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Prieto Otoya TD, McQuaid KT, Paterson NG, Cardin DJ, Kellett A, Cardin CJ. Re-pairing DNA: binding of a ruthenium phi complex to a double mismatch. Chem Sci 2024; 15:9096-9103. [PMID: 38903237 PMCID: PMC11186304 DOI: 10.1039/d4sc01448k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Accepted: 05/11/2024] [Indexed: 06/22/2024] Open
Abstract
We report a crystal structure at atomic resolution (0.9 Å) of a ruthenium complex bound to a consecutive DNA double mismatch, which results in a TA basepair with flipped out thymine, together with the formation of an adenine bulge. The structure shows a form of metalloinsertion interaction of the Λ-[Ru(phen)2phi]2+ (phi = 9,10-phenanthrenediimine) complex at the bulge site. The metal complex interacts with the DNA via the major groove, where specific interactions between the adenines of the DNA and the phen ligands of the complex are formed. One Δ-[Ru(phen)2phi]2+ complex interacts via the minor groove, which shows sandwiching of its phi ligand between the phi ligands of the other two ruthenium complexes, and no interaction of its phen ligands with DNA. To our knowledge, this binding model represents a new form of metalloinsertion in showing major rather than minor groove insertion.
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Affiliation(s)
| | - Kane T McQuaid
- Department of Chemistry, University of Reading Whiteknights Reading, RG6 6AD UK
| | - Neil G Paterson
- Diamond Light Source Ltd Harwell Science and Innovation Campus Didcot Oxfordshire OX11 0DE UK
| | - David J Cardin
- Department of Chemistry, University of Reading Whiteknights Reading, RG6 6AD UK
| | - Andrew Kellett
- SSPC, The Science Foundation Ireland Research Centre for Pharmaceuticals, School of Chemical Sciences, Dublin City University Glasnevin Dublin 9 Ireland
| | - Christine J Cardin
- Department of Chemistry, University of Reading Whiteknights Reading, RG6 6AD UK
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2
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Schlosser J, Ihmels H. Ligands for Abasic Site-containing DNA and their Use as Fluorescent Probes. Curr Org Synth 2023; 20:96-113. [PMID: 35170411 DOI: 10.2174/1570179419666220216091422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Revised: 12/16/2021] [Accepted: 12/16/2021] [Indexed: 12/16/2022]
Abstract
Apurinic and apyrimidinic sites, also referred to as abasic or AP sites, are residues of duplex DNA in which one DNA base is removed from a Watson-Crick base pair. They are formed during the enzymatic repair of DNA and offer binding sites for a variety of guest molecules. Specifically, the AP site may bind an appropriate ligand as a substitute for the missing nucleic base, thus stabilizing the abasic site-containing DNA (AP-DNA). Notably, ligands that bind selectively to abasic sites may be employed for analytical and therapeutical purposes. As a result, there is a search for structural features that establish a strong and selective association of a given ligand with the abasic position in DNA. Against this background, this review provides an overview of the different classes of ligands for abasic site-containing DNA (AP-DNA). This review covers covalently binding substrates, namely amine and oxyamine derivatives, as well as ligands that bind to AP-DNA by noncovalent association, as represented by small heterocyclic aromatic compounds, metal-organic complexes, macrocyclic cyclophanes, and intercalator-nucleobase conjugates. As the systematic development of fluorescent probes for AP-DNA has been somewhat neglected so far, this review article contains a survey of the available reports on the fluorimetric response of the ligand upon binding to the AP-DNA. Based on these data, this compilation shall present a perspective for future developments of fluorescent probes for AP-DNA.
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Affiliation(s)
- Julika Schlosser
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, University of Siegen, Center of Micro- and Nanochemistry and (Bio)Technology (Cμ), Adolf-Reichwein-Str. 2, 57068 Siegen, Germany
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3
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Understanding the role of ancillary ligands in the interaction of Ru(II) complexes with covalent arylamine-DNA adducts. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2021.120681] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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4
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Dayanidhi PD, Vaidyanathan VG. Understanding the ancillary ligand effect on luminescent cyclometalated Ir(III) complex as a reporter for 2-acetylaminofluorene DNA(AAF-dG) adduct. J Biol Inorg Chem 2021; 27:189-199. [PMID: 34843001 DOI: 10.1007/s00775-021-01920-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/17/2021] [Indexed: 11/26/2022]
Abstract
Mutagenic agents such as aromatic amines undergo metabolic activation and produce DNA adducts at C8 position of guanine bases. N-2-acetylaminofluorene (AAF) generates different mutational outcomes when placed at G1, G2, and G3 of a NarI sequence (-G1G2CG3CC/T-). These outcomes are dictated by the conformations adopted by these adducts. Detection of such lesions is of considerable interest owing to their hazardous effects. Here, we report the synthesis of three cyclometalated [Ir(L)2dppz]+ complexes (L = 2-phenylpyridine (ppy) 1; benzo[h]quinoline (bhq) 2; 2-phenylquinoline (pq) 3; dppz = dipyrido[3,2-a:2',3'-c]phenazine) and their interaction with AAF adducted NarI DNA. Remarkably, complexes 1 and 2 displayed dominant 3LC transition characteristic of polar environment despite binding to the adducted sites. On the other hand, complex 3 binds to NarI sequences and behaves as a luminescent reporter for AAF-modified DNA. The results reported here emphasize that molecular light switching phenomenon can be stimulated by switching ancillary ligands and might act as potential probes for covalent-DNA defects.
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Affiliation(s)
- P David Dayanidhi
- Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - V G Vaidyanathan
- Advanced Materials Laboratory, CSIR-Central Leather Research Institute, Adyar, Chennai, 600020, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India.
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5
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Stabilization of an abasic site paired against an unnatural triazolyl nitrobenzene nucleoside. Biophys Chem 2020; 264:106428. [DOI: 10.1016/j.bpc.2020.106428] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Revised: 07/03/2020] [Accepted: 07/03/2020] [Indexed: 11/22/2022]
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6
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Lee YA, Cho HY, Kim SK. Neighboring base sequence effect on DNA damage. J Biomol Struct Dyn 2019; 38:3188-3195. [PMID: 31432766 DOI: 10.1080/07391102.2019.1659186] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Guanine is the most strongly oxidized base in DNA; generation of a guanine radical cation as an intermediate in an oxidation reaction leads to migration through a resulting cationic hole in the DNA π-stack until it is trapped by irreversible reaction with water or other free radicals. In the case of normal sequences, the primary position of Guanine oxidations by one-electron oxidants such as carbonate radical anions, BPT(7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene), and riboflavin are 5'-G in GG doublets and the central G in a GGG triplet. According to results, the properties of guanine oxidation on abasic site containing sequences are independent from the position of AP(apurinic/apyrimidinic) site in the presence of carbonate radical anions under a short irradiation time, although this radical is exposed to solvent by the existence of an abasic site. The lack of abasic site effect on guanine oxidative damage by the carbonate radical may be due to a sequence-independent property of the initial electron transfer rate in the hole injection step, or may relate to an electron transfer mechanism with large reorganization energy dependency. Consequently, the carbonate radical anions may easily migrate to another single G in the charge re-distribution step. Meanwhile, there is a strong dependency on the presence of an AP(apurinic/apyrimidinic) site in the cleavage patterns of guanine oxidations by physically large oxidizing agents, such as BPT(7,8,9,10-tetrahydroxytetrahydrobenzo[a]pyrene) and riboflavin. These radicals show strong AP(apurinic/apyrimidinic) site dependency and clear G-site selectivity.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Young-Ae Lee
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-Buk, Republic of Korea
| | - Ha Young Cho
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-Buk, Republic of Korea
| | - Seog K Kim
- Department of Chemistry, Yeungnam University, Gyeongsan, Gyeong-Buk, Republic of Korea
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7
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Hognon C, Gebus A, Barone G, Monari A. Human DNA Telomeres in Presence of Oxidative Lesions: The Crucial Role of Electrostatic Interactions on the Stability of Guanine Quadruplexes. Antioxidants (Basel) 2019; 8:antiox8090337. [PMID: 31443537 PMCID: PMC6770428 DOI: 10.3390/antiox8090337] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 08/14/2019] [Accepted: 08/20/2019] [Indexed: 01/23/2023] Open
Abstract
By using all atom molecular dynamics simulations, we studied the behavior of human DNA telomere sequences in guanine quadruplex (G4) conformation and in the presence of oxidative lesions, namely abasic sites. In particular, we evidenced that while removing one guanine base induces a significant alteration and destabilization of the involved leaflet, human telomere oligomers tend, in most cases, to maintain at least a partial quadruplex structure, eventually by replacing the empty site with undamaged guanines of different leaflets. This study shows that (i) the disruption of the quadruplex leaflets induces the release of at least one of the potassium cations embedded in the quadruplex channel and that (ii) the electrostatic interactions of the DNA sequence with the aforementioned cations are fundamental to the maintenance of the global quadruplex structure.
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Affiliation(s)
- Cecilia Hognon
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
| | - Adrien Gebus
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France
| | - Giampaolo Barone
- Department of Biological, Chenical and Pharmaceutical Sciences and Technologies, Università di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Antonio Monari
- Université de Lorraine, CNRS, LPCT UMR 7019, F54000 Nancy, France.
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8
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Rono CK, Chu WK, Darkwa J, Meyer D, Makhubela BCE. Triazolyl RuII, RhIII, OsII, and IrIII Complexes as Potential Anticancer Agents: Synthesis, Structure Elucidation, Cytotoxicity, and DNA Model Interaction Studies. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00440] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Charles K. Rono
- Department of Chemistry, University of Johannesburg, Kingsway Campus, 2006 Auckland Park, South Africa
| | - William K. Chu
- Department of Chemistry, University of Johannesburg, Kingsway Campus, 2006 Auckland Park, South Africa
| | - James Darkwa
- Department of Chemistry, University of Johannesburg, Kingsway Campus, 2006 Auckland Park, South Africa
| | - Debra Meyer
- Department of Biochemistry, University of Johannesburg, Kingsway Campus, 2006 Auckland Park, South Africa
| | - Banothile C. E. Makhubela
- Department of Chemistry, University of Johannesburg, Kingsway Campus, 2006 Auckland Park, South Africa
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9
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Boyle KM, Nano A, Day C, Barton JK. Cellular Target of a Rhodium Metalloinsertor is the DNA Base Pair Mismatch. Chemistry 2019; 25:3014-3019. [PMID: 30615818 DOI: 10.1002/chem.201900042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2019] [Indexed: 12/25/2022]
Abstract
Defects in DNA mismatch repair (MMR) are commonly found in various cancers, especially in colorectal cancers. Despite the high prevalence of MMR-deficient cancers, mismatch-targeted therapeutics are limited and diagnostic tools are indirect. Here, we examine the cytotoxic properties of a rhodium metalloinsertor, [Rh(phen)(chrysi)(PPO)]2+ (RhPPO) in 27 diverse colorectal cancer cell lines. Despite the low frequency of genomic mismatches and the non-covalent nature of the RhPPO-DNA lesion, RhPPO is on average five times more potent than cisplatin. Importantly, the biological target and profile for RhPPO differs from that of cisplatin. A fluorescent metalloinsertor, RhCy3, was used to demonstrate that the cellular target of RhPPO is the DNA mismatch. RhCy3 represents a direct probe for MMR-deficiency and correlates directly with the cytotoxicity of RhPPO across different cell lines. Overall, our studies clearly indicate that RhPPO and RhCy3 are promising anticancer and diagnostic probes for MMR-deficient cancers, respectively.
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Affiliation(s)
- Kelsey M Boyle
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California, 91125, USA
| | - Adela Nano
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California, 91125, USA
| | - Catherine Day
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California, 91125, USA
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 East California Boulevard, MC 127-72, Pasadena, California, 91125, USA
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10
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Caron C, Duong XNT, Guillot R, Bombard S, Granzhan A. Interaction of Functionalized Naphthalenophanes with Abasic Sites in DNA: DNA Cleavage, DNA Cleavage Inhibition, and Formation of Ligand–DNA Adducts. Chemistry 2019; 25:1949-1962. [DOI: 10.1002/chem.201805555] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 11/30/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Coralie Caron
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Xuan N. T. Duong
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Régis Guillot
- CNRS UMR8182, Institut de Chimie Moléculaire et des Matériaux d'Orsay (ICMMO)Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Sophie Bombard
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
| | - Anton Granzhan
- CNRS UMR9187, INSERM U1196Institut CuriePSL Research University 91405 Orsay France
- CNRS UMR9187, INSERM U1196Université Paris Sud, Université Paris-Saclay 91405 Orsay France
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11
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Dayanidhi DPE, Malapati RP, Vaidyanathan Ganesan V. Selective recognition of DNA defects by cyclometalated Ir(iii) complexes. Dalton Trans 2019; 48:13536-13540. [DOI: 10.1039/c9dt01225g] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Three different cyclometalated Ir(iii) complexes selectively bind to DNA defects.
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Affiliation(s)
- David Paul Elisa Dayanidhi
- Academy of Scientific and Innovative Research (AcSIR), Advanced Materials Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
| | - Rozaria Pinky Malapati
- Academy of Scientific and Innovative Research (AcSIR), Advanced Materials Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
| | - Vaidyanathan Vaidyanathan Ganesan
- Academy of Scientific and Innovative Research (AcSIR), Advanced Materials Laboratory
- CSIR-Central Leather Research Institute
- Chennai 600 020
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12
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Maisuls I, Cabrerizo FM, David-Gara PM, Epe B, Ruiz GT. DNA Oxidation Photoinduced by Norharmane Rhenium(I) Polypyridyl Complexes: Effect of the Bidentate N,N′-Ligands on the Damage Profile. Chemistry 2018; 24:12902-12911. [DOI: 10.1002/chem.201801272] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 04/15/2018] [Indexed: 11/10/2022]
Affiliation(s)
- Iván Maisuls
- Instituto de Investigaciones Biotecnologicas; Instituto de Tecnologia Chascomus (IIB-INTECH); Universidad Nacional de San Martin (UNSAM); I. Marino, Km 8.2 CC 164 (7130) Chascomus Argentina
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA); Universidad Nacional de la Plata (UNLP); CCT La Plata-CONICET; Diag. 113 y 64, Suc. 4, C.C. 16 (B1906ZAA) La Plata Argentina
| | - Franco M. Cabrerizo
- Instituto de Investigaciones Biotecnologicas; Instituto de Tecnologia Chascomus (IIB-INTECH); Universidad Nacional de San Martin (UNSAM); I. Marino, Km 8.2 CC 164 (7130) Chascomus Argentina
| | - Pedro M. David-Gara
- Centro de Investigaciones Ópticas (CIOP-CONICET-CIC); Universidad Nacional de La Plata; C.C.3 (1897) La Plata Argentina
| | - Bernd Epe
- Institute of Pharmacy and Biochemistry; University of Mainz; Staudingerweg 5 D-55099 Mainz Germany
| | - Gustavo T. Ruiz
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas (INIFTA); Universidad Nacional de la Plata (UNLP); CCT La Plata-CONICET; Diag. 113 y 64, Suc. 4, C.C. 16 (B1906ZAA) La Plata Argentina
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13
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Nano A, Boynton AN, Barton JK. A Rhodium-Cyanine Fluorescent Probe: Detection and Signaling of Mismatches in DNA. J Am Chem Soc 2017; 139:17301-17304. [PMID: 29136382 PMCID: PMC5892186 DOI: 10.1021/jacs.7b10639] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
We report a bifunctional fluorescent probe that combines a rhodium metalloinsertor with a cyanine dye as the fluorescent reporter. The conjugate shows weak luminescence when free in solution or with well matched DNA but exhibits a significant luminescence increase in the presence of a 27-mer DNA duplex containing a central CC mismatch. DNA photocleavage experiments demonstrate that, upon photoactivation, the conjugate cleaves the DNA backbone specifically near the mismatch site on a 27-mer fragment, consistent with mismatch targeting. Fluorescence titrations with the 27-mer duplex containing the CC mismatch reveal a DNA binding affinity of 3.1 × 106 M-1, similar to that of other rhodium metalloinsertors. Fluorescence titrations using genomic DNA extracted from various cell lines demonstrate a clear discrimination in fluorescence between those cell lines that are proficient or deficient in mismatch repair. This differential luminescence reflects the sensitive detection of the mismatchrepair-deficient phenotype.
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Affiliation(s)
- Adela Nano
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, California 91125, United States
| | - Adam N. Boynton
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, California 91125, United States
| | - Jacqueline K. Barton
- California Institute of Technology, Division of Chemistry and Chemical Engineering, Pasadena, California 91125, United States
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14
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Boynton AN, Marcélis L, McConnell AJ, Barton JK. A Ruthenium(II) Complex as a Luminescent Probe for DNA Mismatches and Abasic Sites. Inorg Chem 2017; 56:8381-8389. [PMID: 28657712 PMCID: PMC5516787 DOI: 10.1021/acs.inorgchem.7b01037] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
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[Ru(bpy)2(BNIQ)]2+ (BNIQ = Benzo[c][1,7]naphthyridine-1-isoquinoline), which incorporates the sterically expansive BNIQ ligand, is a
highly selective luminescent probe for DNA mismatches and abasic sites,
possessing a 500-fold higher binding affinity toward these destabilized
regions relative to well-matched base pairs. As a result of this higher
binding affinity, the complex exhibits an enhanced steady-state emission
in the presence of DNA duplexes containing a single base mismatch
or abasic site compared to fully well-matched DNA. Luminescence quenching
experiments with Cu(phen)22+ and [Fe(CN)6]3– implicate binding of the complex to
a mismatch from the minor groove via metalloinsertion. The emission
response of the complex to different single base mismatches, binding
preferentially to the more destabilized mismatches, is also consistent
with binding by metalloinsertion. This work shows that high selectivity
toward destabilized regions in duplex DNA can be achieved through
the rational design of a complex with a sterically expansive aromatic
ligand. The luminescent complex [Ru(bpy)2(BNIQ)]2+ selectivity targets mismatched and abasic sites in duplex
DNA and exhibits an enhanced emission intensity in the presence of
these defect sites relative to well-matched base pairs.
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Affiliation(s)
- Adam N Boynton
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Lionel Marcélis
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Anna J McConnell
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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15
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Aikawa H, Yano A, Nakatani K. A 2,7-diamino-1,4,8-triazanaphthalene derivative selectively binds to cytosine bulge DNA only at a weakly acidic pH. Org Biomol Chem 2017; 15:1313-1316. [PMID: 27847943 DOI: 10.1039/c6ob02273a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The synthesis and properties of 2,7-diamino-1,4,8-triazanaphthalene (azaDANP) are described. AzaDANP is protonated only at a weakly acidic pH to bind to the cytosine bulge DNA duplex selectively. Upon binding of azaDANP to the cytosine bulge DNA, a new absorption band at 407 nm appears, and the absorption change of azaDANP on binding to the target is very sensitive to environmental pH with a bell-shaped pH-absorption profile.
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Affiliation(s)
- H Aikawa
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
| | - A Yano
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
| | - K Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, 8-1 Mihogaoka, Ibaraki 567-0047, Japan.
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16
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Bignon E, Gattuso H, Morell C, Dehez F, Georgakilas AG, Monari A, Dumont E. Correlation of bistranded clustered abasic DNA lesion processing with structural and dynamic DNA helix distortion. Nucleic Acids Res 2016; 44:8588-8599. [PMID: 27587587 PMCID: PMC5063003 DOI: 10.1093/nar/gkw773] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2016] [Accepted: 08/23/2016] [Indexed: 01/08/2023] Open
Abstract
Clustered apurinic/apyrimidinic (AP; abasic) DNA lesions produced by ionizing radiation are by far more cytotoxic than isolated AP lesion entities. The structure and dynamics of a series of seven 23-bp oligonucleotides featuring simple bistranded clustered damage sites, comprising of two AP sites, zero, one, three or five bases 3′ or 5′ apart from each other, were investigated through 400 ns explicit solvent molecular dynamics simulations. They provide representative structures of synthetically engineered multiply damage sites-containing oligonucleotides whose repair was investigated experimentally (Nucl. Acids Res. 2004, 32:5609-5620; Nucl. Acids Res. 2002, 30: 2800–2808). The inspection of extrahelical positioning of the AP sites, bulge and non Watson–Crick hydrogen bonding corroborates the experimental measurements of repair efficiencies by bacterial or human AP endonucleases Nfo and APE1, respectively. This study provides unprecedented knowledge into the structure and dynamics of clustered abasic DNA lesions, notably rationalizing the non-symmetry with respect to 3′ to 5′ position. In addition, it provides strong mechanistic insights and basis for future studies on the effects of clustered DNA damage on the recognition and processing of these lesions by bacterial or human DNA repair enzymes specialized in the processing of such lesions.
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Affiliation(s)
- Emmanuelle Bignon
- Univ Lyon, Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France Institut des Sciences Analytiques, Université de Lyon 1 and CNRS, F-69100, Villeurbanne France
| | - Hugo Gattuso
- Université de Lorraine -Nancy, Theory-Modeling-Simulation SRSMC, F-54506, Vandoeuvre-lès-Nancy, France CNRS, Theory-Modeling-Simulation SRSMC, F-54506, Vandoeuvre-lès-Nancy, France
| | - Christophe Morell
- Institut des Sciences Analytiques, Université de Lyon 1 and CNRS, F-69100, Villeurbanne France
| | - François Dehez
- Université de Lorraine -Nancy, Theory-Modeling-Simulation SRSMC, F-54506, Vandoeuvre-lès-Nancy, France CNRS, Theory-Modeling-Simulation SRSMC, F-54506, Vandoeuvre-lès-Nancy, France
| | - Alexandros G Georgakilas
- DNA damage laboratory, Physics Department, School of Applied Mathematical and Physical Sciences, National Technical University of Athens (NTUA), Zografou 15780, Athens, Greece
| | - Antonio Monari
- Université de Lorraine -Nancy, Theory-Modeling-Simulation SRSMC, F-54506, Vandoeuvre-lès-Nancy, France CNRS, Theory-Modeling-Simulation SRSMC, F-54506, Vandoeuvre-lès-Nancy, France
| | - Elise Dumont
- Univ Lyon, Ens de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F-69342, Lyon, France
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17
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Suć J, Tumir LM, Glavaš-Obrovac L, Jukić M, Piantanida I, Jerić I. The impact of α-hydrazino acids embedded in short fluorescent peptides on peptide interactions with DNA and RNA. Org Biomol Chem 2016; 14:4865-74. [PMID: 27161341 DOI: 10.1039/c6ob00425c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A series of novel hydrazino-based peptidomimetics and analogues comprising N-terminal lysine and C-terminal phenanthridinyl-l-alanine were prepared. The presented results demonstrate the up to now unknown possibility to finely modulate peptide interactions with DNA/RNA by α-hydrazino group insertion and how the different positioning of two α-hydrazino groups in peptides controls binding to various double stranded and single stranded DNA and RNA. All peptidomimetics bind with 1-10 micromolar affinity to ds-DNA/RNA, whereby the binding mode is a combination of electrostatic interactions and hydrophobic interactions within DNA/RNA grooves. Insertion of the α-hydrazino group into the peptide systematically decreased its fluorimetric response to DNA/RNA binding in the order: mono-hydrazino < alternating-hydrazino < sequential-hydrazino group. Binding studies of ss-polynucleotides suggest intercalation of phenanthridine between polynucleotide bases, whereby affinity and fluorimetric response decrease with the number of α-hydrazino groups in the peptide sequence. Particularly interesting was the interaction of two sequential α-hydrazino acids-peptidomimetic with poly rG, characterised by a specific strong increase of CD bands, while all other peptide/ssRNA combinations gave only a CD-band decrease. All mentioned interactions could also be reversibly controlled by adjusting the pH, due to the protonation of the fluorophore.
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Affiliation(s)
- Josipa Suć
- Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, 10000 Zagreb, Croatia.
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18
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Boynton AN, Marcélis L, Barton JK. [Ru(Me4phen)2dppz](2+), a Light Switch for DNA Mismatches. J Am Chem Soc 2016; 138:5020-3. [PMID: 27068529 DOI: 10.1021/jacs.6b02022] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
[Ru(Me4phen)2dppz](2+) serves as a luminescent "light switch" for single base mismatches in DNA. The preferential luminescence enhancement observed with mismatches results from two factors: (i) the complex possesses a 26-fold higher binding affinity toward the mismatch compared to well-matched base pairs, and (ii) the excited state emission lifetime of the ruthenium bound to the DNA mismatch is 160 ns versus 35 ns when bound to a matched site. Results indicate that the complex binds to the mismatch through a metalloinsertion binding mode. Cu(phen)2(2+) quenching experiments show that the complex binds to the mismatch from the minor groove, characteristic of metalloinsertion. Additionally, the luminescence intensity of the complex with DNA containing single base mismatches correlates with the thermodynamic destabilization of the mismatch, also consistent with binding through metalloinsertion. This complex represents a potentially new early cancer diagnostic for detecting deficiencies in mismatch repair.
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Affiliation(s)
- Adam N Boynton
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Lionel Marcélis
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
| | - Jacqueline K Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology , Pasadena, California 91125, United States
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19
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Konda SK, Wang H, Cutts SM, Phillips DR, Collins JG. Binding of pixantrone to DNA at CpA dinucleotide sequences and bulge structures. Org Biomol Chem 2016; 13:5972-82. [PMID: 25929194 DOI: 10.1039/c5ob00526d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The binding of the anti-cancer drug pixantrone to three oligonucleotide sequences, d(TCATATGA)2, d(CCGAGAATTCCGG)2 {double bulge = DB} and the non-self complementary d(TACGATGAGTA) : d(TACCATCGTA) {single bulge = SB}, has been studied by NMR spectroscopy and molecular modelling. The upfield shifts observed for the aromatic resonances of pixantrone upon addition of the drug to each oligonucleotide confirmed the drug bound by intercalation. For the duplex sequence d(TCATATGA)2, NOEs were observed from the pixantrone aromatic H7/8 and aliphatic Ha/Hb protons to the H6/H8 and H1' protons of the C2, A3, T6 and G7 nucleotides, demonstrating that pixantrone preferentially binds at the symmetric CpA sites. However, weaker NOEs observed to various protons from the T4 and A5 residues indicated alternative minor binding sites. NOEs from the H7/H8 and Ha/Hb protons to both major (H6/H8) and minor groove (H1') protons indicated approximately equal proportions of intercalation was from the major and minor groove at the CpA sites. Intermolecular NOEs were observed between the H7/H8 and H4 protons of pixantrone and the A4H1' and G3H1' protons of the oligonucleotide that contains two symmetrically related bulge sites (DB), indicative of binding at the adenine bulge sites. For the oligonucleotide that only contains a single bulge site (SB), NOEs were observed from pixantrone protons to the SB G7H1', A8H1' and G9H1' protons, confirming that the drug bound selectively at the adenine bulge site. A molecular model of pixantrone-bound SB could be constructed with the drug bound from the minor groove at the A8pG9 site that was consistent with the observed NMR data. The results demonstrate that pixantrone preferentially intercalates at adenine bulge sites, compared to duplex DNA, and predominantly from the minor groove.
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Affiliation(s)
- Shyam K Konda
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales, Australian Defence Force Academy, Northcott Drive, Campbell, ACT 2600, Australia.
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20
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Chan K, Yik-Sham Chung C, Wing-Wah Yam V. Parallel folding topology-selective label-free detection and monitoring of conformational and topological changes of different G-quadruplex DNAs by emission spectral changes via FRET of mPPE-Ala-Pt(ii) complex ensemble. Chem Sci 2016; 7:2842-2855. [PMID: 30090278 PMCID: PMC6055111 DOI: 10.1039/c5sc04563k] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2015] [Accepted: 01/05/2016] [Indexed: 12/28/2022] Open
Abstract
The formation of supramolecular assemblies between [Pt(bzimpy-Et){C[triple bond, length as m-dash]CC6H4(CH2NMe3-4)}]Cl2 (1) and mPPE-Ala and the FRET properties of the ensemble have been revealed from the UV-vis absorption, steady-state emission and time-resolved emission decay studies. The two-component mPPE-Ala-1 ensemble has been employed in a "proof-of-principle" concept for label-free detection of G-quadruplex DNAs with the intramolecular propeller parallel folding topology, such as c-myc, in aqueous buffer solution. By the modulation of the aggregation/deaggregation of the polymer-metal complex aggregates and hence the FRET from the mPPE-Ala donor to the aggregated 1 as acceptor, the ensemble has been demonstrated for sensitive and selective label-free detection of c-myc via the monitoring of emission spectral changes of the ensemble. Ratiometric emission of the ensemble at 461 and 662 nm has been shown to distinguish the intramolecular propeller parallel G-quadruplex folding topology of c-myc from other G-quadruplex-forming sequences of different folding topologies, owing to the strong and specific interactions between c-myc and 1 as suggested by the UV-vis absorption and UV melting studies. In addition, the formation of high-order intermolecular multimeric G-quadruplexes from c-myc under molecular crowding conditions has been successfully probed by the ratiometric emission of the ensemble. The conformational and topological transition of human telomeric DNA from the mixed-hybrid form to the intramolecular propeller parallel form, as observed from the circular dichroism spectroscopy, has also been monitored by the ratiometric emission of the ensemble. The ability of the ensemble to detect these conformational and topological transitions of G-quadruplex DNAs has been rationalized by the excellent selectivity and sensitivity of the ensemble towards the intramolecular propeller parallel G-quadruplex DNAs and their high-order intermolecular multimers, which are due to the extra stabilization gained from Pt···Pt and π-π interactions in addition to the electrostatic and hydrophobic interactions found in the polymer-metal complex aggregates.
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Affiliation(s)
- Kevin Chan
- Institute of Molecular Functional Materials (Areas of Excellence Scheme, University Grants Committee (Hong Kong)) , Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
| | - Clive Yik-Sham Chung
- Institute of Molecular Functional Materials (Areas of Excellence Scheme, University Grants Committee (Hong Kong)) , Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
| | - Vivian Wing-Wah Yam
- Institute of Molecular Functional Materials (Areas of Excellence Scheme, University Grants Committee (Hong Kong)) , Department of Chemistry , The University of Hong Kong , Pokfulam Road , Hong Kong , P. R. China .
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21
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Siters KE, Sander SA, Devlin JR, Morrow JR. Bifunctional Zn(II) complexes for recognition of non-canonical thymines in DNA bulges and G-quadruplexes. Dalton Trans 2015; 44:3708-16. [PMID: 25521076 DOI: 10.1039/c4dt03004d] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Six Zn(II) complexes of derivatives of 1,4,7,10-tetraazacyclododecane (cyclen) were studied for binding to DNA sequences containing non-canonical thymines, including a hairpin with a single thymine bulge (T-bulge) and a G-quadruplex (H-telo) containing thymine loops. The cyclen-based macrocycles contained pendents with either two fused rings to give planar groups including quinolinone (QMC), coumarin (MCC) and quinoline (CQC) derivatives or a non-planar dansyl group (DSC). Macrocyclic complexes with three fused rings including an anthraquinone pendent (ATQ) were also studied. All Zn(II) complexes were stable in solution at micromolar concentrations and neutral pH with the Zn(L)(OH2) species prevailing for L = QMC and CQC at pH 7.5 and 100 mM NaCl. Immobilized T-bulge or H-telo G-quadruplex was used to study binding of the complexes by surface plasmon resonance (SPR) for several of the complexes. For the most part, data matched well with that obtained by isothermal calorimetry (ITC) and, for fluorescent complexes, by fluorescence titrations. Data showed that Zn(II) complexes containing planar aromatic pendents with two fused rings bound to T-bulge more tightly than complexes with non-planar pendents such as DSC. The H-telo DNA exhibited multiple binding sites for all complexes containing aromatic pendents. The complexes with two fused rings bound with low micromolar dissociation constants and two binding sites whereas a complex with three fused rings (ATQ) bound to three sites. This study shows that different pendent groups on Zn(II) cyclen complexes impart selectivity for recognition of non-canonical DNA structures.
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Affiliation(s)
- Kevin E Siters
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA.
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22
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Malina J, Scott P, Brabec V. Shape-selective recognition of DNA abasic sites by metallohelices: inhibition of human AP endonuclease 1. Nucleic Acids Res 2015; 43:5297-306. [PMID: 25940617 PMCID: PMC4477665 DOI: 10.1093/nar/gkv438] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/23/2015] [Indexed: 02/07/2023] Open
Abstract
Loss of a base in DNA leading to creation of an abasic (AP) site leaving a deoxyribose residue in the strand, is a frequent lesion that may occur spontaneously or under the action of various physical and chemical agents. Progress in the understanding of the chemistry and enzymology of abasic DNA largely relies upon the study of AP sites in synthetic duplexes. We report here on interactions of diastereomerically pure metallo-helical 'flexicate' complexes, bimetallic triple-stranded ferro-helicates [Fe2(NN-NN)3](4+) incorporating the common NN-NN bis(bidentate) helicand, with short DNA duplexes containing AP sites in different sequence contexts. The results show that the flexicates bind to AP sites in DNA duplexes in a shape-selective manner. They preferentially bind to AP sites flanked by purines on both sides and their binding is enhanced when a pyrimidine is placed in opposite orientation to the lesion. Notably, the Λ-enantiomer binds to all tested AP sites with higher affinity than the Δ-enantiomer. In addition, the binding of the flexicates to AP sites inhibits the activity of human AP endonuclease 1, which is as a valid anticancer drug target. Hence, this finding indicates the potential of utilizing well-defined metallo-helical complexes for cancer chemotherapy.
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Affiliation(s)
- Jaroslav Malina
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic
| | - Peter Scott
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, UK
| | - Viktor Brabec
- Institute of Biophysics, Academy of Sciences of the Czech Republic, v.v.i., Kralovopolska 135, CZ-61265 Brno, Czech Republic
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23
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Kotera N, Poyer F, Granzhan A, Teulade-Fichou MP. Efficient inhibition of human AP endonuclease 1 (APE1) via substrate masking by abasic site-binding macrocyclic ligands. Chem Commun (Camb) 2015; 51:15948-51. [DOI: 10.1039/c5cc06084b] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Bis-naphthalene macrocycles bind to abasic sites in DNA, leading to efficient inhibition of their cleavage by human AP endonuclease 1 (APE1).
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Affiliation(s)
- Naoko Kotera
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
| | - Florent Poyer
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
| | - Anton Granzhan
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
| | - Marie-Paule Teulade-Fichou
- CNRS UMR9187/INSERM U1196 “Chemistry, Modelling and Imaging for Biology”
- Centre de Recherche
- Institut Curie
- 91405 Orsay
- France
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24
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Siters KE, Sander SA, Morrow JR. Selective Binding of Zn 2+Complexes to Non-Canonical Thymine or Uracil in DNA or RNA. PROGRESS IN INORGANIC CHEMISTRY: VOLUME 59 2014. [DOI: 10.1002/9781118869994.ch03] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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25
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Franco D, Vargiu AV, Magistrato A. Ru[(bpy)2(dppz)]2+ and Rh[(bpy)2(chrysi)]3+ Targeting Double Strand DNA: The Shape of the Intercalating Ligand Tunes the Free Energy Landscape of Deintercalation. Inorg Chem 2014; 53:7999-8008. [DOI: 10.1021/ic5008523] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Duvan Franco
- International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste, Italy
| | - Attilio V. Vargiu
- Dipartimento
di Fisica, Università di Cagliari, s.p. Monserrato-Sestu km 0.700, I-09042 Monserrato, Italy
| | - Alessandra Magistrato
- CNR-IOM-DEMOCRITOS c/o International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste, Italy
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26
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Peng J, Shao Y, Liu L, Zhang L, Liu H. Specific recognition of DNA bulge sites by in situ grown fluorescent Ag nanoclusters with high selectivity. Dalton Trans 2014; 43:1534-41. [DOI: 10.1039/c3dt52042k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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27
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Aguiló J, Naeimi A, Bofill R, Mueller-Bunz H, Llobet A, Escriche L, Sala X, Albrecht M. Dinuclear ruthenium complexes containing a new ditopic phthalazin-bis(triazole) ligand that promotes metal–metal interactions. NEW J CHEM 2014. [DOI: 10.1039/c3nj01209c] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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28
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Liu L, Shao Y, Peng J, Liu H, Zhang L. Selective recognition of ds-DNA cavities by a molecular rotor: switched fluorescence of thioflavin T. MOLECULAR BIOSYSTEMS 2013; 9:2512-9. [DOI: 10.1039/c3mb70201d] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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29
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Wu F, Sun Y, Shao Y, Xu S, Liu G, Peng J, Liu L. DNA abasic site-selective enhancement of sanguinarine fluorescence with a large emission shift. PLoS One 2012. [PMID: 23185252 PMCID: PMC3502418 DOI: 10.1371/journal.pone.0048251] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Small molecules that can specifically bind to a DNA abasic site (AP site) have received much attention due to their importance in DNA lesion identification, drug discovery, and sensor design. Herein, the AP site binding behavior of sanguinarine (SG), a natural alkaloid, was investigated. In aqueous solution, SG has a short-wavelength alkanolamine emission band and a long-wavelength iminium emission band. At pH 8.3, SG experiences a fluorescence quenching for both bands upon binding to fully matched DNAs without the AP site, while the presence of the AP site induces a strong SG binding and the observed fluorescence enhancement for the iminium band are highly dependent on the nucleobases flanking the AP site, while the alkanolamine band is always quenched. The bases opposite the AP site also exert some modifications on the SG's emission behavior. It was found that the observed quenching for DNAs with Gs and Cs flanking the AP site is most likely caused by electron transfer between the AP site-bound excited-state SG and the nearby Gs. However, the flanking As and Ts that are not easily oxidized favor the enhanced emission. This AP site-selective enhancement of SG fluorescence accompanies a band conversion in the dominate emission from the alkanolamine to iminium band thus with a large emission shift of about 170 nm. Absorption spectra, steady-state and transient-state fluorescence, DNA melting, and electrolyte experiments confirm that the AP site binding of SG occurs and the stacking interaction with the nearby base pairs is likely to prevent the converted SG iminium form from contacting with water that is thus emissive when the AP site neighbors are bases other than guanines. We expect that this fluorophore would be developed as a promising AP site binder having a large emission shift.
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Affiliation(s)
- Fei Wu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Yanwei Sun
- Chuyang Honors College, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Yong Shao
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
- * E-mail:
| | - Shujuan Xu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Guiying Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Jian Peng
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
| | - Lingling Liu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua, Zhejiang, People's Republic of China
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30
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del Mundo IMA, Siters KE, Fountain MA, Morrow JR. Structural basis for bifunctional zinc(II) macrocyclic complex recognition of thymine bulges in DNA. Inorg Chem 2012; 51:5444-57. [PMID: 22507054 DOI: 10.1021/ic3004245] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The zinc(II) complex of 1-(4-quinoylyl)methyl-1,4,7,10-tetraazacyclododecane (cy4q) binds selectively to thymine bulges in DNA and to a uracil bulge in RNA. Binding constants are in the low-micromolar range for thymine bulges in the stems of hairpins, for a thymine bulge in a DNA duplex, and for a uracil bulge in an RNA hairpin. Binding studies of Zn(cy4q) to a series of hairpins containing thymine bulges with different flanking bases showed that the complex had a moderate selectivity for thymine bulges with neighboring purines. The dissociation constants of the most strongly bound Zn(cy4q)-DNA thymine bulge adducts were 100-fold tighter than similar sequences with fully complementary stems or than bulges containing cytosine, guanine, or adenine. In order to probe the role of the pendent group, three additional zinc(II) complexes containing 1,4,7,10-tetraazacyclododecane (cyclen) with aromatic pendent groups were studied for binding to DNA including 1-(2-quinolyl)methyl-1,4,7,10-tetraazacyclododecane (cy2q), 1-(4-biphenyl)methyl-1,4,7,10-tetraazacyclododecane (cybp), and 5-(1,4,7,10-tetraazacyclododecan-1-ylsulfonyl)-N,N-dimethylnaphthalen-1-amine (dsc). The Zn(cybp) complex binds with moderate affinity but little selectivity to DNA hairpins with thymine bulges and to DNA lacking bulges. Similarly, Zn(dsc) binds weakly both to thymine bulges and hairpins with fully complementary stems. The zinc(II) complex of cy2q has the 2-quinolyl moiety bound to the Zn(II) center, as shown by (1)H NMR spectroscopy and pH-potentiometric titrations. As a consequence, only weak (500 μM) binding is observed to DNA with no appreciable selectivity. An NMR structure of a thymine-bulge-containing hairpin shows that the thymine is extrahelical but rotated toward the major groove. NMR data for Zn(cy4q) bound to DNA containing a thymine bulge is consistent with binding of the zinc(II) complex to the thymine N3(-) and stacking of the quinoline on top of the thymine. The thymine-bulge bound zinc(II) complex is pointed into the major groove, and there are interactions with the guanine positioned 5' to the thymine bulge.
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Affiliation(s)
- Imee Marie A del Mundo
- Department of Chemistry, University at Buffalo, State University of New York, Buffalo, New York 14260, USA
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31
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Nelson KE, Ihms HE, Mazumdar D, Bruesehoff PJ, Lu Y. The importance of peripheral sequences in determining the metal selectivity of an in vitro-selected Co(2+) -dependent DNAzyme. Chembiochem 2012; 13:381-91. [PMID: 22250000 PMCID: PMC3299816 DOI: 10.1002/cbic.201100724] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2011] [Indexed: 11/12/2022]
Abstract
DNAzymes are catalytically active DNA molecules that use metal cofactors for their enzymatic functions. While a growing number of DNAzymes with diverse functions and metal selectivities have been reported, the relationships between metal ion selectivity, conserved sequences and structures responsible for selectivity remain to be elucidated. To address this issue, we report biochemical assays of a family of previously reported in vitro selected DNAzymes. This family includes the clone 11 DNAzyme, which was isolated by positive and negative selection, and the clone 18 DNAzyme, which was isolated by positive selection alone. The clone 11 DNAzyme has a higher selectivity for Co(2+) over Pb(2+) compared with clone 18. The reasons for this difference are explored here through phylogenetic comparison, mutational analysis and stepwise truncation. A novel DNAzyme truncation method incorporated a nick in the middle of the DNAzyme to allow for truncation close to the nicked site while preserving peripheral sequences at both ends of the DNAzyme. The results demonstrate that peripheral sequences within the substrate binding arms, most notably the stem loop, loop II, are sufficient to restore its selectivity for Co(2+) over Pb(2+) to levels observed in clone 11. A comparison of these sequences' secondary structures and Co(2+) selectivities suggested that metastable structures affect metal ion selectivity. The Co(2+) selectivity of the clone 11 DNAzyme showed that the metal ion binding and selectivities of small, in vitro selected DNAzymes may be more complex than previously appreciated, and that clone 11 may be more similar to larger ribozymes than to other small DNAzymes in its structural complexity and behavior. These factors should be taken into account when metal-ion selectivity is required in rationally designed DNAzymes and DNAzyme-based biosensors.
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Affiliation(s)
- Kevin E. Nelson
- Department of Biochemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
- Department of Pediatrics, Primary Children’s Medical Center, University of Utah, 100 North Mario Capecchi Drive, Salt Lake City, UT 84113 (USA)
| | - Hannah E. Ihms
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Debapriya Mazumdar
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Peter J. Bruesehoff
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
| | - Yi Lu
- Department of Biochemistry, University of Illinois, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
- Department of Chemistry, University of Illinois, A322 Chemical and Life Sciences Laboratory, MC-712, Box 8–6, 600 South Mathews Avenue, Urbana, IL 61801 (USA)
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32
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Li F, Weber DK, Morgan JL, Collins JG, Keene FR. An approach to therapeutic agents through selective targeting of destabilised nucleic acid duplex sequences. Dalton Trans 2012; 41:6528-35. [PMID: 22311066 DOI: 10.1039/c2dt12146h] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The binding of ΔΔ/ΛΛ-[{Ru(phen)(2)}(2)(μ-bb(n))](4+) {where phen = 1,10-phenanthroline, bb(n) = 1,n-bis[4(4'-methyl-2,2'-bipyridyl)]-alkane (ΔΔ/ΛΛ-Rubb(n))} to the non-self complementary oligonucleotide 5'-d(CGCGATAAGCCGC·5'-GCGGCATTACGCG) (3-DB) has been examined using a 4',6-diamidino-2-phenylindole dihydrochloride (DAPI) displacement assay. The 3-DB oligonucleotide contains two single adenine bulge nucleotides that are separated by three base pairs. (1)H NMR spectroscopy data demonstrated that the adenine bases are intra-helical and that the segment containing the two bulge nucleotides and the three A·T base pairs between the bulges forms a destabilised segment within the stable duplex oligonucleotide. The DAPI displacement assay demonstrated that ΔΔ-Rubb(7)-bound 3-DB with higher affinity than the other members of the ΔΔ/ΛΛ-Rubb(n) series. Molecular models suggested that the seven-carbon chain length in ΔΔ-Rubb(7) was ideal to span the distance between the two bulge sites. The binding of ΔΔ-Rubb(7) to 3-DB was also studied by (1)H NMR spectroscopy and molecular modelling. The selective changes in chemical shifts for the resonances from 3-DB upon addition of ΔΔ-Rubb(7) suggested that the metal complex specifically bound at the destabilised segment between A(5) and A(19). Observation in NOESY spectra of NOE cross peaks between 3-DB and ΔΔ-Rubb(7) confirmed that one of the ruthenium centres bound at the A(5) bulge site, with the other metal centre positioned at the A(19) bulge. In addition, ΔΔ-Rubb(7) was found to bind chromosomal DNA extracted from a suspension of Staphylococcus aureus that had been incubated with the ruthenium(ii) complex. As inert dinuclear ruthenium(ii) complexes are capable of being transported into a bacterial cell and bind chromosomal DNA, it is possible that they could be developed into anti-microbial agents that specifically target destabilised segments of DNA that are recognised by essential DNA-binding proteins.
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Affiliation(s)
- Fangfei Li
- School of Physical, Environmental and Mathematical Sciences, University of New South Wales, Australian Defence Force Academy, Canberra, ACT 2600, Australia
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Vargiu AV, Magistrato A. Detecting DNA Mismatches with Metallo-Insertors: A Molecular Simulation Study. Inorg Chem 2012; 51:2046-57. [DOI: 10.1021/ic201659v] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Attilio V. Vargiu
- CNR-IOM, Unità Operativa
di Supporto SLACS, c/o Dipartimento di Fisica, Università di Cagliari, s.p. Monserrato-Sestu km 0.7, I-09042 Monserrato,
Italy
| | - Alessandra Magistrato
- CNR-IOM-Democritos,
National
Simulation Center, c/o International School for Advanced Studies (SISSA/ISAS), via Bonomea 265, 34136, Trieste,
Italy
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34
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Wu F, Shao Y, Ma K, Cui Q, Liu G, Xu S. Simultaneous fluorescence light-up and selective multicolor nucleobase recognition based on sequence-dependent strong binding of berberine to DNA abasic site. Org Biomol Chem 2012; 10:3300-7. [DOI: 10.1039/c2ob00028h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
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35
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Chakravarty AR, Roy M. Photoactivated DNA Cleavage and Anticancer Activity of 3d Metal Complexes. PROGRESS IN INORGANIC CHEMISTRY 2011. [DOI: 10.1002/9781118148235.ch3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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36
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Fekry MI, Szekely J, Dutta S, Breydo L, Zang H, Gates KS. Noncovalent DNA binding drives DNA alkylation by leinamycin: evidence that the Z,E-5-(thiazol-4-yl)-penta-2,4-dienone moiety of the natural product serves as an atypical DNA intercalator. J Am Chem Soc 2011; 133:17641-51. [PMID: 21954957 PMCID: PMC3268133 DOI: 10.1021/ja2046149] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Molecular recognition and chemical modification of DNA are important in medicinal chemistry, toxicology, and biotechnology. Historically, natural products have revealed many interesting and unexpected mechanisms for noncovalent DNA binding and covalent DNA modification. The studies reported here characterize the molecular mechanisms underlying the efficient alkylation of duplex DNA by the Streptomyces-derived natural product leinamycin. Previous studies suggested that alkylation of duplex DNA by activated leinamycin (2) is driven by noncovalent association of the natural product with the double helix. This is striking because leinamycin does not contain a classical noncovalent DNA-binding motif, such as an intercalating unit, a groove binder, or a polycation. The experiments described here provide evidence that leinamycin is an atypical DNA-intercalating agent. A competition binding assay involving daunomycin-mediated inhibition of DNA alkylation by leinamycin provided evidence that activated leinamycin binds to duplex DNA with an apparent binding constant of approximately 4.3 ± 0.4 × 10(3) M(-1). Activated leinamycin caused duplex unwinding and hydrodynamic changes in DNA-containing solutions that are indicative of DNA intercalation. Characterization of the reaction of activated leinamycin with palindromic duplexes containing 5'-CG and 5'-GC target sites, bulge-containing duplexes, and 5-methylcytosine-containing duplexes provided evidence regarding the orientation of leinamycin with respect to target guanine residues. The data allow construction of a model for the leinamycin-DNA complex suggesting how a modest DNA-binding constant combines with proper positioning of the natural product to drive efficient alkylation of guanine residues in the major groove of duplex DNA.
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Affiliation(s)
- Mostafa I. Fekry
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
- Cairo University Pharmacognosy Department Faculty of Pharmacy Kasr El-Aini, Cairo, Egypt 11562
| | - Jozsef Szekely
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
| | - Sanjay Dutta
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
| | - Leonid Breydo
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
| | - Hong Zang
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
| | - Kent S. Gates
- University of Missouri–Columbia Departments of Chemistry and Biochemistry 125 Chemistry Building Columbia, MO 65211
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37
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Xu S, Shao Y, Ma K, Cui Q, Liu G, Wu F, Li M. Fluorescence light-up recognition of DNA nucleotide based on selective abasic site binding of an excited-state intramolecular proton transfer probe. Analyst 2011; 136:4480-5. [PMID: 21946800 DOI: 10.1039/c1an15652g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA single-nucleotide polymorphism (SNP) detection has attracted much attention due to mutation-related diseases. Various fluorescence methods for SNP detection have been proposed and many are already in use. However, fluorescence enhancement for signal-on SNP identification without label modification still remains a challenge. Here, we find that the abasic site (AP site) in a DNA duplex can be developed as a binding pocket favorable for the occurrence of the excited-state intramolecular proton transfer (ESIPT) of a 3-hydroxyflavone, fisetin, which is used as a proof of concept for effective SNP identification. Fisetin binding at the AP site is highly selective for target thymine or cytosine facing the AP site by observation of a drastic increase in the ESIPT emission band. In addition, the target recognition selectivity based on this ESIPT process is not affected by flanking bases of the AP site. The binding selectivity of fisetin at the AP site is also confirmed by measurements of fluorescence resonance energy transfer, emission lifetime and DNA melting. The fluorescent signal-on sensing for SNP based on this fluorophore is substantially advantageous over the previously used fluorophores such as the AP site-specific signal-off organic ligands with a similar fluorescing mechanism before and after binding to DNA with hydrogen bonding interaction. We expect that this approach will be employed to develop a practical SNP detection method by locating an AP site toward a target and employing an ESIPT probe as readout.
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Affiliation(s)
- Shujuan Xu
- Institute of Physical Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People's Republic of China
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Palanichamy K, Sreejayan N, Ontko AC. Overcoming cisplatin resistance using gold(III) mimics: anticancer activity of novel gold(III) polypyridyl complexes. J Inorg Biochem 2011; 106:32-42. [PMID: 22112837 DOI: 10.1016/j.jinorgbio.2011.08.013] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2010] [Revised: 08/18/2011] [Accepted: 08/19/2011] [Indexed: 11/27/2022]
Abstract
Gold(III) compounds have been recognized as anticancer agents due to their structural and electronic similarities with currently employed platinum(II) species. An added benefit to gold(III) agents is the ability to overcome cisplatin resistance. This work identified four gold(III) compounds, [Au(Phen)Cl(2)]PF(6), [Au(DPQ)Cl(2)]PF(6), [Au(DPPZ)Cl(2)]PF(6), and [Au(DPQC)Cl(2)]PF(6), (Phen = 1,10-phenanthroline, DPQ = dipyrido[3,2-d:2',3'-f]quinoxaline, DPPZ = dipyrido[3,2-a:2',3'-c] phenazine, DPQC = dipyrido[3,2-d:2',3'-f] cyclohexyl quinoxaline) that exhibited anticancer activity in both cisplatin sensitive and cisplatin resistant ovarian cancer cells. Two of these compounds, [Au(DPQ)Cl(2)]PF(6) (AQ) and [Au(DPPZ)Cl(2)]PF(6) (AZ), displayed exceptional anticancer activity and were the focus of more intensive mechanistic study. At the molecular level, AQ and AZ formed DNA adducts, generated free radicals, and upregulated pro-apoptotic signaling molecules (p53, caspases, PARP, death effectors). Taken together, these two novel gold(III) polypyridyl complexes exhibit potent antitumor activity in cisplatin resistant cancer cells. These activities may be mediated, in part, by the activation of apoptotic signaling.
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Affiliation(s)
- Kamalakannan Palanichamy
- Department of Radiation Oncology, The Ohio State University Medical Center, Columbus, OH 43210, USA
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39
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Lutterman DA, Lazinski-Melanson LA, Asher Y, Johnston DH, Gallucci JC, Turro C. Effect of intraligand π-delocalization on the photophysical properties of two new Ru(II) complexes. J Photochem Photobiol A Chem 2011. [DOI: 10.1016/j.jphotochem.2010.09.025] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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40
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Spencer BR, Kraft BJ, Hughes CG, Pink M, Zaleski JM. Modulating the Light Switch by 3MLCT-3ππ* State Interconversion. Inorg Chem 2010; 49:11333-45. [DOI: 10.1021/ic1011617] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Brigitte R. Spencer
- Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405, United States
| | - Brian J. Kraft
- Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405, United States
| | - Chris G. Hughes
- Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405, United States
| | - Maren Pink
- Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405, United States
| | - Jeffrey M. Zaleski
- Department of Chemistry and Molecular Structure Center, Indiana University, Bloomington, Indiana 47405, United States
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41
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Ghattas W, Müller-Bunz H, Albrecht M. [Ru(bpy)3]2+ Analogues Containing an N-Heterocyclic Carbene Ligand. Organometallics 2010. [DOI: 10.1021/om100925j] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Wadih Ghattas
- School of Chemistry & Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Helge Müller-Bunz
- School of Chemistry & Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
| | - Martin Albrecht
- School of Chemistry & Chemical Biology, University College Dublin, Belfield, Dublin 4, Ireland
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42
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Granzhan A, Largy E, Saettel N, Teulade-Fichou MP. Macrocyclic DNA-mismatch-binding ligands: structural determinants of selectivity. Chemistry 2010; 16:878-89. [PMID: 19938008 DOI: 10.1002/chem.200901989] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Abstract
A collection of 15 homodimeric and 5 heterodimeric macrocyclic bisintercalators was prepared by one- or two-step condensation of aromatic dialdehydes with aliphatic diamines; notably, the heterodimeric scaffolds were synthesized for the first time. The binding of these macrocycles to DNA duplexes containing a mispaired thymine residue (TX), as well as to the fully paired control (TA), was investigated by thermal denaturation and fluorescent-intercalator-displacement experiments. The bisnaphthalene derivatives, in particular, the 2,7-disubstituted ones, have the highest selectivity for the TX mismatches, as these macrocycles show no apparent binding to the fully paired DNA. By contrast, other macrocyclic ligands, as well as seven conventional DNA binders, show lesser or no selectivity for the mismatch sites. The study demonstrates that the topology of the ligands plays a crucial role in determining the mismatch-binding affinity and selectivity of the macrocyclic bisintercalators.
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Affiliation(s)
- Anton Granzhan
- UMR176 CNRS, Institut Curie, Centre de Recherche, Centre Universitaire, 91405 Orsay, France
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43
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Georgiades SN, Vilar R. Interaction of metal complexes with nucleic acids. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b918406f] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Minetti CASA, Remeta DP, Dickstein R, Breslauer KJ. Energetic signatures of single base bulges: thermodynamic consequences and biological implications. Nucleic Acids Res 2010; 38:97-116. [PMID: 19946018 PMCID: PMC2800203 DOI: 10.1093/nar/gkp1036] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2009] [Revised: 10/20/2009] [Accepted: 10/21/2009] [Indexed: 12/24/2022] Open
Abstract
DNA bulges are biologically consequential defects that can arise from template-primer misalignments during replication and pose challenges to the cellular DNA repair machinery. Calorimetric and spectroscopic characterizations of defect-containing duplexes reveal systematic patterns of sequence-context dependent bulge-induced destabilizations. These distinguishing energetic signatures are manifest in three coupled characteristics, namely: the magnitude of the bulge-induced duplex destabilization (DeltaDeltaG(Bulge)); the thermodynamic origins of DeltaDeltaG(Bulge) (i.e. enthalpic versus entropic); and, the cooperativity of the duplex melting transition (i.e. two-state versus non-two state). We find moderately destabilized duplexes undergo two-state dissociation and exhibit DeltaDeltaG(Bulge) values consistent with localized, nearest neighbor perturbations arising from unfavorable entropic contributions. Conversely, strongly destabilized duplexes melt in a non-two-state manner and exhibit DeltaDeltaG(Bulge) values consistent with perturbations exceeding nearest-neighbor expectations that are enthalpic in origin. Significantly, our data reveal an intriguing correlation in which the energetic impact of a single bulge base centered in one strand portends the impact of the corresponding complementary bulge base embedded in the opposite strand. We discuss potential correlations between these bulge-specific differential energetic profiles and their overall biological implications in terms of DNA recognition, repair and replication.
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Affiliation(s)
| | | | | | - Kenneth J. Breslauer
- Department of Chemistry and Chemical Biology, Rutgers – The State University of New Jersey, Piscataway, NJ 08854, USA
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45
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Zeglis BM, Pierre VC, Kaiser JT, Barton JK. A bulky rhodium complex bound to an adenosine-adenosine DNA mismatch: general architecture of the metalloinsertion binding mode. Biochemistry 2009; 48:4247-53. [PMID: 19374348 DOI: 10.1021/bi900194e] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Two crystal structures of Delta-Rh(bpy)(2)(chrysi)(3+) (chrysi is 5,6-chrysenequinone diimine) bound to the oligonucleotide duplex 5'-CGGAAATTACCG-3' containing two adenosine-adenosine mismatches (italics) through metalloinsertion were determined. Diffraction quality crystals with two different space groups (P3(2)21 and P4(3)2(1)2) were obtained under very similar crystallization conditions. In both structures, the bulky rhodium complex inserts into the two mismatched sites from the minor groove side, ejecting the mismatched bases into the major groove. The conformational changes are localized to the mismatched site; the metal complex replaces the mismatched base pair without an increase in base pair rise. The expansive metal complex is accommodated in the duplex by a slight opening in the phosphodiester backbone; all sugars retain a C2'-endo puckering, and flanking base pairs neither stretch nor shear. The structures differ, however, in that in one of the structures, an additional metal complex is bound by intercalation from the major groove at the central 5'-AT-3' step. We conclude that this additional metal complex is intercalated into this central step because of crystal packing forces. The structures described here of Delta-Rh(bpy)(2)(chrysi)(3+) bound to thermodynamically destabilized AA mismatches share critical features with binding by metalloinsertion in two other oligonucleotides containing different single-base mismatches. These results underscore the generality of metalloinsertion as a new mode of noncovalent binding by small molecules with a DNA duplex.
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Affiliation(s)
- Brian M Zeglis
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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46
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Lim MH, Song H, Olmon ED, Dervan EE, Barton JK. Sensitivity of Ru(bpy)2dppz2+ luminescence to DNA defects. Inorg Chem 2009; 48:5392-7. [PMID: 19453124 PMCID: PMC2747521 DOI: 10.1021/ic900407n] [Citation(s) in RCA: 112] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The luminescent characteristics of Ru(bpy)(2)dppz(2+) (dppz = dipyrido[3,2-a:2',3'-c]phenazine), a DNA light switch, were investigated in the presence of oligonucleotides containing single base mismatches or an abasic site. In water, the ruthenium luminescence is quenched, but, bound to well matched duplex DNA, the Ru complex luminesces. Here we show that with DNAs containing a defect, rac-, Delta-, and Lambda-Ru(bpy)(2)dppz(2+) exhibit significant luminescent enhancements above that with well matched DNA. In the presence of a single base mismatch, large luminescent enhancements are evident for the Delta-Ru isomer; the Lambda-isomer shows particularly high luminescence bound to an oligonucleotide containing an abasic site. Similar increases are not evident with two common DNA-binding organic fluorophores, ethidium bromide and TO-PRO-3. Titrations with hairpin oligonucleotides containing a variable mismatch site show correlation between the level of luminescent enhancement and the thermodynamic destabilization associated with the mismatch. This correlation is reminiscent of that found earlier for a bulky rhodium complex that binds mismatched DNA sites through metalloinsertion, where the complex binds the DNA from the minor groove side, ejecting the mismatched bases into the major groove. Differential quenching studies with minor and major groove quenchers and time-resolved emission studies support this metalloinsertion mode for the dppz complex at the defect site. Certainly these data underscore the utility of Ru(bpy)(2)dppz(2+) as a sensitive luminescent reporter of DNA and its defects.
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Affiliation(s)
| | - Hang Song
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Eric D. Olmon
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Elizabeth E. Dervan
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
| | - Jacqueline K. Barton
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California, 91125
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