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Satange R, Rode AB, Hou MH. Revisiting recent unusual drug-DNA complex structures: Implications for cancer and neurological disease diagnostics and therapeutics. Bioorg Med Chem 2022; 76:117094. [PMID: 36410206 DOI: 10.1016/j.bmc.2022.117094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2022] [Revised: 11/07/2022] [Accepted: 11/07/2022] [Indexed: 11/13/2022]
Abstract
DNA plays a crucial role in various biological processes such as protein production, replication, recombination etc. by adopting different conformations. Targeting these conformations by small molecules is not only important for disease therapy, but also improves our understanding of the mechanisms of disease development. In this review, we provide an overview of some of the most recent ligand-DNA complexes that have diagnostic and therapeutic applications in neurological diseases caused by abnormal repeat expansions and in cancer associated with mismatches. In addition, we have discussed important implications of ligands targeting higher-order structures, such as four-way junctions, G-quadruplexes and triplexes for drug discovery and DNA nanotechnology. We provide an overview of the results and perspectives of such structural studies on ligand-DNA interactions.
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Affiliation(s)
- Roshan Satange
- Institute of Genomics and Bioinformatics National Chung Hsing University, Taichung 402, Taiwan; Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan
| | - Ambadas B Rode
- Regional Centre for Biotechnology, NCR Biotech Science Cluster, 3rd Milestone, Faridabad-Gurugram Expressway, Faridabad, Haryana 121001, India
| | - Ming-Hon Hou
- Institute of Genomics and Bioinformatics National Chung Hsing University, Taichung 402, Taiwan; Ph.D. Program in Medical Biotechnology, National Chung Hsing University, Taichung 402, Taiwan; Graduate Institute of Biotechnology, National Chung Hsing University, Taichung 402, Taiwan; Department of Life Sciences, National Chung Hsing University, Taichung 402, Taiwan.
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2
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Dai B, Xu Y, Wang T, Wang S, Tang L, Tang J. Recent Advances in Agglomeration Detection and Dual-Function Application of Surface-Enhanced Raman Scattering (SERS). J Biomed Nanotechnol 2022. [DOI: 10.1166/jbn.2022.3356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Surface-enhanced Raman scattering (SERS) has been widely utilized in early detection of disease biomarkers, cell imaging, and trace contamination detection, owing to its ultra-high sensitivity. However, it is also subject to certain application restrictions in virtue of its expensive
detection equipment and long-term stability of SERS-active substrate. Recently, great progress has been made in SERS technology, represented by agglomeration method. Dual readout signal detection methods are combined with SERS, including electrochemical detection, fluorescence detection, etc.,
establishing a new fantastic viewpoint for application of SERS. In this review, we have made a comprehensive report on development of agglomeration detection and dual-function detection methods based on SERS. The synthesis methods for plasmonic materials and mainstream SERS enhancement mechanism
are also summarized. Finally, the key facing challenges are discussed and prospects are addressed.
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Affiliation(s)
- Bailin Dai
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, National & Local Joint Engineering Research Center for Advanced Packaging Material and Technology, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Yue Xu
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, National & Local Joint Engineering Research Center for Advanced Packaging Material and Technology, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Tao Wang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, National & Local Joint Engineering Research Center for Advanced Packaging Material and Technology, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Shasha Wang
- Engineering Research Center in Biomaterials, Sichuan University, Chengdu 610065, Sichuan, P. R. China
| | - Li Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, National & Local Joint Engineering Research Center for Advanced Packaging Material and Technology, Hunan University of Technology, Zhuzhou 412007, P. R. China
| | - Jianxin Tang
- Hunan Key Laboratory of Biomedical Nanomaterials and Devices, National & Local Joint Engineering Research Center for Advanced Packaging Material and Technology, Hunan University of Technology, Zhuzhou 412007, P. R. China
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Lachance-Brais C, Hennecker CD, Alenaizan A, Luo X, Toader V, Taing M, Sherrill CD, Mittermaier AK, Sleiman HF. Tuning DNA Supramolecular Polymers by the Addition of Small, Functionalized Nucleobase Mimics. J Am Chem Soc 2021; 143:19824-19833. [PMID: 34783562 DOI: 10.1021/jacs.1c08972] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Nucleobase mimicking small molecules able to reconfigure DNA are a recently discovered strategy that promises to extend the structural and functional diversity of nucleic acids. However, only simple, unfunctionalized molecules such as cyanuric acid and melamine have so far been used in this approach. In this work, we show that the addition of substituted cyanuric acid molecules can successfully program polyadenine strands to assemble into supramolecular fibers. Unlike conventional DNA nanostructure functionalization, which typically end-labels DNA strands, our approach incorporates functional groups into DNA with high density using small molecules and results in new DNA triple helices coated with alkylamine or alcohol units that grow into micrometer-long fibers. We find that small changes in the small molecule functional group can result in large structural and energetic variation in the overall assembly. A combination of circular dichroism, atomic force microscopy, molecular dynamics simulations, and a new thermodynamic method, transient equilibrium mapping, elucidated the molecular factors behind these large changes. In particular, we identify substantial DNA sugar and phosphate group deformations to accommodate a hydrogen bond between the phosphate and the small-molecule functional groups, as well as a critical chain length of the functional group which switches this interaction from intra- to interfiber. These parameters allow the controlled formation of hierarchical, hybrid DNA assemblies simply through the addition and variation of small, functionalized molecules.
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Affiliation(s)
| | - Christopher D Hennecker
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Asem Alenaizan
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Xin Luo
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Violeta Toader
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Monica Taing
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - C David Sherrill
- School of Chemistry and Biochemistry, Georgia Institute of Technology, 901 Atlantic Drive, Atlanta, Georgia 30332-0400, United States
| | - Anthony K Mittermaier
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
| | - Hanadi F Sleiman
- Department of Chemistry, McGill University, 801 Sherbrooke St. W., Montreal, QC H3A0B8, Canada
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Abstract
Organophosphorus compounds play a vital role as nucleic acids, nucleotide coenzymes, metabolic intermediates and are involved in many biochemical processes. They are part of DNA, RNA, ATP and a number of important biological elements of living organisms. Synthetic compounds of this class have found practical application as agrochemicals, pharmaceuticals, bioregulators, and othrs. In recent years, a large number of phosphorus compounds containing P-O, P-N, P-C bonds have been isolated from natural sources. Many of them have shown interesting biological properties and have become the objects of intensive scientific research. Most of these compounds contain asymmetric centers, the absolute configurations of which have a significant effect on the biological properties of the products of their transformations. This area of research on natural phosphorus compounds is still little-studied, that prompted us to analyze and discuss it in our review. Moreover natural organophosphorus compounds represent interesting models for the development of new biologically active compounds, and a number of promising drugs and agrochemicals have already been obtained on their basis. The review also discusses the history of the development of ideas about the role of organophosphorus compounds and stereochemistry in the origin of life on Earth, starting from the prebiotic period, that allows us in a new way to consider this most important problem of fundamental science.
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Rousina‐Webb A, Lachance‐Brais C, Rizzuto FJ, Askari MS, Sleiman HF. Transition‐Metal‐Functionalized DNA Double‐Crossover Tiles: Enhanced Stability and Chirality Transfer to Metal Centers. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.201913956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Alexander Rousina‐Webb
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | | | - Felix J. Rizzuto
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Mohammad S. Askari
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
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Rousina‐Webb A, Lachance‐Brais C, Rizzuto FJ, Askari MS, Sleiman HF. Transition‐Metal‐Functionalized DNA Double‐Crossover Tiles: Enhanced Stability and Chirality Transfer to Metal Centers. Angew Chem Int Ed Engl 2020; 59:4091-4098. [DOI: 10.1002/anie.201913956] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2019] [Indexed: 01/08/2023]
Affiliation(s)
- Alexander Rousina‐Webb
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | | | - Felix J. Rizzuto
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Mohammad S. Askari
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
| | - Hanadi F. Sleiman
- Department of Chemistry McGill University 801 Sherbrooke St W Montreal QC H3A 0B8 Canada
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