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Huang SC, Chen CW, Satange R, Hsieh CC, Chang CC, Wang SC, Peng CL, Chen TL, Chiang MH, Horng YC, Hou MH. Targeting DNA junction sites by bis-intercalators induces topological changes with potent antitumor effects. Nucleic Acids Res 2024:gkae643. [PMID: 39036959 DOI: 10.1093/nar/gkae643] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 06/21/2024] [Accepted: 07/09/2024] [Indexed: 07/23/2024] Open
Abstract
Targeting inter-duplex junctions in catenated DNA with bidirectional bis-intercalators is a potential strategy for enhancing anticancer effects. In this study, we used d(CGTATACG)2, which forms a tetraplex base-pair junction that resembles the DNA-DNA contact structure, as a model target for two alkyl-linked diaminoacridine bis-intercalators, DA4 and DA5. Cross-linking of the junction site by the bis-intercalators induced substantial structural changes in the DNA, transforming it from a B-form helical end-to-end junction to an over-wounded side-by-side inter-duplex conformation with A-DNA characteristics and curvature. These structural perturbations facilitated the angled intercalation of DA4 and DA5 with propeller geometry into two adjacent duplexes. The addition of a single carbon to the DA5 linker caused a bend that aligned its chromophores with CpG sites, enabling continuous stacking and specific water-mediated interactions at the inter-duplex contacts. Furthermore, we have shown that the different topological changes induced by DA4 and DA5 lead to the inhibition of topoisomerase 2 activities, which may account for their antitumor effects. Thus, this study lays the foundations for bis-intercalators targeting biologically relevant DNA-DNA contact structures for anticancer drug development.
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Affiliation(s)
- Shih-Chun Huang
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chia-Wei Chen
- Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan
| | - Roshan Satange
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | | | - Chih-Chun Chang
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Shun-Ching Wang
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Chi-Li Peng
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
| | - Tai-Lin Chen
- Post Baccalaureate Medicine, School of Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Ming-Hsi Chiang
- Institute of Chemistry, Academia Sinica, Taipei 11528, Taiwan
| | - Yih-Chern Horng
- Department of Chemistry, National Changhua University of Education, Changhua 50058, Taiwan
| | - Ming-Hon Hou
- Doctoral Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
- Biotechnology Center, National Chung Hsing University, Taichung 402, Taiwan
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2
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McQuaid K, Pipier A, Cardin C, Monchaud D. Interactions of small molecules with DNA junctions. Nucleic Acids Res 2022; 50:12636-12656. [PMID: 36382400 PMCID: PMC9825177 DOI: 10.1093/nar/gkac1043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/13/2022] [Accepted: 10/23/2022] [Indexed: 11/17/2022] Open
Abstract
The four natural DNA bases (A, T, G and C) associate in base pairs (A=T and G≡C), allowing the attached DNA strands to assemble into the canonical double helix of DNA (or duplex-DNA, also known as B-DNA). The intrinsic supramolecular properties of nucleobases make other associations possible (such as base triplets or quartets), which thus translates into a diversity of DNA structures beyond B-DNA. To date, the alphabet of DNA structures is ripe with approximately 20 letters (from A- to Z-DNA); however, only a few of them are being considered as key players in cell biology and, by extension, valuable targets for chemical biology intervention. In the present review, we summarise what is known about alternative DNA structures (what are they? When, where and how do they fold?) and proceed to discuss further about those considered nowadays as valuable therapeutic targets. We discuss in more detail the molecular tools (ligands) that have been recently developed to target these structures, particularly the three- and four-way DNA junctions, in order to intervene in the biological processes where they are involved. This new and stimulating chemical biology playground allows for devising innovative strategies to fight against genetic diseases.
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Affiliation(s)
- Kane T McQuaid
- Department of Chemistry, University of Reading, Whiteknights, Reading RG6 6AD, UK
| | - Angélique Pipier
- Institut de Chimie Moléculaire de l’Université de Bourgogne (ICMUB), CNRS UMR 6302, UBFC Dijon, 21078 Dijon, France
| | - Christine J Cardin
- Correspondence may also be addressed to Christine J. Cardin. Tel: +44 118 378 8215;
| | - David Monchaud
- To whom correspondence should be addressed. Tel: +33 380 399 043;
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3
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Non-G Base Tetrads. MOLECULES (BASEL, SWITZERLAND) 2022; 27:molecules27165287. [PMID: 36014524 PMCID: PMC9414646 DOI: 10.3390/molecules27165287] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/03/2022] [Accepted: 08/11/2022] [Indexed: 11/17/2022]
Abstract
Tetrads (or quartets) are arrangements of four nucleobases commonly involved in the stability of four-stranded nucleic acids structures. Four-stranded or quadruplex structures have attracted enormous attention in the last few years, being the most extensively studied guanine quadruplex (G-quadruplex). Consequently, the G-tetrad is the most common and well-known tetrad. However, this is not the only possible arrangement of four nucleobases. A number of tetrads formed by the different nucleobases have been observed in experimental structures. In most cases, these tetrads occur in the context of G-quadruplex structures, either inserted between G-quartets, or as capping elements at the sides of the G-quadruplex core. In other cases, however, non-G tetrads are found in more unusual four stranded structures, such as i-motifs, or different types of peculiar fold-back structures. In this report, we review the diversity of these non-canonical tetrads, and the structural context in which they have been found.
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Mendes E, Aljnadi IM, Bahls B, Victor BL, Paulo A. Major Achievements in the Design of Quadruplex-Interactive Small Molecules. Pharmaceuticals (Basel) 2022; 15:ph15030300. [PMID: 35337098 PMCID: PMC8953082 DOI: 10.3390/ph15030300] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/17/2022] Open
Abstract
Organic small molecules that can recognize and bind to G-quadruplex and i-Motif nucleic acids have great potential as selective drugs or as tools in drug target discovery programs, or even in the development of nanodevices for medical diagnosis. Hundreds of quadruplex-interactive small molecules have been reported, and the challenges in their design vary with the intended application. Herein, we survey the major achievements on the therapeutic potential of such quadruplex ligands, their mode of binding, effects upon interaction with quadruplexes, and consider the opportunities and challenges for their exploitation in drug discovery.
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Affiliation(s)
- Eduarda Mendes
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
| | - Israa M. Aljnadi
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bárbara Bahls
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Bruno L. Victor
- Faculty of Sciences, BioISI, Biosystems and Integrative Sciences Institute, Universidade de Lisboa, 1749-016 Lisbon, Portugal;
| | - Alexandra Paulo
- Faculty of Pharmacy, Research Institute for Medicines (iMed.Ulisboa), Universidade de Lisboa, 1649-003 Lisbon, Portugal; (E.M.); (I.M.A.); (B.B.)
- Correspondence:
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5
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Intercalative DNA binding of the marine anticancer drug variolin B. Sci Rep 2017; 7:39680. [PMID: 28051169 PMCID: PMC5209663 DOI: 10.1038/srep39680] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Accepted: 11/25/2016] [Indexed: 01/04/2023] Open
Abstract
Variolin B is a rare marine alkaloid that showed promising anti-cancer activity soon after its isolation. It acts as a cyclin-dependent kinase inhibitor, although the precise mechanism through which it exerts the cytotoxic effects is still unknown. The crystal structure of a variolin B bound to a DNA forming a pseudo-Holliday junction shows that this compound can also contribute, through intercalative binding, to either the formation or stabilization of multi-stranded DNA forms.
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6
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Boer DR, Wu L, Lincoln P, Coll M. Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross-Linking of DNA Duplexes. Angew Chem Int Ed Engl 2014; 53:1949-52. [DOI: 10.1002/anie.201308070] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 11/15/2013] [Indexed: 11/07/2022]
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7
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Boer DR, Wu L, Lincoln P, Coll M. Thread Insertion of a Bis(dipyridophenazine) Diruthenium Complex into the DNA Double Helix by the Extrusion of AT Base Pairs and Cross-Linking of DNA Duplexes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201308070] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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8
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Stefan L, Bertrand B, Richard P, Le Gendre P, Denat F, Picquet M, Monchaud D. Assessing the Differential Affinity of Small Molecules for Noncanonical DNA Structures. Chembiochem 2012; 13:1905-12. [DOI: 10.1002/cbic.201200396] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2012] [Indexed: 01/19/2023]
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9
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Abstract
Dynamic combinatorial chemistry (DCC) is a powerful method for the identification of novel ligands for the molecular recognition of receptor molecules. The method relies on self-assembly processes to generate libraries of compounds under reversible conditions, allowing a receptor molecule to select the optimal binding ligand from the mixture. However, while DCC is now an established field of chemistry, there are limited examples of the application of DCC to nucleic acids. The requirement to conduct experiments under physiologically relevant conditions, and avoid reaction with, or denaturation of, the target nucleic acid secondary structure, limits the choice of the reversible chemistry, and presents restrictions on the building block design. This review will summarize recent examples of applications of DCC to the recognition of nucleic acids. Studies with duplex DNA, quadruplex DNA, and RNA have utilized mainly thiol disulfide libraries, although applications of imine libraries, in combination with metal coordination, have been reported. The use of thiol disulfide libraries produces lead compounds with limited biostability, and hence design of stable analogues or mimics is required for many applications.
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Debray J, Zeghida W, Jourdan M, Monchaud D, Dheu-Andries ML, Dumy P, Teulade-Fichou MP, Demeunynck M. Synthesis and evaluation of fused bispyrimidinoacridines as novel pentacyclic analogues of quadruplex-binder BRACO-19. Org Biomol Chem 2009; 7:5219-28. [PMID: 20024118 DOI: 10.1039/b912716j] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The present article reports on the design and the synthesis of a series of mono- and bis-pyrimidinoacridines and their evaluation as a novel family of quadruplex-binders. It is shown that bispyrimidinoacridines represent an interesting compromise between easy synthetic access and efficiency in terms of quadruplex interaction (both affinic and selective), as judged by G4-FID assay and molecular modelling. The present study also highlights that control of the pi-stacking interactions taking place between the ligand and the accessible G-tetrad of a quadruplex-DNA is indeed essential for good recognition but not exclusively (key role of direct and water-mediated H-bonds). The introduction of additional amino side chains, valuable in the acridine series, results here in steric perturbations of the ligand/quadruplex recognition and lowers the quadruplex/duplex selectivity.
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Affiliation(s)
- Julien Debray
- Département Chimie Moléculaire, UMR 5250, CNRS/Université Joseph Fourier, BP 53, 38041 Grenoble cedex 9, France
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11
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12
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Viladoms J, Escaja N, Frieden M, Gómez-Pinto I, Pedroso E, González C. Self-association of short DNA loops through minor groove C:G:G:C tetrads. Nucleic Acids Res 2009; 37:3264-75. [PMID: 19321501 PMCID: PMC2691830 DOI: 10.1093/nar/gkp191] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In addition to the better known guanine-quadruplex, four-stranded nucleic acid structures can be formed by tetrads resulting from the association of Watson-Crick base pairs. When such association occurs through the minor groove side of the base pairs, the resulting structure presents distinctive features, clearly different from quadruplex structures containing planar G-tetrads. Although we have found this unusual DNA motif in a number of cyclic oligonucleotides, this is the first time that this DNA motif is found in linear oligonucleotides in solution, demonstrating that cyclization is not required to stabilize minor groove tetrads in solution. In this article, we have determined the solution structure of two linear octamers of sequence d(TGCTTCGT) and d(TCGTTGCT), and their cyclic analogue d<pCGCTCCGT>, utilizing 2D NMR spectroscopy and restrained molecular dynamics. These three molecules self-associate forming symmetric dimers stabilized by a novel kind of minor groove C:G:G:C tetrad, in which the pattern of hydrogen bonds differs from previously reported ones. We hypothesize that these quadruplex structures can be formed by many different DNA sequences, but its observation in linear oligonucleotides is usually hampered by competing Watson-Crick duplexes.
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Affiliation(s)
- Júlia Viladoms
- Departament de Química Orgànica and IBUB, Universitat de Barcelona, C/. Martí i Franquès 1-11, 08028 Barcelona, Spain
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13
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Brogden A, Hopcroft N, Searcey M, Cardin C. Ligand Bridging of the DNA Holliday Junction: Molecular Recognition of a Stacked-X Four-Way Junction by a Small Molecule. Angew Chem Int Ed Engl 2007. [DOI: 10.1002/ange.200603760] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
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14
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Brogden AL, Hopcroft NH, Searcey M, Cardin CJ. Ligand Bridging of the DNA Holliday Junction: Molecular Recognition of a Stacked-X Four-Way Junction by a Small Molecule. Angew Chem Int Ed Engl 2007; 46:3850-4. [PMID: 17477457 DOI: 10.1002/anie.200603760] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Anna L Brogden
- School of Chemistry, University of Reading, Whiteknights, Reading, Berkshire, RG6 6AD, UK
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15
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Escaja N, Gómez-Pinto I, Pedroso E, Gonzalez C. Four-Stranded DNA Structures Can Be Stabilized by Two Different Types of Minor Groove G:C:G:C Tetrads. J Am Chem Soc 2007; 129:2004-14. [PMID: 17260988 DOI: 10.1021/ja066172z] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Four-stranded nucleic acid structures are central to many processes in biology and in supramolecular chemistry. It has been shown recently that four-stranded DNA structures are not only limited to the classical guanine quadruplex but also can be formed by tetrads resulting from the association of Watson-Crick base pairs. Such an association may occur through the minor or the major groove side of the base pairs. Structures stabilized by minor groove tetrads present distinctive features, clearly different from the canonical guanine quadruplex, making these quadruplexes a unique structural motif. Within our efforts to study the sequence requirements for the formation of this unusual DNA motif, we have determined the solution structure of the cyclic oligonucleotide dpCCGTCCGT by two-dimensional NMR spectroscopy and restrained molecular dynamics. This molecule self-associates, forming a symmetric dimer stabilized by two G:C:G:C tetrads with intermolecular G-C base pairs. Interestingly, although the overall three-dimensional structure is similar to that found in other cyclic and linear oligonucleotides of related sequences, the tetrads that stabilize the structure of dpCCGTCCGT are different to other minor groove G:C:G:C tetrads found earlier. Whereas in previous cases the G-C base pairs aligned directly, in this new tetrad the relative position of the two base pairs is slipped along the axis defined by the base pairs. This is the first time that a quadruplex structure entirely stabilized by slipped minor groove G:C:G:C tetrads is observed in solution or in the solid state. However, an analogous arrangement of G-C base pairs occurs between the terminal residues of contiguous duplexes in some DNA crystals. This structural polymorphism between minor groove GC tetrads may be important in stabilization of higher order DNA structures.
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Affiliation(s)
- Núria Escaja
- Instituto de Química Física "Rocasolano", CSIC, C/, Serrano 119, 28006 Madrid, Spain
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16
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Abstract
Non-covalent DNA-recognition by synthetic agents is surveyed in this tutorial review, and contrasted with biomolecular DNA-recognition. The principles and forces involved in DNA recognition are similar to those seen elsewhere in the wider field of supramolecular chemistry, although the size, surface dimensions and nature of DNA introduce new possibilities and challenges. Recent discoveries of new binding motifs, and new biological structural and genomic information from bioscience, are affording new opportunities for supramolecular chemistry, where shape, fit and orientation play such an important role.
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Affiliation(s)
- Michael J Hannon
- School of Chemistry, University of Birmingham, Edgbaston, Birmingham B15 2TT, UK.
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Hopcroft NH, Brogden AL, Searcey M, Cardin CJ. X-ray crystallographic study of DNA duplex cross-linking: simultaneous binding to two d(CGTACG)2 molecules by a bis(9-aminoacridine-4-carboxamide) derivative. Nucleic Acids Res 2006; 34:6663-72. [PMID: 17145714 PMCID: PMC1751537 DOI: 10.1093/nar/gkl930] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Acridine-4-carboxamides form a class of known DNA mono-intercalating agents that exhibit cytotoxic activity against tumour cell lines due to their ability to inhibit topoisomerases. Previous studies of bis-acridine derivatives have yielded equivocal results regarding the minimum length of linker necessary between the two acridine chromophores to allow bis-intercalation of duplex DNA. We report here the 1.7 A resolution X-ray crystal structure of a six-carbon-linked bis(acridine-4-carboxamide) ligand bound to d(CGTACG)2 molecules by non-covalent duplex cross-linking. The asymmetric unit consists of one DNA duplex containing an intercalated acridine-4-carboxamide chromophore at each of the two CG steps. The other half of each ligand is bound to another DNA molecule in a symmetry-related manner, with the alkyl linker threading through the minor grooves. The two crystallographically independent ligand molecules adopt distinct side chain interactions, forming hydrogen bonds to either O6 or N7 on the major groove face of guanine, in contrast to the semi-disordered state of mono-intercalators bound to the same DNA molecule. The complex described here provides the first structural evidence for the non-covalent cross-linking of DNA by a small molecule ligand and suggests a possible explanation for the inconsistent behaviour of six-carbon linked bis-acridines in previous assays of DNA bis-intercalation.
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Affiliation(s)
- Nicholas H. Hopcroft
- School of Chemistry, University of ReadingWhiteknights, Reading, Berkshire RG6 6AD, UK
| | - Anna L. Brogden
- School of Chemistry, University of ReadingWhiteknights, Reading, Berkshire RG6 6AD, UK
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London29-39 Brunswick Square, London WC1N 1AX, UK
| | - Mark Searcey
- Department of Pharmaceutical and Biological Chemistry, School of Pharmacy, University of London29-39 Brunswick Square, London WC1N 1AX, UK
| | - Christine J. Cardin
- School of Chemistry, University of ReadingWhiteknights, Reading, Berkshire RG6 6AD, UK
- To whom correspondence should be addressed. Tel: +44 118 931 8215; Fax: +44 118 931 6331;
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Valls N, Steiner RA, Wright G, Murshudov GN, Subirana JA. Variable role of ions in two drug intercalation complexes of DNA. J Biol Inorg Chem 2005; 10:476-82. [PMID: 15926069 DOI: 10.1007/s00775-005-0655-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2005] [Accepted: 04/21/2005] [Indexed: 10/25/2022]
Abstract
The crystal structures of the hexamer duplex d(CGTACG)(2) complexed with the intercalating anthraquinone derivative 1,5-bis[3-(diethylamino)propionamido]anthracene-9,10-dione and the acridine derivative 9-acridinyl tetralysine have been solved at 2.0- and 1.4-A resolution, respectively. In both cases, the drugs adopt multiple orientations within a large DNA cavity constituted by two groups of four approximately coplanar bases. Cations play a pivotal role in the crystal structure. Both complexes crystallise in the presence of Co(2+), Ba(2+) and Na(+) ions. They reveal at least two different types of coordination environments: (1) specific sites for Co(2+) interacting with N7 of guanine; (2) a central ionic site formed by four phosphate groups, which can be occupied by different ions. One more ionic site that is not always occupied by ions is also visible in the electron density map. All of them play a role in the crystal structure.
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Affiliation(s)
- Núria Valls
- Departament d'Enginyeria Química, Universitat Politècnica de Catalunya, Avinguda Diagonal 647, 08028 Barcelona, Spain
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19
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Abstract
Fifty years after the publication of the DNA double helix model by Watson and Crick, new nucleic acid structures keep emerging at an ever-increasing rate. The past three years have brought a flurry of new oligonucleotide structures, including those of a Hoogsteen-paired DNA duplex, Holliday junctions, DNA-drug complexes, quadruplexes, a host of RNA motifs and various nucleic acid analogues. Major advances were also made in terms of the structure and function of catalytic RNAs. These range from improved models of the phosphodiester cleavage reactions catalyzed by the hairpin and hepatitis delta virus ribozymes to the visualization of a complete active site of a group I self-splicing intron with bound 5'- and 3'-exons. These triumphs are complemented by a refined understanding of cation-nucleic-acid interactions and new routes to the generation of derivatives for phasing of DNA and RNA structures.
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Affiliation(s)
- Martin Egli
- Department of Biochemistry, Vanderbilt University, School of Medicine, Nashville, TN 37232, USA.
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20
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Nelson SM, Ferguson LR, Denny WA. DNA and the chromosome - varied targets for chemotherapy. CELL & CHROMOSOME 2004; 3:2. [PMID: 15157277 PMCID: PMC421739 DOI: 10.1186/1475-9268-3-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/04/2004] [Accepted: 05/24/2004] [Indexed: 12/29/2022]
Abstract
The nucleus of the cell serves to maintain, regulate, and replicate the critical genetic information encoded by the genome. Genomic DNA is highly associated with proteins that enable simple nuclear structures such as nucleosomes to form higher-order organisation such as chromatin fibres. The temporal association of regulatory proteins with DNA creates a dynamic environment capable of quickly responding to cellular requirements and distress. The response is often mediated through alterations in the chromatin structure, resulting in changed accessibility of specific DNA sequences that are then recognized by specific proteins. Anti-cancer drugs that target cellular DNA have been used clinically for over four decades, but it is only recently that nuclease specific drugs have been developed to not only target the DNA but also other components of the nuclear structure and its regulation. In this review, we discuss some of the new drugs aimed at primary DNA sequences, DNA secondary structures, and associated proteins, keeping in mind that these agents are not only important from a clinical perspective but also as tools for understanding the nuclear environment in normal and cancer cells.
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Affiliation(s)
- Stephanie M Nelson
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
| | - Lynnette R Ferguson
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
| | - William A Denny
- Auckland Cancer Society Research Centre, School of Medical Sciences, The University of Auckland, Private Bag 92019, Auckland 10000, New Zealand
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21
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Thorpe JH, Gale BC, Teixeira SCM, Cardin CJ. Conformational and hydration effects of site-selective sodium, calcium and strontium ion binding to the DNA Holliday junction structure d(TCGGTACCGA)(4). J Mol Biol 2003; 327:97-109. [PMID: 12614611 DOI: 10.1016/s0022-2836(03)00088-3] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
The role of metal ions in determining the solution conformation of the Holliday junction is well established, but to date the picture of metal ion binding from structural studies of the four-way DNA junction is very incomplete. Here we present two refined structures of the Holliday junction formed by the sequence d(TCGGTACCGA) in the presence of Na(+) and Ca(2+), and separately with Sr(2+) to resolutions of 1.85A and 1.65A, respectively. This sequence includes the ACC core found to promote spontaneous junction formation, but its structure has not previously been reported. Almost complete hydration spheres can be defined for each metal cation. The Na(+) sites, the most convincing observation of such sites in junctions to date, are one on either face of the junction crossover region, and stabilise the ordered hydration inside the junction arms. The four Ca(2+) sites in the same structure are at the CG/CG steps in the minor groove. The Sr(2+) ions occupy the TC/AG, GG/CC, and TA/TA sites in the minor groove, giving ten positions forming two spines of ions, spiralling through the minor grooves within each arm of the stacked-X structure. The two structures were solved in the two different C2 lattices previously observed, with the Sr(2+) derivative crystallising in the more highly symmetrical form with two-fold symmetry at its centre. Both structures show an opening of the minor groove face of the junction of 8.4 degrees in the Ca(2+) and Na(+) containing structure, and 13.4 degrees in the Sr(2+) containing structure. The crossover angles at the junction are 39.3 degrees and 43.3 degrees, respectively. In addition to this, a relative shift in the base pair stack alignment of the arms of 2.3A is observed for the Sr(2+) containing structure only. Overall these results provide an insight into the so-far elusive stabilising ion structure for the DNA Holliday junction.
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Affiliation(s)
- James H Thorpe
- School of Chemistry, The University of Reading, Whiteknights, Reading RG6 6AD, UK
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