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Zaccaria F, van der Lubbe SCC, Nieuwland C, Hamlin TA, Fonseca Guerra C. How Divalent Cations Interact with the Internal Channel Site of Guanine Quadruplexes. Chemphyschem 2021; 22:2286-2296. [PMID: 34435425 PMCID: PMC9293024 DOI: 10.1002/cphc.202100529] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 08/24/2021] [Indexed: 11/06/2022]
Abstract
The formation of guanine quadruplexes (GQ) in DNA is crucial in telomere homeostasis and regulation of gene expression. Pollution metals can interfere with these DNA superstructures upon coordination. In this work, we study the affinity of the internal GQ channel site towards alkaline earth metal (Mg2+, Ca2+, Sr2+, and Ba2+), and (post‐)transition metal (Zn2+, Cd2+, Hg2+, and Pb2+) cations using density functional theory computations. We find that divalent cations generally bind to the GQ cavity with a higher affinity than conventional monovalent cations (e. g. K+). Importantly, we establish the nature of the cation‐GQ interaction and highlight the relationship between ionic and nuclear charge, and the electrostatic and covalent interactions. The covalent interaction strength plays an important role in the cation affinity and can be traced back to the relative stabilization of cations’ unoccupied atomic orbitals. Overall, our findings contribute to a deeper understanding of how pollution metals could induce genomic instability.
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Affiliation(s)
- Francesco Zaccaria
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Stephanie C C van der Lubbe
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Celine Nieuwland
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Trevor A Hamlin
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and, Amsterdam Center for Multiscale Modelling, AIMMS, Vrije Universiteit Amsterdam, De Boelelaan 1083, 1081 HV, Amsterdam, The Netherlands.,Leiden Institute of Chemistry, Gorlaeus Laboratories, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
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2
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Hou C, Tsodikov OV. Utilizing guanine-coordinated Zn 2+ ions to determine DNA crystal structures by single-wavelength anomalous diffraction. ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY 2019; 75:32-40. [PMID: 30644843 DOI: 10.1107/s205979831801553x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/02/2018] [Indexed: 11/10/2022]
Abstract
The experimental phase determination of crystal structures of nucleic acids and nucleic acid-ligand complexes would benefit from a facile method. Even for double-stranded DNA, software-generated models are generally insufficiently accurate to serve as molecular replacement search models, necessitating experimental phasing. Here, it is demonstrated that Zn2+ ions coordinated to the N7 atom of guanine bases generate sufficient anomalous signal for single-wavelength anomalous diffraction (SAD) phasing of DNA crystal structures. Using zinc SAD, three crystal structures of double-stranded DNA oligomers, 5'-AGGGATCCCT-3', 5'-GGGATCCC-3' and 5'-GAGGCCTC-3', were determined. By determining the crystal structure of one of these oligomers, GAGGCCTC, in the presence of Mg2+ instead of Zn2+, it was demonstrated that Zn2+ is not structurally perturbing. These structures allowed the analysis of structural changes in the DNA on the binding of analogues of the natural product mithramycin to two of these oligomers, AGGGATCCCT and GAGGCCTC. Zinc SAD may become a routine approach for determining the crystal structures of nucleic acids and their complexes with small molecules.
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Affiliation(s)
- Caixia Hou
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
| | - Oleg V Tsodikov
- Department of Pharmaceutical Sciences, University of Kentucky, Lexington, KY 40536, USA
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3
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Gáliková J, Trávníček Z. Effect of different reaction conditions on the structural diversity of zinc(II) complexes with 9-deazahypoxanthine. Polyhedron 2014. [DOI: 10.1016/j.poly.2014.05.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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4
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Stereospecific intra-molecular interligand interactions affecting base-specific metal bonding to purine nucleobases in the solid state. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.02.008] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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5
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Lai TC, Chen WH, Lee CJ, Wang BC, Wei HH. Structure and magnetic property of μ-alkoxo–μ-6-methoxypurinate double bridged dinuclear copper(II) complex. J Mol Struct 2009. [DOI: 10.1016/j.molstruc.2009.06.041] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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6
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Amo-Ochoa P, Castillo O, Alexandre SS, Welte L, de Pablo PJ, Rodríguez-Tapiador MI, Gómez-Herrero J, Zamora F. Synthesis of Designed Conductive One-Dimensional Coordination Polymers of Ni(II) with 6-Mercaptopurine and 6-Thioguanine. Inorg Chem 2009; 48:7931-6. [DOI: 10.1021/ic900896w] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pilar Amo-Ochoa
- Departamento de Química Inorgánica, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Oscar Castillo
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apartado 644, E-48080 Bilbao, Spain
| | - Simone S. Alexandre
- Universidade Federal de São João Del-Rei, Campus Alto Paraopeba, Ouro Branco, Brazil
| | - Lorena Welte
- Departamento de Química Inorgánica, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Pedro J. de Pablo
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | | | - Julio Gómez-Herrero
- Departamento de Física de la Materia Condensada, Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Félix Zamora
- Departamento de Química Inorgánica, Universidad Autónoma de Madrid, 28049 Madrid, Spain
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7
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Zamora F, Pilar Amo-Ochoa M, Sanz Miguel PJ, Castillo O. From metal-nucleobase chemistry towards molecular wires. Inorganica Chim Acta 2009. [DOI: 10.1016/j.ica.2008.02.029] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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8
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Brancolini G, Di Felice R. Electronic Properties of Metal-Modified DNA Base Pairs. J Phys Chem B 2008; 112:14281-90. [DOI: 10.1021/jp806419t] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Giorgia Brancolini
- National Research Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41100 Modena, Italy
| | - Rosa Di Felice
- National Research Center on nanoStructures and bioSystems at Surfaces (S3) of INFM-CNR, Via Campi 213/A, 41100 Modena, Italy
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Lippert B. Coordinative Bond Formation Between Metal Ions and Nucleic Acid Bases. NUCLEIC ACID–METAL ION INTERACTIONS 2008. [DOI: 10.1039/9781847558763-00039] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Affiliation(s)
- Bernhard Lippert
- Fakultät für Chemie, Technische Universität Dortmund Otto-Hahn-Strasse 6 D-44227 Dortmund Germany
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Choquesillo-Lazarte D, Brandi-Blanco MDP, García-Santos I, González-Pérez JM, Castiñeiras A, Niclós-Gutiérrez J. Interligand interactions involved in the molecular recognition between copper(II) complexes and adenine or related purines. Coord Chem Rev 2008. [DOI: 10.1016/j.ccr.2007.09.018] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Amo-Ochoa P, Castillo O, Sanz Miguel PJ, Zamora F. Unusual Dimeric Zn(II)-cytosine complexes: New models of the interaction of Zn(II) with DNA and RNA. J Inorg Biochem 2008; 102:203-8. [PMID: 17870174 DOI: 10.1016/j.jinorgbio.2007.07.036] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2007] [Revised: 07/24/2007] [Accepted: 07/26/2007] [Indexed: 10/23/2022]
Abstract
Synthesis and crystal structure of two Zn(II) dimer complexes with 1-methylcytosine (1-MeC) are reported. In complex [Zn(2)Cl(4)(mu-1-MeC-O2,N3)(2)] (1), two 1-MeC ligands are bridging two ZnCl(2) moieties. In [Zn(2)(1-MeC-N3)(4)(mu-SO(4))(2)].2H(2)O (2), the sulfates act as bridging ligands and 1-MeC are linked via N3 to Zn(II) as terminal ligands. Both complexes represent the first examples of Zn(II)-pyrimidine dimers. The potential biological significance of 1 and 2 is discussed.
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Affiliation(s)
- Pilar Amo-Ochoa
- Departamento de Tecnología Industrial, Universidad Alfonso X El Sabio, 28691 Villanueva de la Cañada, Madrid, Spain
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12
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Mastropietro TF, Armentano D, Grisolia E, Zanchini C, Lloret F, Julve M, De Munno G. Guanine-containing copper(ii) complexes: synthesis, X-ray structures and magnetic properties. Dalton Trans 2008:514-20. [DOI: 10.1039/b713960h] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Amo-Ochoa P, Sanz Miguel PJ, Castillo O, Sabat M, Lippert B, Zamora F. Interguanine hydrogen-bonding patterns in adducts with water and Zn–purine complexes (purine is 9-methyladenine and 9-methylguanine). Unexpected preference of Zn(II) for adenine-N7 over guanine-N7. J Biol Inorg Chem 2007; 12:543-55. [PMID: 17310379 DOI: 10.1007/s00775-007-0206-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Accepted: 01/08/2007] [Indexed: 11/26/2022]
Abstract
Guanine-guanine hydrogen bonding involving the Watson-Crick edge [N(1)H, N(2)H2] of one base and the Hoogsteen edge (N7, O6) of the other is the dominant association pattern in the solid-state structures of two hydrates of 9-ethylguanine (9-EtGH), and in adducts of 9-methylguanine (9-MeGH) with the Zn compounds [ZnCl2(H2O)(9-MeGH-N7)]*(9-MeGH) as well as [ZnCl2(H2O)(9-MeA-N7)]*2(9-MeGH) (9-MeA is 9-methyladenine). The structures of 9-EtGH*2H2O and 9-EtGH*3.5H2O are dominated by polymeric tape structures of the guanine and extended water clusters. In [ZnCl2(H2O)(9-MeGH-N7)]*(9-MeGH) the metalated guanine is involved in hydrogen bonding (GG3 motif) with a free 9-MeGH, which in turn is centrosymmetrically related to itself via hydrogen bonds involving N2H2 and N3 (GG4 motif). In [ZnCl2(H2O)(9-MeA-N7)]*2(9-MeGH) the metalated adenine base interacts via its Watson-Crick edge [N1, N(6)H2] with the sugar edge [N(2)H2, N3] of one of the guanine nucleobases of the GG pair. Crystallization of [ZnCl2(H2O)(9-MeA-N7)]*2(9-MeGH) from an aqueous solution containing 9-MeGH, 9-MeA, and ZnCl2 is fully unexpected in that the anticipated preference of Zn(II) for guanine-N7 is not realized and instead coordination to adenine-N7 is observed. The relevance of [ZnCl2(H2O)(9-MeGH-N7)]*(9-MeGH) and [ZnCl2(H2O)(9-MeA-N7)]*2(9-MeGH) for metal-containing nucleic acid triplex structures is discussed.
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Affiliation(s)
- Pilar Amo-Ochoa
- Departamento de Tecnología Industrial, Universidad Alfonso X El Sabio, 28691 Villanueva de la Cañada, Madrid, Spain.
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14
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Li L, Murthy NN, Telser J, Zakharov LN, Yap GPA, Rheingold AL, Karlin KD, Rokita SE. Targeted Guanine Oxidation by a Dinuclear Copper(II) Complex at Single Stranded/Double Stranded DNA Junctions. Inorg Chem 2006; 45:7144-59. [PMID: 16933915 DOI: 10.1021/ic0605930] [Citation(s) in RCA: 66] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A dinuclear copper(II) complex [Cu(II)2(PD'O-)(H2O)2](ClO4)3 (5) with terminal Cu(II)-H(2)O moieties and a Cu...Cu distance of 4.13 A (X-ray structure) has been synthesized and characterized by EPR spectroscopy (ferromagnetic coupling observed) and cyclic voltammetry. Dizinc(II) and mononuclear copper(II) analogues [Zn(II)2(PD'O-)(H2O)2]3+ (7) and [Cu(II)(mPD'OH)(H2O)]2+ (6), respectively, have also been synthesized and structurally characterized. Reacting 5/MPA/O(2) (MPA = 3-mercaptopropionic acid) with DNA leads to a highly specific oxidation of guanine (G) at a junction between single- and double-stranded DNA. Mass spectrometric analysis of the major products indicates a gain of +18 and +34 amu relative to initial DNA strands. The most efficient reaction requires G at the first and second unpaired positions of each strand extending from the junction. Less reaction is observed for analogous targets in which the G cluster is farther from the junction or contains less than four Gs. Consistent with our previous systems, the multinuclear copper center is required for selective reaction; mononuclear complex 6 is not effective. Hydrogen peroxide as a substitute for MPA/O2 also does not lead to activity. Structural analysis of a [Cu(II)2(PD'O-)(G)]3+ complex (8) and dizinc analogue [Zn(II)(2)(PD'O-)(G)](ClO4)3 (9) (G = guanosine) reveals coordination of the G O6 and N7 atoms with the two copper (or zinc) centers and suggests that copper-G coordination likely plays a role in recognition of the DNA target. The Cu2-O2 intermediate responsible for guanine oxidation appears to be different from that responsible for direct-strand scission induced by other multinuclear copper complexes; the likely course of reaction is discussed.
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Affiliation(s)
- Lei Li
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA
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15
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Amo-Ochoa P, Alexandre SS, Pastor C, Zamora F. Stabilization of the non-canonical adenine–adeninium base pair by N(7) coordination of Zn(II). J Inorg Biochem 2005; 99:2226-30. [PMID: 16183132 DOI: 10.1016/j.jinorgbio.2005.07.015] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2005] [Revised: 07/26/2005] [Accepted: 07/27/2005] [Indexed: 10/25/2022]
Abstract
A new zinc (II) compound with 9-ethyladenine (9-EtA) of formula [Zn(9-EtA-N7)Cl(3)](9-EtAH) has been synthesized and characterized by X-ray diffraction. Its X-structure consists of an Zn(II) anionic complex and 9-ethyladeninium as counteranion. The Zn(II) complex shows a distorted tetrahedral geometry in which three Cl and an 9-EtA coordinates through N(7) position are the ligands. An indirect chelation via intramolecular H-bond between N(6)H and an Cl ligand is present in the complex. The network of [Zn(9-EtA-N7)Cl(3)](9-EtAH) shows interesting features. Thus, self-association of coordinated adenine-adeninium takes place by H-bonding of N(6)-H...N(1) and N(6)-H...N(7), leading to a polymeric ribbon-like 1D supramolecular arrangement. Ab initio calculations have been applied in order to study the stability of the adenine-adeninium interaction due to the coordination of the Zn(II) to the N(7) position and to compare experimental and theoretical structural data.
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Affiliation(s)
- Pilar Amo-Ochoa
- Departamento de Tecnología Industrial, Universidad Alfonso X El Sabio, 28691 Villanueva de la Cañada, Madrid, Spain
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16
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Western EC, Shaughnessy KH. Inhibitory effects of the guanine moiety on Suzuki couplings of unprotected halonucleosides in aqueous media. J Org Chem 2005; 70:6378-88. [PMID: 16050700 DOI: 10.1021/jo050832l] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
In the Suzuki arylations of unprotected halonucleosides in aqueous media, 8-bromo-2'-deoxyguanosine (8BrdG) couplings were slower to reach completion than the corresponding 8-bromo-2'-deoxyadenosine (8BrdA) couplings. The guanine moiety has an acidic proton, which under our Suzuki conditions (pH congruent with 10) may be deprotonated to give an anion that can coordinate to palladium. The possibility that guanine coordination was responsible for the observed slower rates was explored using additive experiments in which nonhalogenated nucleosides were added to the Suzuki coupling reaction of 8BrdA or 4-bromotoluene and PhB(OH)2 and the reaction progress monitored by HPLC or GC. Adding dG slowed these reactions, and an induction period was observed. The addition of dA or 1-methyl-2'-deoxyguanosine (1MedG) to these couplings did not affect the rate of conversion to product. Guanine coordination was further explored using 13C and 31P NMR spectroscopy, which implies that guanine is coordinating to palladium through N-1 or O-6, or both. Furthermore, the presence of dG inhibited the formation of the active palladium(0) catalytic species, which may account for both the observed induction period and the sluggishness of reactions where guanine is involved.
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Affiliation(s)
- Elizabeth C Western
- Department of Chemistry and the Center for Green Manufacturing, The University of Alabama, Box 870336, Tuscaloosa, Alabama 35487-0336, USA
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17
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Ochoa PA, Rodríguez-Tapiador MI, Alexandre SS, Pastor C, Zamora F. Structural models for the interaction of Cd(II) with DNA: trans-[Cd(9-RGH-N7)2(H2O)4]2+. J Inorg Biochem 2005; 99:1540-7. [PMID: 15927262 DOI: 10.1016/j.jinorgbio.2005.04.014] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2005] [Revised: 04/13/2005] [Accepted: 04/15/2005] [Indexed: 11/30/2022]
Abstract
Reactions of Cd(NO(3))(2) with the model nucleobases 9-alkylguanine in water at neutral pH, give the compounds trans-[Cd(9-RGH-N7)(2)(H(2)O)(4)](NO(3))(2)(R=Me, Et), with the 9-alkylguanine ligands bound to the metal cation at the N(7) position. The X-ray structures of both compounds are reported. The six-coordinate Cd(II) complexes consist of a highly regular octahedral geometry in which the two 9-alkylguanine ligands are in a trans position to each other and approximately collinear with the metal cation. In addition, the networks of both compounds show interesting features. Thus, intramolecular H-bonds between O(6) and a coordinated water molecule are present, and self-association of guanines via H-bonding of N(3)-H...N(2) take place, leading to a 1D supramolecular polymeric ribbon. Density functional theory calculations have been applied to both compounds in order to study the stability of N(7) metalated guanine-guanine associations by comparing experimental and theoretical results. The potential relevance with regard to possible Cd(II)-DNA cross-links is briefly discussed.
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Affiliation(s)
- Pilar Amo Ochoa
- Departamento de Tecnología Industrial, Universidad Alfonso X El Sabio, 28691 Villanueva de la Cañada, Madrid, Spain
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18
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Gordon LE, Harrison WTA. Amino Acid Templating of Inorganic Networks: Synthesis and Structure of l-Asparagine Zinc Phosphite, C4N2O3H8·ZnHPO3. Inorg Chem 2004; 43:1808-9. [PMID: 15018491 DOI: 10.1021/ic0346127] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
C(4)N(2)O(3)H(8).ZnHPO(3) is the first zincophosphite framework to be templated by an amino acid (l-asparagine), which bonds to Zn via a carboxyl O atom. It contains infinite, homochiral, helical 4-ring chains of ZnO(4) and HPO(3) groups, stabilized by intra- and interchain N-H.O hydrogen bonds. Crystal data: C(4)N(2)O(3)H(8).ZnHPO(3), M(r) = 277.49, orthorhombic, P2(1)2(1)2(1) (No. 19), a = 5.0349(2) A, b = 9.4539(4) A, c = 18.6092(8) A, V = 885.79 (6) A(3), Z = 4.
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Affiliation(s)
- Laura E Gordon
- Department of Chemistry, University of Aberdeen, Aberdeen AB24 3UE, Scotland, UK
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