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Malina J, Crowley JD, Brabec V. Interaction of dinuclear Co(III) cylinders with higher-order DNA structures. Chem Biol Interact 2024; 395:111031. [PMID: 38703805 DOI: 10.1016/j.cbi.2024.111031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2024] [Revised: 04/20/2024] [Accepted: 05/01/2024] [Indexed: 05/06/2024]
Abstract
Alternative DNA structures play critical roles in fundamental biological processes linked to human diseases. Thus, targeting and stabilizing these structures by specific ligands could affect the progression of cancer and other diseases. Here, we describe, using methods of molecular biophysics, the interactions of two oxidatively locked [Co2L3]6+ cylinders, rac-2 and meso-1, with diverse alternative DNA structures, such as junctions, G quadruplexes, and bulges. This study was motivated by earlier results demonstrating that both Co(III) cylinders exhibit potent and selective activity against cancer cells, accumulate in the nucleus of cancer cells, and prove to be efficient DNA binders. The results show that the bigger cylinder rac-2 stabilizes all DNA structures, while the smaller cylinder meso-1 stabilizes just the Y-shaped three-way junctions. Collectively, the results of this study suggest that the stabilization of alternative DNA structures by Co(III) cylinders investigated in this work might contribute to the mechanism of their biological activity.
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Affiliation(s)
- Jaroslav Malina
- Czech Academy of Sciences, Institute of Biophysics, CZ-61200, Brno, Czech Republic
| | - James D Crowley
- Department of Chemistry, University of Otago, Dunedin, 9016, Otago, New Zealand
| | - Viktor Brabec
- Czech Academy of Sciences, Institute of Biophysics, CZ-61200, Brno, Czech Republic; Department of Biophysics, Faculty of Science, Palacky University, CZ-78371, Olomouc, Czech Republic.
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Xu G, Zhao J, Liu N, Yang M, Zhao Q, Li C, Liu M. Structure-guided post-SELEX optimization of an ochratoxin A aptamer. Nucleic Acids Res 2019; 47:5963-5972. [PMID: 31062016 PMCID: PMC6582339 DOI: 10.1093/nar/gkz336] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Revised: 03/30/2019] [Accepted: 04/26/2019] [Indexed: 01/10/2023] Open
Abstract
SELEX is the cornerstone for aptamer research with broad applications in biosensors and medicine. To improve the affinity of selected aptamers, we propose a structure-guided post-SELEX approach, an optimization method based on the precise secondary structure of the aptamer–ligand complex. We demonstrate this approach using the Ochratoxin A (OTA) aptamer. Guided by the structure, we designed a new aptamer whose affinity is improved by more than 50-fold. We also determined the high-resolution NMR structure of the new aptamer-OTA complex and elucidated the discriminatory recognition mechanism of one atomic difference between two analogs, OTA and OTB. The aptamer forms an unusual hairpin structure containing an intramolecular triple helix, which is not seen in the previously determined aptamer complex. The π–π stacking, the hydrophobic interaction, hydrogen bonds and halogen bonds between OTA and the aptamer contribute to the recognition of OTA, and the halogen bonds play an important role in discriminating between OTA and OTB. Our results demonstrate that the structure-guided post-SELEX approach improves aptamers affinity. An improved OTA biosensor system might be developed using this new strategy.
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Affiliation(s)
- Guohua Xu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Jiajing Zhao
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
| | - Na Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
| | - Minghui Yang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China
| | - Qiang Zhao
- University of Chinese Academy of Sciences, Beijing 100029, P.R. China.,State Key Laboratory of Environmental Chemistry and Ecotoxicology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing 100085, P.R. China
| | - Conggang Li
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
| | - Maili Liu
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, National Center for Magnetic Resonance in Wuhan, Wuhan National Laboratory for Optoelectronics, Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences, Wuhan 430071, P.R. China.,University of Chinese Academy of Sciences, Beijing 100029, P.R. China
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Peng J, Shao Y, Liu L, Zhang L, Liu H. Specific recognition of DNA bulge sites by in situ grown fluorescent Ag nanoclusters with high selectivity. Dalton Trans 2014; 43:1534-41. [DOI: 10.1039/c3dt52042k] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Sheng J, Gan J, Huang Z. Structure-based DNA-targeting strategies with small molecule ligands for drug discovery. Med Res Rev 2013; 33:1119-73. [PMID: 23633219 DOI: 10.1002/med.21278] [Citation(s) in RCA: 66] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Nucleic acids are the molecular targets of many clinical anticancer drugs. However, compared with proteins, nucleic acids have traditionally attracted much less attention as drug targets in structure-based drug design, partially because limited structural information of nucleic acids complexed with potential drugs is available. Over the past several years, enormous progresses in nucleic acid crystallization, heavy-atom derivatization, phasing, and structural biology have been made. Many complicated nucleic acid structures have been determined, providing new insights into the molecular functions and interactions of nucleic acids, especially DNAs complexed with small molecule ligands. Thus, opportunities have been created to further discover nucleic acid-targeting drugs for disease treatments. This review focuses on the structure studies of DNAs complexed with small molecule ligands for discovering lead compounds, drug candidates, and/or therapeutics.
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Affiliation(s)
- Jia Sheng
- Department of Chemistry, Georgia State University, Atlanta, Georgia 30303, USA
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Ma D, Lin Y, Xiao Z, Kappen L, Goldberg IH, Kallmerten AE, Jones GB. Designed DNA probes from the neocarzinostatin family: impact of glycosyl linkage stereochemistry on bulge base binding. Bioorg Med Chem 2009; 17:2428-32. [PMID: 19243952 DOI: 10.1016/j.bmc.2009.02.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2008] [Revised: 02/02/2009] [Accepted: 02/03/2009] [Indexed: 10/21/2022]
Abstract
Bulged sites in DNA and RNA have become targets for rational drug design due to their suspected involvement in a number of key biomolecular processes. A lead compound, derived from the enediyne natural product NCS-chrom has been used to inform chemical synthesis of a family of designed probes of DNA bulges, one of which shows 80 nM affinity for a two base bulged target. Key contributors to binding of these spirocyclic compounds have been studied in order to correlate affinity and specificity with structural features. Herein, we demonstrate that the glycosyl linkage stereochemistry of the pendant aminofucosyl group plays a pivotal role in binding, and coupled with insight obtained with various bulged targets, will allow rational design of second generation ligands.
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Affiliation(s)
- Dong Ma
- Bioorganic and Medicinal Chemistry Laboratories, Department of Chemistry and Chemical Biology, Northeastern University, 360 Huntington Ave, 101HT, Boston, MA 02115, USA
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Boer DR, Canals A, Coll M. DNA-binding drugs caught in action: the latest 3D pictures of drug-DNA complexes. Dalton Trans 2008:399-414. [PMID: 19122895 DOI: 10.1039/b809873p] [Citation(s) in RCA: 137] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this paper, we review recent DNA-binding agents that are expected to influence the field of DNA-targeting. We restrict ourselves to binders for which the three-dimensional structure in complex with DNA or RNA has been determined by X-ray crystallography or NMR. Furthermore, we primarily focus on unprecedented ways of targeting peculiar DNA structures, such as junctions, quadruplexes, and duplex DNAs different from the B-form. Classical binding modes of small molecular weight compounds to DNA, i.e. groove binding, intercalation and covalent addition are discussed in those cases where the structures represent a novelty. In addition, we review 3D structures of triple-stranded DNA, of the so-called Peptide Nucleic Acids (PNAs), which are oligonucleotide bases linked by a polypeptide backbone, and of aptamers, which are DNA or RNA receptors that are designed combinatorially. A discussion on perspectives in the field of DNA-targeting and on sequence recognition is also provided.
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Affiliation(s)
- D Roeland Boer
- Institute for Research in Biomedicine and Institut de Biologia Molecular de Barcelona (CSIC), Barcelona Science Park, Barcelona, Spain
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Liu L, Yi L, Yang X, Yu Z, Wen X, Xi Z. Synthesis and spectroscopic characterization of binaphthol aminosugars for stimulation of DNA strand slippage synthesis. Tetrahedron 2008. [DOI: 10.1016/j.tet.2008.04.047] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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