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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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Gao M, Harish B, Berghaus M, Seymen R, Arns L, McCallum SA, Royer CA, Winter R. Temperature and pressure limits of guanosine monophosphate self-assemblies. Sci Rep 2017; 7:9864. [PMID: 28852183 PMCID: PMC5574928 DOI: 10.1038/s41598-017-10689-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Accepted: 08/14/2017] [Indexed: 12/31/2022] Open
Abstract
Guanosine monophosphate, among the nucleotides, has the unique property to self-associate and form nanoscale cylinders consisting of hydrogen-bonded G-quartet disks, which are stacked on top of one another. Such self-assemblies describe not only the basic structural motif of G-quadruplexes formed by, e.g., telomeric DNA sequences, but are also interesting targets for supramolecular chemistry and nanotechnology. The G-quartet stacks serve as an excellent model to understand the fundamentals of their molecular self-association and to unveil their application spectrum. However, the thermodynamic stability of such self-assemblies over an extended temperature and pressure range is largely unexplored. Here, we report a combined FTIR and NMR study on the temperature and pressure stability of G-quartet stacks formed by disodium guanosine 5′-monophosphate (Na25′-GMP). We found that under abyssal conditions, where temperatures as low as 5 °C and pressures up to 1 kbar are reached, the self-association of Na25′-GMP is most favoured. Beyond those conditions, the G-quartet stacks dissociate laterally into monomer stacks without significantly changing the longitudinal dimension. Among the tested alkali cations, K+ is the most efficient one to elevate the temperature as well as the pressure limits of GMP self-assembly.
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Affiliation(s)
- Mimi Gao
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Balasubramanian Harish
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, United States
| | - Melanie Berghaus
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Rana Seymen
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Loana Arns
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany
| | - Scott A McCallum
- NMR Facility Center for Biotechnology and Interdisciplinary Science, Rensselaer Polytechnic Institute, Troy, NY, USA
| | - Catherine A Royer
- Center for Biotechnology & Interdisciplinary Studies, Rensselaer Polytechnic Institute, Troy, New York, 12180, United States
| | - Roland Winter
- Physical Chemistry I - Biophysical Chemistry, Faculty of Chemistry and Chemical Biology, Technical University Dortmund, Otto-Hahn-Street 4a, 44227, Dortmund, Germany.
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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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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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Federiconi F, Ausili P, Fragneto G, Ferrero C, Mariani P. Locating counterions in guanosine quadruplexes: a contrast-variation neutron diffraction experiment in condensed hexagonal phase. J Phys Chem B 2007; 109:11037-45. [PMID: 16852345 DOI: 10.1021/jp0501751] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Guanosine, one of the primary components of nucleic acids, self-associates in water to form G-quadruplexes, four-stranded helicoidal aggregates, made by stacked planar tetramers, consisting of four planar guanine molecules. Essential for the stability of these supramolecular aggregates is the presence of monovalent cations. As G-quadruplexes show a lyotropic polymorphism, neutron diffraction, in combination with the H2O/D2O contrast variation technique, has been applied to study the cation structural features of quadruplexes in hexagonal phase at different hydrations and counterion concentrations. The guanosine 5'-monophosphate, dipotassium salt, was considered and G-quadruplexes in hexagonal phase were prepared in the different experimental conditions (contrast, hydration and KCl solution concentration) by using the osmotic stress technique. The calculated scattering length density distribution maps show that counterions fill the helix inner cavity and that atmospheric cations are bound to a second site, close to the external phosphate groups. The site occupancy turned out to be very high: we found on the inner site 0.87 K ions per tetramer in G-quadruplexes prepared in pure water and 0.97 K ions per tetramer in G-quadruplexes prepared in KCl 0.5 M, while in all cases 6 ions per unit cell were detected to occupy the outer sites, partially neutralizing the two formal negative charges per phosphate group. The very large K ions concentration difference between the binding sites and the bulk solution demonstrates that counterions are structurally involved in the formation and in the stabilization of the helices.
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Affiliation(s)
- Francesco Federiconi
- Dipartimento di Scienze Applicate ai Sistemi Complessi and INFM, Università Politecnica delle Marche, Via Ranieri 65, I-60131 Ancona, Italy.
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