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

Abstract

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...

Principles of Nucleic Acid Structure

“…These observations are corroborated by NMR-spectroscopic studies evaluating 3lp_lH and 3lp_l3C heteronuclear coupling (130-132,143-147, 175,176,178,218,293,352-354) as well as lanthanide shift methods (330,354,355) on mono-, oligo-, and polynucleotides. Irrespective of sugar puckering, the atomic chain H4,-C4,-Cs'-Os'-P is predominantly extended, corresponding to + sc orientation for l' and ap for {3 torsion angles.…”

IR Study on the Relaxation of the Phosphate Group of 5‘-dCMP in2H2O and H2O Solutions

“…Crystallographic data on 5‘-dCMP·Na 2 heptahydrate and monohydrate indicate that the compound is orthorhombic, space group P 2 1 2 1 2 1 , showing an unusual gauche−trans conformation around the C4‘−C5‘ bond, and accompanied, however, by a normal C3‘-exo sugar pucker. In relation to the conformational state of the 5‘-ribonucleotides or 5‘-deoxyribonucleotides, it was clearly established by 1 H NMR studies , that the conformational preferences of the phosphate backbone are maintained when going from the crystal to the aqueous solution. Some other conformational studies of 5‘-dCMP by 13 C chemical shifts and 13 C− 31 P coupling constants as a function of pH in aqueous solution point to a preference (70−80%) for the trans orientation of the P5‘−O5‘−C5‘−C4‘ fragment, with little dependence on the nature of the sugar.…”

1H‐NMR studies on nucleotide binding to the catalytic sites of bovine mitochondrial F1‐ATPase

“…The conformations of free 5' -adenine ribonucleotides in solution have been extensively studied by proton NMR spectroscopy [1][2][3]. A favored anti orientation of the base ring with respect to the ribose ring was found (fig.l).…”