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Distinct differences in metal ion specificity of RNA and DNA G-quadruplexes. J Biol Inorg Chem 2016; 21:975-986. [PMID: 27704222 DOI: 10.1007/s00775-016-1393-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 09/02/2016] [Indexed: 01/21/2023]
Abstract
RNA G-quadruplexes, as their well-studied DNA analogs, require the presence of cations to fold and remain stable. This is the first comprehensive study on the interaction of RNA quadruplexes with metal ions. We investigated the formation and stability of two highly conserved and biologically relevant RNA quadruplex-forming sequences (24nt-TERRA and 18nt-NRAS) in the presence of several monovalent and divalent metal ions, namely Li+, Na+, K+, Rb+, Cs+, NH4+, Mg2+, Ca2+, Sr2+, and Ba2+. Circular dichroism was used to probe the influence of these metal ions on the folded fraction of the parallel G-quadruplexes, and UV thermal melting experiments allowed to assess the relative stability of the structures in each cationic condition. Our results show that the RNA quadruplexes are more stable than their DNA counterparts under the same buffer conditions. We have observed that the addition of mainly Na+, K+, Rb+, NH4+, as well as Sr2+ and Ba2+ in water, shifts the equilibrium to the folded quadruplex form, whereby the NRAS sequence responds stronger than TERRA. However, only K+ and Sr2+ lead to a significant increase in the stability of the folded structures, which is consistent with their coordination to the O6 atoms from the G-quartet guanosines. Compared to the respective DNA motives, dNRAS and htelo, the RNA sequences are not stabilized by Na+ ions. Finally, the difference in response between NRAS and TERRA, as well as to the corresponding DNA sequences with respect to different metal ions, could potentially be exploited for selective targeting purposes.
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Farasat R, Yancey B, Vyazovkin S. Loading salts from solutions into nanopores: Model and its test. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.01.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Abstract
Metal ions are inextricably involved with nucleic acids due to their polyanionic nature. In order to understand the structure and function of RNAs and DNAs, one needs to have detailed pictures on the structural, thermodynamic, and kinetic properties of metal ion interactions with these biomacromolecules. In this review we first compile the physicochemical properties of metal ions found and used in combination with nucleic acids in solution. The main part then describes the various methods developed over the past decades to investigate metal ion binding by nucleic acids in solution. This includes for example hydrolytic and radical cleavage experiments, mutational approaches, as well as kinetic isotope effects. In addition, spectroscopic techniques like EPR, lanthanide(III) luminescence, IR and Raman as well as various NMR methods are summarized. Aside from gaining knowledge about the thermodynamic properties on the metal ion-nucleic acid interactions, especially NMR can be used to extract information on the kinetics of ligand exchange rates of the metal ions applied. The final section deals with the influence of anions, buffers, and the solvent permittivity on the binding equilibria between metal ions and nucleic acids. Little is known on some of these aspects, but it is clear that these three factors have a large influence on the interaction between metal ions and nucleic acids.
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Affiliation(s)
- Maria Pechlaner
- Institute of Inorganic Chemistry, University of Zürich, Zürich, Switzerland
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Divalent metal ions tune the self-splicing reaction of the yeast mitochondrial group II intron Sc.ai5γ. J Biol Inorg Chem 2008; 13:1025-36. [DOI: 10.1007/s00775-008-0390-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2008] [Accepted: 05/14/2008] [Indexed: 11/25/2022]
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Burgermeister W, Winkler-Oswatitsch R. Complex formation of monovalent cations with biofunctional ligands. Top Curr Chem (Cham) 2007. [DOI: 10.1007/bfb0111222] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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Freisinger E, Sigel RK. From nucleotides to ribozymes—A comparison of their metal ion binding properties. Coord Chem Rev 2007. [DOI: 10.1016/j.ccr.2007.03.008] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Schuster P, Jakubetz W, Marius W. Molecular models for the solvation of small ions and polar molecules. Top Curr Chem (Cham) 2006:1-107. [PMID: 766305 DOI: 10.1007/bfb0045206] [Citation(s) in RCA: 75] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Ammann D, Bissig R, Güggi M, Pretsch E, Simon W, Borowitz IJ, Weiss L. Preparation of Neutral Ionophores for Alkali and Alkaline Earth Metal Cations and their application in ion selective membrane electrodes. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19750580605] [Citation(s) in RCA: 109] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Bissig R, Oesch U, Pretsch E, Morf WE, Simon W. Einfluss der Lipophilie von 3, 6-Dioxakorksäurediamiden auf ihr Verhalten als Ionophore. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19780610504] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Graf E, Lehn JM. Cryptates Sphériques. Synthèse et Complexes d'Inclusion de Ligands Macrotricycliques Sphériques. Helv Chim Acta 2004. [DOI: 10.1002/hlca.19810640410] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Marcos PM, Ascenso JR, Segurado MA, Pereira J. Synthesis, NMR conformational analysis, complexation and transport studies of an inherently chiral dihomooxacalix[4]arene triester. Tetrahedron 2001. [DOI: 10.1016/s0040-4020(01)00652-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Morf WE, Pretsch E. Reminiscences of Professor Wilhelm Simon and his research work at the ETH Zürich. ELECTROANAL 1995. [DOI: 10.1002/elan.1140070903] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Selke R, Čapka M. Carbohydrate phosphinites as chiral ligands for asymmetric syntheses catalyzed by complexes. ACTA ACUST UNITED AC 1990. [DOI: 10.1016/0304-5102(90)85124-z] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Portmann P, Maruizumi T, Welti M, Badertscher M, Neszmelyi A, Simon W, Pretsch E. Pair potentials for the interaction energy of Li+, Na+, K+, and NH+4with organic molecules. J Chem Phys 1987. [DOI: 10.1063/1.453595] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
Epithelial Na channels are apparently pore-forming membrane proteins which conduct Na much better than any other biologically abundant ion. The conductance to Na can be 100 to 1000 times higher than that to K. The only other ions that can readily get through this channel are protons and Li. Small organic cations cannot pass through the channel, and water may also be impermeant. The selectivity properties of epithelial Na channels appear to be determined by at least three factors: A high field-strength anionic site, most likely a carboxyl residue of glutamic or aspartic acid residues on the channel protein, probably accounts for the high conductance through these channels of Na and Li and to the low conductance of K, Rb and Cs. A restriction in the size of the pore at its narrowest point probably accounts for the low conductance of organic cations as well as the possible exclusion of water molecules. The outer mouth of the channel appears to be negatively charged and may control access to the region of highest selectivity and may serve as a preliminary selectivity filter, attracting cations over anions. These conclusions are illustrated by the cartoon of the channel in Fig. 3. This picture is obviously both fanciful and simplified, but its general points will hopefully be testable. It leaves open a number of important questions, including: does amiloride block the channel by binding within the outer mouth? what does the inner mouth of the channel look like, and does this part of the channel contribute to selectivity? and what, if any, are the interactions between the features of the channel that impart selectivity and those that control the regulation of the channel by hormonal and other factors?
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Delahay P, Dziedzic A. Nonequilibrium electronic polarization of the solvent in photoionization. J Chem Phys 1986. [DOI: 10.1063/1.450539] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Delahay P, Dziedzic A. Solvation and dielectric dispersion in optical electron transfer. J Chem Phys 1984. [DOI: 10.1063/1.448117] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Delahay P, Dziedzic A. Inner‐sphere reorganization in optical electron transfer. J Chem Phys 1984. [DOI: 10.1063/1.446603] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Barthel J, Gores HJ, Schmeer G, Wachter R. Non-aqueous electrolyte solutions in chemistry and modern technology. PHYSICAL AND INORGANIC CHEMISTRY 1983. [DOI: 10.1007/3-540-12065-3_2] [Citation(s) in RCA: 85] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Welti M, Pretsch E, Clementi E, Simon W. Interaction of Ca2+ and Mg2+ with Ionophores Studied by Using a Pair-Potential Model Based onab initio Calculations. Helv Chim Acta 1982. [DOI: 10.1002/hlca.19820650707] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Vögtle F, Weber E. Vielzähnige nichtcyclische Neutralliganden und ihre Komplexierung. Angew Chem Int Ed Engl 1979. [DOI: 10.1002/ange.19790911007] [Citation(s) in RCA: 88] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Corongiu G, Clementi E, Pretsch E, Simon W. Ab initio calculations of the interaction of ions with neutral ligands: I. Pair potentials for Na+/ether, Na+/thioether, and Na+/amide systems. J Chem Phys 1979. [DOI: 10.1063/1.437564] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Jimenez Reyes M, Maddock A, Duplatre G, Schleiffer J. Radiochemical separation of alkali ions by solvent extraction of cryptate complexes. ACTA ACUST UNITED AC 1979. [DOI: 10.1016/0022-1902(79)80054-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Lehn JM, Montavon F. Cryptates. XXV. Stability and selectivity of cation inclusion complexes of polyaza-macrobicyclic ligands. Selective complexation of toxic heavy metal cations. Helv Chim Acta 1978. [DOI: 10.1002/hlca.19780610107] [Citation(s) in RCA: 77] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Kirsch NN, Funck RJ, Pretsch E, Simon W. [Membranc selectivity and syntheses of ionophores for Li+. Stability constants in ethanol (author's transl)]. Helv Chim Acta 1977; 60:2326-33. [PMID: 924806 DOI: 10.1002/hlca.19770600723] [Citation(s) in RCA: 38] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Coordination chemistry of scandium. VIII[1] detection of complex formation in solution by 45Sc NMR spectroscopy. ACTA ACUST UNITED AC 1977. [DOI: 10.1016/0584-8539(77)80034-2] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Kostetsky PV, Ivanov VT, Ovchinnikov YA, Shchembelov G. The nature of the metal-ligand bonding in the complexes of ionophores with alkali metal ions. A quantum mechanical study of the N,N-dimethyl acetamide and methyl acetate interaction with Na(+) and Li(+). FEBS Lett 1973; 30:205-209. [PMID: 11947094 DOI: 10.1016/0014-5793(73)80652-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- P V. Kostetsky
- Shemyakin Institute for Chemistry of Natural Products, USSR Academy of Sciences, Moscow, USSR
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Züst CU, Früh PU, Simon W. Complex formation of macrotetrolide carrier antibiotics with cations studied by microcalorimetry and vapour pressure osmometry. Helv Chim Acta 1973; 56:495-9. [PMID: 4721749 DOI: 10.1002/hlca.19730560144] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Modellrechnungen zur Solvatation einatomiger Ionen (LCAO-MO-Untersuchungen von Molek�lstrukturen VIII). ACTA ACUST UNITED AC 1972. [DOI: 10.1007/bf00641398] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Morf WE, Simon W. [Estimation of alkali and alkaline earth ion selectivity of electrically neutral carrier-antibiotics and model compounds]. Helv Chim Acta 1971; 54:2683-704. [PMID: 5141431 DOI: 10.1002/hlca.19710540832] [Citation(s) in RCA: 106] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Lutz WK, Früh PU, Simon W. Microcalorimetric determination of H 0 , G 0 and S 0 for the interaction of the carrier antibiotics nigericin and monensin with sodium and potassium ions. Helv Chim Acta 1971; 54:2767-70. [PMID: 5141435 DOI: 10.1002/hlca.19710540840] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
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Früh PU, Clerc JT, Simon W. Determination of H o , G o , and S o of the interaction of ions with carrier antibiotics by computerized microcalorimetry. Helv Chim Acta 1971; 54:1445-50. [PMID: 5121752 DOI: 10.1002/hlca.19710540527] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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