Napoli Federico II, Via D. Montesano 49, I-80131 Napoli, Italy
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Varsano D, Di Felice R, Marques MAL, Rubio A. A TDDFT Study of the Excited States of DNA Bases and Their Assemblies. J Phys Chem B 2006; 110:7129-38. [PMID: 16599476 DOI: 10.1021/jp056120g] [Citation(s) in RCA: 104] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchange-correlation functional. Our approach turns out to be a reliable tool to describe the response of the nucleobases. Furthermore, we analyze in detail the impact of hydrogen bonding and pi-stacking in the calculated spectra for both Watson-Crick base pairs and Watson-Crick stacked assemblies. We show that the reduction of the UV absorption intensity (hypochromicity) for light polarized along the base-pair plane depends strongly on the type of interaction. For light polarized perpendicular to the basal plane, the hypochromicity effect is reduced, but another characteristic is found, namely a blue shift of the optical spectrum of the base-assembly compared to that of the isolated bases. The use of optical tools as fingerprints for the characterization of the structure (and type of interaction) is extensively discussed.
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Affiliation(s)
- Daniele Varsano
- Departamento de Física de Materiales, Facultad de Quimicas, Universidad del País Vasco and Donostia International Physics Center (DIPC), 20080 San Sebastian, Spain
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Abstract
We present a comparison between experimental and calculated soft X-ray spectra of DNA's nucleobases, adenine (A), guanine (G), cytosine (C), and thymine (T) using X-ray absorption spectroscopy (XAS) and soft X-ray emission spectroscopy (XES). Spectra of the 1s thresholds of carbon, nitrogen, and oxygen give a complete picture of the occupied and unoccupied partial density of states of the nucleobases. A combination of both Hartree-Fock and density functional theory calculations are used in the comparison to experimental results. Most experimental results agree well with our theoretical calculations for the XAS and XES of all bases. All spectral features are assigned. A comparison of the experimental highest occupied molecular orbital-lowest unoccupied molecular orbital energy gaps is made to the diverse values predicted in the literature.
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Affiliation(s)
- J MacNaughton
- Department of Physics and Engineering Physics, University of Saskatchewan, 116 Science Place, Saskatoon, Saskatchewan S7N 5E2, Canada.
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