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Díaz-Casado L, Serrano-Chacón I, Montalvillo-Jiménez L, Corzana F, Bastida A, Santana AG, González C, Asensio JL. De Novo Design of Selective Quadruplex-Duplex Junction Ligands and Structural Characterisation of Their Binding Mode: Targeting the G4 Hot-Spot. Chemistry 2021; 27:6204-6212. [PMID: 33368678 DOI: 10.1002/chem.202005026] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Indexed: 01/03/2023]
Abstract
Targeting the interface between DNA quadruplex and duplex regions by small molecules holds significant promise in both therapeutics and nanotechnology. Herein, a new pharmacophore is reported, which selectively binds with high affinity to quadruplex-duplex junctions, while presenting a poorer affinity for G-quadruplex or duplex DNA alone. Ligands complying with the reported pharmacophore exhibit a significant affinity and selectivity for quadruplex-duplex junctions, including the one observed in the HIV-1 LTR-III sequence. The structure of the complex between a quadruplex-duplex junction with a ligand of this family has been determined by NMR methods. According to these data, the remarkable selectivity of this structural motif for quadruplex-duplex junctions is achieved through an unprecedented interaction mode so far unexploited in medicinal and biological chemistry: the insertion of a benzylic ammonium moiety into the centre of the partially exposed G-tetrad at the interface with the duplex. Further decoration of the described scaffolds with additional fragments opens up the road to the development of selective ligands for G-quadruplex-forming regions of the genome.
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Affiliation(s)
- Laura Díaz-Casado
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Israel Serrano-Chacón
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Serrano 119., 28006, Madrid, Spain
| | - Laura Montalvillo-Jiménez
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Francisco Corzana
- Department of Chemistry, Centro de Investigación en Síntesis Química, Universidad de La Rioja, Madre de Dios, 53., 26006, Logroño, Spain
| | - Agatha Bastida
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Andrés G Santana
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
| | - Carlos González
- Instituto de Química-Física Rocasolano (IQFR-CSIC), Serrano 119., 28006, Madrid, Spain
| | - Juan Luis Asensio
- Glycochemistry and Molecular Recognition group-Dpt. Bio-Organic Chemistry, Instituto de Química Orgánica General (IQOG-CSIC), Juan de la Cierva 3., 28006, Madrid, Spain
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2
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Gratal PB, Quero JG, Pérez-Redondo A, Gándara Z, Gude L. PhenQE8, a Novel Ligand of the Human Telomeric Quadruplex. Int J Mol Sci 2021; 22:E749. [PMID: 33451070 PMCID: PMC7828518 DOI: 10.3390/ijms22020749] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 12/30/2020] [Accepted: 01/10/2021] [Indexed: 01/02/2023] Open
Abstract
A novel quadruplex ligand based on 1,10-phenanthroline and incorporating two guanyl hydrazone functionalities, PhenQE8, is reported herein. Synthetic access was gained in a two-step procedure with an overall yield of 61%. X-ray diffraction studies revealed that PhenQE8 can adopt an extended conformation that may be optimal to favor recognition of quadruplex DNA. DNA interactions with polymorphic G-quadruplex telomeric structures were studied by different techniques, such as Fluorescence resonance energy transfer (FRET) DNA melting assays, circular dichroism and equilibrium dialysis. Our results reveal that the novel ligand PhenQE8 can efficiently recognize the hybrid quadruplex structures of the human telomeric DNA, with high binding affinity and quadruplex/duplex selectivity. Moreover, the compound shows significant cytotoxic activity against a selected panel of cultured tumor cells (PC-3, HeLa and MCF-7), whereas its cytotoxicity is considerably lower in healthy human cells (HFF-1 and RPWE-1).
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Affiliation(s)
| | | | | | - Zoila Gándara
- Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; (P.B.G.); (J.G.Q.); (A.P.-R.)
| | - Lourdes Gude
- Departamento de Química Orgánica y Química Inorgánica, Instituto de Investigación Química “Andrés M. del Río” (IQAR), Universidad de Alcalá, 28805 Alcalá de Henares, Madrid, Spain; (P.B.G.); (J.G.Q.); (A.P.-R.)
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3
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Chalikian TV, Liu L, Macgregor RB. Duplex-tetraplex equilibria in guanine- and cytosine-rich DNA. Biophys Chem 2020; 267:106473. [PMID: 33031980 DOI: 10.1016/j.bpc.2020.106473] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2020] [Accepted: 09/03/2020] [Indexed: 02/07/2023]
Abstract
Noncanonical four-stranded DNA structures, including G-quadruplexes and i-motifs, have been discovered in the cell and are implicated in a variety of genomic regulatory functions. The tendency of a specific guanine- and cytosine-rich region of genomic DNA to adopt a four-stranded conformation depends on its ability to overcome the constraints of duplex base-pairing by undergoing consecutive duplex-to-coil and coil-to-tetraplex transitions. The latter ability is determined by the balance between the free energies of participating ordered and disordered structures. In this review, we present an overview of the literature on the stability of G-quadruplex and i-motif structures and discuss the extent of duplex-tetraplex competition as a function of the sequence context of the DNA and environmental conditions including temperature, pH, salt, molecular crowding, and the presence of G-quadruplex-binding ligands. We outline how the results of in vitro studies can be expanded to understanding duplex-tetraplex equilibria in vivo.
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Affiliation(s)
- Tigran V Chalikian
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada.
| | - Lutan Liu
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences, Leslie Dan Faculty of Pharmacy, University of Toronto, 144 College Street, Toronto, Ontario M5S 3M2, Canada
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4
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Wang BL, Jiang C. DNA G-Quadruplexes as a Template To Direct Cyanine Dyes To Form H-Aggregates and Application of the Self-Assembly Entity as a New G-Quadruplexes Ligands Screening Platform. Anal Chem 2019; 91:1541-1547. [DOI: 10.1021/acs.analchem.8b04677] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Bo-Lin Wang
- College of Chemistry, Sichuan University, No. 29 Wangjiang Road, Chengdu 610064, China
| | - Chuang Jiang
- College of Chemistry, Sichuan University, No. 29 Wangjiang Road, Chengdu 610064, China
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5
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Wang Z, Li J, Liu JP. Effects of cation charges on the binding of stabilizers with human telomere and TERRA G-quadruplexes. J Biomol Struct Dyn 2018; 37:1908-1921. [DOI: 10.1080/07391102.2018.1471416] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Zhiguo Wang
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University , Hangzhou, Zhejiang 311121, China
| | - Jianfeng Li
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University , Hangzhou, Zhejiang 311121, China
| | - Jun-Ping Liu
- Institute of Ageing Research, School of Medicine, Hangzhou Normal University , Hangzhou, Zhejiang 311121, China
- Department of Immunology, Central Eastern Clinical School, Monash University , Melbourne, Vitoria 3004, Australia
- Hudson Institute of Medical Research , Clayton, Victoria 3168, Australia
- Department of Molecular and Translational Science, Monash University , Clayton, Victoria 3168, Australia
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6
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Paul S, Samanta A. Ground- and Excited-State Interactions of a Psoralen Derivative with Human Telomeric G-Quadruplex DNA. J Phys Chem B 2018; 122:2277-2286. [PMID: 29376354 DOI: 10.1021/acs.jpcb.7b12475] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
G-quadruplex DNA has been a recent target for anticancer agents, and its binding interactions with small molecules, often used as anticancer drugs, have become an important area of research. Considering that psoralens have long been studied in the context of duplex DNA but that very little is known about their potential as G-quadruplex binders and their excited-state interaction with the latter has not been explored, we have studied herein the binding of a planar water-soluble psoralen derivative, 4'-aminomethyl-4,5',8-trimethylpsoralen (AMT), with the 22-mer human telomeric G-quadruplex-forming sequence, AGGG(TTAGGG)3, labeled here as (hTel22), and investigated the consequences of photoexcitation of AMT by calorimetric and spectroscopic techniques. The results show an enthalpy-driven 1:1 binding of AMT with hTel22 via end-stacking mode. Fluorescence quenching experiments on 6-fluorescein amidite-labeled oligomers indicate that the binding site is nearer to the 3' end of hTel22 in the diagonal loop region. Femtosecond time-resolved transient absorption measurements indicate electron transfer from the guanine moiety of hTel22 to photoexcited AMT, leading to the formation of a radical pair species (AMT•-G•+), which survives for 30 ps and is favored by a parallel/quasi-parallel orientation between the two. The findings reveal psoralens as a prospective class of compounds for the development of anticancer therapeutics by targeting the G-quadruplex DNA.
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Affiliation(s)
- Sneha Paul
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
| | - Anunay Samanta
- School of Chemistry, University of Hyderabad , Hyderabad 500046, India
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7
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Lee W, Matsika S. Conformational and electronic effects on the formation of anti cyclobutane pyrimidine dimers in G-quadruplex structures. Phys Chem Chem Phys 2018; 19:3325-3336. [PMID: 28091673 DOI: 10.1039/c6cp05604k] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cyclobutane pyrimidine dimers (CPDs) are the most commonly formed photochemical products when nucleic acids interact with UV radiation. In duplex DNA, the relative inflexible structure allows for only the cis, syn CPD isomer to be formed. G-quadruplex structures, however, have loops that are more flexible and allow for different orientations of the bases to interact. As a result, the highly unusual formation of an anti CPD has been observed in these structures. Due to the close proximity between two opposing loops containing the TTA sequence in two G-quadruplex structures (called "form-3" and "basket"), a high yield of anti CPD formation was expected in these structures. However, while significant yields of anti CPDs are observed in form-3, the anti CPD is hardly observed in the basket structure. To account for this inconsistency, we examine the process of anti CPD formation in form-3 and basket structures using simulations at the atomistic level. Here, we consider the conformational effect using MD simulations, which show whether the formation of the anti CPD is structurally feasible. Quantum mechanical/molecular mechanical (QM/MM) calculations of excited states are also used to consider the electronic effect by an adjacent guanine base which can quench the formation of the anti CPD through charge transfer (CT). Our results are in qualitative agreement with the experimental results, predicting a significant yield of the anti CPD in the form-3 structure and a negligible yield in the basket structure, while they also predict the formation of the cis, syn CPD between two opposing loops in form-3. Most importantly, our simulation results show that the yields of the anti CPD in the G-quadruplex are affected significantly by both conformational and electronic effects.
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Affiliation(s)
- Wook Lee
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
| | - Spiridoula Matsika
- Department of Chemistry, Temple University, Philadelphia, PA 19122, USA.
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8
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Papi F, Bazzicalupi C, Ferraroni M, Massai L, Bertrand B, Gratteri P, Colangelo D, Messori L. [Au(9-methylcaffein-8-ylidene)2
]+
/DNA Tel23 System: Solution, Computational, and Biological Studies. Chemistry 2017; 23:13784-13791. [DOI: 10.1002/chem.201702854] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Indexed: 12/16/2022]
Affiliation(s)
- Francesco Papi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI Italy
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco, Salute del Bambino (NEUROFARBA); Laboratory of Molecular Modeling Cheminformatics & QSAR; Università degli Studi di Firenze; Via Ugo Schiff 6 50019 Sesto Fiorentino (FI Italy
| | - Carla Bazzicalupi
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI Italy
| | - Marta Ferraroni
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI Italy
| | - Lara Massai
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI Italy
| | | | - Paola Gratteri
- Dipartimento di Neuroscienze, Psicologia, Area del Farmaco, Salute del Bambino (NEUROFARBA); Laboratory of Molecular Modeling Cheminformatics & QSAR; Università degli Studi di Firenze; Via Ugo Schiff 6 50019 Sesto Fiorentino (FI Italy
| | - Donato Colangelo
- Dipartimento di Scienze della Salute; Università del Piemonte Orientale ‘A. Avogadro'; Via Solaroli 17 28100 Novara Italy
| | - Luigi Messori
- Dipartimento di Chimica “Ugo Schiff”; Università degli Studi di Firenze; Via della Lastruccia 3 50019 Sesto Fiorentino (FI Italy
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9
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Dehez F, Gattuso H, Bignon E, Morell C, Dumont E, Monari A. Conformational polymorphism or structural invariance in DNA photoinduced lesions: implications for repair rates. Nucleic Acids Res 2017; 45:3654-3662. [PMID: 28334906 PMCID: PMC5397166 DOI: 10.1093/nar/gkx148] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2016] [Accepted: 02/21/2017] [Indexed: 02/01/2023] Open
Abstract
DNA photolesions constitute a particularly deleterious class of molecular defects responsible for the insurgence of a vast majority of skin malignant tumors. Dimerization of two adjacent thymines or cytosines mostly gives rise to cyclobutane pyrimidine dimers (CPD) and pyrimidine(6-4)pyrimidone 64-PP as the most common defects. We perform all-atom classical simulations, up to 2 μs, of CPD and 64-PP embedded in a 16-bp duplex, which reveal the constrasted behavior of the two lesions. In particular we evidence a very limited structural deformation induced by CPD while 64-PP is characterized by a complex structural polymorphism. Our simulations also allow to unify the contrasting experimental structural results obtained by nuclear magnetic resonance or Förster Resonant Energy Transfer method, showing that both low and high bent structures are indeed accessible. These contrasting behaviors can also explain repair resistance or the different replication obstruction, and hence the genotoxicity of these two photolesions.
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Affiliation(s)
- François Dehez
- CNRS, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Université de Lorraine, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Laboratoire International Associé Centre National de la Recherche Scientifique et University of Illinois at Urbana Champaign
| | - Hugo Gattuso
- CNRS, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Université de Lorraine, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France
| | - Emmanuelle Bignon
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, ENS Lyon, Lyon, France.,Université de Lyon, ENS de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F69342 Lyon, France
| | - Christophe Morell
- Institut des Sciences Analytiques, UMR 5280, Université de Lyon1 (UCBL) CNRS, ENS Lyon, Lyon, France
| | - Elise Dumont
- Université de Lyon, ENS de Lyon, CNRS, Université Lyon 1, Laboratoire de Chimie UMR 5182, F69342 Lyon, France
| | - Antonio Monari
- CNRS, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France.,Université de Lorraine, Theory-Modeling-Simulation, SRSMC F-54506 Vandoeuvre-lès-Nancy, France
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10
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Dolinnaya NG, Ogloblina AM, Yakubovskaya MG. Structure, Properties, and Biological Relevance of the DNA and RNA G-Quadruplexes: Overview 50 Years after Their Discovery. BIOCHEMISTRY (MOSCOW) 2017; 81:1602-1649. [PMID: 28260487 PMCID: PMC7087716 DOI: 10.1134/s0006297916130034] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
G-quadruplexes (G4s), which are known to have important roles in regulation of key biological processes in both normal and pathological cells, are the most actively studied non-canonical structures of nucleic acids. In this review, we summarize the results of studies published in recent years that change significantly scientific views on various aspects of our understanding of quadruplexes. Modern notions on the polymorphism of DNA quadruplexes, on factors affecting thermodynamics and kinetics of G4 folding–unfolding, on structural organization of multiquadruplex systems, and on conformational features of RNA G4s and hybrid DNA–RNA G4s are discussed. Here we report the data on location of G4 sequence motifs in the genomes of eukaryotes, bacteria, and viruses, characterize G4-specific small-molecule ligands and proteins, as well as the mechanisms of their interactions with quadruplexes. New information on the structure and stability of G4s in telomeric DNA and oncogene promoters is discussed as well as proof being provided on the occurrence of G-quadruplexes in cells. Prominence is given to novel experimental techniques (single molecule manipulations, optical and magnetic tweezers, original chemical approaches, G4 detection in situ, in-cell NMR spectroscopy) that facilitate breakthroughs in the investigation of the structure and functions of G-quadruplexes.
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Affiliation(s)
- N G Dolinnaya
- Lomonosov Moscow State University, Department of Chemistry, Moscow, 119991, Russia.
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11
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Li YY, Macgregor RB. A Thermodynamic Study of Adenine and Thymine Substitutions in the Loops of the Oligodeoxyribonucleotide HTel. J Phys Chem B 2016; 120:8830-6. [PMID: 27487080 DOI: 10.1021/acs.jpcb.6b05601] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Guanine-rich DNA oligodeoxyribonucleotides (ODN) can form four-stranded structures named quadruplexes (G4s), which are stabilized via the association of four guanine bases. Quadruplexes have a high level of conformational diversity depending on the molecularity, sequence, and the cation conditions of the G4 formation. Monomolecular G4 structures have nonguanine loops that usually consist of between one and four adenine and thymine residues. In the work reported here, we systematically modified the nucleotides in the loops of the 22 nucleotide ODN, HTel, which contains four repeats of the human telomeric sequence, GGGTTA. We studied the effect of different types of bases in the loops on the stability and topology of the G4s formed. We show that lower steric hindrance of pyrimidine residues increases the stability of G4s with a major enthalpic contribution. Stacking of the loop bases onto tetrads could compensate for the loss of rotational freedom. In addition, in the presence of sodium, the stabilities of the G4s are loop dependent. In the presence of potassium, the stability of G4 depend on the sequences of each loop. Lastly, in the presence of potassium ions, the modified HTel ODNs may exist in equilibrium of the two types of the hybrid topology, and these structures are stabilized by the second loop. Modifications of the bases in this loop change the topology and stability of the folded structures.
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Affiliation(s)
- Yang Yun Li
- Department of Pharmaceutical Sciences University of Toronto , 144 College Street, Toronto, Ontario M5S 3M2, Canada
| | - Robert B Macgregor
- Department of Pharmaceutical Sciences University of Toronto , 144 College Street, Toronto, Ontario M5S 3M2, Canada
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12
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Largy E, Mergny JL, Gabelica V. Role of Alkali Metal Ions in G-Quadruplex Nucleic Acid Structure and Stability. Met Ions Life Sci 2016; 16:203-58. [PMID: 26860303 DOI: 10.1007/978-3-319-21756-7_7] [Citation(s) in RCA: 104] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
G-quadruplexes are guanine-rich nucleic acids that fold by forming successive quartets of guanines (the G-tetrads), stabilized by intra-quartet hydrogen bonds, inter-quartet stacking, and cation coordination. This specific although highly polymorphic type of secondary structure deviates significantly from the classical B-DNA duplex. G-quadruplexes are detectable in human cells and are strongly suspected to be involved in a number of biological processes at the DNA and RNA levels. The vast structural polymorphism exhibited by G-quadruplexes, together with their putative biological relevance, makes them attractive therapeutic targets compared to canonical duplex DNA. This chapter focuses on the essential and specific coordination of alkali metal cations by G-quadruplex nucleic acids, and most notably on studies highlighting cation-dependent dissimilarities in their stability, structure, formation, and interconversion. Section 1 surveys G-quadruplex structures and their interactions with alkali metal ions while Section 2 presents analytical methods used to study G-quadruplexes. The influence of alkali cations on the stability, structure, and kinetics of formation of G-quadruplex structures of quadruplexes will be discussed in Sections 3 and 4. Section 5 focuses on the cation-induced interconversion of G-quadruplex structures. In Sections 3 to 5, we will particularly emphasize the comparisons between cations, most often K(+) and Na(+) because of their prevalence in the literature and in cells.
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Affiliation(s)
- Eric Largy
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France.,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France
| | - Jean-Louis Mergny
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
| | - Valérie Gabelica
- ARNA Laboratory, Université Bordeaux, IECB, 2, rue Robert Escarpit, F-33600, Pessac, France. .,ARNA Laboratory, INSERM, U869, F-33000, Bordeaux, France.
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13
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Ogloblina AM, Bannikova VA, Khristich AN, Oretskaya TS, Yakubovskaya MG, Dolinnaya NG. Parallel G-quadruplexes formed by guanine-rich microsatellite repeats inhibit human topoisomerase I. BIOCHEMISTRY (MOSCOW) 2015; 80:1026-38. [DOI: 10.1134/s0006297915080088] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Wang Z, Chen R, Hou L, Li J, Liu JP. Molecular dynamics and principal components of potassium binding with human telomeric intra-molecular G-quadruplex. Protein Cell 2015; 6:423-33. [PMID: 25894091 PMCID: PMC4444812 DOI: 10.1007/s13238-015-0155-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2015] [Accepted: 03/10/2015] [Indexed: 11/29/2022] Open
Abstract
Telomere assumes intra-molecular G-quadruplex that is a significant drug target for inhibiting telomerase maintenance of telomeres in cancer. Metal cations have been recognized as playing important roles in stabilizing G-quadruplex, but their binding processes to human telomeric G-quadruplex remain uncharacterized. To investigate the detailed binding procedures, molecular dynamics simulations were conducted on the hybrid [3 + 1] form-one human telomeric intra-molecular G-quadruplex. We show here that the binding of a potassium ion to a G-tetrad core is mediated by two alternative pathways. Principal component analysis illustrated the dominant concerted motions of G-quadruplex occurred at the loop domains. MM-PBSA calculations revealed that binding was energetically favorable and driven by the electrostatic interactions. The lower binding site was found more constructive favorable for binding. Our data provide useful information on a potassium-mediated stable structure of human telomeric intra-molecular G-quadruplex, implicating in ion disorder associated conformational changes and targeted drug design.
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Affiliation(s)
- Zhiguo Wang
- Institute of Aging Research, School of Medicine, Hangzhou Normal University, Hangzhou, 311121, China,
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15
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Salgado GF, Cazenave C, Kerkour A, Mergny JL. G-quadruplex DNA and ligand interaction in living cells using NMR spectroscopy. Chem Sci 2015; 6:3314-3320. [PMID: 28706695 PMCID: PMC5490339 DOI: 10.1039/c4sc03853c] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2014] [Accepted: 01/13/2015] [Indexed: 12/31/2022] Open
Abstract
Using in-cell NMR spectroscopy to probe ligand binding to a G-quadruplex nucleic acid.
Gathering structural information from biologically relevant molecules inside living cells has always been a challenging task. In this work, we have used multidimensional NMR spectroscopy to probe DNA G-quadruplexes inside living Xenopus laevis oocytes. Some of these structures can be found in key regions of chromosomes. G-quadruplexes are considered potential anticancer therapeutic targets and several lines of evidence indirectly point out roles in key biological processes, such as cell proliferation, genomic instability or replication initiation. However, direct demonstrations of the existence of G-quadruplexes in vivo are scarce. Using SOFAST-HMQC type spectra, we probed a tetramolecular G-quadruplex model made of d(TG4T)4 inside living Xenopus laevis oocytes. Our observations lead us to conclude that the quadruplex structure is formed within the cell and that the intracellular environment preferentially selects a conformation that most resembles the one found in vitro under KCl conditions. We also show for the first time that specific ligands targeting G-quadruplexes can be studied using high resolution NMR directly inside living cells, opening new avenues to study ligand binding discrimination under physiologically relevant conditions with atomic detail.
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Affiliation(s)
- Gilmar F Salgado
- Univ. Bordeaux , ARNA Laboratory , F-33000 Bordeaux , France . .,INSERM , U869 , IECB , F-33600 Pessac , France
| | - Christian Cazenave
- CNRS , Microbiologie Fondamentale et Pathogénicité , UMR 5234 , F-33000 Bordeaux , France.,Univ. Bordeaux , Microbiologie Fondamentale et Pathogénicité , UMR 5234 , F-33000 Bordeaux , France
| | - Abdelaziz Kerkour
- Univ. Bordeaux , ARNA Laboratory , F-33000 Bordeaux , France . .,INSERM , U869 , IECB , F-33600 Pessac , France
| | - Jean-Louis Mergny
- Univ. Bordeaux , ARNA Laboratory , F-33000 Bordeaux , France . .,INSERM , U869 , IECB , F-33600 Pessac , France
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16
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Bonnet R, Lavergne T, Gennaro B, Spinelli N, Defrancq E. Construction of anti-parallel G-quadruplexes through sequential templated click. Chem Commun (Camb) 2015; 51:4850-3. [DOI: 10.1039/c4cc09744k] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Biologically relevant anti-parallel DNA G-quadruplexes were constrained and stabilised onto addressable cyclopeptide scaffolds through sequential oxime and CuAAc reactions.
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Affiliation(s)
- Romaric Bonnet
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Thomas Lavergne
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Béatrice Gennaro
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Nicolas Spinelli
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
| | - Eric Defrancq
- Université Grenoble Alpes
- Département de Chimie Moléculaire
- F-38000 Grenoble
- France
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17
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Liu L, Shao Y, Peng J, Huang C, Liu H, Zhang L. Molecular Rotor-Based Fluorescent Probe for Selective Recognition of Hybrid G-Quadruplex and as a K+ Sensor. Anal Chem 2014; 86:1622-31. [DOI: 10.1021/ac403326m] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Lingling Liu
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Yong Shao
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Jian Peng
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Chaobiao Huang
- Department
of Chemistry, College of Chemistry and Life Sciences, Zhejiang Normal University, Jinhua 321004, People’s Republic of China
| | - Hua Liu
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
| | - Lihua Zhang
- Institute of Physical
Chemistry, Zhejiang Normal University, Jinhua 321004, Zhejiang, People’s Republic of China
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18
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Monaselidze J, Gorgoshidze M, Khachidze D, Kiladze M, Bregadze V, Kiziria E, Margaryan H, Hakobyan N. Conformations of DNA in the presence of nanomole concentrations of Co+2ions and mezo-tetra(4-N-oxyethylpiridil) porphyrin. J Biomol Struct Dyn 2014; 33:267-73. [DOI: 10.1080/07391102.2013.873001] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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19
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Lim KW, Ng VCM, Martín-Pintado N, Heddi B, Phan AT. Structure of the human telomere in Na+ solution: an antiparallel (2+2) G-quadruplex scaffold reveals additional diversity. Nucleic Acids Res 2013; 41:10556-62. [PMID: 23999095 PMCID: PMC3905899 DOI: 10.1093/nar/gkt771] [Citation(s) in RCA: 106] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Single-stranded DNA overhangs at the ends of human telomeric repeats are capable of adopting four-stranded G-quadruplex structures, which could serve as potential anticancer targets. Out of the five reported intramolecular human telomeric G-quadruplex structures, four were formed in the presence of K+ ions and only one in the presence of Na+ ions, leading often to a perception that this structural polymorphism occurs exclusively in the presence of K+ but not Na+. Here we present the structure of a new antiparallel (2+2) G-quadruplex formed by a derivative of a 27-nt human telomeric sequence in Na+ solution, which comprises a novel core arrangement distinct from the known topologies. This structure complements the previously elucidated basket-type human telomeric G-quadruplex to serve as reference structures in Na+-containing environment. These structures, together with the coexistence of other conformations in Na+ solution as observed by nuclear magnetic resonance spectroscopy, establish the polymorphic nature of human telomeric repeats beyond the influence of K+ ions.
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Affiliation(s)
- Kah Wai Lim
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Veronica Chinn Min Ng
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Nerea Martín-Pintado
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Brahim Heddi
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
| | - Anh Tuân Phan
- School of Physical and Mathematical Sciences, Nanyang Technological University, 637371 Singapore, School of Biological Sciences, Nanyang Technological University, 637551 Singapore and Instituto de Química Física Rocasolano, CSIC, 28006 Madrid, Spain
- *To whom correspondence should be addressed. Tel: +65 6514 1915; Fax: +65 6795 7981;
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20
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Marušič M, Veedu RN, Wengel J, Plavec J. G-rich VEGF aptamer with locked and unlocked nucleic acid modifications exhibits a unique G-quadruplex fold. Nucleic Acids Res 2013; 41:9524-36. [PMID: 23935071 PMCID: PMC3814366 DOI: 10.1093/nar/gkt697] [Citation(s) in RCA: 63] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
Abstract
The formation of a single G-quadruplex structure adopted by a promising 25 nt G-rich vascular endothelial growth factor aptamer in a K+ rich environment was facilitated by locked nucleic acid modifications. An unprecedented all parallel-stranded monomeric G-quadruplex with three G-quartet planes exhibits several unique structural features. Five consecutive guanine residues are all involved in G-quartet formation and occupy positions in adjacent DNA strands, which are bridged with a no-residue propeller-type loop. A two-residue D-shaped loop facilitates inclusion of an isolated guanine residue into the vacant spot within the G-quartet. The remaining two G-rich tracts of three residues each adopt parallel orientation and are linked with edgewise and propeller loops. Both 5′ with 3 nt and 3′ with 4 nt overhangs display well-defined conformations, with latter adopting a basket handle topology. Locked residues contribute to thermal stabilization of the adopted structure and formation of structurally pre-organized intermediates that facilitate folding into a single G-quadruplex. Understanding the impact of chemical modifications on folding, thermal stability and structural polymorphism of G-quadruplexes provides means for the improvement of vascular endothelial growth factor aptamers and advances our insights into driving nucleic acid structure by locking or unlocking the conformation of sugar moieties of nucleotides in general.
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Affiliation(s)
- Maja Marušič
- Slovenian NMR Center, National Institute of Chemistry, Hajdrihova 19, SI-1000 Ljubljana, Slovenia, School of Chemistry & Molecular Biosciences, University of Queensland, St Lucia, Brisbane, 4072 Australia, Nucleic Acid Center, Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, 5230 Odense M, Denmark, EN-FIST Center of Excellence, SI-1000 Ljubljana, Slovenia and Faculty of Chemistry and Chemical Technology, University of Ljubljana, SI-1000 Ljubljana, Slovenia
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21
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Buscaglia R, Miller MC, Dean WL, Gray RD, Lane AN, Trent JO, Chaires JB. Polyethylene glycol binding alters human telomere G-quadruplex structure by conformational selection. Nucleic Acids Res 2013; 41:7934-46. [PMID: 23804761 PMCID: PMC3763525 DOI: 10.1093/nar/gkt440] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Polyethylene glycols (PEGs) are widely used to perturb the conformations of nucleic acids, including G-quadruplexes. The mechanism by which PEG alters G-quadruplex conformation is poorly understood. We describe here studies designed to determine how PEG and other co-solutes affect the conformation of the human telomeric quadruplex. Osmotic stress studies using acetonitrile and ethylene glycol show that conversion of the ‘hybrid’ conformation to an all-parallel ‘propeller’ conformation is accompanied by the release of about 17 water molecules per quadruplex and is energetically unfavorable in pure aqueous solutions. Sedimentation velocity experiments show that the propeller form is hydrodynamically larger than hybrid forms, ruling out a crowding mechanism for the conversion by PEG. PEGs do not alter water activity sufficiently to perturb quadruplex hydration by osmotic stress. PEG titration experiments are most consistent with a conformational selection mechanism in which PEG binds more strongly to the propeller conformation, and binding is coupled to the conformational transition between forms. Molecular dynamics simulations show that PEG binding to the propeller form is sterically feasible and energetically favorable. We conclude that PEG does not act by crowding and is a poor mimic of the intranuclear environment, keeping open the question of the physiologically relevant quadruplex conformation.
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Affiliation(s)
- Robert Buscaglia
- James Graham Brown Cancer Center, University of Louisville, 505 S. Hancock, Louisville, KY, 40202
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22
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Larsen AF, Nielsen MC, Ulven T. Tetrasubstituted Phenanthrolines as Highly Potent, Water-Soluble, and Selective G-Quadruplex Ligands. Chemistry 2012; 18:10892-902. [DOI: 10.1002/chem.201200081] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2012] [Revised: 04/29/2012] [Indexed: 11/11/2022]
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23
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Wang SR, Zhang D, Luo FL, Liu L, Weng XC, Huang J, Li GR, Zhang XL, Zhou X. Some cationic porphyrins: synthesis, stabilization of G-quadruplexes, and down-regulation of c-myc in Hep G2 cells. J PORPHYR PHTHALOCYA 2012. [DOI: 10.1142/s1088424609001121] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The stabilization of G-quadruplex DNA represents an attractive strategy for the design and development of novel antitumor drugs. In the present work, we have designed and synthesized nine cationic porphyrins, each with four side arms at their meso positions. The interactions of these porphyrins with both human telomeric DNA and NHE III1 G-quadruplexes were measured by various DNA binding assays, including polymerase stop assay, circular dichroism (CD) and CD melting assay. We then proceeded to investigate their effects on the expression of c-myc oncogene in the Hep G2 cell line. The experimental results indicate that these porphyrins are capable of effectively inducing or stabilizing both human telomeric and NHE III1 G-quadruplexes in the presence or absence of metal ions. Furthermore, we have discovered that porphyrins with a stronger stabilizing effect on c-myc G-quadruplexes lead to more pronounced down-regulation of the c-myc oncogene in the Hep G2 cell line.
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Affiliation(s)
- Shao R. Wang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Dan Zhang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Feng L. Luo
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, P.R. China
| | - Lin Liu
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Xiao C. Weng
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Jing Huang
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Guo R. Li
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
| | - Xiao L. Zhang
- State Key Laboratory of Virology, Department of Immunology, Hubei Province Key Laboratory of Allergy and Immunology, Wuhan University School of Medicine, Wuhan 430071, P.R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences, Wuhan University, Hubei, Wuhan 430072, P.R. China
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24
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Xu L, Xu Z, Shang Y, Feng S, Zhou X. Structural polymorphism of human telomere G-quadruplex induced by a pyridyl carboxamide molecule. Bioorg Med Chem Lett 2012; 22:2988-92. [DOI: 10.1016/j.bmcl.2012.02.030] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/09/2012] [Accepted: 02/13/2012] [Indexed: 01/02/2023]
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25
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Wu J, Fu Y, He Z, Han Y, Zheng L, Zhang J, Li W. Growth mechanisms of fluorescent silver clusters regulated by polymorphic DNA templates: a DFT study. J Phys Chem B 2012; 116:1655-65. [PMID: 22242908 DOI: 10.1021/jp206251v] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
The aggregation behaviors of silver atoms modulated by polymorphic DNA templates involving i-motif, G-quadruplex, and the Watson-Crick duplex, were investigated by using the density functional theory (DFT) calculations, combining with the experimental characterizations of CD, UV, fluorescence measurements and TEM, in order to understand the reason in the molecular level that polymorphic DNA templates affect the fluorescence emitting species of Ag nanomaterials. First, the affinity sites of silver ions on different DNA templates were analyzed by using DFT calculations, and the conformational variations of DNA templates caused by silver ions and atoms were disclosed. Second, the aggregation behaviors of silver atoms constrained by the polymorphic DNA templates were studied by DFT modeling, and distinct fluorescence property of nanosilvers templated by polymorphic DNA were evaluated using the time-dependent DFT calculations. It is illustrated that with the DNA template adopting i-motif or the duplex the silver atoms tend to aggregate inside the encapsulated spaces of nucleobases, and the formed silver nanoclusters are positively charged with high fluorescent spectral features; whereas with the template of the G-quadruplex the silver atoms are preferential to aggregate outside of the G-tetrad, which results in the formation of larger silver crystals without fluorescence property. The results obtained here are useful to explore the nucleation and growth mechanism of silver nanomaterials regulated by the structure-specific DNA templates, which is important to rational design of desirable fluorescent emitters for sensing in the field from biology to nanoscience.
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Affiliation(s)
- Jiangjiexing Wu
- Key Laboratory for Green Chemical Technology MOE, Tianjin University, Tianjin 300072, People's Republic of China
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26
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Sun H, Xiang J, Li Q, Liu Y, Li L, Shang Q, Xu G, Tang Y. Recognize three different human telomeric G-quadruplex conformations by quinacrine. Analyst 2012; 137:862-7. [PMID: 22223064 DOI: 10.1039/c2an15870a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Recognition of different human telomeric G-quadruplex structures has been a very important task for developing anti-cancer drug design. However, it also is a very challenging question since multiple conformational isomers of telomeric G-quadruplexes coexist under some conditions. Here, three different conformations including parallel, antiparallel, and mixed-type telomeric G-quadruplex structures have been well recognized by quinacrine (QNA) through monitoring its absorption, fluorescence, and fluorescence lifetime spectra. The multiple structures of H22 G-quadruplexes under physiological K(+) conditions could also be easily determined to coexist as mixed-type and antiparallel G-quadruplexes. The recognition mechanism based on the different binding affinity and binding sites has been further elucidated by association with the nuclear magnetic resonance (NMR) results.
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Affiliation(s)
- Hongxia Sun
- National Laboratory for Molecular Sciences, Center for Molecular Sciences, Institute of Chemistry Chinese Academy of Sciences, Beijing, 100190, PR China
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27
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Abstract
G-quadruplex ligands are potential anticancer agents as telomerase inhibitors and potential transcriptional regulators of oncogenes. The search for best-in-class drugs is addressed to identify small molecules able to promote and stabilize G-quadruplex structures. What features should the G-quadruplex ligands possess? They should have selective antiproliferative effects on cancer cells and induce telomerase inhibition or oncogene suppression. One of the main challenges in their design and synthesis is to make the ligands selective for G-quadruplex DNA. These features should be amplified by careful analyses of physico-chemical aspects of G-quadruplex-drug interactions. In particular, the study of the energetics of G-quadruplex-drug interactions can enhance drug design by providing thermodynamic parameters that give quantitative information on the biomolecular interactions important for binding. The main methodologies used to gain information on energetics of binding are based on spectroscopic or calorimetric principles. Spectroscopic techniques such as fluorescence and circular dichroism are rapid and cheap methods, but are not sufficient to characterize completely the thermodynamics of interaction. Calorimetric techniques such as isothermal titration calorimetry offer a direct measure of binding enthalpy, in addition to the stoichiometry and affinity constants. With the complete thermodynamic signature of drug-target interaction, dissecting the enthalpic and entropic components of binding is possible, which can be a useful aid to decision-making during drug optimization.
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Affiliation(s)
- Concetta Giancola
- Dipartimento di Scienze Chimiche, Università degli Studi di Napoli "Federico II", Via Cintia, 80126, Napoli, Italy,
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28
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Monaselidze J, Kiziria E, Gorgoshidze M, Khachidze D, Kiladze M, Lomidze E, Margaryan H, Hakobyan N. CD and DSC Investigation of Individual and Complex Influence of Meso-Tetra(4-Oxiethylpyridil) Porphyrin (TOEPyP4) and Its Zn-Complex on DNA. ACTA ACUST UNITED AC 2012. [DOI: 10.4236/ajac.2012.310092] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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29
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Dhamodharan V, Harikrishna S, Jagadeeswaran C, Halder K, Pradeepkumar PI. Selective G-quadruplex DNA Stabilizing Agents Based on Bisquinolinium and Bispyridinium Derivatives of 1,8-Naphthyridine. J Org Chem 2011; 77:229-42. [DOI: 10.1021/jo201816g] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- V. Dhamodharan
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - S. Harikrishna
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - C. Jagadeeswaran
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - K. Halder
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
| | - P. I. Pradeepkumar
- Department
of Chemistry, Indian Institute of Technology Bombay, Mumbai 400076, India
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30
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Cang X, Šponer J, Cheatham TE. Insight into G-DNA structural polymorphism and folding from sequence and loop connectivity through free energy analysis. J Am Chem Soc 2011; 133:14270-9. [PMID: 21761922 PMCID: PMC3168932 DOI: 10.1021/ja107805r] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
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The lengths of G-tracts and their connecting loop sequences determine G-quadruplex folding and stability. Complete understanding of the sequence–structure relationships remains elusive. Here, single-loop G-quadruplexes were investigated using explicit solvent molecular dynamics (MD) simulations to characterize the effect of loop length, loop sequence, and G-tract length on the folding topologies and stability of G-quadruplexes. Eight loop types, including different variants of lateral, diagonal, and propeller loops, and six different loop sequences [d0 (i.e., no intervening residues in the loop), dT, dT2, dT3, dTTA, and dT4] were considered through MD simulation and free energy analysis. In most cases the free energetic estimates agree well with the experimental observations. The work also provides new insight into G-quadruplex folding and stability. This includes reporting the observed instability of the left propeller loop, which extends the rules for G-quadruplex folding. We also suggest a plausible explanation why human telomere sequences predominantly form hybrid-I and hybrid-II type structures in K+ solution. Overall, our calculation results indicate that short loops generally are less stable than longer loops, and we hypothesize that the extreme stability of sequences with very short loops could possibly derive from the formation of parallel multimers. The results suggest that free energy differences, estimated from MD and free energy analysis with current force fields and simulation protocols, are able to complement experiment and to help dissect and explain loop sequence, loop length, and G-tract length and orientation influences on G-quadruplex structure.
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Affiliation(s)
- Xiaohui Cang
- Department of Medicinal Chemistry, College of Pharmacy, Skaggs Hall 201, University of Utah, Salt Lake City, Utah 84112, USA
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31
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Xing X, Wang X, Wang X, Xu L, Tai Y, Dai L, Zheng X, Mao W, Xu X, Zhou X. Light-driven conformational regulation of human telomeric G-quadruplex DNA in physiological conditions. Org Biomol Chem 2011; 9:6639-45. [PMID: 21850352 DOI: 10.1039/c1ob05939d] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Human telomeric G-quadruplexes have raised broad interest not just due to their involvement in the regulation of gene expressions and telomerase activities but also because of their application in nanoarchitectures. Herein, three azobenzene derivatives 1-3 were synthesized with different substituent groups and their photo-isomerization properties were investigated by UV/Vis spectroscopy. Then circular dichroism spectroscopy (CD), fluorescence experiments and native-gel electrophoresis were performed to evaluate their capabilities of conformational photo-regulation both in the absence and presence of metal ions. The results suggested that the compounds synthesized can successfully regulate the conformation of human telomeric G-quadruplex DNA in K(+) conditions to some extent. This work will initiate the possibility for the design and intriguing application of light-induced switching to photoregulate the conformation of G-quadruplex DNA under physiological conditions, providing a possible pathway to control G-quadruplex conformation in biological applications and also expanding the potential use of G-quadruplexes in nanomachines.
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Affiliation(s)
- Xiwen Xing
- College of Chemistry and Molecular Sciences, Key Laboratory of Biomedical Polymers of Ministry of Education, Wuhan University, Hubei, Wuhan 430072, PR China
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32
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Xue Y, Liu JQ, Zheng KW, Kan ZY, Hao YH, Tan Z. Kinetic and Thermodynamic Control of G-Quadruplex Folding. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201101759] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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33
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Xue Y, Liu JQ, Zheng KW, Kan ZY, Hao YH, Tan Z. Kinetic and Thermodynamic Control of G-Quadruplex Folding. Angew Chem Int Ed Engl 2011; 50:8046-50. [DOI: 10.1002/anie.201101759] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2011] [Revised: 05/30/2011] [Indexed: 12/18/2022]
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34
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Yue DJE, Lim KW, Phan AT. Formation of (3+1) G-quadruplexes with a long loop by human telomeric DNA spanning five or more repeats. J Am Chem Soc 2011; 133:11462-5. [PMID: 21702440 DOI: 10.1021/ja204197d] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Structural studies of human telomeric repeats represent an active field of research with potential applications toward the development of specific telomeric quadruplex-targeting drugs for anticancer treatment. To date, high-definition structures were limited to DNA sequences containing up to four GGGTTA repeats. Here we investigate the formation of G-quadruplexes in sequences spanning five to seven human telomeric repeats using NMR, UV, and CD spectroscopy. A (3+1) G-quadruplex with a long propeller loop was isolated from a five-repeat sequence utilizing a guanine-to-inosine substitution. A simple approach of selective site-specific labeling of guanine residues was devised to rigorously determine the folding topology of the oligonucleotide. The same scaffold could be extrapolated to six- and seven-repeat sequences. Our results suggest that long human telomeric sequences consisting of five or more GGGTTA repeats could adopt (3+1) G-quadruplex structures harboring one or more repeat(s) within a single loop. We report on the formation of a Watson-Crick duplex within the long propeller loop upon addition of the complementary strand, demonstrating that the long loop could serve as a new recognition motif.
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Affiliation(s)
- Doris Jia En Yue
- School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
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35
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Prakash A, Kieken F, Marky LA, Borgstahl GEO. Stabilization of a G-Quadruplex from Unfolding by Replication Protein A Using Potassium and the Porphyrin TMPyP4. J Nucleic Acids 2011; 2011:529828. [PMID: 21772995 PMCID: PMC3136172 DOI: 10.4061/2011/529828] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2010] [Revised: 03/17/2011] [Accepted: 04/01/2011] [Indexed: 11/20/2022] Open
Abstract
Replication protein A (RPA) plays an essential role in DNA replication by binding and unfolding non-canonical single-stranded DNA (ssDNA) structures. Of the six RPA ssDNA binding domains (labeled A-F), RPA-CDE selectively binds a G-quadruplex forming sequence (5′-TAGGGGAAGGGTTGGAGTGGGTT-3′ called Gq23). In K+, Gq23 forms a mixed parallel/antiparallel conformation, and in Na+ Gq23 has a less stable (TM lowered by ∼20°C), antiparallel conformation. Gq23 is intramolecular and 1D NMR confirms a stable G-quadruplex structure in K+. Full-length RPA and RPA-CDE-core can bind and unfold the Na+ form of Gq23 very efficiently, but complete unfolding is not observed with the K+ form. Studies with G-quadruplex ligands, indicate that TMPyP4 has a thermal stabilization effect on Gq23 in K+, and inhibits complete unfolding by RPA and RPA-CDE-core. Overall these data indicate that G-quadruplexes present a unique problem for RPA to unfold and ligands, such as TMPyP4, could possibly hinder DNA replication by blocking unfolding by RPA.
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Affiliation(s)
- Aishwarya Prakash
- The Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, 987696 Nebraska Medical Center, Omaha, NE 68198-7696, USA
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Prislan I, Khutsishvili I, Marky LA. Interaction of minor groove ligands with G-quadruplexes: thermodynamic contributions of the number of quartets, T-U substitutions, and conformation. Biochimie 2011; 93:1341-50. [PMID: 21684318 DOI: 10.1016/j.biochi.2011.06.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2011] [Accepted: 06/01/2011] [Indexed: 10/18/2022]
Abstract
In the presence of specific metal ions, DNA oligonucleotides containing guanine repeat sequences can adopt G-quadruplex structures. In this work, we used a combination of spectroscopic and calorimetric techniques to investigate the conformation and unfolding thermodynamics of the K(+)-form of five G-quadruplexes with sequences: d(G(2)T(2)G(2)TGTG(2)T(2)G(2)), G2, d(G(3)T(2)G(3)TGTG(3)T(2)G(3)), G3, their analogs where T is replaced with U, G2-U and G3-U, and r(G(2)U(2)G(2)UGUG(2)U(2)G(2)), rG2. These G-quadruplexes show CD spectra characteristic of the "chair" conformation (G2 and G2-U), or "basket" conformation (rG2); or a mixture of these two conformers (G3 and G3-U). Thermodynamic profiles show that the favorable folding of each G-quadruplex results from the typical compensation of a favorable enthalpy and unfavorable entropy contributions. G-quadruplex stability increase in the following order (in ΔG°(20)): rG2 (-1.3 kcal/mol) < G2 < G2-U <G3-U (chair) < G3 (chair) <G3-U (basket) < G3 (basket) (-8.6 kcal/mol), due to favorable enthalpy contribution from the stacking of G-quartets. We used ITC to determine thermodynamic binding profiles for the interaction of the minor groove ligands, netropsin and distamycin, with each G-quadruplex. Both ligands bind with high exothermic enthalpies (~ -10.8 kcal/mol), 1:1 stoichiometries, and weak affinities (~8 × 10(4) M(-1)). The similarity of the binding thermodynamic profiles, together with the absence of induced Cotton effects, indicates a surface or outside binding mode. We speculate that the top and bottom surfaces of the G-quadruplex comprise the potential MGBL binding sites, where the ligand lies on the surface forming van der Waals interactions with the guanines of the G-quartets and loop nucleotides.
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Affiliation(s)
- Iztok Prislan
- Department of Pharmaceutical Sciences, University of Nebraska Medical Center, 986025 Nebraska Medical Center, Omaha, NE 68198-6025, USA
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Xu Y. Chemistry in human telomere biology: structure, function and targeting of telomere DNA/RNA. Chem Soc Rev 2011; 40:2719-40. [DOI: 10.1039/c0cs00134a] [Citation(s) in RCA: 249] [Impact Index Per Article: 19.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Prislan I, Lah J, Milanic M, Vesnaver G. Kinetically governed polymorphism of d(G₄T₄G₃) quadruplexes in K+ solutions. Nucleic Acids Res 2010; 39:1933-42. [PMID: 21113023 PMCID: PMC3061076 DOI: 10.1093/nar/gkq867] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
It has been generally recognized that understanding the molecular basis of some important cellular processes is hampered by the lack of knowledge of forces that drive spontaneous formation/disruption of G-quadruplex structures in guanine-rich DNA sequences. According to numerous biophysical and structural studies G-quadruplexes may occur in the presence of K(+) and Na(+) ions as polymorphic structures formed in kinetically governed processes. The reported kinetic models suggested to describe this polymorphism should be considered inappropriate since, as a rule, they include bimolecular single-step associations characterized by negative activation energies. In contrast, our approach in studying polymorphic behavior of G-quadruplexes is based on model mechanisms that involve only elementary folding/unfolding transitions and structural conversion steps that are characterized by positive activation energies. Here, we are investigating a complex polymorphism of d(G(4)T(4)G(3)) quadruplexes in K(+) solutions. On the basis of DSC, circular dichroism and UV spectroscopy and polyacrylamide gel electrophoresis experiments we propose a kinetic model that successfully describes the observed thermally induced conformational transitions of d(G(4)T(4)G(3)) quadruplexes in terms of single-step reactions that involve besides single strands also one tetramolecular and three bimolecular quadruplex structures.
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Affiliation(s)
- Iztok Prislan
- Faculty of Chemistry and Chemical Technology, Physical Chemistry, University of Ljubljana, Askerceva, Slovenia
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Forsha SJ, Panyutin IV, Neumann RD, Panyutin IG. Intracellular traffic of oligodeoxynucleotides in and out of the nucleus: effect of exportins and DNA structure. Oligonucleotides 2010; 20:277-84. [PMID: 20946012 DOI: 10.1089/oli.2010.0255] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The delivery of oligodeoxynucleotides (ODNs) into cells is widely utilized for antisense, antigene, aptamer, and similar approaches to regulate gene and protein activities based upon the ODNs' sequence-specific recognition. Short pieces of DNA can also be generated in biological processes, for example, after degradation of viral or bacterial DNA. However, the mechanisms that regulate intracellular trafficking and localization of ODNs are not fully understood. Here we study the effects of major transporters of microRNA, exportin-1 (Exp1) and exportin-5 (Exp5), on the transport of single-stranded ODNs in and out of the nucleus. For this, we employed a fluorescent microscopy-based assay to quantitatively measure the redistribution of ODNs between the nucleus and cytoplasm of live cells. By measuring the fluorescent signal of the nuclei we observed that after delivery into cells via cationic liposomes ODNs rapidly accumulated inside nuclei. However, after removal of the ODN/liposome containing media, we found re-localization of ODNs from the nuclei to cytoplasm of the cells over the time course of several hours. Downregulation of the Exp5 gene by siRNA resulted in a slight increase of ODN uptake into the nucleus, but the kinetics of ODN efflux to the cytoplasm was not affected. Inhibition of Exp1 with leptomycin B somewhat slowed down the clearance of ODNs from the nucleus; however, within 6 hours most of the ODN were still being cleared form the nucleus. ODNs that could form intramolecular G-quadruplex structures behaved differently. They also accumulated in nuclei, although at a lesser extent than unstructured ODN, but they remained there for up to 20 hours after transfection, causing significant cell death. We conclude that Exp1 and Exp5 are not the major transporters of our ODNs out of the nucleus, and that the transport of ODNs is strongly affected by their secondary structure.
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Affiliation(s)
- Stephen J Forsha
- Radiology and Imaging Sciences Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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Monchaud D, Granzhan A, Saettel N, Guédin A, Mergny JL, Teulade-Fichou MP. "One ring to bind them all"-part I: the efficiency of the macrocyclic scaffold for g-quadruplex DNA recognition. J Nucleic Acids 2010; 2010. [PMID: 20725629 PMCID: PMC2915875 DOI: 10.4061/2010/525862] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Accepted: 02/18/2010] [Indexed: 01/01/2023] Open
Abstract
Macrocyclic scaffolds are particularly attractive for designing selective G-quadruplex ligands essentially because, on one hand, they show a poor affinity for the “standard” B-DNA conformation and, on the other hand, they fit nicely with the external G-quartets of quadruplexes. Stimulated by the pioneering studies on the cationic porphyrin TMPyP4 and the natural product telomestatin, follow-up studies have developed, rapidly leading to a large diversity of macrocyclic structures with remarkable-quadruplex binding properties and biological activities. In this review we summarize the current state of the art in detailing the three main categories of quadruplex-binding macrocycles described so far (telomestatin-like polyheteroarenes, porphyrins and derivatives, polyammonium cyclophanes), and in addressing both synthetic issues and biological aspects.
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Affiliation(s)
- David Monchaud
- Section Recherche, Institut Curie, CNRS UMR176, Centre Universitaire Paris XI, Batiment 110, 91405 Orsay, France
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Sannohe Y, Sugiyama H. Overview of formation of G-quadruplex structures. ACTA ACUST UNITED AC 2010; Chapter 17:Unit 17.2.1-17. [PMID: 20201027 DOI: 10.1002/0471142700.nc1702s40] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
There are many structures that can be adopted by nucleic acids other than the Watson-Crick duplex. In particular, a noncanonical four-stranded topology, called a G-quadruplex, is of great interest because of its roles in key biological processes such as the maintenance of telomeres and regulation of gene transcription. This review describes the condition for forming the G-quadruplex structure, G-quadruplex-forming sequences, and methods for studying the structures.
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Li MH, Luo Q, Li ZS. Molecular Dynamics Study on the Interactions of Porphyrin with Two Antiparallel Human Telomeric Quadruplexes. J Phys Chem B 2010; 114:6216-24. [DOI: 10.1021/jp101373p] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Ming-Hui Li
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Quan Luo
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s Republic of China
| | - Ze-Sheng Li
- Institute of Theoretical Chemistry, State Key Laboratory of Theoretical and Computational Chemistry, Jilin University, Changchun 130023, People’s Republic of China
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Yoon JM, Kang HJ, Sung JH, Park HJ, Hohng SC. Highly Polymorphic G-quadruplexes in the c-MYC Promoter. B KOREAN CHEM SOC 2010. [DOI: 10.5012/bkcs.2010.31.04.1025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Onyshchenko MI, Gaynutdinov TI, Englund EA, Appella DH, Neumann RD, Panyutin IG. Stabilization of G-quadruplex in the BCL2 promoter region in double-stranded DNA by invading short PNAs. Nucleic Acids Res 2010; 37:7570-80. [PMID: 19820116 PMCID: PMC2794188 DOI: 10.1093/nar/gkp840] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Numerous regulatory genes have G-rich regions that can potentially form quadruplex structures, possibly playing a role in transcription regulation. We studied a G-rich sequence in the BCL2 gene 176-bp upstream of the P1 promoter for G-quadruplex formation. Using circular dichroism (CD), thermal denaturation and dimethyl sulfate (DMS) footprinting, we found that a single-stranded oligonucleotide with the sequence of the BCL2 G-rich region forms a potassium-stabilized G-quadruplex. To study G-quadruplex formation in double-stranded DNA, the G-rich sequence of the BCL2 gene was inserted into plasmid DNA. We found that a G-quadruplex did not form in the insert at physiological conditions. To induce G-quadruplex formation, we used short peptide nucleic acids (PNAs) that bind to the complementary C-rich strand. We examined both short duplex-forming PNAs, complementary to the central part of the BCL2 gene, and triplex-forming bis-PNAs, complementary to sequences adjacent to the G-rich BCL2 region. Using a DMS protection assay, we demonstrated G-quadruplex formation within the G-rich sequence from the promoter region of the human BCL2 gene in plasmid DNA. Our results show that molecules binding the complementary C-strand facilitate G-quadruplex formation and introduce a new mode of PNA-mediated sequence-specific targeting.
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Affiliation(s)
- Mykola I. Onyshchenko
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Timur I. Gaynutdinov
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ethan A. Englund
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Daniel H. Appella
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ronald D. Neumann
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
| | - Igor G. Panyutin
- Department of Radiology and Imaging Sciences, Clinical Center and Laboratory of Bioorganic Chemistry, NIDDK, National Institutes of Health, Bethesda, MD 20892, USA
- *To whom correspondence should be addressed. Tel: +1 301 496 8308; Fax: +1 301 480 9712;
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Martino L, Pagano B, Fotticchia I, Neidle S, Giancola C. Shedding light on the interaction between TMPyP4 and human telomeric quadruplexes. J Phys Chem B 2010; 113:14779-86. [PMID: 19824637 DOI: 10.1021/jp9066394] [Citation(s) in RCA: 126] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
The nature of the binding mode and stoichiometry of the TMPyP4 cationic porphyrin to G-quadruplex structures continues to be controversial, with no consensus model to date, especially for intramolecular G-quadruplexes from human telomeric sequences. Those sequences possess intricate polymorphism in solution that appears to be reduced under molecular crowding conditions in which the parallel structure appears to be the most populated one. We have performed a systematic study, in dilute solution and under molecular crowding conditions, of the binding reactions between TMPyP4 and four G-quadruplexes formed by different truncations of human telomeric DNA, with 5'- or 3'-flanking bases, using isothermal titration calorimetry and circular dichroism. The results clearly indicate that all of these G-quadruplexes are able to bind up to four TMPyP4 molecules. CD studies show that interaction with TMPyP4 promotes the conversion of the hybrid structures to an antiparallel conformation in dilute solution, while under molecular crowding conditions the interaction does not promote any conformational change. ITC reveals in both cases that the binding process comprises two sequential events, a first in which one molecule of TMPyP4 interacts with the quadruplex structures and a second in which three other molecules bind to the structures. The selectivity of TMPyP4 for the quadruplex relative to duplex DNA was also investigated under molecular crowding conditions showing that TMPyP4 has enhanced selectivity for quadruplex DNA compared to the duplex structure. This finding reinforces the potential applications of TMPyP4.
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Affiliation(s)
- Luigi Martino
- Dipartimento di Chimica P. Corradini, Università degli Studi di Napoli Federico II, via Cintia, I-80126, Napoli, Italy
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Gray RD, Petraccone L, Trent JO, Chaires JB. Characterization of a K+-induced conformational switch in a human telomeric DNA oligonucleotide using 2-aminopurine fluorescence. Biochemistry 2010; 49:179-94. [PMID: 19961180 DOI: 10.1021/bi901357r] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Human telomeric DNA consists of tandem repeats of the DNA sequence d(GGGTTA). Oligodeoxynucleotide telomere models such as d[A(GGGTTA)(3)GGG] (Tel22) fold in a cation-dependent manner into quadruplex structures consisting of stacked G-quartets linked by d(TTA) loops. NMR has shown that in Na(+) solutions Tel22 forms a "basket" topology of four antiparallel strands; in contrast, Tel22 in K(+) solutions consists of a mixture of unknown topologies. Our previous studies on the mechanism of folding of Tel22 and similar telomere analogues utilized changes in UV absorption between 270 and 325 nm that report primarily on G-quartet formation and stacking showed that quadruplex formation occurs within milliseconds upon mixing with an appropriate cation. In this study, we assess the dynamics and equilibria of folding of specific loops by using Tel22 derivatives in which the dA residues were serially substituted with the fluorescent reporter base, 2-aminopurine (2-AP). Tel22 folding induced by Na(+) or K(+) assessed by changes in 2-AP fluorescence consists of at least three kinetic steps with time constants spanning a range from milliseconds to several hundred seconds. Na(+)-dependent equilibrium titrations of Tel22 folding could be approximated as a cooperative two-state process. In contrast, K(+)-dependent folding curves were biphasic, revealing that different conformational ensembles are present in 1 and 30 mM K(+). This conclusion was confirmed by (1)H NMR. Molecular dynamics simulations revealed a K(+) binding pocket in Tel22 located near dA1 that is specific for the so-called hybrid-1 conformation in which strand 1 is in a parallel arrangement. The possible presence of this topologically specific binding site suggests that K(+) may play an allosteric role in regulating telomere conformation and function by modulating quadruplex tertiary structure.
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Affiliation(s)
- Robert D Gray
- James Graham Brown Cancer Center, University of Louisville, Louisville, Kentucky 40202, USA
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Hong Y, Xiong H, Lam J, Häußler M, Liu J, Yu Y, Zhong Y, Sung H, Williams I, Wong K, Tang B. Fluorescent Bioprobes: Structural Matching in the Docking Processes of Aggregation-Induced Emission Fluorogens on DNA Surfaces. Chemistry 2010; 16:1232-45. [DOI: 10.1002/chem.200900778] [Citation(s) in RCA: 158] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Gaynutdinov TI, Brown P, Neumann RD, Panyutin IG. Duplex formation at the 5' end affects the quadruplex conformation of the human telomeric repeat overhang in sodium but not in potassium. Biochemistry 2009; 48:11169-77. [PMID: 19856972 DOI: 10.1021/bi901063g] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Human telomeres contain numerous copies of the (TTAGGG)(n).(AATCCC)(n) repeated sequence with multiple TTAGGG repeats in 3' single-stranded overhangs. Single-stranded oligonucleotides consisting of four TTAGGG repeats can fold into various intramolecular quadruplex structures stabilized by quartets of guanines. The quadruplex structures are believed to play a role in telomere functions and considered as targets for anticancer drug design. In an effort to create a more realistic model of telomeric DNA, we designed oligonucleotides containing a duplex region at the 5' end and four telomeric repeats in the 3' overhang. We applied CD spectroscopy and (125)I radioprobing to determine the conformation of the quadruplexes formed in the 3' overhangs. We found that in the presence of NaCl the conformation of the quadruplex changes with formation of the 5' duplex and depends on the position of the interface between the duplex and the 3' telomeric sequence. When the duplex region extended to the first T of the first TTAGGG repeat, both CD and radioprobing data are consistent with the parallel propeller conformation of the overhang. In the presence of KCl, formation of the duplex at the 5' end of DNA molecules did not change the fold of the quadruplex in the overhang which was interpreted as a mixture of two isomers of 3+1 conformation regardless of the duplex-overhang interface position. Our results demonstrate that the interface between the duplex and single-stranded overhang can affect the conformation of the telomeric quadruplex.
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Affiliation(s)
- Timur I Gaynutdinov
- Department of Radiology and Imaging Sciences, Clinical Center, National Institutes of Health, Bethesda, Maryland 20892-1180, USA
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Abstract
Telomeres play an important role in cellular aging and cancer. Human telomeric DNA and RNA G-rich sequences are capable of forming a four-stranded structure, known as the G-quadruplex. Such a structure might be important for telomere biology and a good target for drug design. This minireview describes the structural diversity or conservation of DNA and RNA human telomeric G-quadruplexes, discusses structural views on targeting these G-quadruplexes and presents some future challenges for structural studies.
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Affiliation(s)
- Anh Tuân Phan
- Division of Physics & Applied Physics, School of Physical & Mathematical Sciences, Nanyang Technological University, Singapore.
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Renciuk D, Kejnovská I, Skoláková P, Bednárová K, Motlová J, Vorlícková M. Arrangements of human telomere DNA quadruplex in physiologically relevant K+ solutions. Nucleic Acids Res 2009; 37:6625-34. [PMID: 19717545 PMCID: PMC2770667 DOI: 10.1093/nar/gkp701] [Citation(s) in RCA: 159] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
The arrangement of the human telomeric quadruplex in physiologically relevant conditions has not yet been unambiguously determined. Our spectroscopic results suggest that the core quadruplex sequence G3(TTAG3)3 forms an antiparallel quadruplex of the same basket type in solution containing either K+ or Na+ ions. Analogous sequences extended by flanking nucleotides form a mixture of the antiparallel and hybrid (3 + 1) quadruplexes in K+-containing solutions. We, however, show that long telomeric DNA behaves in the same way as the basic G3(TTAG3)3 motif. Both G3(TTAG3)3 and long telomeric DNA are also able to adopt the (3 + 1) quadruplex structure: Molecular crowding conditions, simulated here by ethanol, induced a slow transition of the K+-stabilized quadruplex into the hybrid quadruplex structure and then into a parallel quadruplex arrangement at increased temperatures. Most importantly, we demonstrate that the same transitions can be induced even in aqueous, K+-containing solution by increasing the DNA concentration. This is why distinct quadruplex structures were detected for AG3(TTAG3)3 by X-ray, nuclear magnetic resonance and circular dichrosim spectroscopy: Depending on DNA concentration, the human telomeric DNA can adopt the antiparallel quadruplex, the (3 + 1) structure, or the parallel quadruplex in physiologically relevant concentrations of K+ ions.
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