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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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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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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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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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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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Kuriabova T, Betterton MD, Glaser MA. Linear aggregation and liquid-crystalline order: comparison of Monte Carlo simulation and analytic theory. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/c0jm02355h] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Mariani P, Spinozzi F, Federiconi F, Amenitsch H, Spindler L, Drevensek-Olenik I. Small angle X-ray scattering analysis of deoxyguanosine 5'-monophosphate self-assembing in solution: nucleation and growth of G-quadruplexes. J Phys Chem B 2009; 113:7934-44. [PMID: 19435359 DOI: 10.1021/jp809734p] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
To solve details of the self-assembling process of guanosine in diluted aqueous solution and to derive a thermodynamical model for quadruplex formation, the structural behavior of deoxyguanosine 5'-monophosphate has been analyzed by in-solution small angle X-ray scattering. The experiments have been performed as a function of guanosine concentration and at fixed guanosine concentration but in the presence of varying amounts of KCl. As a result, the self-assembling process, in terms of both aggregate particle fractions and aggregate length, has been observed to be strongly dependent on composition and largely affected by excess potassium ions in the solution. In particular, the different aggregate forms have been resolved and their concentration derived as a function of sample composition. In accordance with a hierarchical aggregation process, a nucleation and elongation mechanism has been used to derive the thermodynamical parameters for self-assembling. The results show that the annealing and fragmentation steps play an important role in the aggregation process.
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Affiliation(s)
- Paolo Mariani
- Dipartimento SAIFET, Università Politecnica delle Marche and CNISM, Research Unit of Ancona, Via Brecce Bianche, I-60131 Ancona, Italy.
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Martín-Rapún R, Byelov D, Palmans ARA, de Jeu WH, Meijer EW. Lyomesophases of C3-symmetrical bipyridine-based discs in alkanes: an X-ray diffraction study. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2009; 25:8794-8801. [PMID: 20050050 DOI: 10.1021/la9003017] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The importance of the role of alkane solvents in the self-assembly process of pi-conjugated molecules is well recognized but hardly understood. Here we present our results on the X-ray diffraction studies that we conducted to gain insight into the supramolecular structure of mixtures of a bipyridine-based molecule (1) with alkanes. Independent of the alkane used (linear or branched), above x(w) > 0.06 (with x(w) being the weight fraction of 1) the mixtures show lyotropic liquid-crystalline behavior. The nature of the lyomesophase depends only on x(w) and not on the nature of the alkane (linear or branched). A columnar rectangular phase is present when x(w) > 0.66. Upon dilution of 1, a columnar hexagonal phase is assigned first (0.50 < x(w) < 0.65), and finally a columnar nematic phase is observed when x(w) < 0.50. Concentration-dependent SAXD measurements revealed that the dilution of 1 can be viewed as a swelling process. First, solvent molecules occupy space between the columns formed by 1, which are not disrupted. This process can quantitatively be described by a 2D swelling model. Only at lower concentrations does 3D swelling start as the columns start breaking into shorter fragments.
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Affiliation(s)
- Rafael Martín-Rapún
- Laboratory of Macromolecular and Organic Chemistry, Eindhoven University of Technology, P.O. Box 513, 5600 MB Eindhoven, The Netherlands
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Rudd L, Lee DJ, Kornyshev AA. On the physical nature of mesophases of guanosine gels. Phys Chem Chem Phys 2006; 8:4347-58. [PMID: 16986078 DOI: 10.1039/b601018k] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The unusual columnar aqueous mesophases of self-assembled guanosine stacks, such as 2'-deoxyguanosine 5'-monophosphate and 2'-deoxyguanosine 3'-monophosphate, are analyzed in terms of a general theory of azimuthal correlations between the charged helices. This theory considers forces, specific to the helical structure of each macromolecule, which depend on the azimuthal orientations of the molecules about their long axes. More specifically, in determining the magnitudes and decay lengths of these helix specific forces we utilize the Kornyshev-Leikin theory of electrostatic interaction between helical macromolecules and quantitatively fit experimental data. Together with explaining a number of the observed features of these mesophases, several new effects are predicted. Possible limitations and developments of our theoretical model are discussed, as well as new experiments to test the implications of the theory.
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Affiliation(s)
- Laura Rudd
- Department of Chemistry, Faculty of Natural Sciences, Imperial College London, London, UK SW7 2AZ
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Pieraccini S, Gottarelli G, Mariani P, Masiero S, Saturni L, Spada GP. Columnar lyomesophases formed in hydrocarbon solvents by chiral lipophilic guanosine-alkali metal complexes. Chirality 2001; 13:7-12. [PMID: 11135408 DOI: 10.1002/1520-636x(2001)13:1<7::aid-chir3>3.0.co;2-m] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The lipophilic guanosine derivative 1 acts as a self-assembled ionophore and, in the presence of alkali metal ions, forms chiral polymeric structures in organic solvents. These polymeric columnar aggregates are comprised of G-quartets held together by alkali metal ions which are located inside the tubular structure; the quartets are surrounded by hydrocarbon chains. In hydrocarbon solvents, these columnar aggregates form lyomesophases of the cholesteric and hexagonal type. Copyright 2000 Wiley-Liss, Inc.
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Affiliation(s)
- S Pieraccini
- Università di Bologna, Dipartimento di Chimica Organica 'A. Mangini', Bologna, Italy
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Mariani P, Ciuchi F, Saturni L. Helix-specific interactions induce condensation of guanosine four-stranded helices in concentrated salt solutions. Biophys J 1998; 74:430-5. [PMID: 9449343 PMCID: PMC1299395 DOI: 10.1016/s0006-3495(98)77800-2] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Deoxyguanosine-5'-monophosphate in water self-associates into stable structures, which include liquid-crystalline hexagonal and cholesteric phases. The structural unit is a four-stranded helix, composed of stacked Hoogsteen-bonded guanosine quartets. By using the osmotic stress method, we recently measured the force between helices in KCl solutions up to 2 M. In addition to the long-range electrostatic force, a short-range hydration repulsive contribution was recognized. The hydration repulsion is exponential, and shows a decay length independent from the ionic strength of the solution. Here, we report that more concentrated KCl solutions cause condensation of the guanosine helix in a hexagonal phase with constant equilibrium separation of approximately 7 A between helix surfaces. Long-range attraction, which induces the self-assembly, and short-range repulsion, which prevents the contact between the helices, are implied. By using osmotic stress, the force needed to push helices closer from the spontaneously assumed position has been measured. The attractive force was then estimated as a difference between the net force and the repulsive contribution, revealing an exponential decay length about two times larger than that of the short-range repulsion. The agreement with the helix interaction theory introduced recently by Kornyshev and Leikin (Kornyshev, A. A., and S. Leikin, 1997. Theory of interaction between helical molecules. J. Phys. Chem. 107:3656-3674) suggests that the repulsive and attractive forces originate from helix-specific interactions.
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Affiliation(s)
- P Mariani
- Istituto di Scienze Fisiche, Facoltà di Medicina e Chirurgia, Università di Ancona, Italy.
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Gottarelli G, Proni G, Spada GP, Bonazzi S, Garbesi A, Ciuchi F, Mariani P. The self-assembly and liquid crystal formation of d(GpGpApGpG). Biopolymers 1997. [DOI: 10.1002/(sici)1097-0282(19971015)42:5<561::aid-bip6>3.0.co;2-o] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Itri R, Amaral LQ, Mariani P. Structure of the hexagonal phase of the sodium dodecyl sulfate and water system. PHYSICAL REVIEW. E, STATISTICAL PHYSICS, PLASMAS, FLUIDS, AND RELATED INTERDISCIPLINARY TOPICS 1996; 54:5211-5216. [PMID: 9965702 DOI: 10.1103/physreve.54.5211] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Mariani P, Saturni L. Measurement of intercolumnar forces between parallel guanosine four-stranded helices. Biophys J 1996; 70:2867-74. [PMID: 8744324 PMCID: PMC1225266 DOI: 10.1016/s0006-3495(96)79856-9] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
The deoxyguanosine-5'-monophosphate in aqueous solution self-associates into stable structures, which include hexagonal and cholesteric columnar phases. The structural unit is a four-stranded helix, composed of a stacked array of Hoogsteen-bonded guanosine quartets. We have measured by osmotic stress method the force per unit length versus interaxial distance between helices in the hexagonal phase under various ionic conditions. Two contributions have been recognized: the first one is purely electrostatic, is effective at large distances, and shows a strong dependence on the salt concentration of the solution. The second contribution is short range, dominates at interaxial separations smaller than about 30-32 A, and rises steeply as the columns approach each other, preventing the coalescence of the helices. This repulsion has an exponential nature and shows a magnitude and a decay length insensitive to the ionic strength of the medium. Because these features are distinctive of the hydration force detected between phospholipid bilayers or between several linear macromolecules (DNA, polysaccharides, collagen), we conclude that the dominant force experienced by deoxyguanosine helices approaching contact is hydration repulsion. The observed decay length of about 0.7 A has been rationalized to emerge from the coupling between the 3-A decay length of water solvent and the helically ordered structure of the hydrophilic groups on the opposing surfaces. The present results agree with recent measurements, also showing the dependence of the hydration force decay on the structure of interacting surfaces and confirm the correlations between force and structure.
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Affiliation(s)
- P Mariani
- Istituto di Scienze Fisiche, Facoltà di Medicina e Chirurgia, Università di Ancona, Italy.
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