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Bertini L, Libera V, Catalini S, Schirò G, Orecchini A, Campanella R, Arciuolo V, Pagano B, Petrillo C, De Michele C, Comez L, Paciaroni A. Hindered intermolecular stacking of anti-parallel telomeric G-quadruplexes. J Chem Phys 2024; 161:105101. [PMID: 39248241 DOI: 10.1063/5.0225371] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Accepted: 08/21/2024] [Indexed: 09/10/2024] Open
Abstract
Telomeric G-quadruplexes (G4s) are non-canonical DNA structures composed of TTAGGG repeats. They are extensively studied both as biomolecules key for genome stability and as promising building blocks and functional elements in synthetic biology and nanotechnology. This is why it is extremely important to understand how the interaction between G4s is affected by their topology. We used small-angle x-ray scattering to investigate the end-to-end stacking of antiparallel telomeric G-quadruplexes formed by the sequence AG3(T2AG3)3. To represent the experimental data, we developed a highly efficient coarse-grained fitting tool, which successfully described the samples as an equilibrium mixture of monomeric and dimeric G4 species. Our findings indicate that the antiparallel topology prevents the formation of long multimeric structures under self-crowding conditions, unlike the hybrid/parallel structures formed by the same DNA sequence. This result supports the idea that the stacking of monomeric G-quadruplexes is strongly affected by the presence of diagonal loops.
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Affiliation(s)
- Luca Bertini
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
| | - Valeria Libera
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
| | - Sara Catalini
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
| | - Giorgio Schirò
- Univ. Grenoble Alpes, CEA, CNRS, Institut de Biologie Structurale, F-38044 Grenoble, France
| | - Andrea Orecchini
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
| | - Renzo Campanella
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
| | - Valentina Arciuolo
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Bruno Pagano
- Department of Pharmacy, University of Naples Federico II, 80131 Naples, Italy
| | - Caterina Petrillo
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
| | | | - Lucia Comez
- CNR-IOM c/o Department of Physics and Geology, University of Perugia, 06123 Perugia, Italy
| | - Alessandro Paciaroni
- Department of Physics and Geology, University of Perugia, via Alessandro Pascoli, 06123 Perugia, Italy
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2
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Huang Y, Liang Q, Yin H, Zhang X, Gao R, Pan J, Liang K, Jiang L, Kong B. pH Modulation of Super-Assembled Heteromembranes for Sustainable Chiral Sensing. ACS NANO 2024; 18:12547-12559. [PMID: 38695563 DOI: 10.1021/acsnano.4c02720] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/15/2024]
Abstract
Enantioselective sensing and separation represent formidable challenges across a diverse range of scientific domains. The advent of hybrid chiral membranes offers a promising avenue to address these challenges, capitalizing on their unique characteristics, including their heterogeneous structure, porosity, and abundance of chiral surfaces. However, the prevailing fabrication methods typically involve the initial preparation of achiral porous membranes followed by subsequent modification with chiral molecules, limiting their synthesis flexibility and controllability. Moreover, existing chiral membranes struggle to achieve coupled-accelerated enantioseparation (CAE). Here, we report a replacement strategy to controllably produce mesoscale and chiral silica-carbon (MCSC) hybrid membranes that comprise chiral pores by interfacial superassembly on a macroporous alumina (AAO) membrane, in which both ion- and enantiomers can be effectively and selectively transported across the membrane. As a result, the heterostructured hybrid membrane (MCSC/AAO) exhibits enhanced selectivity for cations and enantiomers of amino acids, achieving CAE for amino acids with an isoelectric point (pI) exceeding 7. Interestingly, the MCSC/AAO system demonstrates enhanced pH-sensitive enantioseparation compared to chiral mesoporous silica/AAO (CMS/AAO) with significant improvements of 78.14, 65.37, and 14.29% in the separation efficiency, separation factor, and permeate flux, respectively. This work promises to advance the synthesis of two or more component-integrated chiral nanochannels with multifunctional properties and allows a better understanding of the origins of the homochiral hybrid membranes.
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Affiliation(s)
- Yanan Huang
- Department of Chemistry, Shanghai Key Lab of Molecular Catalysis and Innovative Materials, iChEM, Fudan University, Shanghai 200433, P. R. China
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Qirui Liang
- Qingdao Innovation and Development Center, Harbin Engineering University, Qingdao 266400, P. R. China
| | - Haibo Yin
- State Key Joint Laboratory of Environment Simulation and Pollution Control, School of Environment, Tsinghua University, Beijing 100084, P. R. China
| | - Xin Zhang
- Department of Chemistry, Shanghai Key Lab of Molecular Catalysis and Innovative Materials, iChEM, Fudan University, Shanghai 200433, P. R. China
| | - Ruihua Gao
- State Key Laboratory of Molecular Engineering of Polymers, Department of Macromolecular Science, Fudan University, Shanghai 200433, P. R. China
| | - Jianming Pan
- School of Chemistry and Chemical Engineering, Jiangsu University, Zhenjiang 212013, P. R. China
| | - Kang Liang
- School of Chemical Engineering, Graduate School of Biomedical Engineering, The University of New South Wales, Sydney, NSW 2052, Australia
| | - Lei Jiang
- Beijing National Laboratory for Molecular Sciences (BNLMS), Key Laboratory of Organic Solids, Institute of Chemistry, Chinese Academy of Science, Beijing 100190, P. R. China
| | - Biao Kong
- Department of Chemistry, Shanghai Key Lab of Molecular Catalysis and Innovative Materials, iChEM, Fudan University, Shanghai 200433, P. R. China
- Yiwu Research Institute of Fudan University, Yiwu, Zhejiang 322000, P. R. China
- Shandong Fudan Research Institute, Jinan 250014, P. R. China
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3
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Pepe A, Moretti P, Yoneda JS, Carducci F, Itri R, Mariani P. Self-oriented anisotropic structure of G-hydrogels as a delicate balance between attractive and repulsive forces. NANOSCALE 2023; 15:15196-15205. [PMID: 37624640 DOI: 10.1039/d3nr01348k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/27/2023]
Abstract
Guanine (G) hydrogels are very attractive materials made by the supramolecular organization of G-derivatives in water. In this paper, hydrogels composed of guanosine 5'-monophosphate (GMP) and guanosine (Gua), that make long, flexible and knotted G-quadruplexes, were investigated by small- and wide-angle X-ray scattering (SAXS and WAXS) to comprehend the origin of their unique orientational properties. The SAXS intensity, analysed at a fixed scattering vector modulus Q as a function of polar angle, allowed us to derive the Maier-Saupe orientation parameter m. The strong dependence of m on hydrogel composition and temperature demonstrated that the preferred orientation is controlled by the quadruplex surface charge and flexibility. Indeed, a possible correlation between the orientation parameter m and the quadruplex-to-quadruplex lateral interactions was explored. Results confirmed that the balance between attractive and repulsive interactions plays a main role in the orientational anisotropy: quadruplex clusters lose their orientational properties when attractive interactions decrease. The key role of the number of negative charges per unit length of the G-quadruplex filaments was confirmed by Atomic Force Microscopy (AFM) observations. Indeed, directionality histograms showed that in the presence of a large amount of Gua, G-quadruplexes follow preferential orientations other than those related to the strong interactions with the K+ pattern on the mica surface. The fact that lateral quadruplex-to-quadruplex interactions, even in the presence of external (opposing) forces, can tune the hydrogel alignment in a given preferred direction provides novel possibilities for scaffold/3D printing applications.
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Affiliation(s)
- Alessia Pepe
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Paolo Moretti
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Juliana S Yoneda
- Department of Applied Physics, Institute of Physics, University of São Paulo, São Paulo, Brazil
- Brazilian Synchrotron Light Laboratory (LNLS), Brazilian Center for Research in Energy and Materials (CNPEM), Campinas, Brazil
| | - Federica Carducci
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
| | - Rosangela Itri
- Department of Applied Physics, Institute of Physics, University of São Paulo, São Paulo, Brazil
| | - Paolo Mariani
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, via Brecce Bianche, 60131 Ancona, Italy.
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4
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Paparini S, Virga EG. Shape bistability in 2D chromonic droplets. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:495101. [PMID: 34517353 DOI: 10.1088/1361-648x/ac2645] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 09/13/2021] [Indexed: 06/13/2023]
Abstract
An extensive experimental study of the shapes of two-dimensional bipolar droplets of the chromonic nematic phase of disodium cromoglycate (DSCG) sandwiched between glass plates, by Kimet alwas published in (2013J. Phys.: Condens. Matter25404202). The paper includes a mathematical model of this system. We have extended this study by further theoretical modelling. Our results are in good, quantitative agreement with the experimental data. The model has produced what promises to be a more accurate estimate for the isotropic surface tension at the nematic/isotropic solution interface-and predicts a regime of shape bistability (which has not yet been observed) for larger droplets, where tactoids (pointed, zeppelin-shaped droplets) and smooth-edged discoids can coexist in equilibrium. The general method presented in this paper is also applied to the tactoids formed by F-actin filaments in solution, for which an estimate is given for the value of the isotropic surface tension at the nematic/isotropic interface.
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Affiliation(s)
- Silvia Paparini
- Dipartimento di Matematica, Università di Pavia, Via Ferrata 5, 27100 Pavia, Italy
| | - Epifanio G Virga
- Dipartimento di Matematica, Università di Pavia, Via Ferrata 5, 27100 Pavia, Italy
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5
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Paparini S, Virga EG. Nematic tactoid population. Phys Rev E 2021; 103:022707. [PMID: 33736001 DOI: 10.1103/physreve.103.022707] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2020] [Accepted: 01/27/2021] [Indexed: 01/02/2023]
Abstract
Tactoids are pointed, spindlelike droplets of nematic liquid crystal in an isotropic fluid. They have long been observed in inorganic and organic nematics, in thermotropic phases as well as lyotropic colloidal aggregates. The variational problem of determining the optimal shape of a nematic droplet is formidable and has only been attacked in selected classes of shapes and director fields. Here, by considering a special class of admissible solutions for a bipolar droplet, we study the prevalence in the population of all equilibrium shapes of each of the three that may be optimal (tactoids primarily among them). We show how the prevalence of a shape is affected by a dimensionless measure α of the drop's volume and the ratios k_{24} and k_{3} of the saddle-splay constant K_{24} and the bending constant K_{33} of the material to the splay constant K_{11}. Tactoids, in particular, prevail for α⪅16.2+0.3k_{3}-(14.9-0.1k_{3})k_{24}. Our class of shapes (and director fields) is sufficiently different from those employed so far to unveil a rather different role of K_{24}.
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Affiliation(s)
- Silvia Paparini
- Dipartimento di Matematica, Università di Pavia, Via Ferrata 5, 27100 Pavia, Italy
| | - Epifanio G Virga
- Dipartimento di Matematica, Università di Pavia, Via Ferrata 5, 27100 Pavia, Italy
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6
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Gao C, Liu Z, Hou H, Ding J, Chen X, Xie C, Song Z, Hu Z, Feng M, Mohamed HI, Xu S, Parkinson GN, Haider S, Wei D. BMPQ-1 binds selectively to (3+1) hybrid topologies in human telomeric G-quadruplex multimers. Nucleic Acids Res 2020; 48:11259-11269. [PMID: 33080032 PMCID: PMC7672424 DOI: 10.1093/nar/gkaa870] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 09/23/2020] [Accepted: 10/14/2020] [Indexed: 12/21/2022] Open
Abstract
A single G-quadruplex forming sequence from the human telomere can adopt six distinct topologies that are inter-convertible under physiological conditions. This presents challenges to design ligands that show selectivity and specificity towards a particular conformation. Additional complexity is introduced in differentiating multimeric G-quadruplexes over monomeric species, which would be able to form in the single-stranded 3′ ends of telomeres. A few ligands have been reported that bind to dimeric quadruplexes, but their preclinical pharmacological evaluation is limited. Using multidisciplinary approaches, we identified a novel quinoline core ligand, BMPQ-1, which bound to human telomeric G-quadruplex multimers over monomeric G-quadruplexes with high selectivity, and induced the formation of G-quadruplex DNA along with the related DNA damage response at the telomere. BMPQ-1 reduced tumor cell proliferation with an IC50 of ∼1.0 μM and decreased tumor growth rate in mouse by half. Biophysical analysis using smFRET identified a mixture of multiple conformations coexisting for dimeric G-quadruplexes in solution. Here, we showed that the titration of BMPQ-1 shifted the conformational ensemble of multimeric G-quadruplexes towards (3+1) hybrid-2 topology, which became more pronounced as further G-quadruplex units are added.
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Affiliation(s)
- Chao Gao
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong AgriculturalUniversity, Wuhan, 430070, China.,College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhu Liu
- National Key Laboratory of Crop Genetic Improvement, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Haitao Hou
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Jieqin Ding
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Xin Chen
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Congbao Xie
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zibing Song
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhe Hu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingqian Feng
- College of Life Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Hany I Mohamed
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,Chemistry Department, Faculty of Science, Benha University, Benha 13518, Egypt
| | - Shengzhen Xu
- Department of Chemistry, College of Science, Huazhong Agricultural University, Wuhan 430070, China
| | - Gary N Parkinson
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Shozeb Haider
- UCL School of Pharmacy, University College London, 29-39 Brunswick Square, London WC1N 1AX, UK
| | - Dengguo Wei
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan 430070, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, Huazhong AgriculturalUniversity, Wuhan, 430070, China
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7
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Baldassarri EJ, Ortore MG, Spinozzi F, Round A, Ferrero C, Mariani P. K vs. Na Effects on the Self-Assembly of Guanosine 5'-Monophosphate: A Solution SAXS Structural Study +. NANOMATERIALS (BASEL, SWITZERLAND) 2020; 10:E629. [PMID: 32231081 PMCID: PMC7221663 DOI: 10.3390/nano10040629] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2020] [Revised: 03/18/2020] [Accepted: 03/20/2020] [Indexed: 12/18/2022]
Abstract
The hierarchical process of guanosine (G) self-assembly, leading in aqueous solution and in the presence of metal cations to the formation of G-quadruplexes, represents an intriguing topic both for the biological correlation with telomerase activity and for the nano-technological applications, as demonstrated by the current measured in a quadruplex wire 100 nm long. Similar to G-rich DNA sequences and G-oligonucleotides, the guanosine 5'-monophosphate (GMP) self-aggregates in water to form quadruplexes. However, due to the absence of a covalent axial backbone, this system can be very useful to understand the chemical-physical conditions that govern the guanosine supramolecular aggregation. We have then investigated by in-solution Synchrotron Small Angle X-ray Scattering technique the role of different cations in promoting the quadruplex formation as a function of concentration and temperature. Results show how potassium, with its peculiar biological traits, favours the G-quadruplex elongation process in respect to other cations (Na + , but also NH 4 + and Li + ), determining the longest particles in solution. Moreover, the formation and the elongation of G-quadruplexes have been demonstrated to be controlled by both GMP concentration and excess cation content, even if they specifically contribute to these processes in different ways. The occurrence of condensed liquid crystalline phases was also detected, proving that excess cations play also unspecific effects on the effective charges on the G-quadruplex surface.
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Affiliation(s)
- Enrico Junior Baldassarri
- Marche Structural Biology Center, Department of Life and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Maria Grazia Ortore
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Francesco Spinozzi
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
| | - Adam Round
- European XFEL, SPB/SFX Instrument, 22869 Schenefeld, Germany
| | - Claudio Ferrero
- European Synchrotron Radiation Facility-E.S.R.F., 38043 Grenoble, France
| | - Paolo Mariani
- Department of Life and Environmental Sciences, Università Politecnica delle Marche, 60131 Ancona, Italy
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8
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Pieraccini S, Campitiello M, Carducci F, Davis JT, Mariani P, Masiero S. Playing supramolecular dominoes with light: building and breaking a photoreversible G-quadruplex made from guanosine, boric acid and an azobenzene. Org Biomol Chem 2020; 17:2759-2769. [PMID: 30785179 DOI: 10.1039/c9ob00193j] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Addition of azobenzene-derivative 1 in its E configuration to an aqueous solution containing various guanosine borate esters induces a helical G-quartet based self-organization, stabilized by intercalation of the dye. The process is driven, in a domino fashion, by the initial host-guest interaction between the dye and a specific guanosine borate diester, whose structure can be thus assigned. This inclusion complex templates the formation of G-quartets. The quartets, in turn, pile up to form a supramolecular G-quadruplex structure, in which other G species present in solution are progressively included. The G-quadruplex can be reversibly broken and reformed by photoisomerization of the dye. This hierarchical and photosensitive self-assembly is unprecedented for simple guanosine derivatives.
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Affiliation(s)
- Silvia Pieraccini
- Dipartimento di Chimica "Giacomo Ciamician", Università di Bologna, v. S. Giacomo, 11-40126 Bologna, Italy.
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9
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Gonnelli A, Pieraccini S, Baldassarri EJ, Funari S, Masiero S, Ortore MG, Mariani P. Metallo-responsive self-assembly of lipophilic guanines in hydrocarbon solvents: a systematic SAXS structural characterization. NANOSCALE 2020; 12:1022-1031. [PMID: 31845695 DOI: 10.1039/c9nr08556d] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Lipophilic guanines (LipoGs) in aprotic solvents undergo different self-assembly processes based on different H-bonded motifs. Cylindrical nanotubes made by π-π stacked guanine tetramers (G-quadruplexes) and flat, tape-like aggregates (G-ribbons) have been observed depending on the presence of alkali metal ions. To obtain information on the structural properties and stability of these LipoG aggregates, Small-Angle X-ray Scattering (SAXS) experiments have been performed in dodecane, both in the presence and in the absence of potassium ions. As a result, the occurrence of the two different metallo-responsive architectures (nanoribbons or columnar nanotubes) was confirmed and we reported here for the first time a systematic study on the dependence of the aggregate properties on composition, temperature and molecular unit structure. Even if dodecane was selected to favour LipoG solubility, a strong tendency to self-organize into ordered lyotropic phases was indeed detected.
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Affiliation(s)
- Adriano Gonnelli
- Dipartimento di Scienze della Vita e dell'Ambiente, Biophysics Research Group, Università Politecnica delle Marche, Via Brecce Bianche, 60131 Ancona, Italy.
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10
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Bianchi F, Comez L, Biehl R, D’Amico F, Gessini A, Longo M, Masciovecchio C, Petrillo C, Radulescu A, Rossi B, Sacchetti F, Sebastiani F, Violini N, Paciaroni A. Structure of human telomere G-quadruplex in the presence of a model drug along the thermal unfolding pathway. Nucleic Acids Res 2018; 46:11927-11938. [PMID: 30407585 PMCID: PMC6294516 DOI: 10.1093/nar/gky1092] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2018] [Revised: 09/28/2018] [Accepted: 10/19/2018] [Indexed: 12/21/2022] Open
Abstract
A multi-technique approach, combining circular dichroism spectroscopy, ultraviolet resonance Raman spectroscopy and small angle scattering techniques, has been deployed to elucidate how the structural features of the human telomeric G-quadruplex d[A(GGGTTA)3GGG] (Tel22) change upon thermal unfolding. The system is studied both in the free form and when it is bound to Actinomycin D (ActD), an anticancer ligand with remarkable conformational flexibility. We find that at room temperature binding of Tel22 with ActD involves end-stacking upon the terminal G-tetrad. Structural evidence for drug-driven dimerization of a significant fraction of the G-quadruplexes is provided. When the temperature is raised, both free and bound Tel22 undergo melting through a multi-state process. We show that in the intermediate states of Tel22 the conformational equilibrium is shifted toward the (3+1) hybrid-type, while a parallel structure is promoted in the complex. The unfolded state of the free Tel22 is consistent with a self-avoiding random-coil conformation, whereas the high-temperature state of the complex is observed to assume a quite compact form. Such an unprecedented high-temperature arrangement is caused by the persistent interaction between Tel22 and ActD, which stabilizes compact conformations even in the presence of large thermal structural fluctuations.
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Affiliation(s)
- Federico Bianchi
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Lucia Comez
- IOM-CNR c/o Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Ralf Biehl
- JCNS & ICS, Forschungszentrum Jülich GmbH, Leo-Brandt Strasse, 52425 Jülich, Germany
| | - Francesco D’Amico
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Alessandro Gessini
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Marialucia Longo
- JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Claudio Masciovecchio
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Caterina Petrillo
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Aurel Radulescu
- JCNS at Heinz Maier-Leibnitz Zentrum (MLZ), Forschungszentrum Juelich GmbH, Lichtenbergstrasse 1, 85748 Garching, Germany
| | - Barbara Rossi
- Elettra-Sincrotrone Trieste, Strada Statale 14 - km 163,5 in AREA Science Park, 34149 Basovizza, Trieste, Italy
| | - Francesco Sacchetti
- Dipartimento di Fisica e Geologia, Università di Perugia, 06123 Perugia, Italy
| | - Federico Sebastiani
- Lehrstuhl für Physikalische Chemie 2, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Nicolò Violini
- JCNS, Forschungszentrum Jülich GmbH, Leo-Brandt Strasse, 52425 Jülich, Germany
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11
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Nguyen KT, De Michele C. Nematic liquid crystals of bifunctional patchy spheres. THE EUROPEAN PHYSICAL JOURNAL. E, SOFT MATTER 2018; 41:141. [PMID: 30552517 DOI: 10.1140/epje/i2018-11750-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Accepted: 11/09/2018] [Indexed: 06/09/2023]
Abstract
Anisotropic interactions can bring about the formation, through self-assembly, of semi-flexible chains, which in turn can give rise to nematic phases for suitable temperatures and concentrations. A minimalist model constituted of hard cylinders decorated with attractive sites has been already extensively studied numerically. Simulation data shows that a theoretical approach recently proposed is able to properly capture the physical properties of these self-assembly-driven liquid crystals. Here, we investigated a simpler model constituted of bifunctional Kern-Frenkel hard spheres which does not possess steric anisotropy but which can undergo a istropic-nematic transition as a result of their self-assembly into semi-flexible chains. For this model we compare an accurate numerical estimate of isotropic-nematic phase boundaries with theoretical predictions. The theoretical treatment, originally proposed for cylinder-like particles, has been greatly simplified and its predictions are in good agreement with numerical results. Finally, we also assess a crucial, and not obvious, hypothesis used in the theory, i.e. the ability of the Onsager trial function to properly model particle orientation in the presence of aggregation, that has not been properly checked yet.
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Affiliation(s)
- Khanh Thuy Nguyen
- Dipartimento di Fisica, "Sapienza" Università di Roma, P.le A. Moro 2, 00185, Roma, Italy
| | - Cristiano De Michele
- Dipartimento di Fisica, "Sapienza" Università di Roma, P.le A. Moro 2, 00185, Roma, Italy.
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12
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Sticking and stacking: Persistent ordering of fragmented DNA analogs. Proc Natl Acad Sci U S A 2018; 115:8652-8654. [PMID: 30093389 DOI: 10.1073/pnas.1810662115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
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13
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Backbone-free duplex-stacked monomer nucleic acids exhibiting Watson-Crick selectivity. Proc Natl Acad Sci U S A 2018; 115:E7658-E7664. [PMID: 29967169 PMCID: PMC6099888 DOI: 10.1073/pnas.1721369115] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The columnar liquid crystal phases reported here are physical associations of the smallest molecular species to self-assemble into the duplex base-paired stacked columnar double-helical structures of nucleic acids. These assemblies of monomers can provide starting states capable of partitioning appropriate molecules from solution with a high degree of selectivity, acting as pathways for the prebiotic appearance of molecular selection, self-assembly, and, ultimately, of the sequence-directed assembly of polymers. We demonstrate that nucleic acid (NA) mononucleotide triphosphates (dNTPs and rNTPs), at sufficiently high concentration and low temperature in aqueous solution, can exhibit a phase transition in which chromonic columnar liquid crystal ordering spontaneously appears. Remarkably, this polymer-free state exhibits, in a self-assembly of NA monomers, the key structural elements of biological nucleic acids, including: long-ranged duplex stacking of base pairs, complementarity-dependent partitioning of molecules, and Watson–Crick selectivity, such that, among all solutions of adenosine, cytosine, guanine, and thymine NTPs and their binary mixtures, duplex columnar ordering is most stable in the A-T and C-G combinations.
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14
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Carducci F, Yoneda JS, Itri R, Mariani P. On the structural stability of guanosine-based supramolecular hydrogels. SOFT MATTER 2018; 14:2938-2948. [PMID: 29611597 DOI: 10.1039/c8sm00299a] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Supramolecular hydrogels formed from the self-assembly of low molecular weight derivatives are very attractive systems, because of their potential applications in nano- and bio-technology. In this paper, the stable and transparent hydrogels observed in binary mixtures of guanosine derivatives (G), namely guanosine 5'-monophosphate (GMP) and guanosine (Gua), dissolved in water (at volume fractions larger than 0.95), were investigated by microscopy techniques and Small Angle X-ray Scattering (SAXS). The results confirm the presence of G-quadruplexes, chiral cylindrical rods obtained by the regular stacking of self-assembled planar cyclic guanosine quartets. However, the addition of Gua determines the formation of very stable hydrogels able to trap large amounts of water (up to a volume fraction of 0.99) and characterised by an unusual anisotropic order. A modified lateral helix-to-helix interaction pattern, tuned by Gua, is suggested to be responsible for the supramolecular gelation and the stability of the hydrogels during swelling.
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Affiliation(s)
- Federica Carducci
- Dipartimento di Scienze della Vita e dell'Ambiente, Molecular Biophysics Group, Università Politecnica delle Marche, Via Brecce Bianche, I-60131 Ancona, Italy.
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15
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Fraccia TP, Smith GP, Bethge L, Zanchetta G, Nava G, Klussmann S, Clark NA, Bellini T. Liquid Crystal Ordering and Isotropic Gelation in Solutions of Four-Base-Long DNA Oligomers. ACS NANO 2016; 10:8508-16. [PMID: 27571250 DOI: 10.1021/acsnano.6b03622] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Liquid crystal ordering is reported in aqueous solutions of the oligomer 5'-ATTAp-3' and of the oligomer 5'-GCCGp-3'. In both systems, we quantitatively interpret ordering as stemming from the chaining of molecules via a "running-bond" type of pairing, a self-assembly process distinct from the duplex aggregation previously reported for longer oligonucleotides. While concentrated solutions of 5'-ATTAp-3' show only a columnar liquid crystal phase, solutions of 5'-GCCGp-3' display a rich phase diagram, featuring a chiral nematic phase analogous to those observed in solutions of longer oligonucleotides and two unconventional phases, a columnar crystal and, at high concentration, an isotropic amorphous gel. The appearance of these phases, which can be interpreted on the basis of features of 5'-GCCGp-3'molecular structure, suggests distinctive assembly motifs specific to ultrashort oligonucleotides.
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Affiliation(s)
- Tommaso P Fraccia
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano , via Fratelli Cervi 93, I-20090 Segrate (Milan), Italy
- Dipartimento di Scienze Umane e Promozione della Qualità della Vita, Università San Raffaele di Roma , via di Val Cannuta, 247, I-00166 Rome, Italy
| | - Gregory P Smith
- Department of Physics and Liquid Crystal Materials Research Center, University of Colorado , Boulder, Colorado 80309-0390, United States
| | - Lucas Bethge
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Giuliano Zanchetta
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano , via Fratelli Cervi 93, I-20090 Segrate (Milan), Italy
| | - Giovanni Nava
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano , via Fratelli Cervi 93, I-20090 Segrate (Milan), Italy
| | - Sven Klussmann
- NOXXON Pharma AG, Max-Dohrn-Strasse 8-10, 10589 Berlin, Germany
| | - Noel A Clark
- Department of Physics and Liquid Crystal Materials Research Center, University of Colorado , Boulder, Colorado 80309-0390, United States
| | - Tommaso Bellini
- Dipartimento di Biotecnologie Mediche e Medicina Traslazionale, Università di Milano , via Fratelli Cervi 93, I-20090 Segrate (Milan), Italy
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16
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X-ray characterization of mesophases of human telomeric G-quadruplexes and other DNA analogues. Sci Rep 2016; 6:27079. [PMID: 27249961 PMCID: PMC4890033 DOI: 10.1038/srep27079] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2016] [Accepted: 05/13/2016] [Indexed: 01/13/2023] Open
Abstract
Observed in the folds of guanine-rich oligonucleotides, non-canonical G-quadruplex structures are based on G-quartets formed by hydrogen bonding and cation-coordination of guanosines. In dilute 5'-guanosine monophosphate (GMP) solutions, G-quartets form by the self-assembly of four GMP nucleotides. We use x-ray diffraction to characterize the columnar liquid-crystalline mesophases in concentrated solutions of various model G-quadruplexes. We then probe the transitions between mesophases by varying the PEG solution osmotic pressure, thus mimicking in vivo molecular crowding conditions. Using the GMP-quadruplex, built by the stacking of G-quartets with no covalent linking between them, as the baseline, we report the liquid-crystalline phase behaviors of two other related G-quadruplexes: (i) the intramolecular parallel-stranded G-quadruplex formed by the 22-mer four-repeat human telomeric sequence AG3(TTAG3)3 and (ii) the intermolecular parallel-stranded G-quadruplex formed by the TG4T oligonucleotides. Finally, we compare the mesophases of the G-quadruplexes, under PEG-induced crowding conditions, with the corresponding mesophases of the canonical duplex and triplex DNA analogues.
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17
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Vissers T, Smallenburg F, Munaò G, Preisler Z, Sciortino F. Cooperative polymerization of one-patch colloids. J Chem Phys 2015; 140:144902. [PMID: 24735313 DOI: 10.1063/1.4869834] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
We numerically investigate cooperative polymerization in an off-lattice model based on a pairwise additive potential using particles with a single attractive patch that covers 30% of the colloid surface. Upon cooling, these particles self-assemble into small clusters which, below a density-dependent temperature, spontaneously reorganize into long straight tubes. We evaluate the partition functions of clusters of all sizes to provide an accurate description of the chemical reaction constants governing this process. Our calculations show that, for intermediate sizes, the partition functions retain contributions from two different structures, differing in both energy and entropy. We illustrate the microscopic mechanism behind the complex polymerization process in this system and provide a detailed evaluation of its thermodynamics.
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Affiliation(s)
- Teun Vissers
- Sapienza, Università di Roma, Piazzale Aldo Moro 2, 00185, Roma, Italy
| | - Frank Smallenburg
- Sapienza, Università di Roma, Piazzale Aldo Moro 2, 00185, Roma, Italy
| | - Gianmarco Munaò
- Sapienza, Università di Roma, Piazzale Aldo Moro 2, 00185, Roma, Italy
| | - Zdeněk Preisler
- Sapienza, Università di Roma, Piazzale Aldo Moro 2, 00185, Roma, Italy
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18
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Bueno-Alejo CJ, Villaescusa LA, Garcia-Bennett AE. Supramolecular transcription of guanosine monophosphate into mesostructured silica. Angew Chem Int Ed Engl 2014; 53:12106-10. [PMID: 25213316 DOI: 10.1002/anie.201407005] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Indexed: 01/04/2023]
Abstract
There is large interest in replicating biological supramolecular structures in inorganic materials that are capable of mimicking biological properties. The use of 5-guanosine monophosphate in the presence of Na(+) and K(+) ions as a supramolecular template for the synthesis of well-ordered mesostructured materials is reported here. Mesostructured particles with the confined template exhibit high structural order at both meso- and atomic scales, with a lower structural symmetry in the columnar mesophase. Although a chiral space group can not be deduced from X-ray diffraction, analysis by electron microscopy and circular dichroism confirms a chiral stacking arrangement along the c-axis. Guanosine monophosphate based mesophases thus illustrate the possibility for specific molecular imprinting of mesoporous materials by genetic material and the potential for higher definition in molecular recognition.
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Affiliation(s)
- Carlos J Bueno-Alejo
- Centro de Reconocimiento Molecular y Desarrollo (IDM), UPV-UV, Camino de Vera, 46022 Valencia (Spain)
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19
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Bueno-Alejo CJ, Villaescusa LA, Garcia-Bennett AE. Supramolecular Transcription of Guanosine Monophosphate into Mesostructured Silica. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407005] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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20
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Spinozzi F, Ferrero C, Ortore MG, De Maria Antolinos A, Mariani P. GENFIT: software for the analysis of small-angle X-ray and neutron scattering data of macro-molecules in solution. J Appl Crystallogr 2014; 47:1132-1139. [PMID: 24904247 PMCID: PMC4038801 DOI: 10.1107/s1600576714005147] [Citation(s) in RCA: 71] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2013] [Accepted: 03/06/2014] [Indexed: 12/25/2022] Open
Abstract
Many research topics in the fields of condensed matter and the life sciences are based on small-angle X-ray and neutron scattering techniques. With the current rapid progress in source brilliance and detector technology, high data fluxes of ever-increasing quality are produced. In order to exploit such a huge quantity of data and richness of information, wider and more sophisticated approaches to data analysis are needed. Presented here is GENFIT, a new software tool able to fit small-angle scattering data of randomly oriented macromolecular or nanosized systems according to a wide list of models, including form and structure factors. Batches of curves can be analysed simultaneously in terms of common fitting parameters or by expressing the model parameters via physical or phenomenological link functions. The models can also be combined, enabling the user to describe complex heterogeneous systems.
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Affiliation(s)
- Francesco Spinozzi
- Department DiSVA, Marche Polytechnic University and CNISM, Via Brecce Bianche, I-60131 Ancona, Italy
| | | | - Maria Grazia Ortore
- Department DiSVA, Marche Polytechnic University and CNISM, Via Brecce Bianche, I-60131 Ancona, Italy
| | | | - Paolo Mariani
- Department DiSVA, Marche Polytechnic University and CNISM, Via Brecce Bianche, I-60131 Ancona, Italy
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21
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Nguyen KT, Sciortino F, De Michele C. Self-assembly-driven nematization. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2014; 30:4814-4819. [PMID: 24701976 DOI: 10.1021/la500127n] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
The anisotropy of attractive interactions between particles can favor, through a self-assembly process, the formation of linear semi-flexible chains. In the appropriate temperatures and concentration ranges, the growing aspect ratio of the aggregates can induce formation of a nematic phase, as recently experimentally observed in several biologically relevant systems. We present here a numerical study of the isotropic-nematic phase boundary for a model of bifunctional polymerizing hard cylinders, to provide an accurate benchmark for recent theoretical approaches and to assess their ability to capture the coupling between self-assembly and orientational ordering. The comparison indicates the importance of properly modeling excluded volume and orientational entropy and provides a quantitative confirmation of some theoretical predictions.
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Affiliation(s)
- Khanh Thuy Nguyen
- Dipartimento di Fisica, and ‡Istituto dei Sistemi Complessi (ISC)-Consiglio Nazionale delle Ricerche (CNR), "Sapienza" Università di Roma , Piazzale Aldo Moro 5, 00185 Rome, Italy
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22
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Kim YK, Shiyanovskii SV, Lavrentovich OD. Morphogenesis of defects and tactoids during isotropic-nematic phase transition in self-assembled lyotropic chromonic liquid crystals. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2013; 25:404202. [PMID: 24025849 DOI: 10.1088/0953-8984/25/40/404202] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
We explore the structure of nuclei and topological defects in the first-order phase transition between the nematic (N) and isotropic (I) phases in lyotropic chromonic liquid crystals (LCLCs). The LCLCs are formed by self-assembled molecular aggregates of various lengths and show a broad biphasic region. The defects emerge as a result of two mechanisms: (1) surface-anisotropy that endows each N nucleus ('tactoid') with topological defects thanks to preferential (tangential) orientation of the director at the closed I-N interface, and (2) Kibble mechanism with defects forming when differently oriented N tactoids merge with each other. Different scenarios of phase transition involve positive (N-in-I) and negative (I-in-N) tactoids with nontrivial topology of the director field and also multiply connected tactoid-in-tactoid configurations. The closed I-N interface limiting a tactoid shows a certain number of cusps; the lips of the interface on the opposite sides of the cusp make an angle different from π. The N side of each cusp contains a point defect-boojum. The number of cusps shows how many times the director becomes perpendicular to the I-N interface when one circumnavigates the closed boundary of the tactoid. We derive conservation laws that connect the number of cusps c to the topological strength m of defects in the N part of the simply connected and multiply connected tactoids. We demonstrate how the elastic anisotropy of the N phase results in non-circular shape of the disclination cores. A generalized Wulff construction is used to derive the shape of I and N tactoids as a function of I-N interfacial tension anisotropy in the approximation of frozen director field of various topological charges m. The complex shapes and structures of tactoids and topological defects demonstrate an important role of surface anisotropy in morphogenesis of phase transitions in liquid crystals.
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Affiliation(s)
- Young-Ki Kim
- Liquid Crystal Institute and Chemical Physics Interdisciplinary Program, Kent State University, Kent, OH 44242, USA
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23
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Wu YL, Brown KE, Wasielewski MR. Extending Photoinduced Charge Separation Lifetimes by Using Supramolecular Design: Guanine–Perylenediimide G-Quadruplex. J Am Chem Soc 2013; 135:13322-5. [DOI: 10.1021/ja407648d] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Yi-Lin Wu
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER)
Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Kristen E. Brown
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER)
Center, Northwestern University, Evanston, Illinois 60208-3113, United States
| | - Michael R. Wasielewski
- Department of Chemistry and Argonne-Northwestern Solar Energy Research (ANSER)
Center, Northwestern University, Evanston, Illinois 60208-3113, United States
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24
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Lima FS, Cuccovia IM, Horinek D, Amaral LQ, Riske KA, Schreier S, Salinas RK, Bastos EL, Pires PAR, Bozelli JC, Favaro DC, Rodrigues ACB, Dias LG, El Seoud OA, Chaimovich H. Effect of counterions on the shape, hydration, and degree of order at the interface of cationic micelles: the triflate case. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2013; 29:4193-4203. [PMID: 23473070 DOI: 10.1021/la304658e] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Specific ion effects in surfactant solutions affect the properties of micelles. Dodecyltrimethylammonium chloride (DTAC), bromide (DTAB), and methanesulfonate (DTAMs) micelles are typically spherical, but some organic anions can induce shape or phase transitions in DTA(+) micelles. Above a defined concentration, sodium triflate (NaTf) induces a phase separation in dodecyltrimethylammonium triflate (DTATf) micelles, a phenomenon rarely observed in cationic micelles. This unexpected behavior of the DTATf/NaTf system suggests that DTATf aggregates have unusual properties. The structural properties of DTATf micelles were analyzed by time-resolved fluorescence quenching, small-angle X-ray scattering, nuclear magnetic resonance, and electron paramagnetic resonance and compared with those of DTAC, DTAB, and DTAMs micelles. Compared to the other micelle types, the DTATf micelles had a higher average number of monomers per aggregate, an uncommon disk-like shape, smaller interfacial hydration, and restricted monomer chain mobility. Molecular dynamic simulations supported these observations. Even small water-soluble salts can profoundly affect micellar properties; our data demonstrate that the -CF3 group in Tf(-) was directly responsible for the observed shape changes by decreasing interfacial hydration and increasing the degree of order of the surfactant chains in the DTATf micelles.
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Affiliation(s)
- Filipe S Lima
- Instituto de Química, Universidade de São Paulo, São Paulo, Brazil
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25
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Röttger K, Schwalb NK, Temps F. Electronic Deactivation of Guanosine in Extended Hydrogen-Bonded Self-Assemblies. J Phys Chem A 2013; 117:2469-78. [DOI: 10.1021/jp3095193] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Katharina Röttger
- Institut für
Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr.
40, D-24098 Kiel, Germany
| | - Nina K. Schwalb
- Institut für
Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr.
40, D-24098 Kiel, Germany
| | - Friedrich Temps
- Institut für
Physikalische Chemie, Christian-Albrechts-Universität zu Kiel, Olshausenstr.
40, D-24098 Kiel, Germany
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26
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Gonnelli A, Ortore MG, Baldassarri EJ, Spada GP, Pieraccini S, Perone RC, Funari SS, Mariani P. Small-angle X-ray scattering study of self-assembling lipophilic guanines in organic solvents: G-quadruplex formation and cation effects in cyclohexane. J Phys Chem B 2013; 117:1095-103. [PMID: 23294474 DOI: 10.1021/jp3121929] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Lipophilic guanilic derivatives (lipoGs) dissolved in organic solvents can undergo different self-assembly pathways based on different H-bonded motifs, e.g., the cyclic discrete G-quartet, which forms in the presence of alkali-metal ions, and the "infinite" tape-like G-ribbon observed in the absence of ions. Using in-solution small-angle X-ray scattering, we analyzed a series of lipoGs dissolved in cyclohexane in the presence of different salts. The formation of G-quartet based supramolecular aggregates has been confirmed, evidencing the coexistence equilibrium of octamers and noncovalent molecular nanowires (the so-called G-quadruplexes). By global fitting the scattering data, the concentration of the two kinds of particles as well as the nanowire length have been derived as a function of temperature for the different compounds and salts. The thermodynamic parameters show that the self-assembly aggregation process is enthalpy driven, while the observed enthalpy-entropy compensation suggests that similar stacking interactions control the self-assembly of the different compounds. However, the strength of the stacking interactions, and then the nanowire stability, depends on the nature of templating cations and on their capacity to fill the central cavity of quadruplexes, with the order Sr(+) < Na(+) ≲ K(+).
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Affiliation(s)
- A Gonnelli
- Dipartimento di Scienze della Vita e dell'Ambiente, Biophysics Research Group, Università Politecnica delle Marche, via Brecce Bianche, I-60131 Ancona, Italy
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27
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Ortore MG, Spinozzi F, Vilasi S, Sirangelo I, Irace G, Shukla A, Narayanan T, Sinibaldi R, Mariani P. Time-resolved small-angle x-ray scattering study of the early stage of amyloid formation of an apomyoglobin mutant. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2011; 84:061904. [PMID: 22304113 DOI: 10.1103/physreve.84.061904] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Revised: 09/22/2011] [Indexed: 05/31/2023]
Abstract
The description of the fibrillogenesis pathway and the identification of "on-pathway" or "off-pathway" intermediates are key issues in amyloid research as they are concerned with the mechanism for onset of certain diseases and with therapeutic treatments. Recent results on the fibril formation process revealed an unexpected complexity both in the number and in the types of species involved, but the early aggregation events are still largely unknown, mainly because of their experimental inaccessibility. To provide information on the early stage events of self-assembly of an amyloidogenic protein, during the so-called lag phase, stopped-flow time-resolved small angle x-ray scattering (SAXS) experiments were performed. Using a global fitting analysis, the structural and aggregation properties of the apomyoglobin W7FW14F mutant, which is monomeric and partly folded at acidic pH but forms amyloid fibrils after neutralization, were derived from the first few milliseconds onward. SAXS data indicated that the first aggregates appear in less than 20 ms after the pH jump to neutrality and further revealed the simultaneous presence of diverse species. In particular, worm-like unstructured monomers, very large assemblies, and elongated particles were detected, and their structural features and relative concentrations were derived as a function of time on the basis of our model. The final results show that, during the lag phase, early assembling occurs due to the presence of transient monomeric species very prone to association and through successive competing aggregation and rearrangement processes leading to coexisting on-pathway and off-pathway transient species.
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Affiliation(s)
- Maria Grazia Ortore
- Department of Life and Environmental Sciences, Marche Polytechnic University and CNISM, Ancona, Italy.
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28
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Federiconi F, Mattioni M, Baldassarri EJ, Ortore MG, Mariani P. How soft are biological helices? A measure of axial and lateral force constants in folate quadruplexes by high-pressure X-ray diffraction. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2011; 40:1225-35. [PMID: 21713534 DOI: 10.1007/s00249-011-0717-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Revised: 05/14/2011] [Accepted: 05/20/2011] [Indexed: 01/04/2023]
Abstract
Alkaline folates self-associate in aqueous solutions to form columnar lyotropic phases. Such phases are made by quadruplexes, which are supramolecular helicoidal structures formed by a stacked array of folate tetramers. High-pressure synchrotron X-ray diffraction is used to analyze alkaline folate quadruplex stability and energetics. Diffraction data show that both inter-helical lateral and tetramer stacking distances decrease as a function of pressure. Lateral and axial quadruplex compressibilities and force constants have been derived and strong correlation between the strength of tetramer stacking and pressure effects demonstrated. In particular, quadruplex rigidity increases by changing Na+ to K+ and by adding excess KCl, as a consequence of increased stacking interactions and quadruplex elongation.
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29
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Park HS, Kang SW, Tortora L, Kumar S, Lavrentovich OD. Condensation of self-assembled lyotropic chromonic liquid crystal sunset yellow in aqueous solutions crowded with polyethylene glycol and doped with salt. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2011; 27:4164-4175. [PMID: 21391644 DOI: 10.1021/la200505y] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
We use optical and fluorescence microscopy, densitometry, cryo-transmission electron microscopy (cryo-TEM), spectroscopy, and synchrotron X-ray scattering to study the phase behavior of the reversible self-assembled chromonic aggregates of an anionic dye Sunset Yellow (SSY) in aqueous solutions crowded with an electrically neutral polymer polyethylene glycol (PEG) and doped with the salt NaCl. PEG causes the isotropic SSY solutions to condense into a liquid-crystalline region with a high concentration of SSY aggregates, coexisting with a PEG-rich isotropic (I) region. PEG added to the homogeneous nematic (N) phase causes separation into the coexisting N and I domains; the SSY concentration in the N domains is higher than the original concentration of PEG-free N phase. Finally, addition of PEG to the highly concentrated homogeneous N phase causes separation into the coexisting columnar hexagonal (C) phase and I phase. This behavior can be qualitatively explained by the depletion (excluded volume) effects that act at two different levels: at the level of aggregate assembly from monomers and short aggregates and at the level of interaggregate packing. We also show a strong effect of a monovalent salt NaCl on phase diagrams that is different for high and low concentrations of SSY. Upon the addition of salt, dilute I solutions of SSY show appearance of the condensed N domains, but the highly concentrated C phase transforms into a coexisting I and N domains. We suggest that the salt-induced screening of electric charges at the surface of chromonic aggregates leads to two different effects: (a) increase of the scission energy and the contour length of aggregates and (b) decrease of the persistence length of SSY aggregates.
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Affiliation(s)
- Heung-Shik Park
- Liquid Crystal Institute and Chemical Physics Interdisciplinary Program, Kent State University, Kent, Ohio 44242, United States
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Hu J, Fang M, Cheng Y, Zhang J, Wu Q, Xu T. Host-guest chemistry of dendrimer-drug complexes. 4. An in-depth look into the binding/encapsulation of guanosine monophosphate by dendrimers. J Phys Chem B 2010; 114:7148-57. [PMID: 20446745 DOI: 10.1021/jp1007889] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
In the present study, we investigated the host-guest chemistry of dendrimer/guanosine monophosphate (GMP) and present an in-depth look into the binding/encapsulation of GMP by dendrimers using NMR studies. (1)H NMR spectra showed a significant downfield shift of methylene protons in the outmost layer of the G5 dendrimer, indicating the formation of ion pairs between cationic amine groups of dendrimer and anionic phosphate groups of GMP. Chemical shift titration results showed that the binding constant between G5 dendrimer and GMP is 17,400 M(-1) and each G5 dendrimer has 107 binding sites. The binding of GMP to dendrimers prevents its aggregation in aqueous solutions and thereby enhances its stability. Nuclear Overhauser effect measurements indicated that a GMP binding and encapsulation balance occurs on the surface and in the interior of dendrimer. The binding/encapsulation transitions can be easily tailored by altering the surface and interior charge densities of the dendrimer. All these findings provide a new insight into the host-guest chemistry of dendrimer/guest complexes and may play important roles in the study of dendrimer/DNA aggregates by a "bottom-up" strategy.
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Affiliation(s)
- Jingjing Hu
- CAS Key Laboratory of Soft Matter Chemistry, School of Chemistry and Material Science, University of Science and Technology of China, Hefei, Anhui, 230026, People's Republic of China
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Mariani P, Spinozzi F, Federiconi F, Ortore MG, Amenitsch H, Spindler L, Drevensek-Olenik I. Guanosine quadruplexes in solution: a small-angle x-ray scattering analysis of temperature effects on self-assembling of deoxyguanosine monophosphate. J Nucleic Acids 2010; 2010. [PMID: 20725625 PMCID: PMC2915817 DOI: 10.4061/2010/472478] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2010] [Accepted: 03/26/2010] [Indexed: 11/20/2022] Open
Abstract
We investigated quadruplex formation in aqueous solutions of 2′-deoxyriboguanosine 5′-monophosphate, d(pG), which takes place in the absence of the covalent axial backbone. A series of in-solution small angle X-ray scattering experiments on d(pG) have been performed as a function of temperature in the absence
of excess salt, at a concentration just above the critical one at which self-assembling occurs. A global fit
approach has been used to derive composition and size distribution of the scattering particles as a function
of temperature. The obtained results give thermodynamical justification for the observed phase-behavior,
indicating that octamer formation is essential for quadruplex elongation. Our investigation shows that d(pG)
quadruplexes are very suitable to assess the potential of G-quadruplex formation and to study the self-assembling thermodynamics.
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Affiliation(s)
- P Mariani
- Physical Science Section, Research Unit of Ancona, SAIFET Department, CNISM, Marche Polytechnic University, Via Brecce Bianche, 60131 Ancona, Italy
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Li Z, Buerkle LE, Orseno MR, Streletzky KA, Seifert S, Jamieson AM, Rowan SJ. Structure and gelation mechanism of tunable guanosine-based supramolecular hydrogels. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2010; 26:10093-10101. [PMID: 20384308 DOI: 10.1021/la100211y] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
The mechanism of gelation of 50/50 w/w mixtures of guanosine (G) and 2',3',5'-tri-O-acetylguanosine (TAcG) in aqueous 0.354 M KCl was investigated using a combination of static light scattering (SLS), polarized and depolarized dynamic light scattering (VV and VH DLS), small-angle neutron and X-ray scattering (SANS and SAXS), and viscometric experiments. SLS and viscometry show a dramatic increase in apparent molecular weight and hydrodynamic volume at 0.2 wt % and 0.3 wt %, respectively, indicating the critical concentration for self-association of G/TAcG quartets into columnar assemblies lies below 0.2 wt %. Above this concentration, SANS and SAXS generate complementary information on the structure of the individual columnar stacks. VV and VH DLS results indicate bimodal correlation functions, whose properties suggest, respectively, translational and rotational diffusion of a bimodal distribution of particles. The fast mode appears to originate from fibrillar agglomerates of G/TAcG columnar quartet assemblies, while the slow mode comes from microgel domains. Guinier plot analysis of the SLS data probes the internal structure of the microgel domains. Collectively, the results suggest that sol and microgel phases coexist below the macroscopic gel point, and that the sol phase contains individual columnar stacks of G/TAcG quartets and fibrillar aggregates formed via lateral aggregation of these columnar assemblies. With increasing concentration, the DLS data indicate a progressive increase in the volume fraction of microgel domains, which ultimately leads to macroscopic gelation. Prior observation of a transient network contribution to the gel rheology at low temperature is attributed to the presence of individual columnar stacks within the gel network.
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Affiliation(s)
- Zheng Li
- Department of Macromolecular Science and Engineering, Case Western Reserve University, Cleveland, Ohio 44106, USA
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On the structure and excited electronic state lifetimes of cytidine self-assemblies with extended hydrogen-bonding networks. J Photochem Photobiol A Chem 2009. [DOI: 10.1016/j.jphotochem.2009.09.011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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