Regular Article
Supramolecular arrangement of guanosine/5′-guanosine monophosphate binary mixtures studied by methods of circular dichroism
Jana Novotná,
Iryna Goncharova,
Marie Urbanová,
Jana Novotná
Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
Search for more papers by this authorIryna Goncharova
Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
Search for more papers by this authorCorresponding Author
Marie Urbanová
Department of Physics and Measurements, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
Marie Urbanová, Department of Physics and Measurements, Institute of Chemical Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic. E-mail:[email protected]Search for more papers by this authorJana Novotná,
Iryna Goncharova,
Marie Urbanová,
Jana Novotná
Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
Search for more papers by this authorIryna Goncharova
Department of Analytical Chemistry, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
Search for more papers by this authorCorresponding Author
Marie Urbanová
Department of Physics and Measurements, Institute of Chemical Technology, Prague, Prague 6, Czech Republic
Marie Urbanová, Department of Physics and Measurements, Institute of Chemical Technology, Prague, Technická 5, Prague 6, 166 28, Czech Republic. E-mail:[email protected]Search for more papers by this authorAbstract
Self-assembly of molecules is one of the fundamental processes in biology and in supramolecular chemistry. Guanosine (Guo) and its derivatives are among the widely studied molecules because of self-assembly abilities. Their tetrameric associates are the nature of telomeric DNA, and furthermore they are fundamental building blocks of supramolecular reversible gels, which may arise in certain physical and chemical conditions. Although poorly soluble in water, Guo forms interesting structures with guanosine 5′-monophosphate salt (GMP) in the TRIS buffer. We used electronic circular dichroism and vibrational circular dichroism to describe the thermal response of gels formed by the Guo/GMP binary mixture. Using these complementary techniques suitable to study conformational changes of chiral compounds, we obtained information about the involvement of functional groups and weak interactions in the guanosine quartet (G4) and stacked G4 structures. Chirality 24:432–438, 2012. © 2012 Wiley Periodicals, Inc.
Literature cited
- 1 Guschlbauer W, Chantot JF, Thiele D. Four-stranded nucleic acid structures 25 years later: from guanosine gels to telomer DNA. J Biomol Struct Dyn 1990; 8: 491–511.
- 2 Davis JT. G-Quartets 40 years later: from 5′-GMP to molecular biology and supramolecular chemistry. Angew Chem Int Ed 2004; 43: 668–698.
- 3 Wong A, Ida R, Spindler L, Wu G. Disodium guanosine 5′-monophosphate self-associates into nanoscale cylinders at pH 8: a combined diffusion NMR spectroscopy and dynamic light scattering study. J Am Chem Soc 2005; 127: 6990–6998.
- 4 Bouhoutsos-Brown E, Marshall CL, Pinnavaia TJ. Structure-directing properties of Na+ in the solution ordering of guanosine 5′-monophosphate. Stoichiometry of aggregation, binding to ethidium, and modes of Na+ complexation. J Am Chem Soc 1982; 104: 6576–6584.
- 5 Setnička V, Urbanová M, Volka K, Nampally S, Lehn JM. Investigation of guanosine-quartet assemblies by vibrational and electronic circular dichroism spectroscopy, a novel approach for studying supramolecular entities. Chem Eur J 2006; 12: 8735–8743.
- 6 Setnička V, Nový J, Böhm S, Sreenivasachary N, Urbanová M, Volka K. Molecular structure of guanine-quartet supramolecular assemblies in a gel-state based on a DFT calculation of infrared and vibrational circular dichroism spectra. Langmuir 2008; 24: 7520–7527.
- 7 Gottarelli G, Lena S, Masiero S, Pieraccini S, Spada GP. The use of circular dichroism spectroscopy for studying the chiral molecular self-assembly: an overview. Chirality 2008; 20: 471–485.
- 8 Wu G, Wong A. Direct detection of the bound sodium ions in self-assembled 5′-GMP gels: a solid-state 23NA NMR approach. Chem Commun 2001; 24: 2658–2659.
- 9 Manet I, Francini L, Masiero S, Pieraccini S, Spada GP, Gottarelli G. An ESI-MS and NMR study of the self-assembly of guanosine derivatives. Helv Chim Acta 2001; 84: 2096–2107.
- 10 Sreenivasachary N, Lehn JM. Gelation-driven component selection in the generation of constitutional dynamic hydrogels based on guanine-quartet formation. Proc Natl Acad Sci USA 2005; 102: 5938–5943.
- 11 Pinnavaia TJ, Marshall CL, Mettler CM, Fisk CL, Todd Miles H, Becker ED. Alkali metal ion specificity in the solution ordering of a nucleotide, 5′-guanosine monophosphate [21]. J Am Chem Soc 1978; 100: 3625–3627.
- 12 Wong A, Wu G. Selective binding of monovalent cations to the stacking G-quartet structure formed by guanosine 5′-monophosphate: a solid-state NMR study. J Am Chem Soc 2003; 125: 13895–13905.
- 13 Cheong C, Moore PB. Solution structure of an unusually stable RNA tetraplex containing G- and U-quartet structures. Biochemistry 1992; 31: 8406–8414.
- 14 Wong A, Fettinger JC, Forman SL, Davis JT, Wu G. The sodium ions inside a lipophilic G-quadruplex channel as probed by solid-state 23Na NMR. J Am Chem Soc 2002; 124: 742–743.
- 15 Ida R, Wu G. Solid-state 87Rb NMR signatures for rubidium cations bound to a G-quadruplex. Chem Commun 2005; 4294–4296.
- 16 Kwan ICM, Mo X, Wu G. Probing hydrogen bonding and ion–carbonyl interactions by solid-state 17O NMR spectroscopy: G-ribbon and G-quartet. J Am Chem Soc 2007; 129: 2398–2407.
- 17 Detellier C, Laszlo P. Role of alkali metal and ammonium cations in the self-assembly of the 5′-guanosine monophosphate dianion. J Am Chem Soc 1980; 102: 1135–1141.
- 18 Petersen SB, Led JJ, Johnston ER, Grant DM. NMR studies of self-association of disodium guanosine 5′-monophosphate. J Am Chem Soc 1982; 104: 5007–5015.
- 19 Walmsley JA, Barr RG, Bouhoutsos-Brown E, Pinnavaia TJ. Ordered forms of dianionic guanosine 5′-monophosphate with Na+ as the structure director. 1H and 31P NMR studies of hydrogen bonding and comparisons of stacked tetramer and stacked dimer models. J Phys Chem 1984; 88: 2599–2605.
- 20 Fukushima K, Iwahashi H. 1:1 complex of guanine quartet with alkali metal cations detected by electrospray ionization mass spectrometry. Chem Commun 2000; 895–896.
- 21 Fisk CL, Becker ED, Miles HT, Pinnavaia TJ. Self-structured guanosine 5′-monophosphate. A 13C and 1H magnetic resonance study. J Am Chem Soc 1982; 104: 3307–3314.
- 22 Audet P, Lacroix C, Paquin C. Continuous fermentation of a supplemented whey permeate medium with immobilized Streptococcus salivarius subsp. thermophilus. Int Dairy J 1992; 2: 1–15.
- 23 Jurga-Nowak H, Banachowicz E, Dobek A, Patkowski A. Supramolecular guanosine 5′-monophosphate structures in solution. Light scattering study. J Phys Chem B 2004; 108: 2744–2750.
- 24 Pinnavaia TJ, Miles HT, Becker ED. Self-assembled 5′-guanosine monophosphate. Nuclear magnetic resonance evidence for a regular, ordered structure and slow chemical exchange [29]. J Am Chem Soc 1975; 97: 7198–7200.
- 25 Wu G, Kwan ICM. Helical structure of disodium 5′-guanosine monophosphate self-assembly in neutral solution. J Am Chem Soc 2009; 131: 3180–3182.
- 26 Yu E, Nakamura D, DeBoyace K, Neisius AW, McGown LB. Tunable thermoassociation of binary guanosine gels. J Phys Chem B 2008; 112: 1130–1134.
- 27 Weiss RGTP. Molecular gels: materials with self-assembled fibrillar networks. The Netherlands: Springer; 2006. p. 978.
- 28 Urbanová M, Maloň P. Analytical methods in supramolecular chemistry. In: CA Schalley, editor. Weinheim: Wiley-VCH; 2007. p 265–304.
- 29 Berova N, Nakanishi K, Woody RW. Circular dichroism: principles and applications. New York: John Wiley and Sons; 2000. p. 877.
- 30 Buffeteau T, Ducasse L, Brizard A, Huc I, Oda R. Density functional theory calculations of vibrational absorption and circular dichroism spectra of dimethyl-l-tartrate. J Phys Chem A 2004; 108: 4080–4086.
- 31 Tinoco I. Exciton contribution to optical rotation of polymers. Radiat Res 1963; 20: 133–138.
- 32 Harada N, Nakanishi K. Circular dichroic spectroscopy: exciton coupling in organic stereochemistry. New York, Mill Valley: University Science Books; 1983.
- 33 Nový J, Böhm S, Králová J, Král V, Urbanová M. Formation and temperature stability of G-quadruplex structures studied by electronic and vibrational circular dichroism spectroscopy combined with ab initio calculations. Biopolymers 2008; 89: 144–152.
- 34 Forman SL, Fettinger JC, Pieraccini S, Gottarelli G, Davis JT. Toward artificial ion channels: a lipophilic G-quadruplex. J Am Chem Soc 2000; 122: 4060–4067.
- 35 Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz Jr KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc 1995; 117: 5179–5197.
- 36 Gottarelli G, Proni G, Spada GP. The effect of ions on the chiral self-assembly and liquid crystal formation of 2′-deoxyguanosine 3′-and 5′-phosphates. Enantiomer 1996; 1: 201–209.
- 37 Gottarelli G, Spada GP. The stepwise supramolecular organisation of guanosine derivatives. Chem Rec 2004; 4: 39–49.
