1
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Zhao T, Wu W, Yang C. Chiroptical regulation of macrocyclic arenes with flipping-induced inversion of planar chirality. Chem Commun (Camb) 2023; 59:11469-11483. [PMID: 37691554 DOI: 10.1039/d3cc03829g] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/12/2023]
Abstract
Studies on various macrocyclic arenes have received increasing attention due to their straightforward syntheses, convenient derivatization, and unique complexation properties. Represented by pillar[n]arenes, several distinctive macrocyclic arenes have recently emerged with the following characteristics: they possess a pair of enantiomeric planar chiral conformations, and interconversion between these enantiomeric conformations can be achieved through the flipping of ring units. Complexation of a chiral guest with these macrocyclic arenes will lead to a shift of the equilibrium between the Rp and Sp conformers, leading to intriguing possibilities for chiral induction and sensing. By the introduction of bulky substituents on the rims, employing rotaxanation or pseudocatenation, planar chirality could be locked, enabling the enantiomeric separation of the chiral structures. The induced or separated chiral conformers/compounds exhibit significant chiroptical properties. These macrocyclic arenes, with flipping-induced inversion of planar chirality, demonstrated intriguing chiral induction dynamics and kinetics. In this featured review, we systematically summarize the progress in chiroptical induction/regulation of these macrocyclic arenes, particularly in the fields of chiral sensing, molecular machines, molecular recognition, and assembly.
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Affiliation(s)
- Ting Zhao
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry Institution, Sichuan University Chengdu, Chengdu 610064, China.
| | - Wanhua Wu
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry Institution, Sichuan University Chengdu, Chengdu 610064, China.
| | - Cheng Yang
- Key Laboratory of Green Chemistry & Technology of Ministry of Education, College of Chemistry Institution, Sichuan University Chengdu, Chengdu 610064, China.
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2
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He S, Jiang Z, Dou X, Gao L, Feng C. Chiral Supramolecular Assemblies: Controllable Construction and Biological Activity. Chempluschem 2023; 88:e202300226. [PMID: 37438864 DOI: 10.1002/cplu.202300226] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 06/28/2023] [Accepted: 07/10/2023] [Indexed: 07/14/2023]
Abstract
Chiral supramolecular assemblies with helical structures (e. g., proteins with α-helix, DNA with double helix, collagen with triple-helix) as the central structure motifs in biological systems play a crucial role in various physiological activities of living organisms. Variations in chiral structure can cause many abnormal physiological activities. To gain insight into the construction, structural transition, and related physiological functions of these complex helix in natural systems, it is necessary to fabricate artificial supramolecular assemblies with controllable helix orientation as research platform. This review discusses recent advances in chiral supramolecular assembly, including the precise construction and regulation of assembled chiral nanostructures with tunable chirality. Chiral structure-dependent biological activities, including cell proliferation, cell differentiation, antibacterial activity and tissue regeneration, are also discussed. This review not only contributes to further understanding of the importance of chirality in the physiological environment, but also plays an important role in the development of chiral biomedical materials for the treatment of diseases (e. g., tissue engineering regeneration, stem cell transplantation therapy).
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Affiliation(s)
- Sijia He
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Zichao Jiang
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Xiaoqiu Dou
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Laiben Gao
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
| | - Chuanliang Feng
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, 200240, P. R. China
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3
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Fu L, Wang R, Zhu Q, Gu Y, Zheng L, Chen Y, Jiang J, Ma J. Planar Chirality for Acid/Base Responsive Macrocyclic Pillararenes Induced by Amino Acid Derivatives: Molecular Dynamics Simulations and Machine Learning. J Chem Theory Comput 2023. [PMID: 37154217 DOI: 10.1021/acs.jctc.2c01265] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Chirality is ubiquitous in nature, ranging from a DNA helix to a biological macromolecule, snail's shell, and even a galaxy. However, the precise control of chirality at the nanoscale is a challenge due to the structure complexity of supramolecular assemblies, the small energy differences between different enantiomers, and the difficulty in obtaining polymorphic crystals. The planar chirality of water-soluble pillar[5]arenes (called WP5-Na with Na ions in the side chain) host triggered by the addition of chiral L-amino acid hydrochloride (L-AA-OEt) guests and acid/base is rationalized by the relative stability of different chiral isomers, being estimated by molecular dynamics (MD) simulations and quantum chemical calculations. As an increase in the pH value, the change from a positive to a negative value of the free energy difference (ΔG) between two conformations, pR-WP5-Na⊃L-AA-OEt and pS-WP5-Na⊃L-AA-OEt, suggests an inversed preference of the pS-WP5-Na conformer induced by the deprotonated L-arginine ethyl ester (L-Arg-OEt) at pH = 14, which is supported by the circular dichroism (CD) experiments. On the basis of 2256 WP5-Na⊃L-Ala-OEt and 3299 WP5-Na⊃L-Arg-OEt conformers sampled from MD, the gradient boosting regression (GBR) model exhibits a satisfactory performance (R2 = 0.91) in predicting the chirality of WP5-Na complexations using host-guest binding descriptors, including the geometry matching and binding sites and modes (electrostatics and hydrogen bonding). The machine learning model also performs well on external tests of different hosts (using different side chains and cavity sizes) with the addition of 22 other different guests, with the average chirality prediction accuracy of ML versus experimental CD determinations of 92.8%. The easily accessible host-guest features, binding position coordination and size matching between the cavity and guest, exhibit a close correlation to the chirality of different macrocyclic molecules, water-soluble pillar[6]arenes (WP6) versus WP5, in complexation with different amino acid guests. The exploration of efficient host-guest features in ML displays the great potential of building a large space of various assembled systems and accelerating the on-demand design of chiral supramolecular systems at the nanoscale.
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Affiliation(s)
- Lulu Fu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Ranran Wang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Qiang Zhu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yuming Gu
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Lifeng Zheng
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Yuan Chen
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
| | - Juli Jiang
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
- MaAnShan High-Tech Research Institute of Nanjing University, MaAnShan 238200, P. R. China
| | - Jing Ma
- Key Laboratory of Mesoscopic Chemistry of Ministry of Education, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, P. R. China
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4
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Stimuli-responsive chirality inversion of metallohelices and related dynamic metal complexes. Coord Chem Rev 2022. [DOI: 10.1016/j.ccr.2022.214582] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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5
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Tomassi S, Ieranò C, Del Bene A, D’Aniello A, Napolitano M, Rea G, Auletta F, Portella L, Capiluongo A, Mazzarella V, Russo R, Chambery A, Scala S, Di Maro S, Messere A. Tailoring the Structure of Cell Penetrating DNA and RNA Binding Nucleopeptides. Int J Mol Sci 2022; 23:ijms23158504. [PMID: 35955638 PMCID: PMC9369335 DOI: 10.3390/ijms23158504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Revised: 07/28/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
Synthetic nucleic acid interactors represent an exciting research field due to their biotechnological and potential therapeutic applications. The translation of these molecules into drugs is a long and difficult process that justifies the continuous research of new chemotypes endowed with favorable binding, pharmacokinetic and pharmacodynamic properties. In this scenario, we describe the synthesis of two sets of homo-thymine nucleopeptides, in which nucleobases are inserted in a peptide structure, to investigate the role of the underivatized amino acid residue and the distance of the nucleobase from the peptide backbone on the nucleic acid recognition process. It is worth noting that the CD spectroscopy investigation showed that two of the reported nucleopeptides, consisting of alternation of thymine functionalized L-Orn and L-Dab and L-Arg as underivatized amino acids, were able to efficiently bind DNA and RNA targets and cross both cell and nuclear membranes.
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Affiliation(s)
- Stefano Tomassi
- Department of Pharmacy, University of Naples “Federico” II, Via D. Montesano 49, 80131 Napoli, Italy;
| | - Caterina Ieranò
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Alessandra Del Bene
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Antonia D’Aniello
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Maria Napolitano
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Giuseppina Rea
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Federica Auletta
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Luigi Portella
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Anna Capiluongo
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Vincenzo Mazzarella
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Rosita Russo
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Angela Chambery
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
| | - Stefania Scala
- Molecular Immunology and Immunoregulation, Istituto Nazionale Tumori “Fondazione G. Pascale”, IRCCS-Napoli, 80131 Naples, Italy; (C.I.); (M.N.); (G.R.); (F.A.); (L.P.); (A.C.); (S.S.)
| | - Salvatore Di Maro
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
- Correspondence: (S.D.M.); (A.M.)
| | - Anna Messere
- Department of Environmental, Biological and Pharmaceutical Sciences and Technologies, University of Campania “Luigi Vanvitelli”, Via Vivaldi 43, 81100 Caserta, Italy; (A.D.B.); (A.D.); (V.M.); (R.R.); (A.C.)
- Correspondence: (S.D.M.); (A.M.)
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Sakai N, Assies L, Matile S. G‐Quartets, 4‐Way Junctions and Triple Helices but Not DNA Duplexes: Planarization of Twisted Push‐Pull Flipper Probes by Surface Recognition Rather Than Physical Compression. Helv Chim Acta 2022. [DOI: 10.1002/hlca.202200052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Naomi Sakai
- University of Geneva: Universite de Geneve Department of Organic Chemistry SWITZERLAND
| | - Lea Assies
- University of Geneva: Universite de Geneve Department of Organic Chemistry SWITZERLAND
| | - Stefan Matile
- University of Geneva Department of Organic Chemistry Quai Ernest-Ansermet 30 CH-1211 Geneva SWITZERLAND
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7
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Rangel VM, Gu L, Chen G, Chen QH, Xue L. 5-Substituted 3, 3', 4', 7-tetramethoxyflavonoids - A novel class of potent DNA triplex specific binding ligands. Bioorg Med Chem Lett 2022; 61:128608. [PMID: 35143982 DOI: 10.1016/j.bmcl.2022.128608] [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: 11/23/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 11/18/2022]
Abstract
Herein, we present a class of potent triplex DNA binding ligands derived from the natural product quercetin, which is the first of its kind that has ever been reported in the literature. The binding of 5-substituted quercetin derivatives (3, 3', 4', 7-tetramethoxyflavonoids) to triplex and duplex DNA was investigated using several biophysical tools, including thermal denaturation monitored by UV, circular dichroism, differential scanning calorimetry, and isothermal titration calorimetry. Experimental data reveal that several 5-substituted 3, 3', 4', 7-tetramethoxyflavonoids have remarkable effects on binding to DNA triple helices, and they do not influence the double-helical DNA structures. A few derivatives such as compounds 5 and 7 have comparable (if not better) binding affinities to neomycin, a well-known DNA triplex binding ligand, under the same conditions. The amino-containing side chains at the 5-position of 3, 3', 4', 7-tetramethoxyflavonoids are crucial for the observed binding affinity and specificity.
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Affiliation(s)
- Vanessa M Rangel
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Landy Gu
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA
| | - Guanglin Chen
- Department of Chemistry, California State University, Fresno, CA 93740, USA
| | - Qiao-Hong Chen
- Department of Chemistry, California State University, Fresno, CA 93740, USA
| | - Liang Xue
- Department of Chemistry, University of the Pacific, 3601 Pacific Avenue, Stockton, CA 95211, USA.
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8
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Sahoo D, Benny R, Ks NK, De S. Stimuli-Responsive Chiroptical Switching. Chempluschem 2021; 87:e202100322. [PMID: 34694736 DOI: 10.1002/cplu.202100322] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2021] [Revised: 09/23/2021] [Indexed: 12/16/2022]
Abstract
"Chirality" governs many fundamental properties in chemistry and biochemistry. While early investigations on stereochemistry are primarily dedicated to static chirality, there is an increasing interest in the field of dynamic chirality (chiral switches). These chiral switches are essential in controlling the directionality in molecular motors. Dynamic chiralities are equally crucial in switchable stereoselectivity, switchable asymmetric catalysis and enantioselective separation. Herein, we limit our discussion to recent advances on stimuli-induced chiroptical switching of axial, helical, and planar chirality in response to external stimuli. We also discuss a few examples of applications of the switchable chirality.
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Affiliation(s)
- Diptiprava Sahoo
- School of Chemistry, Indian Institute of Science Education and, Research Thiruvananthapuram (IISER-TVM), Thiruvananthapuram, 695551, India
| | - Renitta Benny
- School of Chemistry, Indian Institute of Science Education and, Research Thiruvananthapuram (IISER-TVM), Thiruvananthapuram, 695551, India
| | - Nithish Kumar Ks
- School of Chemistry, Indian Institute of Science Education and, Research Thiruvananthapuram (IISER-TVM), Thiruvananthapuram, 695551, India
| | - Soumen De
- School of Chemistry, Indian Institute of Science Education and, Research Thiruvananthapuram (IISER-TVM), Thiruvananthapuram, 695551, India
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9
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Chen JF, Ding JD, Wei TB. Pillararenes: fascinating planar chiral macrocyclic arenes. Chem Commun (Camb) 2021; 57:9029-9039. [PMID: 34498646 DOI: 10.1039/d1cc03778a] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Chiral macrocycles possess significant value in chiral science and supramolecular chemistry. Pillararenes, as a class of relatively young supramolecular macrocyclic hosts, have been widely used for host-guest recognition and self-assembly. Since the position of substituents on the benzene rings breaks the molecular symmetry (symmetric plane and symmetric center), pillararenes possess planar chirality. However, it is a great challenge to synthesize stable and resolvable enantiomers because of the easy rotation of the phenylene group. In this review, we summarize the construction methods of resolvable chiral pillararenes. We also focus on their applications in enantioselective recognition, chiral switches, chirality sensing, asymmetric catalysis, circularly polarized luminescence, metal-organic frameworks, and highly permeable membranes. Finally, we discuss the future research perspectives in this field of pillararene-based planar chiral materials. We hope that this review will encourage more researchers to work in this exciting field.
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Affiliation(s)
- Jin-Fa Chen
- Beijing Key Laboratory of Photoelectronic/Electrophotonic Conversion Materials, Key Laboratory of Cluster Science of the Ministry of Education, School of Chemistry and Chemical Engineering, Beijing Institute of Technology of China, Beijing, 102488, China
| | - Jin-Dong Ding
- Shaanxi Key Laboratory of National Products & Chemical Biology, College of Chemistry & Pharmacy, Northwest A&F University, Yangling, 712100, P. R. China
| | - Tai-Bao Wei
- Key Laboratory of Eco-Environment-Related Polymer Materials, Ministry of Education of China, Key Laboratory of Polymer Materials of Gansu Province, College of Chemistry and Chemical Engineering, Northwest Normal University, Lanzhou, Gansu, 730070, P. R. China.
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10
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Zhang Y, Qin M, Xing C, Zhao C, Dou X, Feng CL. Rational Fabrication of Multiple Dimensional Assemblies from Tryptophan-Based Racemate. Chemistry 2021; 27:14911-14920. [PMID: 34347917 DOI: 10.1002/chem.202102145] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Indexed: 11/07/2022]
Abstract
Fabricating structural complex assemblies from simple amino acid-based derivatives is attracting great research interests due to their easy accessibility and preparation. However, the morphological regulation of racemates (an equimolar mixture of enantiomers) were largely overlooked. In this work, through rational modulation of kinetic and thermodynamic parameters, we achieved multiple dimensional architectures employing tryptophan-based racemate (RPWM). Upon assembling, 1D bundled nanofibers, 2D lamellar nanostructure and 3D urchin-like microflowers could be obtained depending on the solvents used. The corresponding morphology evolutions were successfully illustrated by changing the enantiomeric excess (ee) value. Moreover, for RPWM, uniform 0D nanospheres were formed in H 2 O under 4 ℃, which could spontaneously convert into lamella under ambient temperature. Taking advantages of its temperature-responsive phase change behavior, RPWM assemblies exhibited excellent removal efficiency for organic dye RhB, and could be reused for several consecutive cycles without significant changes in its removal performance. Taken together, it's rational to envision that the engineering of racemates assembly pathways can greatly increase the robustness in a wide variety of supramolecular materials and further lead to their blooming versatile applications.
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Affiliation(s)
- Yaqian Zhang
- Shanghai Jiao Tong University, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, P.R. China 200240, Shanghai, CHINA
| | - Minggao Qin
- Shanghai Jiao Tong University, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, P.R. China 200240, Shanghai, CHINA
| | - Chao Xing
- Shanghai Jiao Tong University, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, P.R. China 200240, Shanghai, CHINA
| | - Changli Zhao
- Shanghai Jiao Tong University, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, P.R. China 200240, Shanghai, CHINA
| | - Xiaoqiu Dou
- Shanghai Jiao Tong University, School of Materials Science and Engineering, Shanghai Jiao Tong University, 800 Dongchuan Road, Shanghai, P.R. China 200240, Shanghai, CHINA
| | - Chuan Liang Feng
- Shanghai Jiaotong University, Materials Science and Engineering Technology, Dongchuan Road 800, 200240, Shanghai, CHINA
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11
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Lousen B, Pedersen SK, Răsădean DM, Pantoş GD, Pittelkow M. Triggering G-Quadruplex Conformation Switching with [7]Helicenes. Chemistry 2021; 27:6064-6069. [PMID: 33326174 DOI: 10.1002/chem.202004990] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Indexed: 12/14/2022]
Abstract
The dynamic interplay between two types of chiral structures; fully conjugated racemic hetero[7]helicenes and DNA strands prone to fold into G-quadruplex structures is described. Both the [7]helicenes and the G-quadruplex DNA structures exist in more than one conformation in solution. We show that the structures interact with and stabilise each other, mutually amplifying and stabilising certain conformations at increased temperatures. The [7]helicene ligands L1 and L2 stabilise the parallel conformation of k-ras significantly, whereas hybrid (K+ ) and antiparallel (Na+ ) h-telo G-quadruplexes are stabilised upon conformational switching into altered G-quadruplex conformations. Both L1 and L2 induce parallel G-quadruplexes from hybrid structures (K+ ) and L1 induces hybrid G-quadruplexes from antiparallel conformations (Na+ ). Enantioselective binding of one helicene enantiomer is observed for helicene ligand L2, and VTCD melting experiments are used to estimate the racemisation barrier of the helicene.
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Affiliation(s)
- Bodil Lousen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Stephan K Pedersen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Dora M Răsădean
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - G Dan Pantoş
- Department of Chemistry, University of Bath, Claverton Down, Bath, BA2 7AY, UK
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
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12
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Exploration of head-to-tail and head-to-head isomers of a guanine quadruplex platinum-based binder. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2020.120236] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Zheng L, Guo S, Wang C, Wang Y, Fan Y, Chen X, Zhang K, Jiang H. Distance-Dependent Chiral Communication between Two Quinoline Oligoamide Foldamers Connected by Alkyl Chains. Chempluschem 2021; 86:340-346. [PMID: 33624952 DOI: 10.1002/cplu.202000824] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/13/2021] [Indexed: 11/09/2022]
Abstract
A series of macrocycles that contain two quinoline oligoamide foldamers (QOFs) using various length of alkyl chains as linkers (2, 3, 6, 8 or 12 hydrocarbons) were synthesized. The two QOFs interact with each other through the linkers and the intramolecular helix chiral communications between the two QOFs were studied by 1 H NMR spectroscopy and crystal structures. Investigations show that the intensity of the intramolecular helix chiral communications between the two QOFs is dependent on the length of the linkers, and the interaction between the two QOFs increases with decreasing length of the linkers. When the length of the linkers decreased to C2 linkers, only one conformer is present in solution. Moreover, increasing the length of the foldamers would enhance the intramolecular helix chiral communication if the linkers are short, indicating that the length of the foldamers also has significant impact on intramolecular helix chiral communication.
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Affiliation(s)
- Lu Zheng
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China.,School of Pharmacy, Jiangsu Ocean University, Lianyungang, 222005, P. R. China
| | - Shengzhu Guo
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China
| | - Chu Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Yanru Wang
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Yanqing Fan
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Xuebo Chen
- College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
| | - Kun Zhang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China
| | - Hua Jiang
- School of Biotechnology and Health Sciences, Wuyi University, Jiangmen, 529020, P. R. China.,International Healthcare Innovation Institute (Jiangmen), Jiangmen, 529040, P. R. China.,College of Chemistry, Beijing Normal University, Beijing, 100875, P. R. China
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14
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A Multiple Chirality Switching Device for Spatial Light Modulators. Angew Chem Int Ed Engl 2021. [DOI: 10.1002/ange.202009916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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15
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Yang G, Yu Y, Yang B, Lu T, Cai Y, Yin H, Zhang H, Zhang NN, Li L, Zhang YM, Zhang SXA. A Multiple Chirality Switching Device for Spatial Light Modulators. Angew Chem Int Ed Engl 2021; 60:2018-2023. [PMID: 32885573 DOI: 10.1002/anie.202009916] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2020] [Revised: 08/24/2020] [Indexed: 12/25/2022]
Abstract
A new and simple strategy towards electric-field-driven multiple chirality switching device has been designed and fabricated by combining a newly synthesized base-responsive chiroptical polymer switch (R-FLMA) and p-benzoquinone (p-BQ) via proton-coupled electron transfer (PCET) mechanism. Clear and stable triple chirality states (silence, positive, negative) of this device in visible band can be regulated reversibly (>1000 cycles) by adjusting voltage programs. Furthermore, such chiral switching phenomena are also accompanied by apparent changes of color and fluorescence. More importantly, the potential application of this device for a spatial light modulator has also been demonstrated.
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Affiliation(s)
- Guojian Yang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, P. R. China.,College of Chemistry, Jilin University, Changchun, P. R. China
| | - Yang Yu
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, P. R. China.,College of Chemistry, Jilin University, Changchun, P. R. China
| | - Baige Yang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, P. R. China.,College of Chemistry, Jilin University, Changchun, P. R. China
| | - Tong Lu
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, P. R. China.,College of Chemistry, Jilin University, Changchun, P. R. China
| | - Yiru Cai
- College of Chemistry, Jilin University, Changchun, P. R. China
| | - Hang Yin
- Institute of Atom and Molecular Physics, Jilin University, Changchun, P. R. China
| | - Huiqi Zhang
- College of Chemistry, Jilin University, Changchun, P. R. China
| | - Ning-Ning Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, P. R. China.,College of Chemistry, Jilin University, Changchun, P. R. China
| | - Li Li
- College of Chemistry, Jilin University, Changchun, P. R. China.,State Key Laboratory of Inorganic Synthesis and Preparative Chemistry, Jilin University, Changchun, P. R. China
| | - Yu-Mo Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, P. R. China.,College of Chemistry, Jilin University, Changchun, P. R. China
| | - Sean Xiao-An Zhang
- State Key Laboratory of Supramolecular Structure and Materials, Jilin University, Changchun, P. R. China.,College of Chemistry, Jilin University, Changchun, P. R. China
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16
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Tan L, Zhang J. A phenolic hydroxyl in the ortho- and meta-positions on the main ligands effect on the interactions of [Ru(phen) 2(o-HPIP)] 2+ and [Ru(phen) 2(m-HPIP)] 2+ with the poly(U)·poly(A)*poly(U) triplex. J Inorg Biochem 2020; 213:111268. [PMID: 33065523 DOI: 10.1016/j.jinorgbio.2020.111268] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 09/23/2020] [Accepted: 09/27/2020] [Indexed: 01/14/2023]
Abstract
The association of two ruthenium(II) complexes [Ru(phen)2(o-HPIP)]2+ (Ru1; phen = 1,10-phenanthroline, o-HPIP = 2-(2-hydroxyphenyl)-imidazo[4,5-f][1,10] phenanthroline) and [Ru(phen)2(m-HPIP)]2+ (Ru2; m-HPIP = 2-(3-hydroxyphenyl)-imidazo[4,5-f][1,10]phenan- throline) with the RNA poly(U)·poly(A)⁎poly(U) triplex has been investigated by spectrophotometric titrations and melting experiments in this work. All experimental data reveal an intercalative triplex-binding mode of the two complexes, whereas the binding constant for Ru1 is significantly higher than that for Ru2. Circular dichroism spectroscopic investigations show that the two complexes could bind to the chiral environment of the triplex, but the triplex perturbation effects induced by Ru1 are more marked. Thermal denaturation experiments demonstrate that both Ru1 and Ru2 display a large binding preference and stabilizing effect for the third strand over the Watson-Crick base-paired duplex of the triplex. However, the third-strand stabilizing effect of Ru1 is much more effective than that of Ru2. The obtained results suggest that positions of the phenolic group on the main ligands have significant effect on the binding of the two complexes with poly(U)·poly(A)⁎poly(U) triplex.
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Affiliation(s)
- Lifeng Tan
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China; Key Lab of Environment-friendly Chemistry and Application in Ministry of Education, Xiangtan University, Xiangtan 411105, People's Republic of China.
| | - Jingwen Zhang
- College of Chemistry, Xiangtan University, Xiangtan 411105, People's Republic of China
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17
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Chloro-Substituted Naphthyridine Derivative and Its Conjugate with Thiazole Orange for Highly Selective Fluorescence Sensing of an Orphan Cytosine in the AP Site-Containing Duplexes. APPLIED SCIENCES-BASEL 2020. [DOI: 10.3390/app10124133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Fluorescent probes with the binding selectivity to specific structures in DNAs or RNAs have gained much attention as useful tools for the study of nucleic acid functions. Here, chloro-substituted 2-amino-5,7-dimethyl-1,8-naphthyridine (ClNaph) was developed as a strong and highly selective binder for target orphan cytosine opposite an abasic (AP) site in the DNA duplexes. ClNaph was then conjugated with thiazole orange (TO) via an alkyl spacer (ClNaph–TO) to design a light-up probe for the detection of cytosine-related mutations in target DNA. In addition, we found the useful binding and fluorescence signaling of the ClNaph–TO conjugate to target C in AP site-containing DNA/RNA hybrid duplexes with a view toward sequence analysis of microRNAs.
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18
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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 PMCID: PMC6851491 DOI: 10.1016/j.bbamcr.2019.118539] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [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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19
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Amouzadeh Tabrizi M, Ferré-Borrull J, Marsal LF. Highly sensitive aptasensor based on interferometric reflectance spectroscopy for the determination of amyloid β as an Alzheimer's disease biomarkers using nanoporous anodic alumina. Biosens Bioelectron 2019; 137:279-286. [PMID: 31125817 DOI: 10.1016/j.bios.2019.04.050] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2019] [Revised: 04/08/2019] [Accepted: 04/23/2019] [Indexed: 02/06/2023]
Abstract
It is well known that Alzheimer's disease is one of the global challenges for the 21st century. Therefore, it is urgent to develop a reliable biosensor for the detection of this disease. Here in, we have developed for the first time, an aptasensor based on interferometric reflectance spectroscopy (IRS) for the determination of amyloid β (Aβ) oligomers that is an Alzheimer's disease biomarker. For this purpose, the nanoporous anodic alumina (NAA) was first fabricated. After that, the pore walls of the NAA were modified with (3-aminopropyl) trimethoxysilane (NAA-NH2). The amino-terminal aptamers probe were then attached to the pore walls of the NAA-NH2 by using glutaraldehyde (GA) as the cross-linking agent. Subsequently, methylene blue (MB) was immobilized into the aptamer as the photo-probe, generating the MB/G-quadruplex complex. Since MB has a high absorption coefficient, the intensity of the reflected white light to the charge-coupled device (CCD) detector decreased. In the presence of the Aβ oligomers that have high affinity to the immobilized aptamer, the MB/quadruplex complex broke and MB washed away from the aptasensor. Therefore, the intensity of the reflected white light to the CCD detector increased. The increased signal intensity of the aptasensor has a logarithmic relationship with the concentration of Aβ oligomers. The proposed aptasensor exhibited a good response to the concentration of Aβ oligomers in the range of 0.5-50.0 μg × mL-1. The experimental detection limit was of 0.02 μg × mL-1 (at 3σ/S). The proposed optical aptasensor exhibited good selectivity, linear range, and stability.
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Affiliation(s)
- Mahmoud Amouzadeh Tabrizi
- Departamento de Ingeniería Electrónica, Eléctrica y Automática, Universitat Rovira i Virgili, Avda. Països Catalans 26, 43007 Tarragona, Spain
| | - Josep Ferré-Borrull
- Departamento de Ingeniería Electrónica, Eléctrica y Automática, Universitat Rovira i Virgili, Avda. Països Catalans 26, 43007 Tarragona, Spain
| | - Lluis F Marsal
- Departamento de Ingeniería Electrónica, Eléctrica y Automática, Universitat Rovira i Virgili, Avda. Països Catalans 26, 43007 Tarragona, Spain.
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20
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Zhang J, Liu Q, Wu W, Peng J, Zhang H, Song F, He B, Wang X, Sung HHY, Chen M, Li BS, Liu SH, Lam JWY, Tang BZ. Real-Time Monitoring of Hierarchical Self-Assembly and Induction of Circularly Polarized Luminescence from Achiral Luminogens. ACS NANO 2019; 13:3618-3628. [PMID: 30835442 DOI: 10.1021/acsnano.9b00218] [Citation(s) in RCA: 75] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
Constructing artificial helical structures through hierarchical self-assembly and exploring the underlying mechanism are important, and they help gain insight from the structures, processes, and functions from the biological helices and facilitate the development of material science and nanotechnology. Herein, the two enantiomers of chiral Au(I) complexes ( S)-1 and ( R)-1 were synthesized, and they exhibited impressive spontaneous hierarchical self-assembly transitions from vesicles to helical fibers. An impressive chirality inversion and amplification was accompanied by the assembly transition, as elucidated by the results of in situ and time-dependent circular dichroism spectroscopy and scanning electron microscope imaging. The two enantiomers could serve as ideal chiral templates to co-assemble with other achiral luminogens to efficiently induce the resulting co-assembly systems to show circularly polarized luminescence (CPL). Our work has provided a simple but efficient way to explore the sophisticated self-assembly process and presented a facile and effective strategy to fabricate architectures with CPL properties.
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Affiliation(s)
- Jing Zhang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Qiuming Liu
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen 518060 , China
- Center for Aggregation-Induced Emission, SCUT-HKUST Joint Research Institute, State Key Laboratory of Luminescent Materials and Devices , South China University of Technology , Guangzhou 510640 , China
| | - Wenjie Wu
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Junhui Peng
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Haoke Zhang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Fengyan Song
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Benzhao He
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Xiaoyan Wang
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , China
| | - Herman H-Y Sung
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Ming Chen
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Bing Shi Li
- College of Chemistry and Environmental Engineering , Shenzhen University , Shenzhen 518060 , China
| | - Sheng Hua Liu
- Key Laboratory of Pesticide and Chemical Biology, Ministry of Education, College of Chemistry , Central China Normal University , Wuhan 430079 , China
| | - Jacky W Y Lam
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
| | - Ben Zhong Tang
- Department of Chemistry, Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Institute for Advanced Study, and Department of Chemical and Biological Engineering , The Hong Kong University of Science and Technology , Clear Water Bay , Kowloon , 999077 , Hong Kong, China
- Center for Aggregation-Induced Emission, SCUT-HKUST Joint Research Institute, State Key Laboratory of Luminescent Materials and Devices , South China University of Technology , Guangzhou 510640 , China
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21
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Kousar A, Feng C. Controlled mechanical properties and supramolecular chirality of hydrogels via pH change. MethodsX 2019; 6:417-423. [PMID: 30899678 PMCID: PMC6406592 DOI: 10.1016/j.mex.2019.02.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2019] [Accepted: 02/17/2019] [Indexed: 12/23/2022] Open
Abstract
In order to widen the use of soft materials in tissue engineering and life sciences, hydrogels with improved mechanical properties and controlled chirality are critical to achieve. A methodology is presented to enhance the mechanical properties and gain the control of chirality of two component hydrogels by merely varying the solution pH. pH change has been used as a way to ionize the specific functionalities into positive and negative charges. These positive and negative charges are crucial to provide a surge of electrostatic interactions to the components, imparting the improvement in stability and regulating their optical activity. Our goal is to throw light on the significance of opposite charges in the hydrogels for achievement of desired properties. •Role of ionisable groups is crucial to control viscoelastic and optical properties of supramolecular hydrogels.•Increasing the pH of the solution increases the number of negative ions by affecting the ionisable moieties, which interact with the positive charges in the solution.•Zeta potential of both materials has been analysed to ensure the presence of charged species.
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Affiliation(s)
- Ayesha Kousar
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiaotong University, Dongchuan Rd 800, 200240, Shanghai, China
| | - Chuanliang Feng
- State Key Lab of Metal Matrix Composites, School of Materials Science and Engineering, Shanghai Jiaotong University, Dongchuan Rd 800, 200240, Shanghai, China
- Henan Univ, Collaborat Innovat Ctr Nano Funct Mat & Applicat, Key Lab Special Funct Mat, Kaifeng 475004, China
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22
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Wang R, Wu X, Zhu X, Shi H, Zhou X. A photoregulated split aptaswitch for small molecules with improved sensitivity. Chem Commun (Camb) 2019; 55:9555-9558. [DOI: 10.1039/c9cc04083h] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Here we show the design of a photoregulated split aptaswitch (PSA) for the challenging small-molecule biorecognition and its sensing application.
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Affiliation(s)
- Ruoyu Wang
- State Key Joint Laboratory of ESPC
- Center for Sensor Technology of Environment and Health School of Environment
- Tsinghua University
- Beijing 100084
- China
| | - Xueqi Wu
- State Key Joint Laboratory of ESPC
- Center for Sensor Technology of Environment and Health School of Environment
- Tsinghua University
- Beijing 100084
- China
| | - Xiyu Zhu
- State Key Joint Laboratory of ESPC
- Center for Sensor Technology of Environment and Health School of Environment
- Tsinghua University
- Beijing 100084
- China
| | - Hanchang Shi
- State Key Joint Laboratory of ESPC
- Center for Sensor Technology of Environment and Health School of Environment
- Tsinghua University
- Beijing 100084
- China
| | - Xiaohong Zhou
- State Key Joint Laboratory of ESPC
- Center for Sensor Technology of Environment and Health School of Environment
- Tsinghua University
- Beijing 100084
- China
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23
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Lin Q, Gao L, Kauffmann B, Zhang J, Ma C, Luo D, Gan Q. Helicity adaptation within a quadruply stranded helicate by encapsulation. Chem Commun (Camb) 2018; 54:13447-13450. [PMID: 30431027 DOI: 10.1039/c8cc07932c] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The helicity of a quadruply stranded M2L4 helicate consisting of an aromatic amide bidendate ligand is flexible due to the twisting of the amide moieties and can be tuned by the encapsulated anions. This study reveals the multiple interplays and complementarities between the anions as well as between the anions and the helicate, which are synthetically responsive to the ultimate conformation of the helicate.
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Affiliation(s)
- Qi Lin
- Hubei Key Laboratory of Bioinorganic Chemistry & Materia Medica, School of Chemistry and Chemical Engineering, Huazhong University of Science and Technology, Wuhan 430074, P. R. China.
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24
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Lee E, Ju H, Park IH, Jung JH, Ikeda M, Kuwahara S, Habata Y, Lee SS. pseudo[1]Catenane-Type Pillar[5]thiacrown Whose Planar Chiral Inversion is Triggered by Metal Cation and Controlled by Anion. J Am Chem Soc 2018; 140:9669-9677. [DOI: 10.1021/jacs.8b05751] [Citation(s) in RCA: 70] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Eunji Lee
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, S. Korea
| | - Huiyeong Ju
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, S. Korea
| | - In-Hyeok Park
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, S. Korea
| | - Jong Hwa Jung
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, S. Korea
| | - Mari Ikeda
- Department of Chemistry, Education Center, Faculty of Engineering, Chiba Institute of Technology, 2-1-1 Shibazono, Narashino, Chiba 275-0023, Japan
| | - Shunsuke Kuwahara
- Department of Chemistry, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Yoichi Habata
- Department of Chemistry, Faculty of Science, Toho University, 2-2-1 Miyama, Funabashi, Chiba 274-8510, Japan
| | - Shim Sung Lee
- Department of Chemistry and Research Institute of Natural Science, Gyeongsang National University, Jinju 52828, S. Korea
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25
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Dudek M, Deiana M, Pokladek Z, Mlynarz P, Samoc M, Matczyszyn K. Light-driven chiroptical photoswitchable DNA assemblies mediated by bioinspired photoresponsive molecules. NANOSCALE 2018; 10:11302-11306. [PMID: 29892748 DOI: 10.1039/c8nr01784k] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
Abstract
We show that the incorporation of chiral bioinspired photochromic compounds into inherently chiral DNA matrices enables the building of smart nanoscale photoswitchable chiroptical assemblies tunable over a wide range of wavelengths. Moreover, the use of light as external trigger affords precise control of the resulting hybrid DNA nanostructures, and their chiroptical activities can be spatially modulated without photochemical fatigue.
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Affiliation(s)
- Marta Dudek
- Advanced Materials Engineering and Modelling Group, Faculty of Chemistry, Wroclaw University of Science and Technology, Wyb. Wyspianskiego 27, 50-370 Wroclaw, Poland.
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26
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Roviello GN. Novel insights into nucleoamino acids: biomolecular recognition and aggregation studies of a thymine-conjugated L-phenyl alanine. Amino Acids 2018; 50:933-941. [PMID: 29766280 DOI: 10.1007/s00726-018-2562-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 03/28/2018] [Indexed: 01/30/2023]
Abstract
This article deals with the synthesis in solid phase and characterization of a nucleoamino amide, based on a phenylalaninamide moiety which was N-conjugated to a thymine nucleobase. In analogy to the natural nucleobase-amino acid conjugates, endowed with a wide range of biological properties, the nucleoamino amide interacts with single-stranded nucleic acids as verified in DNA- and RNA-binding assays conducted by CD and UV spectroscopies. These technologies were used to show also that this conjugate binds serum proteins altering significantly their secondary structure, as evidenced by CD and UV using BSA as a model. The biomolecular recognition seems to rely on the ability of the novel compound to bind aromatic and heteroaromatic moieties in protein and nucleic acids, not hindered by its propensity to self-assemble in aqueous solution, behavior suggested by dynamic light scattering (DLS) and CD spectroscopy in concentration- and temperature-dependent experiments. Finally, the high stability in human serum concurs to define the picture of the nucleoamino amide: this enzymatically stable drug candidate could interfere with protein and single-stranded nucleic acid-driven biological processes, particularly those associated with mRNA poly(A) tail, and its self-assembling nature, in analogy to other L-Phe-based systems, discloses new scenarios in drug delivery technology.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini-CNR (UOS Napoli centro), 80134, Naples, Italy.
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27
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Saftić D, Ban Ž, Matić J, Tumirv LM, Piantanida I. Conjugates of Classical DNA/RNA Binder with Nucleobase: Chemical, Biochemical and Biomedical Applications. Curr Med Chem 2018; 26:5609-5624. [PMID: 29737251 DOI: 10.2174/0929867325666180508090640] [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: 02/07/2018] [Revised: 03/27/2018] [Accepted: 04/10/2018] [Indexed: 11/22/2022]
Abstract
Among the most intensively studied classes of small molecules (molecular weight < 650) in biomedical research are small molecules that non-covalently bind to DNA/RNA, and another intensively studied class is nucleobase derivatives. Both classes have been intensively elaborated in many books and reviews. However, conjugates consisting of DNA/RNA binder covalently linked to nucleobase are much less studied and have not been reviewed in the last two decades. Therefore, this review summarized reports on the design of classical DNA/RNA binder - nucleobase conjugates, as well as data about their interactions with various DNA or RNA targets, and even in some cases protein targets are involved. According to these data, the most important structural aspects of selective or even specific recognition between small molecule and target are proposed, and where possible related biochemical and biomedical aspects were discussed. The general conclusion is that this, rather new class of molecules showed an amazing set of recognition tools for numerous DNA or RNA targets in the last two decades, as well as few intriguing in vitro and in vivo selectivities. Several lead research lines show promising advancements toward either novel, highly selective markers or bioactive, potentially druggable molecules.
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Affiliation(s)
- Dijana Saftić
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Željka Ban
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Josipa Matić
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Lidija-Marija Tumirv
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
| | - Ivo Piantanida
- Division of Organic Chemistry and Biochemistry, Ruder Boskovic Institute; 10002 Zagreb, Croatia
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Musumeci D, Roviello V, Roviello GN. DNA- and RNA-binding ability of oligoDapT, a nucleobase-decorated peptide, for biomedical applications. Int J Nanomedicine 2018; 13:2613-2629. [PMID: 29750033 PMCID: PMC5936014 DOI: 10.2147/ijn.s156381] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Background Nucleobase-bearing peptides and their interaction with DNA and RNA are an important topic in the development of therapeutic approaches. On one hand, they are highly effective for modulating the nucleic-acid-based biological processes. On the other hand, they permit to overcome some of the main factors limiting the therapeutic efficacy of natural oligonucleotides, such as their rapid degradation by nucleases. Methods and results This article describes the synthesis and characterization of a novel thymine-bearing nucleoamino acid based on the l-diaminopropionic acid (l-Dap) and its solid phase oligomerization to α-peptides (oligoDapT), characterized using mass spectrometry, spectroscopic techniques, and scanning electron microscopy (SEM) analysis. The interaction of the obtained nucleopeptide with DNA and RNA model systems as both single strands (dA12, rA12, and poly(rA)) and duplex structures (dA12/dT12 and poly(rA)/poly(rU)) was investigated by means of circular dichroism (CD) and ultraviolet (UV) experiments. From the analysis of our data, a clear ability of the nucleopeptide to bind nucleic acids emerged, with oligoDapT being able to form stable complexes with both unpaired and double-stranded DNA and RNA. In particular, dramatic changes in the dA12/dT12 and poly(rA)/poly(rU) structures were observed as a consequence of the nucleopeptide binding. CD titrations revealed that multiple peptide units bound all the examined nucleic acid targets, with TLdap/A or TLdap/A:T(U) ratios >4 in case of oligoDapT/DNA and ~2 in oligoDapT/RNA complexes. Conclusion Our findings seem to indicate that Dap-based nucleopeptides are interesting nucleic acid binding-tools to be further explored with the aim to efficiently modulate DNA- and RNA-based biological processes.
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Affiliation(s)
- Domenica Musumeci
- CNR-Institute of Biostructure and Bioimaging, Naples, Italy.,Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Valentina Roviello
- Analytical Chemistry for the Environment and Centro Servizi Metereologici Avanzati, University of Naples Federico II, Naples, Italy
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Chen Z, Liu C, Cao F, Ren J, Qu X. DNA metallization: principles, methods, structures, and applications. Chem Soc Rev 2018; 47:4017-4072. [DOI: 10.1039/c8cs00011e] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
This review summarizes the research activities on DNA metallization since the concept was first proposed in 1998, covering the principles, methods, structures, and applications.
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Affiliation(s)
- Zhaowei Chen
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Chaoqun Liu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Fangfang Cao
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Jinsong Ren
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
| | - Xiaogang Qu
- Laboratory of Chemical Biology and State Key Laboratory of Rare Earth Resources Utilization
- Changchun Institute of Applied Chemistry
- Chinese Academy of Science
- Changchun
- P. R. China
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30
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Kokan Z, Perić B, Vazdar M, Marinić Ž, Vikić-Topić D, Meštrović E, Kirin SI. Metal-induced supramolecular chirality inversion of small self-assembled molecules in solution. Chem Commun (Camb) 2017; 53:1945-1948. [DOI: 10.1039/c6cc09203a] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first example of supramolecular chirality inversion of small self-assembled ligands in solution by complexation to metal ions is presented.
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31
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Sato Y, Saito H, Aoki D, Teramae N, Nishizawa S. Lysine linkage in abasic site-binding ligand-thiazole orange conjugates for improved binding affinity to orphan nucleobases in DNA/RNA hybrids. Chem Commun (Camb) 2016; 52:14446-14449. [PMID: 27901527 DOI: 10.1039/c6cc07236d] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Introduction of lysine linkage in the conjugate between abasic site-binding ligands and thiazole orange significantly improved the binding affinity for target orphan adenine or uracil nucleobase in DNA/RNA hybrids.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Hiroki Saito
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Daisuke Aoki
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Norio Teramae
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
| | - Seiichi Nishizawa
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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32
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Musumeci D, Roviello GN, Rigione G, Capasso D, Di Gaetano S, Riccardi C, Roviello V, Montesarchio D. Benzodifuran Derivatives as Potential Antiproliferative Agents: Possible Correlation between Their Bioactivity and Aggregation Properties. Chempluschem 2016; 82:251-260. [PMID: 31961558 DOI: 10.1002/cplu.201600547] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2016] [Indexed: 01/24/2023]
Abstract
To further explore the properties and bioactivity of benzodifurans, three compounds in this class were synthesised and characterised using spectroscopic and spectrometric techniques, as well as SEM and thermogravimetric analysis. The synthesised compounds showed interesting antiproliferative activity on different human cancer cells (HeLa, Hep-G2, WM266), whereas no relevant cytotoxic effect was observed on healthy control cells. To study the possible mechanism of action of the benzodifurans, their ability to bind various model DNA systems, their aggregation properties, and their ability to bind biologically relevant metal ions was evaluated. The molecules were found to form monodisperse nanoaggregates stable at physiological temperature, which are likely related to the observed bioactivity.
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Affiliation(s)
- Domenica Musumeci
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Naples, Italy.,Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Giovanni N Roviello
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Giuseppina Rigione
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Naples, Italy
| | - Domenica Capasso
- Department of Pharmacy, University of Naples Federico II, Via D. Montesano 49, 80131, Naples, Italy
| | - Sonia Di Gaetano
- Institute of Biostructures and Bioimaging, CNR, Via Mezzocannone 16, 80134, Naples, Italy
| | - Claudia Riccardi
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Naples, Italy
| | - Valentina Roviello
- Centro Regionale di Competenza (CRdC) Tecnologie, Via Nuova Agnano 11, 80125, Naples, Italy
| | - Daniela Montesarchio
- Department of Chemical Sciences, University of Naples Federico II, Via Cintia 21, 80126, Naples, Italy
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Pradhan AB, Bhuiya S, Haque L, Das S. Spectroscopic study on the binding of chelerythrine with duplex poly (rA): A model of RNA intercalation. Int J Biol Macromol 2016; 95:340-347. [PMID: 27884672 DOI: 10.1016/j.ijbiomac.2016.11.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Revised: 11/16/2016] [Accepted: 11/17/2016] [Indexed: 10/20/2022]
Abstract
Here we have reported a detail study on the interaction of the benzophenanthridine alkaloid chelerythrine (CHL) with double stranded polyriboadenylic acid [ds poly (rA)] by exploiting various spectroscopic techniques. The alkaloid shows high binding affinity (binding constant is 1.10×105M-1) towards the double stranded RNA as revealed from Scatchard plot. The binding was confirmed by hypochromic effect in the UV-vis spectrum of CHL, increase in fluorescence intensity of CHL and perturbations of the circular dichroism (CD) spectrum of ds poly (rA). Later fluorescence quenching, cooperative CD melting transition, viscometric and molecular modeling studies establish the fact that the alkaloid binds to the ds poly (rA) by the mechanism of intercalation. Thermodynamic parameters obtained from the isothermal titration calorimetric (ITC) study show that the binding is favoured by negative enthalpy and small positive entropy changes. This report may be a model for intercalation of small molecule like CHL to the double stranded 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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Zhao D, van Leeuwen T, Cheng J, Feringa BL. Dynamic control of chirality and self-assembly of double-stranded helicates with light. Nat Chem 2016; 9:250-256. [PMID: 28221361 DOI: 10.1038/nchem.2668] [Citation(s) in RCA: 159] [Impact Index Per Article: 19.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2015] [Accepted: 10/05/2016] [Indexed: 12/23/2022]
Abstract
Helicity switching in biological and artificial systems is a fundamental process that allows for the dynamic control of structures and their functions. In contrast to chemical approaches to responsive behaviour in helicates, the use of light as an external stimulus offers unique opportunities to invert the chirality of helical structures in a non-invasive manner with high spatiotemporal precision. Here, we report that unidirectional rotary motors with connecting oligobipyridyl ligands, which can dynamically change their chirality upon irradiation, assemble into metal helicates that are responsive to light. The motor function controls the self-assembly process as well as the helical chirality, allowing switching between oligomers and double-stranded helicates with distinct handedness. The unidirectionality of the light-induced motion governs the sequence of programmable steps, enabling the highly regulated self-assembly of fully responsive helical structures. This discovery paves the way for the future development of new chirality-dependent photoresponsive systems including smart materials, enantioselective catalysts and light-driven molecular machines.
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Affiliation(s)
- Depeng Zhao
- Centre for Systems Chemistry, Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Thomas van Leeuwen
- Centre for Systems Chemistry, Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Jinling Cheng
- Centre for Systems Chemistry, Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
| | - Ben L Feringa
- Centre for Systems Chemistry, Stratingh Institute for Chemistry and Zernike Institute for Advanced Materials, Faculty of Mathematics and Natural Sciences, University of Groningen, Nijenborgh 4, 9747 AG Groningen, the Netherlands
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35
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Zhao C, Sun Y, Ren J, Qu X. Recent progress in lanthanide complexes for DNA sensing and targeting specific DNA structures. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.04.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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36
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Mukherjee S, Dohno C, Asano K, Nakatani K. Cyclic mismatch binding ligand CMBL4 binds to the 5'-T-3'/5'-GG-3' site by inducing the flipping out of thymine base. Nucleic Acids Res 2016; 44:7090-9. [PMID: 27466390 PMCID: PMC5009760 DOI: 10.1093/nar/gkw672] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2016] [Revised: 07/15/2016] [Accepted: 07/19/2016] [Indexed: 12/13/2022] Open
Abstract
A newly designed cyclic bis-naphthyridine carbamate dimer CMBL4: with a limited conformational flexibility was synthesized and characterized. Absorption spectra revealed that two naphthyridines in CMBL4: were stacked on each other in aqueous solutions. The most efficient binding of CMBL4: to DNA was observed for the sequence 5'-T-3'/5'-GG-3' (T/GG) with the formation of a 1:1 complex, which is one of possible structural elements involved in the higher order structures of (TGG)n repeat DNA triggering the genome microdeletion. Surface plasmon resonance assay also showed the binding of CMBL4: with TGG repeat DNA. Potassium permanganate oxidation studies of CMBL4: -bound duplex containing the T/GG site showed that the CMBL4: -binding accelerated the oxidation of thymine at that site, which suggests the flipping out of the thymine base from a π-stack. Preferential binding was observed for CMBL4: compared with its acyclic variants, which suggests the marked significance of the macrocyclic structure for the recognition of the T/GG site.
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Affiliation(s)
- Sanjukta Mukherjee
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Chikara Dohno
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kaori Asano
- Comprehensive Analysis Center, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research (ISIR), Osaka University, 8-1 Mihogaoka, Ibaraki, Osaka 567-0047, Japan
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37
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Lv Z, Chen Z, Shao K, Qing G, Sun T. Stimuli-Directed Helical Chirality Inversion and Bio-Applications. Polymers (Basel) 2016; 8:polym8080310. [PMID: 30974585 PMCID: PMC6432277 DOI: 10.3390/polym8080310] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 08/09/2016] [Accepted: 08/12/2016] [Indexed: 12/21/2022] Open
Abstract
Helical structure is a sophisticated ubiquitous motif found in nature, in artificial polymers, and in supramolecular assemblies from microscopic to macroscopic points of view. Significant progress has been made in the synthesis and structural elucidation of helical polymers, nevertheless, a new direction for helical polymeric materials, is how to design smart systems with controllable helical chirality, and further use them to develop chiral functional materials and promote their applications in biology, biochemistry, medicine, and nanotechnology fields. This review summarizes the recent progress in the development of high-performance systems with tunable helical chirality on receiving external stimuli and discusses advances in their applications as drug delivery vesicles, sensors, molecular switches, and liquid crystals. Challenges and opportunities in this emerging area are also presented in the conclusion.
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Affiliation(s)
- Ziyu Lv
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
| | - Zhonghui Chen
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
| | - Kenan Shao
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
| | - Guangyan Qing
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
| | - Taolei Sun
- State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
- School of Chemistry, Chemical Engineering and Life Science, Wuhan University of Technology, 122 Luoshi Road, Wuhan 430070, China.
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38
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A pH-responsive activatable aptamer probe for targeted cancer imaging based on i-motif-driven conformation alteration. Sci China Chem 2016. [DOI: 10.1007/s11426-016-5575-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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39
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Roviello GN, Roviello V, Autiero I, Saviano M. Solid phase synthesis of TyrT, a thymine-tyrosine conjugate with poly(A) RNA-binding ability. RSC Adv 2016; 6:27607-27613. [PMID: 29057072 PMCID: PMC5647564 DOI: 10.1039/c6ra00294c] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/01/2016] [Indexed: 01/15/2023] Open
Abstract
TyrT nucleoamino amide interacts with poly(A) RNA.
The present work deals with the synthesis and characterization of a novel nucleoamino acid derivative based on a l-tyrosine moiety to which a thymine nucleobase was anchored by means of an amide bond to the N-alpha group. This derivative, denominated by us TyrT, belongs to the family of the nucleobase–amino acid conjugates that show a wide range of biological activities, frequently associated with their ability to interact with nucleic acids. In this respect, the interaction of TyrT with poly(A), a proposed RNA target for anticancer strategies, was studied by circular dichroism (CD) which suggested its ability to bind this RNA. Moreover, the modification of the morphology of a sample of TyrT in the presence of poly(A) was visualised by scanning electron microscopy (SEM) which was in agreement with the evidence that the thyminyl l-tyrosine interacts with poly(A). Finally, computational analyses have been performed to hypothesize the binding mode from a structural point of view, suggesting that the binding is mainly kept via hydrophobic contacts, reproducing a stacking-like interaction between the thymine ring of TyrT and the two successive adenine rings of a poly(A) model.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR (UOS Napoli Centro) , 80134 Napoli , Italy . ; ; Tel: +39-81-2534585
| | - Valentina Roviello
- Dipartimento di Ingegneria Chimica , dei Materiali e della Produzione Industriale (DICMaPI) , Università di Napoli "Federico II" , 80125 Napoli , Italy
| | - Ida Autiero
- Istituto di Biostrutture e Bioimmagini - CNR (UOS Napoli Centro) , 80134 Napoli , Italy . ; ; Tel: +39-81-2534585
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Roviello GN, Vicidomini C, Di Gaetano S, Capasso D, Musumeci D, Roviello V. Solid phase synthesis and RNA-binding activity of an arginine-containing nucleopeptide. RSC Adv 2016; 6:14140-14148. [PMID: 29057071 PMCID: PMC5635565 DOI: 10.1039/c5ra25809j] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2015] [Accepted: 01/15/2016] [Indexed: 01/22/2023] Open
Abstract
Here we report the solid phase synthesis and characterization (LC-ESIMS, CD) of a cationic nucleobase-containing α-peptide, composed of both l-arginine residues and l-lysine-based nucleoamino acids sequentially present in the structure. The binding properties of this novel basic nucleopeptide towards nucleic acids were investigated by CD spectroscopy which revealed the ability of the thymine-containing oligomer to bind both adenine-containing DNA (dA12) and RNA (poly rA) molecules inducing high conformational variations in the nucleic acid structures. Moreover, the artificial oligonucleotide inhibited the enzymatic activity of HIV reverse transcriptase, opening the door to the exploitation of novel antiviral strategies inspired to this molecular tool.
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Affiliation(s)
- G N Roviello
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - C Vicidomini
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - S Di Gaetano
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
| | - D Capasso
- Università di Napoli "Federico II" , Dipartimento di Farmacia , 80134 Napoli , Italy
| | - D Musumeci
- CNR , Istituto di Biostrutture e Bioimmagini - (Mezzacannone site and Headquarters) , 80134 Napoli , Italy . ; ; Tel: +39-081-2534585
- Università di Napoli "Federico II" , Dipartimento di Scienze Chimiche , 80126 Napoli , Italy
| | - V Roviello
- Università di Napoli "Federico II" , Dipartimento di Ingegneria Chimica , dei Materiali e della Produzione Industriale (DICMaPI) , 80125 Napoli , Italy
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Xu L, Shen X, Hong S, Wang J, Zhou L, Chen X, Pei R. Thiazole Orange as a Fluorescent Light-Up Probe for the i-Motif and its Application to the Development of a Molecular Logic System. ASIAN J ORG CHEM 2015. [DOI: 10.1002/ajoc.201500347] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]
Affiliation(s)
- Lijun Xu
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 P.R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Xiaoqiang Shen
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 P.R. China
| | - Shanni Hong
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 P.R. China
| | - Jine Wang
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 P.R. China
| | - Lu Zhou
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 P.R. China
| | - Xing Chen
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 P.R. China
| | - Renjun Pei
- Key Laboratory of Nano-Bio Interface, Division of Nanobiomedicine; Suzhou Institute of Nano-Tech and Nano-Bionics; Chinese Academy of Sciences; Suzhou 215123 P.R. China
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Sato Y, Sato T, Sato T, Nishizawa S, Teramae N. The effect of LNA nucleobases as enhancers for the binding of amiloride to an abasic site in DNA/DNA and DNA/RNA duplexes. Org Biomol Chem 2015; 12:7250-6. [PMID: 25101634 DOI: 10.1039/c4ob00977k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We report on a significant effect of locked nucleic acid (LNA) nucleobases on the binding of amiloride for abasic site (AP)-containing DNA duplexes. Fluorescence titration experiments showed that the binding affinity of amiloride for the target thymine (T) opposite an AP site significantly improves for the DNA duplexes possessing LNA nucleobases that flank the AP site, compared to the corresponding normal DNA duplexes. In particular, LNA flanking nucleobases on both 5'- and 3'-sides of the AP site are found to be effective for the enhancement of the binding affinity. From thermodynamic characterization of the amiloride binding, the loss in the binding entropy is remarkably reduced for the LNA-containing DNA duplexes, which is indeed responsible for the enhanced affinity of amiloride. Moreover, such an effect of LNA nucleobases was also observed for amiloride binding to DNA/RNA hybrid duplexes.
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Affiliation(s)
- Yusuke Sato
- Department of Chemistry, Graduate School of Science, Tohoku University, Sendai 980-8578, Japan.
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Lönnberg T, Hutchinson M, Rokita S. Selective Alkylation of C-Rich Bulge Motifs in Nucleic Acids by Quinone Methide Derivatives. Chemistry 2015. [PMID: 26220692 DOI: 10.1002/chem.201502014] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A quinone methide precursor featuring a bis-cyclen anchoring moiety has been synthesized and its capacity to alkylate oligonucleotide targets quantified in the presence and absence of divalent metal ions (Zn(2+) , Ni(2+) and Cd(2+) ). The oligonucleotides were designed for testing the sequence and secondary structure specificity of the reaction. Gel electrophoretic analysis revealed predominant alkylation of C-rich bulges, regardless of the presence of divalent metal ions or even the bis-cyclen anchor. This C-selectivity appears to be an intrinsic property of the quinone methide electrophile as reflected by its reaction with an equimolar mixture of the 2'-deoxynucleosides. Only dA-N1 and dC-N3 alkylation products were detected initially and only the dC adduct persisted for detection under conditions of the gel electrophoretic analysis.
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Affiliation(s)
- Tuomas Lönnberg
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218 (USA). .,Department of Chemistry, University of Turku, 20014 Turku (Finland).
| | - Mark Hutchinson
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218 (USA)
| | - Steven Rokita
- Department of Chemistry, Johns Hopkins University, Baltimore, Maryland 21218 (USA)
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Roviello GN, Musumeci D, Roviello V, Pirtskhalava M, Egoyan A, Mirtskhulava M. Natural and artificial binders of polyriboadenylic acid and their effect on RNA structure. BEILSTEIN JOURNAL OF NANOTECHNOLOGY 2015; 6:1338-1347. [PMID: 26199837 PMCID: PMC4505092 DOI: 10.3762/bjnano.6.138] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2014] [Accepted: 05/22/2015] [Indexed: 06/10/2023]
Abstract
The employment of molecular tools with nucleic acid binding ability to specifically control crucial cellular functions represents an important scientific area at the border between biochemistry and pharmaceutical chemistry. In this review we describe several molecular systems of natural or artificial origin, which are able to bind polyriboadenylic acid (poly(rA)) both in its single-stranded or structured forms. Due to the fundamental role played by the poly(rA) tail in the maturation and stability of mRNA, as well as in the initiation of the translation process, compounds able to bind this RNA tract, influencing the mRNA fate, are of special interest for developing innovative biomedical strategies mainly in the field of anticancer therapy.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy
| | - Domenica Musumeci
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy
- Dipartimento di Scienze Chimiche, Università di Napoli “Federico II”, 80126 Napoli, Italy
| | - Valentina Roviello
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale (DICMaPI), Università di Napoli “Federico II”, 80125 Napoli, Italy
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Roviello GN, Musumeci D, Roviello V. Cationic peptides as RNA compaction agents: a study on the polyA compaction activity of a linear alpha,epsilon-oligo-L-lysine. Int J Pharm 2015; 485:244-8. [PMID: 25772417 DOI: 10.1016/j.ijpharm.2015.03.011] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Revised: 03/05/2015] [Accepted: 03/09/2015] [Indexed: 11/16/2022]
Abstract
In this work, we investigate the compaction activity of a sequential alpha,epsilon-peptide composed of l-lysines towards two RNA targets, in view of its possible pharmaceutical application in RNA-targeting and RNA delivery. The basic oligolysine, object of the present study, proved not only to be efficient in compacting the single-stranded polyA RNA, but also to strongly interact with the polyA·polyU complex, as evidenced by CD-binding and UV-melting experiments. In particular, the marked differences in the CD spectra of the RNA targets upon addition of the peptide, as well as the different UV melting behaviour for the polyA·polyU complex in the presence and absence of the peptide, sustain the hypothesis of a strong RNA compaction capacity of the alpha,epsilon-oligolysine. Finally, by using HPLC analysis, we found a good resistance of the peptide against the lytic action of human serum, an important requirement in view of in vitro/in vivo biological assays.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy.
| | - Domenica Musumeci
- Istituto di Biostrutture e Bioimmagini - CNR, via Mezzocannone 16, 80134 Napoli, Italy; Dipartimento di Scienze Chimiche, Università di Napoli "Federico II", 80126 Napoli, Italy
| | - Valentina Roviello
- Dipartimento di Ingegneria Chimica, dei Materiali e della Produzione Industriale(DICMaPI), Università di Napoli "Federico II", 80125 Napoli, Italy
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Prakasam T, Lusi M, Nauha E, Olsen JC, Sy M, Platas-Iglesias C, Charbonnière LJ, Trabolsi A. Dynamic stereoisomerization in inherently chiral bimetallic [2]catenanes. Chem Commun (Camb) 2015; 51:5840-3. [PMID: 25664727 DOI: 10.1039/c4cc07392d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Stereoisomerization and the unprecedented phenomenon of metal translocation in the absence of redox processes were probed in two inherently chiral bimetallic [2]catenanes by using a combination of variable-temperature (1)H NMR and CD spectroscopies, X-ray crystallography, and DFT calculations.
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Affiliation(s)
- Thirumurugan Prakasam
- Centre for Science and Engineering, New York University Abu Dhabi (NYUAD), United Arab Emirates.
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Novotna J, Laguerre A, Granzhan A, Pirrotta M, Teulade-Fichou MP, Monchaud D. Cationic azacryptands as selective three-way DNA junction binding agents. Org Biomol Chem 2015; 13:215-22. [DOI: 10.1039/c4ob01846j] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Azacryptands are promising candidates for assessing the therapeutic potential of three-way DNA junctions.
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Affiliation(s)
- Jana Novotna
- Institute of Molecular Chemistry
- University of Dijon
- Dijon
- France
- Department of Analytical Chemistry
| | | | | | - Marc Pirrotta
- Institute of Molecular Chemistry
- University of Dijon
- Dijon
- France
| | | | - David Monchaud
- Institute of Molecular Chemistry
- University of Dijon
- Dijon
- France
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Vargiu AV, Magistrato A. Atomistic-Level Portrayal of Drug-DNA Interplay: A History of Courtships and Meetings Revealed by Molecular Simulations. ChemMedChem 2014; 9:1966-81. [DOI: 10.1002/cmdc.201402203] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2014] [Indexed: 12/19/2022]
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Roviello GN, Roviello V, Musumeci D, Pedone C. Synthesis of a novel benzodifuran derivative and its molecular recognition of poly rA RNA. Biol Chem 2014; 394:1235-9. [PMID: 23729622 DOI: 10.1515/hsz-2013-0154] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2013] [Accepted: 05/28/2013] [Indexed: 11/15/2022]
Abstract
In this manuscript, we describe a synthetic approach to a novel benzodifuran derivative as well as CD studies regarding its ability to interact with DNA and RNA. After the chemical synthesis and ESI-MS and NMR characterization, this heteroaromatic molecule was investigated by CD spectroscopy in order to evaluate it as a potential nucleic acid binder. Interestingly, the benzodifuran compound was found to be able to induce conformational changes in both DNA and RNA homoadenine molecules forming in the latter case a complex with a 6:1 benzodifuran/nucleobase stoichiometric ratio, as evidenced by CD titration experiments.
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Affiliation(s)
- Giovanni N Roviello
- Istituto di Biostrutture e Bioimmagini, CNR, Via Mezzocannone 16, I-80134 Napoli, Italy.
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