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Matić J, Piotrowski P, Vrban L, Kobetić R, Vianello R, Jurić I, Fabijanić I, Pernar Kovač M, Brozovic A, Piantanida I, Schmuck C, Radić Stojković M. Distinctive Nucleic Acid Recognition by Lysine-Embedded Phenanthridine Peptides. Int J Mol Sci 2024; 25:4866. [PMID: 38732083 PMCID: PMC11084427 DOI: 10.3390/ijms25094866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 04/25/2024] [Accepted: 04/27/2024] [Indexed: 05/13/2024] Open
Abstract
Three new phenanthridine peptide derivatives (19, 22, and 23) were synthesized to explore their potential as spectrophotometric probes for DNA and RNA. UV/Vis and circular dichroism (CD) spectra, mass spectroscopy, and computational analysis confirmed the presence of intramolecular interactions in all three compounds. Computational analysis revealed that compounds alternate between bent and open conformations, highlighting the latter's crucial influence on successful polynucleotide recognition. Substituting one glycine with lysine in two regioisomers (22, 23) resulted in stronger binding interactions with DNA and RNA than for a compound containing two glycines (19), thus emphasizing the importance of lysine. The regioisomer with lysine closer to the phenanthridine ring (23) exhibited a dual and selective fluorimetric response with non-alternating AT and ATT polynucleotides and induction of triplex formation from the AT duplex. The best binding constant (K) with a value of 2.5 × 107 M-1 was obtained for the interaction with AT and ATT polynucleotides. Furthermore, apart from distinguishing between different types of ds-DNA and ds-RNA, the same compound could recognize GC-rich DNA through distinct induced CD signals.
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Affiliation(s)
- Josipa Matić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Patryciusz Piotrowski
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Lucija Vrban
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Renata Kobetić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Robert Vianello
- Laboratory for the Computational Design and Synthesis of Functional Materials, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (L.V.); (R.V.)
| | - Ivona Jurić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Ivana Fabijanić
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Margareta Pernar Kovač
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Anamaria Brozovic
- Division of Molecular Biology, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (M.P.K.); (A.B.)
| | - Ivo Piantanida
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
| | - Carsten Schmuck
- Institute for Organic Chemistry, University of Duisburg-Essen, Universitätsstrasse 7, 45141 Essen, Germany; (P.P.)
| | - Marijana Radić Stojković
- Laboratory for Biomolecular Interactions and Spectroscopy, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička Cesta 54, 10000 Zagreb, Croatia; (J.M.); (R.K.); (I.J.); (I.F.); (I.P.)
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Ranjan N, Arya DP. Parallel G-quadruplex recognition by neomycin. Front Chem 2023; 11:1232514. [PMID: 37671393 PMCID: PMC10475565 DOI: 10.3389/fchem.2023.1232514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 07/25/2023] [Indexed: 09/07/2023] Open
Abstract
G-quadruplex-forming nucleic acids have evolved to have applications in biology, drug design, sensing, and nanotechnology, to name a few. Together with the structural understanding, several attempts have been made to discover and design new classes of chemical agents that target these structures in the hope of using them as future therapeutics. Here, we report the binding of aminoglycosides, in particular neomycin, to parallel G-quadruplexes that exist as G-quadruplex monomers, dimers, or compounds that have the propensity to form dimeric G-quadruplex structures. Using a combination of calorimetric and spectroscopic studies, we show that neomycin binds to the parallel G-quadruplex with affinities in the range of Ka ∼ 105-108 M-1, which depends on the base composition, ability to form dimeric G-quadruplex structures, salt, and pH of the buffer used. At pH 7.0, the binding of neomycin was found to be electrostatically driven potentially through the formation of ion pairs formed with the quadruplex. Lowering the pH resulted in neomycin's association constants in the range of Ka ∼ 106-107 M-1 in a salt dependent manner. Circular dichroism (CD) studies showed that neomycin's binding does not cause a change in the parallel conformation of the G-quadruplex, yet some binding-induced changes in the intensity of the CD signals were seen. A comparative binding study of neomycin and paromomycin using d(UG4T) showed paromomycin binding to be much weaker than neomycin, highlighting the importance of ring I in the recognition process. In toto, our results expanded the binding landscape of aminoglycosides where parallel G-quadruplexes have been discovered as one of the high-affinity sites. These results may offer a new understanding of some of the undesirable functions of aminoglycosides and help in the design of aminoglycoside-based G-quadruplex binders of high affinity.
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Affiliation(s)
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States
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Yuan F, Liu X, Tan L. Binding and stabilization effect of arene ruthenium(Ⅱ) polypyridyl complexes toward the triple-helical RNA poly(U)•poly(A)⁎poly(U). Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Wang H, Liu X, Tan L. A naked-eye colorimetric molecular "light switch" based on ruthenium(II) polypyridyl complex [Ru(phen) 2ttbd] 2+ as binder and stabilizer for RNA duplex and triplex. Int J Biol Macromol 2022; 215:571-578. [PMID: 35752337 DOI: 10.1016/j.ijbiomac.2022.06.119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/14/2022] [Accepted: 06/16/2022] [Indexed: 11/05/2022]
Abstract
Binding of [Ru(phen)2ttbd]2+ (phen = 1,10-phenanthroline, ttbd = 4-(6-propenylpyrido-[3,2-a]- phenzain-10-yl-benzene-1,2-diamine) to the RNA triplex poly(U-A*U) (herein "-" and "*" refer to the Watson-Crick and Hoogsteen binding, respectively) and the duplex poly(A-U) have been investigated by spectral technology and viscosity method. Analysis of spectral titrations and viscosity experiments as well as melting measurements suggest that [Ru(phen)2ttbd]2+ binds to the studied RNA triplex and duplex through intercalation, while its binding constant toward the triplex is greater than the duplex. Luminescent titrations indicate that [Ru(phen)2ttbd]2+ can act as a molecular "light switch" for the two RNAs and the switch effect can be detected by the naked-eye. Moreover, the "light switch" can be repeatedly cycled off and on by adjusting the pH of the solution, whereas color change in the case of the triplex is more significant compared with the duplex. To our knowledge, [Ru(phen)2ttbd]2+ is the first small molecule capable of serving as a pH-controlled reversible visual molecular "light switch" for both the RNA triplex poly(U-A*U) and duplex poly(A-U). Thermal denaturation experiments suggest that [Ru(phen)2ttbd]2+ can obviously increase the triplex stabilization, while it stabilizing third-strand is more marked in comparison with the template duplex of the triplex, indicating this complex preferentially binds to third-strand. The obtained results may be useful for understanding the binding of Ru(II) polypyridyl complexes to RNAs.
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Affiliation(s)
- Hui Wang
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Lifeng Tan
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China.
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Zhang C, Liu X, Tan L. Interaction of arene ruthenium(II) complexes [(η 6-C 6H 6)Ru(L)Cl]PF 6 (L = o-fpip and p-fpip) with the RNA triplex poly(U)*poly(A)•poly(U). J Inorg Biochem 2022; 232:111813. [PMID: 35405487 DOI: 10.1016/j.jinorgbio.2022.111813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 03/26/2022] [Accepted: 03/31/2022] [Indexed: 11/25/2022]
Abstract
To comprehend the binding properties of η6-arene Ru(II) complexes with poly(U)*poly(A)•poly(U) triplex, two arene Ru(II) complexes with different fluorine substituent positions, [(η6-C6H6)Ru(o-fpip)Cl]PF6 (Ru1,η6-C6H6 = benzene ring, o-fpip = 2-(2'‑fluorine) imidazo [4,5-f] Biver et al. (2008), Gupta et al. (2012) [1, 10] phenanthroline) and [(η6-C6H6)Ru(p-fpip)Cl]PF6 (Ru2,η6-C6H6 = benzene ring, o-fpip = 2-(4'‑fluorine) imidazo [4,5-f] Biver et al. (2008), Gupta et al. (2012) [1, 10] phenanthroline), have been synthesized and characterized in this study. The binding of Ru1 and Ru2 with poly(U)*poly(A)•poly(U) triplex has been investigated by viscosity measurement and spectroscopic methods. Analysis of UV-Vis absorption spectral titrations suggests that Ru1 and Ru2 bind to the triplex through an intercalative mode, but the binding affinity of Ru2 is slightly higher than that of Ru1, which is also verified by viscosity and EB (ethidium bromide) competition measurements. Furthermore, the thermal denaturation experiment shows that Ru1 and Ru2 increase the third-strand stabilization to a similar extent. Interestingly, the two complexes have essentially no effect on the stabilization of the template duplex. Considering the structure of Ru1 and Ru2, conceivably besides the intercalation of ligand, the force stabilizing the triplex should also involve covalent binding and electrostatic interaction. The obtained results will contribute to our understanding of the interaction of arene Ru(II) complexes with the poly(U)*poly(A)•poly(U) triplex.
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Affiliation(s)
- Chengqing Zhang
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Lifeng Tan
- Key Lab of Environment-friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, People's Republic of China.
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Recognition of ATT Triplex and DNA:RNA Hybrid Structures by Benzothiazole Ligands. Biomolecules 2022; 12:biom12030374. [PMID: 35327566 PMCID: PMC8945811 DOI: 10.3390/biom12030374] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 02/21/2022] [Accepted: 02/22/2022] [Indexed: 11/17/2022] Open
Abstract
Interactions of an array of nucleic acid structures with a small series of benzothiazole ligands (bis-benzothiazolyl-pyridines—group 1, 2-thienyl/2-benzothienyl-substituted 6-(2-imidazolinyl)benzothiazoles—group 2, and three 2-aryl/heteroaryl-substituted 6-(2-imidazolinyl)benzothiazoles—group 3) were screened by competition dialysis. Due to the involvement of DNA:RNA hybrids and triplex helices in many essential functions in cells, this study’s main aim is to detect benzothiazole-based moieties with selective binding or spectroscopic response to these nucleic structures compared to regular (non-hybrid) DNA and RNA duplexes and single-stranded forms. Complexes of nucleic acids and benzothiazoles, selected by this method, were characterized by UV/Vis, fluorescence and circular dichroism (CD) spectroscopy, isothermal titration calorimetry, and molecular modeling. Two compounds (1 and 6) from groups 1 and 2 demonstrated the highest affinities against 13 nucleic acid structures, while another compound (5) from group 2, despite lower affinities, yielded higher selectivity among studied compounds. Compound 1 significantly inhibited RNase H. Compound 6 could differentiate between B- (binding of 6 dimers inside minor groove) and A-type (intercalation) helices by an induced CD signal, while both 5 and 6 selectively stabilized ATT triplex in regard to AT duplex. Compound 3 induced strong condensation-like changes in CD spectra of AT-rich DNA sequences.
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Largy E, König A, Ghosh A, Ghosh D, Benabou S, Rosu F, Gabelica V. Mass Spectrometry of Nucleic Acid Noncovalent Complexes. Chem Rev 2021; 122:7720-7839. [PMID: 34587741 DOI: 10.1021/acs.chemrev.1c00386] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Nucleic acids have been among the first targets for antitumor drugs and antibiotics. With the unveiling of new biological roles in regulation of gene expression, specific DNA and RNA structures have become very attractive targets, especially when the corresponding proteins are undruggable. Biophysical assays to assess target structure as well as ligand binding stoichiometry, affinity, specificity, and binding modes are part of the drug development process. Mass spectrometry offers unique advantages as a biophysical method owing to its ability to distinguish each stoichiometry present in a mixture. In addition, advanced mass spectrometry approaches (reactive probing, fragmentation techniques, ion mobility spectrometry, ion spectroscopy) provide more detailed information on the complexes. Here, we review the fundamentals of mass spectrometry and all its particularities when studying noncovalent nucleic acid structures, and then review what has been learned thanks to mass spectrometry on nucleic acid structures, self-assemblies (e.g., duplexes or G-quadruplexes), and their complexes with ligands.
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Affiliation(s)
- Eric Largy
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Alexander König
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Anirban Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Debasmita Ghosh
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Sanae Benabou
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
| | - Frédéric Rosu
- Univ. Bordeaux, CNRS, INSERM, IECB, UMS 3033, F-33600 Pessac, France
| | - Valérie Gabelica
- Univ. Bordeaux, CNRS, INSERM, ARNA, UMR 5320, U1212, IECB, F-33600 Pessac, France
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Ponti F, Campolungo M, Melchiori C, Bono N, Candiani G. Cationic lipids for gene delivery: many players, one goal. Chem Phys Lipids 2021; 235:105032. [PMID: 33359210 DOI: 10.1016/j.chemphyslip.2020.105032] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2020] [Revised: 11/23/2020] [Accepted: 12/19/2020] [Indexed: 12/28/2022]
Abstract
Lipid-based carriers represent the most widely used alternative to viral vectors for gene expression and gene silencing purposes. This class of non-viral vectors is particularly attractive for their ease of synthesis and chemical modifications to endow them with desirable properties. Despite combinatorial approaches have led to the generation of a large number of cationic lipids displaying different supramolecular structures and improved behavior, additional effort is needed towards the development of more and more effective cationic lipids for transfection purposes. With this review, we seek to highlight the great progress made in the design of each and every constituent domain of cationic lipids, that is, the chemical structure of the headgroup, linker and hydrophobic moieties, and on the specific effect on the assembly with nucleic acids. Since the complexity of such systems is known to affect their performances, the role of formulation, stability and phase behavior on the transfection efficiency of such assemblies will be thoroughly discussed. Our objective is to provide a conceptual framework for the development of ever more performing lipid gene delivery vectors.
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Affiliation(s)
- Federica Ponti
- GenT LΛB, Dept. of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, 20131, Milan, Italy; Laboratory for Biomaterials and Bioengineering, Canada Research Chair I in Biomaterials and Bioengineering for the Innovation in Surgery, Dept. Min-Met-Materials Engineering, Research Center of CHU de Quebec, Division of Regenerative Medicine, Laval University, Quebec City, QC, Canada
| | - Matilde Campolungo
- GenT LΛB, Dept. of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, 20131, Milan, Italy
| | - Clara Melchiori
- GenT LΛB, Dept. of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, 20131, Milan, Italy
| | - Nina Bono
- GenT LΛB, Dept. of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, 20131, Milan, Italy.
| | - Gabriele Candiani
- GenT LΛB, Dept. of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, 20131, Milan, Italy.
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Jiang L, Liu X, Tan L. Synthesis and characterization of chiral Ru(II) polypyridyl complexes and their binding and stabilizing effects toward triple-helical RNA. J Inorg Biochem 2020; 213:111263. [PMID: 33011626 DOI: 10.1016/j.jinorgbio.2020.111263] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Revised: 09/10/2020] [Accepted: 09/21/2020] [Indexed: 01/11/2023]
Abstract
Two novel chiral Ru(II) complexes, Λ- and Δ-[Ru(bpy)2(7-CF3-dppz)]2+ (Λ-1 and Δ-1; bpy = 2,2'-bipyridine, 7-CF3-dppz = 7-trifluoromethyl-dipyrido[3,2-a:2',3'-c]phenazine), were synthesized and characterized in this work. The binding and stabilizing effects of Λ-1 and Δ-1 toward the RNA poly(U)•poly(A)*poly(U) triplex were studied by various biophysical techniques. Absorption spectra and fluorescence quenching indicates that the binding affinity of Δ-1 is slightly higher than that Λ-1. Both enantiomers induce significant positive viscosity changes that are indicative of intercalative binding, whereas changes in the relative viscosities of the triplex are found to be more pronounced with Δ-1. Melting experiments indicate that the triplex stabilization effects of both enantiomers are significantly different from each other. With Λ-1, the stabilization of the Watson-Crick base-paired duplex (the template duplex) of the triplex shows a moderate increase, whereas the stabilization of the Hoogsteen base-paired strand (third-strand) exhibits slight decrease under the same conditions, suggesting Λ-1 prefers to stabilize the template duplex rather than third-strand. In stark contrast to Λ-1, Δ-1 can not only strongly stabilize the template duplex, but also moderately increase the third-strand stabilization, even so, which imply that Δ-1 also prefer to stabilize the template duplex instead of the third-strand. These suggest that the [Ru(bpy)2(7-CF3-dppz)]2+ is similar as a non-specific metallointercalator the triplex studied in this work. Combined with our recent research, the obtained results further indicate that Δ- enantiomers rather than Λ-ones of Ru(II) polypyridyl complexes usually exhibit stronger binding and stabilizing effects toward the triplex.
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Affiliation(s)
- Lijuan Jiang
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Xiaohua Liu
- Academic Affairs Office, Xiangtan University, Xiangtan 411105, People's Republic of China
| | - Lifeng Tan
- Key Lab of Environment-friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, People's Republic of China; Key Laboratory for Green Organic Synthesis and Application of Hunan Province, Xiangtan University, Xiangtan 411105, People's Republic of China.
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Brown JA. Unraveling the structure and biological functions of RNA triple helices. WILEY INTERDISCIPLINARY REVIEWS-RNA 2020; 11:e1598. [PMID: 32441456 PMCID: PMC7583470 DOI: 10.1002/wrna.1598] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Revised: 04/06/2020] [Accepted: 04/15/2020] [Indexed: 02/06/2023]
Abstract
It has been nearly 63 years since the first characterization of an RNA triple helix in vitro by Gary Felsenfeld, David Davies, and Alexander Rich. An RNA triple helix consists of three strands: A Watson–Crick RNA double helix whose major‐groove establishes hydrogen bonds with the so‐called “third strand”. In the past 15 years, it has been recognized that these major‐groove RNA triple helices, like single‐stranded and double‐stranded RNA, also mediate prominent biological roles inside cells. Thus far, these triple helices are known to mediate catalysis during telomere synthesis and RNA splicing, bind to ligands and ions so that metabolite‐sensing riboswitches can regulate gene expression, and provide a clever strategy to protect the 3′ end of RNA from degradation. Because RNA triple helices play important roles in biology, there is a renewed interest in better understanding the fundamental properties of RNA triple helices and developing methods for their high‐throughput discovery. This review provides an overview of the fundamental biochemical and structural properties of major‐groove RNA triple helices, summarizes the structure and function of naturally occurring RNA triple helices, and describes prospective strategies to isolate RNA triple helices as a means to establish the “triplexome”. This article is categorized under:RNA Structure and Dynamics > RNA Structure and Dynamics RNA Structure and Dynamics > RNA Structure, Dynamics and Chemistry RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems
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Affiliation(s)
- Jessica A Brown
- Department of Chemistry and Biochemistry, University of Notre Dame, Notre Dame, Indiana, USA
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11
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Ranjan N, Andreasen KF, Arora Y, Xue L, Arya DP. Surface Dependent Dual Recognition of a G-quadruplex DNA With Neomycin-Intercalator Conjugates. Front Chem 2020; 8:60. [PMID: 32117884 PMCID: PMC7028757 DOI: 10.3389/fchem.2020.00060] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2019] [Accepted: 01/20/2020] [Indexed: 01/17/2023] Open
Abstract
G-quadruplexes have been characterized as structures of vital importance in the cellular functioning of several life forms. They have subsequently been established to serve as a therapeutic target of several diseases including cancer, HIV, tuberculosis and malaria. In this paper, we report the binding of aminosugar-intercalator conjugates with a well-studied anti-parallel G-quadruplex derived from Oxytricha Nova G-quadruplex DNA. Of the four neomycin-intercalator conjugates studied with varying surface areas, BQQ-neomycin conjugate displayed the best binding to this DNA G-quadruplex structure with an association constant of Ka = (1.01 ±0.03) × 107 M−1 which is nearly 100-fold higher than the binding of neomycin to this quadruplex. The binding of BQQ-neomycin displays a binding stoichiometry of 1:1 indicating the presence of a single and unique binding site for this G-quadruplex. In contrast, the BQQ-neomycin displays very weak binding to the bacterial A-site rRNA sequence showing that BQQ-does not enhance the neomycin binding to its natural target, the bacterial rRNA A-site. The BQQ-neomycin conjugate is prone to aggregation even at low micromolar concentrations (4 μM) leading to some ambiguities in the analysis of thermal denaturation profiles. Circular dichroism experiments showed that binding of BQQ-neomycin conjugate causes some structural changes in the quadruplex while still maintaining the overall anti-parallel structure. Finally, the molecular docking experiments suggest that molecular surface plays an important role in the recognition of a second site on the G-quadruplex. Overall, these results show that molecules with more than one binding moieties can be made to specifically recognize G-quadruplexes with high affinities. The dual binding molecules comprise of quadruplex groove binding and intercalator units, and the molecular surface of the intercalator plays an important part in enhancing binding interaction to the G-quadruplex structure.
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Affiliation(s)
- Nihar Ranjan
- Laboratory for Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States.,Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, India
| | - Katrine F Andreasen
- Laboratory for Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States
| | - Yashaswina Arora
- Department of Medicinal Chemistry, National Institute of Pharmaceutical Education and Research, Raebareli, India
| | - Liang Xue
- Laboratory for Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States
| | - Dev P Arya
- Laboratory for Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, United States
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Del Mundo IMA, Vasquez KM, Wang G. Modulation of DNA structure formation using small molecules. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2019; 1866:118539. [PMID: 31491448 DOI: 10.1016/j.bbamcr.2019.118539] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 08/20/2019] [Accepted: 08/24/2019] [Indexed: 02/06/2023]
Abstract
Genome integrity is essential for proper cell function such that genetic instability can result in cellular dysfunction and disease. Mutations in the human genome are not random, and occur more frequently at "hotspot" regions that often co-localize with sequences that have the capacity to adopt alternative (i.e. non-B) DNA structures. Non-B DNA-forming sequences are mutagenic, can stimulate the formation of DNA double-strand breaks, and are highly enriched at mutation hotspots in human cancer genomes. Thus, small molecules that can modulate the conformations of these structure-forming sequences may prove beneficial in the prevention and/or treatment of genetic diseases. Further, the development of molecular probes to interrogate the roles of non-B DNA structures in modulating DNA function, such as genetic instability in cancer etiology are warranted. Here, we discuss reported non-B DNA stabilizers, destabilizers, and probes, recent assays to identify ligands, and the potential biological applications of these DNA structure-modulating molecules.
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Affiliation(s)
- Imee M A Del Mundo
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
| | - Karen M Vasquez
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - Guliang Wang
- Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, Dell Pediatric Research Institute, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA
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13
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Watkins D, Maiti K, Arya DP. Aminoglycoside Functionalization as a Tool for Targeting Nucleic Acids. Methods Mol Biol 2019; 1973:147-162. [PMID: 31016700 DOI: 10.1007/978-1-4939-9216-4_9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Aminoglycoside functionalization as a tool for targeting natural and unnatural nucleic acids holds great promise in their development as diagnostic probes and medicinally relevant compounds. Simple synthetic procedures designed to easily and quickly manipulate amino sugar (neomycin, kanamycin) to more powerful and selective ligands are presented in this chapter. We describe representative procedures for (a) aminoglycoside conjugation and (b) preliminary screening for their nucleic acid binding and selectivity.
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Affiliation(s)
- Derrick Watkins
- Department of Chemistry, Clemson University, Clemson, SC, USA
| | | | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, USA.
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14
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Thamban Chandrika N, Garneau-Tsodikova S. Comprehensive review of chemical strategies for the preparation of new aminoglycosides and their biological activities. Chem Soc Rev 2018; 47:1189-1249. [PMID: 29296992 PMCID: PMC5818290 DOI: 10.1039/c7cs00407a] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
A systematic analysis of all synthetic and chemoenzymatic methodologies for the preparation of aminoglycosides for a variety of applications (therapeutic and agricultural) reported in the scientific literature up to 2017 is presented. This comprehensive analysis of derivatization/generation of novel aminoglycosides and their conjugates is divided based on the types of modifications used to make the new derivatives. Both the chemical strategies utilized and the biological results observed are covered. Structure-activity relationships based on different synthetic modifications along with their implications for activity and ability to avoid resistance against different microorganisms are also presented.
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Affiliation(s)
- Nishad Thamban Chandrika
- Department of Pharmaceutical Sciences, College of Pharmacy, University of Kentucky, Lexington, KY 40536-0596, USA.
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15
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Bhuiya S, Haque L, Goswami R, Das S. Multispectroscopic and Theoretical Exploration of the Comparative Binding Aspects of Bioflavonoid Fisetin with Triple- and Double-Helical Forms of RNA. J Phys Chem B 2017; 121:11037-11052. [DOI: 10.1021/acs.jpcb.7b07972] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Sutanwi Bhuiya
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Lucy Haque
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Rapti Goswami
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
| | - Suman Das
- Department of Chemistry, Jadavpur University, Raja S.C. Mullick Road, Jadavpur, Kolkata 700032, India
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16
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Pradhan AB, Bhuiya S, Haque L, Das S. Role of hydroxyl groups in the B-ring of flavonoids in stabilization of the Hoogsteen paired third strand of Poly(U).Poly(A)*Poly(U) triplex. Arch Biochem Biophys 2017; 637:9-20. [PMID: 29162368 DOI: 10.1016/j.abb.2017.11.008] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 11/10/2017] [Accepted: 11/15/2017] [Indexed: 12/12/2022]
Abstract
We have reported the interaction of two flavonoids namely quercetin (Q) and morin (M) with double stranded poly(A).poly(U) (herein after A.U) and triple stranded poly(U).poly(A)*poly(U) (herein after U.A*U, dot represents the Watson-Crick and asterisk represents Hoogsteen base pairing respectively) in this article. It has been observed that relative positions of hydroxyl groups on the B-ring of the flavonoids affect the stabilization of RNA. The double strand as well as the triple strand of RNA-polymers become more stabilized in presence of Q, however both the duplex and triplex remain unaffected in presence of M. The presence of catechol moiety on the B-ring of Q is supposed to be responsible for the stabilization. Moreover, after exploiting a series of biophysical experiments, it has been found that, triple helical RNA becomes more stabilized over its parent duplex in presence of Q. Fluorescence quenching, viscosity measurement and helix melting results establish the fact that Q binds with both forms of RNA through the mode of intercalation while M does not bind at all to either forms of RNA.
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Affiliation(s)
- Ankur Bikash Pradhan
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Sutanwi Bhuiya
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Lucy Haque
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
| | - Suman Das
- Department of Chemistry, Jadavpur University, Raja S. C. Mullick Road, Jadavpur, Kolkata 700 032, India.
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17
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Gómez Ramos LM, Degtyareva NN, Kovacs NA, Holguin SY, Jiang L, Petrov AS, Biesiada M, Hu MY, Purzycka KJ, Arya DP, Williams LD. Eukaryotic Ribosomal Expansion Segments as Antimicrobial Targets. Biochemistry 2017; 56:5288-5299. [PMID: 28895721 DOI: 10.1021/acs.biochem.7b00703] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Diversity in eukaryotic rRNA structure and function offers possibilities of therapeutic targets. Unlike ribosomes of prokaryotes, eukaryotic ribosomes contain species-specific rRNA expansion segments (ESs) with idiosyncratic structures and functions that are essential and specific to some organisms. Here we investigate expansion segment 7 (ES7), one of the largest and most variable expansions of the eukaryotic ribosome. We hypothesize that ES7 of the pathogenic fungi Candida albicans (ES7CA) could be a prototypic drug target. We show that isolated ES7CA folds reversibly to a native-like state. We developed a fluorescence displacement assay using an RNA binding fluorescent probe, F-neo. F-neo binds tightly to ES7CA with a Kd of 2.5 × 10-9 M but binds weakly to ES7 of humans (ES7HS) with a Kd estimated to be greater than 7 μM. The fluorescence displacement assay was used to investigate the affinities of a library of peptidic aminosugar conjugates (PAs) for ES7CA. For conjugates with highest affinities for ES7CA (NeoRH, NeoFH, and NeoYH), the lowest dose needed to induce mortality in C. albicans (minimum inhibitory concentration, MIC) was determined. PAs with the lowest MIC values were tested for cytotoxicity in HEK293T cells. Molecules with high affinity for ES7CA in vitro induce mortality in C. albicans but not in HEK293T cells. The results are consistent with the hypothesis that ESs represent useful targets for chemotherapeutics directed against eukaryotic pathogens.
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Affiliation(s)
- Lizzette M Gómez Ramos
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 315 Ferst Drive NW, Atlanta, Georgia 30332-0363, United States.,School of Chemical and Biomolecular Engineering, Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Natalya N Degtyareva
- NUBAD, LLC , 900 B West Farris Road, Greenville, South Carolina 29605, United States
| | - Nicholas A Kovacs
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 315 Ferst Drive NW, Atlanta, Georgia 30332-0363, United States
| | - Stefany Y Holguin
- School of Chemical and Biomolecular Engineering, Georgia Institute of Technology , 311 Ferst Drive NW, Atlanta, Georgia 30332-0100, United States
| | - Liuwei Jiang
- Department of Chemistry, Clemson University , 436 Hunter Laboratories, Clemson, South Carolina 29634-0973, United States
| | - Anton S Petrov
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 315 Ferst Drive NW, Atlanta, Georgia 30332-0363, United States
| | - Marcin Biesiada
- RNA Structure and Function Laboratory, Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan 61-704, Poland
| | - Michael Y Hu
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 315 Ferst Drive NW, Atlanta, Georgia 30332-0363, United States
| | - Katarzyna J Purzycka
- RNA Structure and Function Laboratory, Institute of Bioorganic Chemistry, Polish Academy of Sciences , Poznan 61-704, Poland
| | - Dev P Arya
- NUBAD, LLC , 900 B West Farris Road, Greenville, South Carolina 29605, United States.,Department of Chemistry, Clemson University , 436 Hunter Laboratories, Clemson, South Carolina 29634-0973, United States
| | - Loren Dean Williams
- School of Chemistry and Biochemistry, Georgia Institute of Technology , 315 Ferst Drive NW, Atlanta, Georgia 30332-0363, United States
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18
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Patwardhan NN, Ganser LR, Kapral GJ, Eubanks CS, Lee J, Sathyamoorthy B, Al-Hashimi HM, Hargrove AE. Amiloride as a new RNA-binding scaffold with activity against HIV-1 TAR. MEDCHEMCOMM 2017; 8:1022-1036. [PMID: 28798862 PMCID: PMC5546750 DOI: 10.1039/c6md00729e] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/31/2016] [Accepted: 03/14/2017] [Indexed: 12/23/2022]
Abstract
Diversification of RNA-targeted scaffolds offers great promise in the search for selective ligands of therapeutically relevant RNA such as HIV-1 TAR. We herein report the establishment of amiloride as a novel RNA-binding scaffold along with synthetic routes for combinatorial C(5)- and C(6)-diversification. Iterative modifications at the C(5)- and C(6)- positions yielded derivative 24, which demonstrated a 100-fold increase in activity over the parent dimethylamiloride in peptide displacement assays. NMR chemical shift mapping was performed using the 2D SOFAST- [1H-13C] HMQC NMR method, which allowed for facile and rapid evaluation of binding modes for all library members. Cheminformatic analysis revealed distinct differences between selective and non-selective ligands. In this study, we evolved dimethylamiloride from a weak TAR ligand to one of the tightest binding selective TAR ligands reported to date through a novel combination of synthetic methods and analytical techniques. We expect these methods to allow for rapid library expansion and tuning of the amiloride scaffold for a range of RNA targets and for SOFAST NMR to allow unprecedented evaluation of small molecule:RNA interactions.
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Affiliation(s)
- Neeraj N. Patwardhan
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Laura R. Ganser
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Gary J. Kapral
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Christopher S. Eubanks
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
| | - Janghyun Lee
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Bharathwaj Sathyamoorthy
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Hashim M. Al-Hashimi
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
| | - Amanda E. Hargrove
- Department of Chemistry
, Duke University
,
Durham
, North Carolina 27708
, USA
.
; Tel: +1 919 660 1522
- Department of Biochemistry
, Duke University Medical Center
,
Durham
, North Carolina 27708
, USA
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19
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Self-assembling complexes between binary mixtures of lipids with different linkers and nucleic acids promote universal mRNA, DNA and siRNA delivery. J Control Release 2017; 249:131-142. [DOI: 10.1016/j.jconrel.2017.01.041] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 01/28/2017] [Indexed: 12/18/2022]
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20
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Li Y, Syed J, Sugiyama H. RNA-DNA Triplex Formation by Long Noncoding RNAs. Cell Chem Biol 2016; 23:1325-1333. [DOI: 10.1016/j.chembiol.2016.09.011] [Citation(s) in RCA: 110] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/29/2016] [Accepted: 09/26/2016] [Indexed: 01/06/2023]
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21
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Kumar S, Ranjan N, Kellish P, Gong C, Watkins D, Arya DP. Multivalency in the recognition and antagonism of a HIV TAR RNA-TAT assembly using an aminoglycoside benzimidazole scaffold. Org Biomol Chem 2016; 14:2052-6. [PMID: 26765486 DOI: 10.1039/c5ob02016f] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Recognition of RNA by high-affinity binding small molecules is crucial for expanding existing approaches in RNA recognition, and for the development of novel RNA binding drugs. A novel neomycin dimer benzimidazole conjugate 5 (DPA 83) was synthesized by conjugating a neomycin-dimer with a benzimidazole alkyne using click chemistry to target multiple binding sites on HIV TAR RNA. Ligand 5 significantly enhances the thermal stability of HIV TAR RNA and interacts stoichiometrically with HIV TAR RNA with a low nanomolar affinity. 5 displayed enhanced binding compared to its individual building blocks including the neomycin dimer azide and benzimidazole alkyne. In essence, a high affinity multivalent ligand was designed and synthesized to target HIV TAR RNA.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
| | - Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA. and Nubad LLC, 900 B West Faris Road, Greenville, SC 29630, USA
| | - Patrick Kellish
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
| | - Changjun Gong
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
| | | | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, USA.
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22
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Mével M, Haudebourg T, Colombani T, Peuziat P, Dallet L, Chatin B, Lambert O, Berchel M, Montier T, Jaffrès PA, Lehn P, Pitard B. Important role of phosphoramido linkage in imidazole-based dioleyl helper lipids for liposome stability and primary cell transfection. J Gene Med 2016; 18:3-15. [PMID: 26519353 DOI: 10.1002/jgm.2869] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Revised: 10/28/2015] [Accepted: 10/29/2015] [Indexed: 01/30/2023] Open
Abstract
BACKGROUND To optimize synthetic gene delivery systems, there is a need to develop more efficient lipid formulations. Most cationic lipid formulations contain 'helper' neutral lipids because of their ability to increase DNA delivery, in particular by improving endosomal escape of DNA molecules via the pH-buffering effect of protonatable groups and/or fusion with the lipid bilayer of endosomes. METHODS We evaluated the influence of the linker structure between the two oleyl chains in the helper lipid on transfection efficiency in cell lines, as well as in primary cells (hepatocytes/cardiomyocytes). We reported the synthesis of two new pH-buffering imidazole helper lipids characterized by a polar headgroup containing one (compound 6) or two (compound 5) imidazole groups and two oleyl chains linked by an amide group. We studied their association with the aminoglycoside lipidic derivative dioleylsuccinylparomomycin (DOSP), which contains two oleyl chains linked to the aminoglycoside polar headgroup via an amide function. We compared the morphology and transfection properties of such binary liposomes of DOSP/5 and DOSP/6 with those of liposomes combining DOSP with another imidazole-based dioleyl helper lipid (MM27) in which a phosphoramido group acts as a linker between the two oleyl chains and imidazole function. RESULTS The phosphoramido linker in the helper lipid induces a major difference in terms of morphology and resistance to decomplexation at physical pH for DOSP/helper lipid complexes. CONCLUSIONS This hybrid dioleyl linker composition of DOSP/MM27 led to higher transfection efficiency in cell lines and in primary cells compared to complexes with homogeneous dioleyl linker.
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Affiliation(s)
- Mathieu Mével
- Unité INSERM UMR 1087, CNRS UMR 6291, Nantes, France
- Université de Nantes, l'institut du thorax, Nantes, France
| | - Thomas Haudebourg
- Unité INSERM UMR 1087, CNRS UMR 6291, Nantes, France
- Université de Nantes, l'institut du thorax, Nantes, France
| | - Thibault Colombani
- Unité INSERM UMR 1087, CNRS UMR 6291, Nantes, France
- Université de Nantes, l'institut du thorax, Nantes, France
| | - Pauline Peuziat
- Unité INSERM UMR 1087, CNRS UMR 6291, Nantes, France
- Université de Nantes, l'institut du thorax, Nantes, France
| | - Laurence Dallet
- Unité INSERM UMR 1087, CNRS UMR 6291, Nantes, France
- Université de Nantes, l'institut du thorax, Nantes, France
- CBMN UMR-CNRS 5248 IECB, Université de Bordeaux 1-IPB, Pessac, France
| | - Benoît Chatin
- Unité INSERM UMR 1087, CNRS UMR 6291, Nantes, France
- Université de Nantes, l'institut du thorax, Nantes, France
| | - Olivier Lambert
- CBMN UMR-CNRS 5248 IECB, Université de Bordeaux 1-IPB, Pessac, France
| | - Mathieu Berchel
- UMR CNRS 6521, IFR 148 ScInBioS, Université de Bretagne Occidentale, Université Européenne de Bretagne, Brest, France
| | - Tristan Montier
- Unité INSERM 1078, IFR 148 ScInBioS, Université de Bretagne Occidentale, Université Européenne de Bretagne, Brest Cedex, France
- Service de Génétique Moléculaire et d'histocompatibilité, CHUR, Brest, France
| | - Paul-Alain Jaffrès
- UMR CNRS 6521, IFR 148 ScInBioS, Université de Bretagne Occidentale, Université Européenne de Bretagne, Brest, France
| | - Pierre Lehn
- Unité INSERM 1078, IFR 148 ScInBioS, Université de Bretagne Occidentale, Université Européenne de Bretagne, Brest Cedex, France
| | - Bruno Pitard
- Unité INSERM UMR 1087, CNRS UMR 6291, Nantes, France
- Université de Nantes, l'institut du thorax, Nantes, France
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23
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Kumar S, Newby Spano M, Arya DP. Shape readout of AT-rich DNA by carbohydrates. Biopolymers 2016; 101:720-32. [PMID: 24281844 DOI: 10.1002/bip.22448] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2013] [Revised: 11/10/2013] [Accepted: 11/23/2013] [Indexed: 12/16/2022]
Abstract
Gene expression can be altered by small molecules that target DNA; sequence as well as shape selectivities are both extremely important for DNA recognition by intercalating and groove-binding ligands. We have characterized a carbohydrate scaffold (1) exhibiting DNA "shape readout" properties. Thermodynamic studies with 1 and model duplex DNAs demonstrate the molecule's high affinity and selectivity towards B* form (continuous AT-rich) DNA. Isothermal titration calorimetry (ITC), circular dichroism (CD) titration, ultraviolet (UV) thermal denaturation, and Differential Scanning Calorimetry were used to characterize the binding of 1 with a B* form AT-rich DNA duplex d[5'-G2 A6 T6 C2 -3']. The binding constant was determined using ITC at various temperatures, salt concentrations, and pH. ITC titrations were fit using a two-binding site model. The first binding event was shown to have a 1:1 binding stoichiometry and was predominantly entropy-driven with a binding constant of approximately 10(8) M(-1) . ITC-derived binding enthalpies were used to obtain the binding-induced change in heat capacity (ΔCp ) of -225 ± 19 cal/mol·K. The ionic strength dependence of the binding constant indicated a significant electrolytic contribution in ligand:DNA binding, with approximately four to five ion pairs involved in binding. Ligand 1 displayed a significantly higher affinity towards AT-tract DNA over sequences containing GC inserts, and binding experiments revealed the order of binding affinity for 1 with DNA duplexes: contiguous B* form AT-rich DNA (d[5'-G2 A6 T6 C2 -3']) >B form alternate AT-rich DNA (d[5'-G2 (AT)6 C2- 3']) > A form GC-rich DNA (d[5'-A2 G6 C6 T2 -3']), demonstrating the preference of ligand 1 for B* form DNA.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC, 29634
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24
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Jiménez-Moreno E, Montalvillo-Jiménez L, Santana AG, Gómez AM, Jiménez-Osés G, Corzana F, Bastida A, Jiménez-Barbero J, Cañada FJ, Gómez-Pinto I, González C, Asensio JL. Finding the Right Candidate for the Right Position: A Fast NMR-Assisted Combinatorial Method for Optimizing Nucleic Acids Binders. J Am Chem Soc 2016; 138:6463-74. [DOI: 10.1021/jacs.6b00328] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- Ester Jiménez-Moreno
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | | | - Andrés G. Santana
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Ana M. Gómez
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Gonzalo Jiménez-Osés
- Departamento de Química y Centro de Investigación en
Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
- Institute of Biocomputation and Physics of Complex Systems
(BIFI), University of Zaragoza, BIFI-IQFR (CSIC), 50018 Zaragoza, Spain
| | - Francisco Corzana
- Departamento de Química y Centro de Investigación en
Síntesis Química, Universidad de La Rioja, 26006 Logroño, La Rioja, Spain
| | - Agatha Bastida
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
| | - Jesús Jiménez-Barbero
- Centro de Investigaciones Biológicas (CIB-CSIC), Ramiro de Maeztu 9, 28040 Madrid, Spain
- Center for Cooperative Research in Biosciences (CIC-bioGUNE), 48160 Derio, Bizkaia, Spain
- Basque Foundation for Science, Ikerbasque, 48013 Bilbao, Bizkaia, Spain
| | | | - Irene Gómez-Pinto
- Instituto de Química-Física Rocasolano (IQFR-CSIC), C/ Serrano 119, 28006 Madrid, Spain
| | - Carlos González
- Instituto de Química-Física Rocasolano (IQFR-CSIC), C/ Serrano 119, 28006 Madrid, Spain
| | - Juan Luis Asensio
- Instituto de Química Orgánica (IQOG-CSIC), Juan de la Cierva 3, 28006 Madrid, Spain
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25
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Haque L, Bhuiya S, Tiwari R, Pradhan AB, Das S. Biophysical insight into the interaction of the bioflavonoid kaempferol with triple and double helical RNA and the dual fluorescence behaviour of kaempferol. RSC Adv 2016. [DOI: 10.1039/c6ra12445c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Binding of kaempferol with triple and double helical RNA.
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Affiliation(s)
- Lucy Haque
- Department of Chemistry
- Jadavpur University
- Jadavpur
- India
| | | | - Richa Tiwari
- Department of Chemistry
- Jadavpur University
- Jadavpur
- India
| | | | - Suman Das
- Department of Chemistry
- Jadavpur University
- Jadavpur
- India
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26
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A pH Sensitive High-Throughput Assay for miRNA Binding of a Peptide-Aminoglycoside (PA) Library. PLoS One 2015; 10:e0144251. [PMID: 26656788 PMCID: PMC4699463 DOI: 10.1371/journal.pone.0144251] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2015] [Accepted: 11/16/2015] [Indexed: 11/19/2022] Open
Abstract
MicroRNAs (miRNA) are small RNAs that have a regulatory role in gene expression. Because of this regulatory role, miRNAs have become a new target for therapeutic compounds. Here, we outline an approach to target specific miRNAs using a high throughput capable assay and a 215 compound peptidic-aminosugar (PA) library. Aminosugars have been shown in a number of recent reports as important lead compounds that bind miRNA. In order to screen for compounds that bind miRNA, we have developed a high throughput displacement assay using a fluorescein-neomycin conjugated molecule (F-neo) as a probe for competitive miRNA binding compounds. We have applied the F-neo assay to four different miRNA constructs and the assay is applicable to most miRNAs, at various stages of processing. The results of the screen were validated by the determination of the IC50 for a select group of compounds from the library. For example, we identified eight compounds that bind to hsa-miR 504 with higher affinity than the parent neomycin. From the F-neo displacement assay we found that the number of binding sites differs for each miRNA, and the binding sites appear to differ both physically and chemically, with different affinity of the compounds resulting from the size of the molecule as well as the chemical structure. Additionally, the affinity of the compounds was dependent on the identity and position of the amino acid position of conjugation and the affinity of the compounds relative to other compounds in the library was miRNA dependent with the introduction of a second amino acid.
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Kumar S, Spano MN, Arya DP. Influence of linker length in shape recognition of B* DNA by dimeric aminoglycosides. Bioorg Med Chem 2015; 23:3105-9. [PMID: 26025072 DOI: 10.1016/j.bmc.2015.04.082] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2015] [Revised: 04/22/2015] [Accepted: 04/30/2015] [Indexed: 10/23/2022]
Abstract
DNA-protein recognition has shown us the importance of DNA shapes in the recognition process. Specific high-affinity targeting of DNA shapes by small molecules is desirable for many biological applications that involve regulation of DNA based processes. Here, the effect of linker length and rigidity on the affinity of a conjugated neomycin dimer for a specific DNA shape (B* form) AT-rich DNA was explored. Binding constants approximating 10(8)M(-1) for optimal linker lengths of 18-19 atoms are reported herein.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States
| | | | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634, United States.
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28
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Tumir LM, Radić Stojković M, Piantanida I. Come-back of phenanthridine and phenanthridinium derivatives in the 21st century. Beilstein J Org Chem 2014; 10:2930-54. [PMID: 25550761 PMCID: PMC4273281 DOI: 10.3762/bjoc.10.312] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 11/21/2014] [Indexed: 12/23/2022] Open
Abstract
Phenanthridine derivatives are one of the most intensively studied families of biologically active compounds with efficient DNA binding capability. Attracting attention since DNA structure discovery (1960s), they were early recognized as a symbol of DNA intercalative binding, for many decades applied as gold-standard DNA- and RNA-fluorescent markers (ethidium bromide), probes for cell viability (propidium iodide), but also “ill-famed” for various toxic (genotoxic) and mutagenic effects. After two decades of low interest, the discovery of phenanthridine alkaloids and new studies of antiparasitic/antitumor properties of phenanthridine derivatives resulted in the strong increase of the scientific interest about the turn of this century. Here are summarized phenanthridine-related advances in the 21st century (2000-present period) with emphasis on the supramolecular interactions and bioorganic chemistry, as well as novel or improved synthetic approaches.
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Affiliation(s)
- Lidija-Marija Tumir
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| | - Marijana Radić Stojković
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
| | - Ivo Piantanida
- Laboratory for Study of Interactions of Biomacromolecules, Division of Organic Chemistry and Biochemistry, Ruđer Bošković Institute, Bijenička cesta 54, PO Box 180, HR-10002 Zagreb, Croatia
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29
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Grandhi TSP, Mallik A, Lin KN, Miryala B, Potta T, Tian Y, Rege K. Aminoglycoside antibiotic-derived anion-exchange microbeads for plasmid DNA binding and in situ DNA capture. ACS APPLIED MATERIALS & INTERFACES 2014; 6:18577-89. [PMID: 25314226 DOI: 10.1021/am503240q] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Plasmid DNA (pDNA) therapeutics are being investigated for gene therapy and DNA vaccines against diseases including cancer, cystic fibrosis and AIDS. In addition, several applications in modern biotechnology require pDNA for transient protein production. Here, we describe the synthesis, characterization, and evaluation of microbeads ("Amikabeads") derived from the aminoglycoside antibiotic amikacin for pDNA binding and in situ DNA capture from mammalian cells. The parental aminoglycoside-derived microbeads (Amikabeads-P) acted as anion-exchange materials, and demonstrated high capacities for binding pDNA. Binding of pDNA was significantly enhanced following quaternization of the amines on the microbeads (Amikabeads-Q). Amikabeads were further employed for the disruption and extraction of DNA from mammalian cells, indicating their utility for in situ DNA capture. Our results indicate that Amikabeads are a novel material, with multiple reactive groups for further conjugation, and can have several applications in plasmid DNA biotechnology.
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Affiliation(s)
- Taraka Sai Pavan Grandhi
- Harrington Biomedical Engineering, School of Biological and Health Systems Engineering ‡Chemical Engineering, School for Engineering of Matter, Transport, and Energy, Arizona State University , Tempe, Arizona 85287, United States
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Nakano M, Tateishi-Karimata H, Tanaka S, Sugimoto N. Affinity of Molecular Ions for DNA Structures Is Determined by Solvent-Accessible Surface Area. J Phys Chem B 2014; 118:9583-94. [DOI: 10.1021/jp505107g] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
| | | | - Shigenori Tanaka
- Graduate
School of System Informatics, Department of Computational Science, Kobe University, 1-1, Rokkodai, Nada-ku, Kobe 657-8501, Japan
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31
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Kellish PC, Kumar S, Mack TS, Spano MN, Hennig M, Arya DP. Multivalent Amino Sugars to Recognize Different TAR RNA Conformations. MEDCHEMCOMM 2014; 5:1235-1246. [PMID: 27076899 DOI: 10.1039/c4md00165f] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Neomycin dimers synthesized using "click chemistry" with varying functionality and length in the linker region have been shown to be effective in targeting the HIV-1 TAR RNA region of the HIV virus. TAR (Transactivation Response) RNA region, a 59 base pair stem loop structure located at the 5'-end of all nascent viral transcripts interacts with its target, a key regulatory protein, Tat, and necessitates the replication of HIV-1 virus. Ethidium bromide displacement and FRET competition assays have revealed nanomolar binding affinity between neomycin dimers and wildtype TAR RNA while in case of neomycin, only a weak binding was detected. Here, NMR and FID-based comparisons reveal an extended binding interface for neomycin dimers involving the upper stem of the TAR RNA thereby offering an explanation for increased affinities. To further explore the potential of these modified aminosugars we have extended binding studies to include four TAR RNA mutants that display conformational differences with minimal sequence variation. The differences in binding between neomycin and neomycin dimers is characterized with TAR RNA mutants that include mutations to the bulge region, hairpin region, and both the bulge and hairpin regions. Our results demonstrate the effect of these mutations on neomycin binding and our results show that linker functionalities between dimeric units of neomycin can distinguish between the conformational differences of mutant TAR RNA structures.
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Affiliation(s)
- Patrick C Kellish
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
| | - Todd S Mack
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 70 President St., Charleston, SC 29425
| | | | - Mirko Hennig
- Department of Biochemistry and Molecular Biology, Medical University of South Carolina, 70 President St., Charleston, SC 29425
| | - Dev P Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States; NUBAD, LLC, 900B West Faris Rd., Greenville, SC 29605
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32
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Dudek M, Romanowska J, Wituła T, Trylska J. Interactions of amikacin with the RNA model of the ribosomal A-site: computational, spectroscopic and calorimetric studies. Biochimie 2014; 102:188-202. [PMID: 24769038 DOI: 10.1016/j.biochi.2014.03.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2013] [Accepted: 03/20/2014] [Indexed: 10/25/2022]
Abstract
Amikacin is a 2-deoxystreptamine aminoglycoside antibiotic possessing a unique l-HABA (l-(-)-γ-amino-α-hydroxybutyric acid) group and applied in the treatment of hospital-acquired infections. Amikacin influences bacterial translation by binding to the decoding region of the small ribosomal subunit that overlaps with the binding site of aminoacylated-tRNA (A-site). Here, we have characterized thermodynamics of interactions of amikacin with a 27-mer RNA oligonucleotide mimicking the aminoglycoside binding site in the bacterial ribosome. We applied isothermal titration and differential scanning calorimetries, circular dichroism and thermal denaturation experiments, as well as computer simulations. Thermal denaturation studies have shown that amikacin affects only slightly the melting temperatures of the A-site mimicking RNA model suggesting a moderate stabilization of RNA by amikacin. Isothermal titration calorimetry gives the equilibrium dissociation constants for the binding reaction between amikacin and the A-site oligonucleotide in the micromolar range with a favorable enthalpic contribution. However, for amikacin we observe a positive entropic contribution to binding, contrary to other aminoglycosides, paromomycin and ribostamycin. Circular dichroism spectra suggest that the observed increase in entropy is not caused by structural changes of RNA because amikacin binding does not destabilize the helicity of the RNA model. To investigate the origins of this positive entropy change we performed all-atom molecular dynamics simulations in explicit solvent for the 27-mer RNA oligonucleotide mimicking one A-site and the crystal structure of an RNA duplex containing two A-sites. We observed that the diversity of the conformational states of the l-HABA group sampled in the simulations of the complex was larger than for the free amikacin in explicit water. Therefore, the larger flexibility of the l-HABA group in the bound form may contribute to an increase of entropy upon binding.
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Affiliation(s)
- Marta Dudek
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland; Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawińskiego 5a, 02-106 Warsaw, Poland; First Faculty of Medicine, Department of Hematology, Oncology and Internal Diseases, Medical University of Warsaw, Al. Żwirki i Wigury 61, 02-091 Warsaw, Poland
| | - Julia Romanowska
- Department of Biophysics, Faculty of Physics, University of Warsaw, Hoża 69, 00-681 Warsaw, Poland; Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, Pawińskiego 5a, 02-106 Warsaw, Poland
| | - Tomasz Wituła
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland
| | - Joanna Trylska
- Centre of New Technologies, University of Warsaw, Al. Żwirki i Wigury 93, 02-089 Warsaw, Poland.
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33
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Willis B, Arya DP. Recognition of RNA duplex by a neomycin–Hoechst 33258 conjugate. Bioorg Med Chem 2014; 22:2327-32. [DOI: 10.1016/j.bmc.2014.02.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2013] [Revised: 01/27/2014] [Accepted: 02/06/2014] [Indexed: 01/01/2023]
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Comparable stability of Hoogsteen and Watson-Crick base pairs in ionic liquid choline dihydrogen phosphate. Sci Rep 2014; 4:3593. [PMID: 24399194 PMCID: PMC3884231 DOI: 10.1038/srep03593] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Accepted: 12/03/2013] [Indexed: 02/06/2023] Open
Abstract
The instability of Hoogsteen base pairs relative to Watson-Crick base pairs has limited biological applications of triplex-forming oligonucleotides. Hydrated ionic liquids (ILs) provide favourable environments for a wide range of chemical reactions and are known to impact the stabilities of Watson-Crick base pairs. We found that DNA triplex formation was significantly stabilized in hydrated choline dihydrogen phosphate as compared with an aqueous buffer at neutral pH. Interestingly, the stability of Hoogsteen base pairs was found to be comparable with that of Watson-Crick base pairs in the hydrated IL. Molecular dynamics simulations of a DNA triplex in the presence of choline ions revealed that the DNA triplex was stabilized because of the binding of choline ion around the third strand in the grooves. Our finding will facilitate the development of new DNA materials. Our data also indicate that triplex formation may be stabilized inside cells where choline ions and their derivatives are abundant in vivo.
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35
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Targeting C-myc G-quadruplex: dual recognition by aminosugar-bisbenzimidazoles with varying linker lengths. Molecules 2013; 18:14228-40. [PMID: 24252993 PMCID: PMC6270413 DOI: 10.3390/molecules181114228] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2013] [Revised: 11/04/2013] [Accepted: 11/08/2013] [Indexed: 12/01/2022] Open
Abstract
G-quadruplexes are therapeutically important biological targets. In this report, we present biophysical studies of neomycin-Hoechst 33258 conjugates binding to a G-quadruplex derived from the C-myc promoter sequence. Our studies indicate that conjugation of neomycin to a G-quadruplex binder, Hoechst 33258, enhances its binding. The enhancement in G-quadruplex binding of these conjugates varies with the length and composition of the linkers joining the neomycin and Hoechst 33258 units.
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36
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Biver T. Stabilisation of non-canonical structures of nucleic acids by metal ions and small molecules. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.04.016] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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37
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Affiliation(s)
- Yuhao Du
- College of Chemistry and Molecular Sciences; Wuhan University; Hubei; Wuhan; 430072; P. R. China
| | - Xiang Zhou
- College of Chemistry and Molecular Sciences; Wuhan University; Hubei; Wuhan; 430072; P. R. China
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38
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Beck A, Vijayanathan V, Thomas T, Thomas TJ. Ionic microenvironmental effects on triplex DNA stabilization: cationic counterion effects on poly(dT)·poly(dA)·poly(dT). Biochimie 2013; 95:1310-8. [PMID: 23454377 DOI: 10.1016/j.biochi.2013.02.012] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2012] [Accepted: 02/18/2013] [Indexed: 12/18/2022]
Abstract
The structure and conformation of nucleic acids are influenced by metal ions, polyamines, and the microenvironment. In poly(purine) · poly(pyrimidine) sequences, triplex DNA formation is facilitated by metal ions, polyamines and other ligands. We studied the effects of mono- and di-valent metal ions, and ammonium salts on the stability of triple- and double-stranded structures formed from poly(dA) and poly(dT) by measuring their respective melting temperatures. In the presence of metal ions, the absorbance versus temperature profile showed two transitions: Tm1 for triplex to duplex and single stranded DNA, and Tm2 for duplex DNA melting to single stranded DNA. Monovalent cations (Li(+), Na(+), K(+), Rb(+), Cs(+) and [Formula: see text] ) promoted triplex DNA at concentrations ≥150 mM. Tm1 varied from 49.8 °C in the presence of 150 mM Li(+) to 30.6 °C in the presence of 150 mM K(+). [Formula: see text] was very effective in stabilizing triplex DNA and its efficacy decreased with increasing substitution of the hydrogen atoms with methyl, ethyl, propyl and butyl groups. As in the case of monovalent cations, a concentration-dependent increase in Tm1 was observed with divalent ions and triplex DNA stabilization decreased in the order: Mg(2+) > Ca(2+) > Sr(2+) > Ba(2+). All positively charged cations increased the melting temperature of duplex DNA. Values of Δn (number of ions released) on triplex DNA melting were 0.46 ± 0.06 and 0.18 ± 0.02, respectively, for mono- and di-valent cations, as calculated from 1/Tm1 versus ln[M(+,2+)] plots. The corresponding values for duplex DNA were 0.25 ± 0.02 and 0.12 ± 0.02, respectively, for mono- and di-valent cations. Circular dichroism spectroscopic studies showed distinct conformational changes in triplex DNA stabilized by alkali metal and ammonium ions. Our results might be useful in developing triplex forming oligonucleotide based gene silencing techniques.
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Affiliation(s)
- Amanda Beck
- Department of Medicine, University of Medicine and Dentistry of New Jersey, Robert Wood Johnson Medical School, 125 Paterson St, New Brunswick, NJ 08903, USA
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39
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Charles I, Davis E, Arya DP. Efficient stabilization of phosphodiester (PO), phosphorothioate (PS), and 2'-O-methoxy (2'-OMe) DNA·RNA hybrid duplexes by amino sugars. Biochemistry 2012; 51:5496-505. [PMID: 22639785 DOI: 10.1021/bi3004507] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Antisense strategies that target DNA·RNA hybrid structures offer potential for the development of new therapeutic drugs. The α-sarcin loop region of the 23S [corrected] rRNA domain has been shown to be a high value target for such strategies. Herein, aminoglycoside interaction with three RNA·DNA α-sarcin targeted duplexes (rR·dY, rR·S-dY, and rR·2'OMe-rY) have been investigated to determine the overall effect of aminoglycoside interaction on the stability, affinity, and conformation of these hybrid duplexes. To this end, UV thermal denaturation, circular dichroism spectroscopy, fluorescence intercalator displacement, and ITC as well as DSC calorimetry experiments were carried out. The results suggest the following. (1) Of all the aminoglycosides studied, neomycin confers the highest thermal stability on all three hybrid duplexes studied. (2) There is no appreciable difference in aminoglycoside-induced thermal stability between the unmodified rR·dY and phophorothioate modified rR·S-dY duplexes. (3) The rR·2'OMe-rY duplexes thermal stability is slightly less than the other two hybrids. (4) In all three duplexes, aminoglycoside-induced thermal stability decreased as the number of amino groups decreased. (5) CD scans revealed similar spectra for the rR·dY and rR·S-dY duplexes as well as a more pronounced A-form signal for the rR·2'OMe-rY duplex. (6) FID assays paralleled the CD results, yielding similar affinity values between the rR·dY and rR·S-dY duplexes and higher affinities with the rR·2'OMe-rY duplex. (7) The overall affinity trend between aminoglycosides and the three duplexes was determined to be neomycin > paromomycin > neamine > ribostamycin. (8) ITC K(a) values revealed similar binding constants for the rR·dY and rR·S-dY duplexes with rR·dY having a K(1) of (1.03 ± 0.58) × 10(7) M(-1) and K(2) of (1.13 ± 0.07) × 10(5) M(-1) while rR·S-dY produced a K(1) of (1.17 ± 0.54) × 10(7) M(-1) and K(2) of (1.27 ± 0.69) × 10(5) M(-1). (8) The rR·2'OMe-rY produced a slightly higher binding constant values with a K(1) of (1.25 ± 0.24) × 10(7) M(-1) and K(2) of (3.62 ± 0.18) × 10(5) M(-1). (9) The ΔT(m)-derived K(Tm) of 3.81 × 10(7) M(-1) for rR·S-dY was in relative agreement with the corresponding K(1) of 1.17 × 10(7) M(-1) derived constant from the fitted ITC. These results illustrate that the increased DNA·RNA hybrid duplex stability in the presence of aminoglycosides can help extend the roles of aminoglycosides in designing modified ODNs for targeting RNA.
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Affiliation(s)
- I Charles
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, South Carolina 29634, United States
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40
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Chang YM, Chen CKM, Hou MH. Conformational changes in DNA upon ligand binding monitored by circular dichroism. Int J Mol Sci 2012; 13:3394-3413. [PMID: 22489158 PMCID: PMC3317384 DOI: 10.3390/ijms13033394] [Citation(s) in RCA: 129] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2012] [Revised: 02/22/2012] [Accepted: 02/24/2012] [Indexed: 11/16/2022] Open
Abstract
Circular dichroism (CD) spectroscopy is an optical technique that measures the difference in the absorption of left and right circularly polarized light. This technique has been widely employed in the studies of nucleic acids structures and the use of it to monitor conformational polymorphism of DNA has grown tremendously in the past few decades. DNA may undergo conformational changes to B-form, A-form, Z-form, quadruplexes, triplexes and other structures as a result of the binding process to different compounds. Here we review the recent CD spectroscopic studies of the induction of DNA conformational changes by different ligands, which includes metal derivative complex of aureolic family drugs, actinomycin D, neomycin, cisplatin, and polyamine. It is clear that CD spectroscopy is extremely sensitive and relatively inexpensive, as compared with other techniques. These studies show that CD spectroscopy is a powerful technique to monitor DNA conformational changes resulting from drug binding and also shows its potential to be a drug-screening platform in the future.
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Affiliation(s)
- Yu-Ming Chang
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; E-Mails: (Y.-M.C.); (C.K.-M.C.)
| | - Cammy K.-M. Chen
- Institute of Biological Chemistry, Academia Sinica, Taipei 115, Taiwan; E-Mails: (Y.-M.C.); (C.K.-M.C.)
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics, National Chung Hsing University, Taichung 402, Taiwan
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Kumar S, Kellish P, Robinson WE, Wang D, Appella DH, Arya DP. Click dimers to target HIV TAR RNA conformation. Biochemistry 2012; 51:2331-47. [PMID: 22339203 DOI: 10.1021/bi201657k] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A series of neomycin dimers have been synthesized using "click chemistry" with varying functionality and length in the linker region to target the human immunodeficiency virus type 1 (HIV-1) TAR RNA region of the HIV virus. The TAR (Trans-Activation Responsive) RNA region, a 59 bp stem-loop structure located at the 5'-end of all nascent viral transcripts, interacts with its target, a key regulatory protein, Tat, and necessitates the replication of HIV-1. Neomycin, an aminosugar, has been shown to exhibit multiple binding sites on TAR RNA. This observation prompted us to design and synthesize a library of triazole-linked neomycin dimers using click chemistry. The binding between neomycin dimers and TAR RNA was characterized using spectroscopic techniques, including FID (fluorescent intercalator displacement), a FRET (fluorescence resonance energy transfer) competitive assay, circular dichroism (CD), and UV thermal denaturation. UV thermal denaturation studies demonstrate that binding of neomycin dimers increases the melting temperature (T(m)) of the HIV TAR RNA up to 10 °C. Ethidium bromide displacement (FID) and a FRET competition assay revealed nanomolar binding affinity between neomycin dimers and HIV TAR RNA, while in case of neomycin, only weak binding was detected. More importantly, most of the dimers exhibited lower IC(50) values toward HIV TAR RNA, when compared to the fluorescent Tat peptide, and show increased selectivity over mutant TAR RNA. Cytopathic effects investigated using MT-2 cells indicate a number of the dimers with high affinity toward TAR show promising anti-HIV activity.
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina 29634, United States
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42
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Paromomycin and neomycin B derived cationic lipids: Synthesis and transfection studies. J Control Release 2012; 158:461-9. [DOI: 10.1016/j.jconrel.2011.12.019] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2011] [Revised: 12/12/2011] [Accepted: 12/17/2011] [Indexed: 11/21/2022]
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Wongsurawat T, Jenjaroenpun P, Kwoh CK, Kuznetsov V. Quantitative model of R-loop forming structures reveals a novel level of RNA-DNA interactome complexity. Nucleic Acids Res 2011; 40:e16. [PMID: 22121227 PMCID: PMC3258121 DOI: 10.1093/nar/gkr1075] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
R-loop is the structure co-transcriptionally formed between nascent RNA transcript and DNA template, leaving the non-transcribed DNA strand unpaired. This structure can be involved in the hyper-mutation and dsDNA breaks in mammalian immunoglobulin (Ig) genes, oncogenes and neurodegenerative disease related genes. R-loops have not been studied at the genome scale yet. To identify the R-loops, we developed a computational algorithm and mapped R-loop forming sequences (RLFS) onto 66,803 sequences defined by UCSC as 'known' genes. We found that ∼59% of these transcribed sequences contain at least one RLFS. We created R-loopDB (http://rloop.bii.a-star.edu.sg/), the database that collects all RLFS identified within over half of the human genes and links to the UCSC Genome Browser for information integration and visualisation across a variety of bioinformatics sources. We found that many oncogenes and tumour suppressors (e.g. Tp53, BRCA1, BRCA2, Kras and Ptprd) and neurodegenerative diseases related genes (e.g. ATM, Park2, Ptprd and GLDC) could be prone to significant R-loop formation. Our findings suggest that R-loops provide a novel level of RNA-DNA interactome complexity, playing key roles in gene expression controls, mutagenesis, recombination process, chromosomal rearrangement, alternative splicing, DNA-editing and epigenetic modifications. RLFSs could be used as a novel source of prospective therapeutic targets.
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Affiliation(s)
- Thidathip Wongsurawat
- Department of Genome and Gene Expression Data Analysis, Bioinformatics Institute, Singapore 138671
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45
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Zhang L, Peng J, Tang J, Yuan B, He R, Xiao Y. Description and validation of coupling high performance liquid chromatography with resonance Rayleigh scattering in aminoglycosides determination. Anal Chim Acta 2011; 706:199-204. [DOI: 10.1016/j.aca.2011.09.025] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2011] [Revised: 09/09/2011] [Accepted: 09/15/2011] [Indexed: 11/29/2022]
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46
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Xi H, Davis E, Ranjan N, Xue L, Hyde-Volpe D, Arya DP. Thermodynamics of nucleic acid "shape readout" by an aminosugar. Biochemistry 2011; 50:9088-113. [PMID: 21863895 PMCID: PMC3673541 DOI: 10.1021/bi201077h] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Recognition of nucleic acids is important for our understanding of nucleic acid structure as well as for our understanding of nucleic acid-protein interactions. In addition to the direct readout mechanisms of nucleic acids such as H-bonding, shape recognition of nucleic acids is being increasingly recognized as playing an equally important role in DNA recognition. Competition dialysis, UV, flourescent intercalator displacement (FID), computational docking, and calorimetry studies were conducted to study the interaction of neomycin with a variety of nucleic acid conformations (shapes). At pH 5.5, the results suggest the following. (1) Neomycin binds three RNA structures [16S A site rRNA, poly(rA)·poly(rA), and poly(rA)·poly(rU)] with high affinities (K(a) ~ 10(7) M(-1)). (2) The binding of neomycin to A-form GC-rich oligomer d(A(2)G(15)C(15)T(2))(2) has an affinity comparable to those of RNA structures. (3) The binding of neomycin to DNA·RNA hybrids shows a 3-fold variance that can be attributed to their structural differences [for poly(dA)·poly(rU), K(a) = 9.4 × 10(6) M(-1), and for poly(rA)·poly(dT), K(a) = 3.1 × 10(6) M(-1)]. (4) The interaction of neomycin with DNA triplex poly(dA)·2poly(dT) yields a binding affinity (K(a)) of 2.4 × 10(5) M(-1). (5) Poly(dA-dT)(2) shows the lowest association constant for all nucleic acids studied (K(a) < 10(5)). (6) Neomycin binds to G-quadruplexes with K(a) values of ~10(4)-10(5) M(-1). (7) Computational studies show that the decrease in major groove width in the B to A transition correlates with increasing neomycin affinity. Neomycin's affinity for various nucleic acid structures can be ranked as follows: RNAs and GC-rich d(A(2)G(15)C(15)T(2))(2) structures > poly(dA)·poly(rU) > poly(rA)·poly(dT) > T·A-T triplex, G-quadruplex, B-form AT-rich, or GC-rich DNA sequences. The results illustrate the first example of a small molecule-based "shape readout" of different nucleic acid conformations.
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Affiliation(s)
- Hongjuan Xi
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Erik Davis
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Nihar Ranjan
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Liang Xue
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - David Hyde-Volpe
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
| | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, South Carolina, 29634
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Kumar S, Xue L, Arya DP. Neomycin-neomycin dimer: an all-carbohydrate scaffold with high affinity for AT-rich DNA duplexes. J Am Chem Soc 2011; 133:7361-75. [PMID: 21524066 PMCID: PMC3641821 DOI: 10.1021/ja108118v] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
A dimeric neomycin-neomycin conjugate 3 with a flexible linker, 2,2'-(ethylenedioxy)bis(ethylamine), has been synthesized and characterized. Dimer 3 can selectively bind to AT-rich DNA duplexes with high affinity. Biophysical studies have been performed between 3 and different nucleic acids with varying base composition and conformation by using ITC (isothermal calorimetry), CD (circular dichroism), FID (fluorescent intercalator displacement), and UV (ultraviolet) thermal denaturation experiments. A few conclusions can be drawn from this study: (1) FID assay with 3 and polynucleotides demonstrates the preference of 3 toward AT-rich sequences over GC-rich sequences. (2) FID assay and UV thermal denaturation experiments show that 3 has a higher affinity for the poly(dA)·poly(dT) DNA duplex than for the poly(dA)·2poly(dT) DNA triplex. Contrary to neomycin, 3 destabilizes poly(dA)·2poly(dT) triplex but stabilizes poly(dA)·poly(dT) duplex, suggesting the major groove as the binding site. (3) UV thermal denaturation studies and ITC experiments show that 3 stabilizes continuous AT-tract DNA better than DNA duplexes with alternating AT bases. (4) CD and FID titration studies show a DNA binding site size of 10-12 base pairs/drug, depending upon the structure/sequence of the duplex for AT-rich DNA duplexes. (5) FID and ITC titration between 3 and an intramolecular DNA duplex [d(5'-A(12)-x-T(12)-3'), x = hexaethylene glycol linker] results in a binding stoichiometry of 1:1 with a binding constant ∼10(8) M(-1) at 100 mM KCl. (6) FID assay using 3 and 512 hairpin DNA sequences that vary in their AT base content and placement also show a higher binding selectivity of 3 toward continuous AT-rich than toward DNA duplexes with alternate AT base pairs. (7) Salt-dependent studies indicate the formation of three ion pairs during binding of the DNA duplex d[5'-A(12)-x-T(12)-3'] and 3. (8) ITC-derived binding constants between 3 and DNA duplexes have the following order: AT continuous, d[5'-G(3)A(5)T(5)C(3)-3'] > AT alternate, d[5'-G(3)(AT)(5)C(3)-3'] > GC-rich d[5'-A(3)G(5)C(5)T(3)-3']. (9) 3 binds to the AT-tract-containing DNA duplex (B* DNA, d[5'-G(3)A(5)T(5)C(3)-3']) with 1 order of magnitude higher affinity than to a DNA duplex with alternating AT base pairs (B DNA, d[5'-G(3)(AT)(5)C(3)-3']) and with almost 3 orders of magnitude higher affinity than a GC-rich DNA (A-form, d[5'-A(3)G(5)C(5)T(3)-3']).
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Affiliation(s)
- Sunil Kumar
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634
| | | | - Dev P. Arya
- Laboratory of Medicinal Chemistry, Department of Chemistry, Clemson University, Clemson, SC 29634
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Xue L, Ranjan N, Arya DP. Synthesis and spectroscopic studies of the aminoglycoside (neomycin)--perylene conjugate binding to human telomeric DNA. Biochemistry 2011; 50:2838-49. [PMID: 21329360 DOI: 10.1021/bi1017304] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Synthesis of a novel perylene-neomycin conjugate (3) and the properties of its binding to human telomeric G-quadruplex DNA, 5'-d[AG3(T2AG3)3] (4), are reported. Various spectroscopic techniques were employed to characterize the binding of conjugate 3 to 4. A competition dialysis assay revealed that 3 preferentially binds to 4, in the presence of other nucleic acids, including DNA, RNA, DNA-RNA hybrids, and other higher-order structures (single strands, duplexes, triplexes, other G-quadruplexes, and the i-motif). UV thermal denaturation studies showed that thermal stabilization of 4 increases as a function of the increasing concentration of 3. The fluorescence intercalator displacement (FID) assay displayed a significantly tighter binding of 3 with 4 as compared to its parent constituents [220-fold stronger than neomycin (1) and 4.5-fold stronger than perylene diamine (2), respectively]. The binding of 3 with 4 resulted in pronounced changes in the molar ellipticity of the DNA absorption region as confirmed by circular dichroism. The UV-vis absorption studies of the binding of 3 to 4 resulted in a red shift in the spectrum of 3 as well as a marked hypochromic change in the perylene absorption region, suggesting that the ligand-quadruplex interaction involves stacking of the perylene moiety. Docking studies suggest that the perylene moiety serves as a bridge that end stacks on 4, making contacts with two thymine bases in the loop, while the two neomycin moieties branch into the grooves of 4.
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Affiliation(s)
- Liang Xue
- Laboratories of Medicinal Chemistry, Clemson University, Clemson, South Carolina 29634, United States
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49
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Abstract
A DNA duplex can be recognized sequence-specifically in the major groove by an oligodeoxynucleotide (ODN). The resulting structure is a DNA triple helix, or triplex. The scientific community has invested significant research capital in the study of DNA triplexes because of their robust potential for providing new applications, including molecular biology tools and therapeutic agents. The triplex structures have inherent instabilities, however, and the recognition of DNA triplexes by small molecules has been attempted as a means of strengthening the three-stranded complex. Over the decades, the majority of work in the field has focused on heterocycles that intercalate between the triplex bases. In this Account, we present an alternate approach to recognition and stabilization of DNA triplexes. We show that groove recognition of nucleic acid triple helices can be achieved with aminosugars. Among these aminosugars, neomycin is the most effective aminoglycoside (groove binder) for stabilizing a DNA triple helix. It stabilizes both the TAT triplex and mixed-base DNA triplexes better than known DNA minor groove binders (which usually destabilize the triplex) and polyamines. Neomycin selectively stabilizes the triplex (TAT and mixed base) without any effect on the DNA duplex. The selectivity of neomycin likely originates from its potential and shape complementarity to the triplex Watson-Hoogsteen groove, making it the first molecule that selectively recognizes a triplex groove over a duplex groove. The groove recognition of aminoglycosides is not limited to DNA triplexes, but also extends to RNA and hybrid triple helical structures. Intercalator-neomycin conjugates are shown to simultaneously probe the base stacking and groove surface in the DNA triplex. Calorimetric and spectrosocopic studies allow the quantification of the effect of surface area of the intercalating moiety on binding to the triplex. These studies outline a novel approach to the recognition of DNA triplexes that incorporates the use of noncompeting binding sites. These principles of dual recognition should be applicable to the design of ligands that can bind any given nucleic acid target with nanomolar affinities and with high selectivity.
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50
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Zhao C, Qu K, Xu C, Ren J, Qu X. Triplex inducer-directed self-assembly of single-walled carbon nanotubes: a triplex DNA-based approach for controlled manipulation of nanostructures. Nucleic Acids Res 2011; 39:3939-48. [PMID: 21227925 PMCID: PMC3089474 DOI: 10.1093/nar/gkq1347] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
As a promising strategy for artificially control of gene expression, reversible assembly of nanomaterials and DNA nanomachine, DNA triplex formation has received much attention. Carbon nanotubes as gene and drug delivery vector or as ‘building blocks’ in nano/microelectronic devices have been successfully explored. Therefore, studies on triplex DNA-based carbon nanotube hybrid materials are important for development of smart nanomaterials and for gene therapy. In this report, a small molecule directed single-walled carbon nanotubes (SWNTs) self-assembly assay has been developed by disproportionation of SWNTs–dT22·dA22 duplex into triplex dT22·dA22·dT22 and dA22 by a triplex formation inducer, coralyne. This has been studied by circular dichroism, light scattering (LS) spectroscopy, scanning electron microscopy (SEM), atomic force microscopy (AFM), electrophoretic mobility shift assay and supported by using DNA random sequence. In contrast, SWNTs do not aggregate under the same experimental conditions when the small molecules used can not induce dT22·dA22·dT22 triplex formation. Therefore, this novel small molecule-directed SWNTs self-assembly assay has also been used for screening of triplex inducers in our studies.
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Affiliation(s)
- Chao Zhao
- Laboratory of Chemical Biology, Division of Biological Inorganic Chemistry, State Key Laboratory of Rare Earth Resource Utilization, Changchun Institute of Applied Chemistry, Chinese Academy of Sciences, Changchun, Jilin 130022, China
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