Physico-chemical properties of nucleosides

Chantot, J F; Sarocchi, Marie-Thérèse; Guschlbauer, Wilhelm

doi:10.1016/s0300-9084(71)80101-3

Cited by 57 publications

(25 citation statements)

References 18 publications

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“…pH titrations of the nucleotides in the presence of a lanthanide were carried out. These experiments with the guanine nucleotides are difficult due to their marked tendency to form gels, especially in the pH range 1-6 [15]. Due to this limitation low concen- trations of both the nucleotides and the lanthanide ions were used.…”

Section: Effect Of P H On Shift Ratiosmentioning

confidence: 99%

Nuclear-Magnetic-Resonance Studies of 5'-Ribonucleotide and 5'-Deoxyribonucleotide Conformations in Solution Using the Lanthanide Probe Method

et al. 1978

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icleo tide WILLIAMSThe conformations of the metal-bound 5 '-ribonucleotides and 5 '-deoxyribonucleotides in aqueous solution at different pH values have been studied using the lanthanide probe method. The conformational analysis, based on mixing different conformations in fast exchange within the nuclear magnetic resonance time scale, agrees well with the results from coupling constants, nuclear Overhauser effects and spin-lattice relaxation times, obtained for the metal-fixed systems. The equilibrium between the two basic conformational combinations for the 5 '-nucleotides, anti-(N G? S ) -gg-g'g' and syn-(NG?S)-gt-g'g' depends on the nature of the furanose ring, the base and also on the state of base protonation and phosphate ionization. The effect of base protonation is particularly strong for the guanine nucleotides.The conformations of free 5 '-ribonucleotides and deoxyribonucleotides in solution have been extensively studied by nuclear magnetic resonance (NMR) spectroscopy, due to the importance of these molecules as the simplest constituents of naturally occurring nucleic acids. Most of these studies have been based on the interpretation of experimental NMR parameters for the isolated nucleotides, such as chemical shifts, vicinal spin-spin coupling constants, nuclear Overhauser enhancements and nuclear relaxation rates [I, 11 -13,281 (and references in [I]). A different general method for the determination of the conformation of metal-bound flexible molecules in solution, using the lanthanide cations (Ln3 ') as shift and relaxation NMR probes has been described and applied to some nucleotide monophosphatates [2-41.In this paper the lanthanide probe method is applied to the comparative study of the conformations in aqueous solution of the eight metal-bound 5'-mOnOnucleotides which occur in ribonucleic and deoxyribonucleic acids : the nucleotides of adenosine (5'-AMP), guanosine (5'-GMP), cytidine (5'-CMP), uridine (5 '-UMP), 2'-deoxyadenosine (5 '-dAMP), 2'-deoxyguanosine (5'-dGMP), 2'-deoxycytidine (5'-dCMP) and thymidine (5'-dTMP).The conformational conclusions obtained from the lanthanide data are compared with independent NMR Ahbrevintion. NMR, nuclear magnetic resonance work, especially coupling constants and nuclear Overhauser enhancement data, as there must be at least a qualitative agreement for the metal-bound systems between the conclusions from the different methods [5,6]. From this comparison, an assessment of the different NMR conformational methods in solution is attempted. Finally the results in aqueous solution are compared with the available information on the crystal structure of metal-bound 5 '-mononucleotides from X-ray diffraction data and with the data on the metal-free systems. MATERIALS AND METHODS'H NMR spectra were obtained at 90 MHz using a Bruker HFX 90 spectrometer and at 270 MHz using an Oxford Instruments superconducting magnet and a modified Bruker HFX 90 console. Both spectrometers were operated in the Fourier transform mode, using a Nicolet 1085 computer. The observation o...

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Section: Effect Of P H On Shift Ratiosmentioning

confidence: 99%

Nuclear-Magnetic-Resonance Studies of 5'-Ribonucleotide and 5'-Deoxyribonucleotide Conformations in Solution Using the Lanthanide Probe Method

et al. 1978

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“…Thus, even in the presence of the poly(C), which creates a large driving force for formation of the very stable poly(G).poly(C) structure, poly(G) persists in metastable, self-associated conformations to rather high temperatures. Guanine residues can aggregate into a number of structures, involving several possible base pairing schemes (Gellert et al, 1962;Pochon & Michelson, 1965;Chantot et al, 1971). One can devise G * G base pairs in which protons participate in H bonding and are thus essential for the G. G formation.…”

Section: (C) Metastable Quanine -Gumande Structures May Underlie the Hymentioning

confidence: 99%

Metastable secondary structures in ribosomal RNA molecular hysteresis in the acid-base titration of Escherichia coli ribosomal RNA

Revzin

Neumann

Katchalsky

1973

Journal of Molecular Biology

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The metastable conformational states which underlie the hysteresis displayed by Escherichia coli ribosomal RNA in its pH titration in the acid range have been analyzed in terms of acid-stable RNA secondary structures. Sedimentation measurements show that the phenomenon is ktramolecular, so that analysis of the hysteresis loops can, in principle, reveal details of molecular architecture. Hysteresis cycles obtained spectrophotometrically and potentiometrically were compared for RNA in solutions of different ionic strengths and ionic compositions. The effect is much smaller at lower ionic strength and disappears in the absence of magnesium ions. The curve followed upon addition of acid appears to reflect the equilibrium state of the system at each pH value. On the "base branch" of the loop, a slow absorbance change (complete in hours) was observed after the pH was raised by addition of a portion of base. This slow process is attributed to the annealing of "mismatched" multihelical regions of the ribosomal RNA. Certain regions, however, remain in metastable configurations for days and it is these long-lived non-equilibrium structures that underlie the hysteresis. Titration at 35°C gave hysteresis loops of the same size and shape as at 20°C ; indeed, we found that the metastabilities are not removed even at 80°C. Ultraviolet light absorbance difference spectra at 80°C between solutions at the same pH, but on different branches of the cycle, give insight into the nature of the metastable conformation(s).Our experimental observations lead us to propose that the hysteresis is due to the formation at acidic pH of double-helical structures involving protonated guanine and adenine base pairs. The G.G pairs seem especially important to account for the very high thermal stability, as well as for the fact that the structures formed at a given pH value as acid is added dissociate only at higher pH values when the solution is titrated with base. Titrations of transfer RNA, along with literature data on 16 S rRNA primary structure, imply that the metastable regions in rRNA may consist of perhaps 10 to 15 base pairs.

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“…As monomer concentration is increased, the G-tetrads stack upon themselves through p-p coupling to form columnar, helical structures [18][19][20][21][22][23]. These structures are generally stabilized by centrally located metal cations such as K 1 that are coordinated to oxygen atoms in the guanosine monomers [19][20][21][22][23]. An important feature of G-gels is their tunability as a function of temperature, pH, guanosine compound concentration and cation content [18][19][20][21][22][23].…”

Section: Introductionmentioning

confidence: 99%

Chiral selectivity of guanosine media in capillary electrophoresis

Dong

McGown

2011

Electrophoresis

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Gels formed by self-association of monomeric guanosine compounds join numerous other agents such as cyclodextrins, crown ethers, chiral surfactants, antibiotics, proteins, and polysaccharides for chiral separations. Guanosine gels (G-gels) are self-assembled networks of hydrogen-bonded tetrads formed by guanosine nucleotides and their derivatives. The tetrads stack upon themselves to form columnar, helical aggregates that are stabilized by π-π interactions and centrally located cations. Previous work showed the effectiveness of G-gels formed by guanosine-5'-monophophate for separation of the enantiomers of the cationic drug propranolol using capillary electrophoresis. Subsequently, it was found that not all chiral compounds could be resolved into their enantiomers, leading us to investigate in this work the structural features that appear to be correlated to enantiomerically selective interactions of chiral compounds with G-gels. For those compounds (anionic 1,1'-binaphthyl-2,2'-diyl hydrogen phosphate and zwitterionic tryptophan) for which enantiomeric resolution was achieved, the effects of experimental conditions and G-gel composition were examined. For other compounds with no net charge (hydrobenzoin and zwitterionic amino acids and derivatives), the migration times were used as an indicator of the extent of interaction with the G-gel run buffer. It was found that the extent of interaction alone does not determine the chiral selectivity of the G-gel, indicating that the mechanism of chiral separation involves particular structural characteristics of the chiral compounds.

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Physico-chemical properties of nucleosides

Cited by 57 publications

References 18 publications

Nuclear-Magnetic-Resonance Studies of 5'-Ribonucleotide and 5'-Deoxyribonucleotide Conformations in Solution Using the Lanthanide Probe Method

Nuclear-Magnetic-Resonance Studies of 5'-Ribonucleotide and 5'-Deoxyribonucleotide Conformations in Solution Using the Lanthanide Probe Method

Metastable secondary structures in ribosomal RNA molecular hysteresis in the acid-base titration of Escherichia coli ribosomal RNA

Chiral selectivity of guanosine media in capillary electrophoresis

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