Investigation of self-association of molecules of desoxytetraribonucleoside triphosphates d(GpCpGpC) in solution by means of one-dimensional and two-dimensional1H NMR spectrometry

Veselkov, A. N.; Davis, Darryl N.; Parkes, Harold G.; Dymant, L. N.; Sigaev, V. A.

doi:10.1007/bf00748050

J Struct Chem

1992

DOI: 10.1007/bf00748050

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Investigation of self-association of molecules of desoxytetraribonucleoside triphosphates d(GpCpGpC) in solution by means of one-dimensional and two-dimensional1H NMR spectrometry

A. N. Veselkov¹,

Darryl N. Davis²,

Harold G. Parkes³

et al.

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1994

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“…These calculations are based on the following assumptions: .1) the chemical shifts represent time-averaged values, b) the equilibria are independent and both can be described formally by a two-state model, and c) van' t Hoff conditions prevail. In a recent study of d(GCGC)(44), it was shown that this relationship (ln (KA) = f(l/T)) Downloaded by [New York University] at 12:…”

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confidence: 97%

Thermodynamic and Structural Properties of r(ACC) as Revealed by Ultraviolet Electronic Absorption, Circular Dichroism,¹H-NMR Spectroscopy and Monte Carlo Simulations

Bouchemal-Chibani

Lebrun²,

Penhoat³

et al. 1994

Journal of Biomolecular Structure and Dynamics

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UV absorption, circular dichroism (CD) and 1H NMR, associated with Monte Carlo (MC) molecular structure simulations have been applied to the study of the trinucleoside diphosphate: r(ACC). The MC study which has been conducted as a function of temperature, is based on random variations of the nucleotide conformational angles, i.e. phosphodiester chain torsional angles and sugar pucker pseudorotational angles. All of the chemical bond lengths and valence angles remained fixed during the structural simulation, except those of the sugar pucker. Six different initial structures have been selected in order to explore the molecular conformational space as completely as possible. This simulation procedure led to distinct families of equilibrium conformations at 283, 298 and 318 K. The thermodynamical parameters such as variations in entropy, enthalpy and also melting temperature (delta SX0, delta HX0 and Tm) of the stacking (X) equilibrium were obtained from UV absorption and circular dichroism (CD) spectra recorded over a 80K temperature range. Chemical shifts (delta), vicinal coupling constants (3Jk,l), and cross-relaxation rate (sigma k,l) of trimers were measured at 400.13 MHz over a range of concentrations (2-13 mM) and temperatures (283-333K). Least-squares fitting of the experimental chemical shifts to simple models of association (A) and stacking equilibria allowed separation of the variations in the delta values (delta delta X and delta delta A) due to either phenomenon. The three NMR data sets (delta delta X, 3Jk,l, and sigma k,l) were then evaluated for the minima conformers obtained with the MC stimulations. Theoretical values of delta delta X were estimated using the results of an ab initio study while the coupling constant data were simulated with Karplus-type equations. Finally, the relaxation data were simulated from the distance matrices using treatment for cases of both slow conformational exchange accompanied by rapid small-amplitude fluctuations about the minima structures. A consistent picture of the large amplitude deformations (torsional angle variation) of these trimers has emerged from the present study. Optimized conformational blends at 283,296 and 318K were obtained by least-squares fitting of the experimental data to the theoretical ones, while considering the populations as adjustable parameters. As it would be expected, the right-handed helical conformation (A-RNA type) is found to be the major stacked species, in the temperature range of 283 to 318K. Limited evidence for bulged structures has been obtained, whereas novel reverse-stacked and half-stacked conformers also presented theoretical data compatible with the NMR observables of aqueous r(ACC).

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confidence: 97%

Thermodynamic and Structural Properties of r(ACC) as Revealed by Ultraviolet Electronic Absorption, Circular Dichroism,¹H-NMR Spectroscopy and Monte Carlo Simulations

Bouchemal-Chibani

Lebrun²,

Penhoat³

et al. 1994

Journal of Biomolecular Structure and Dynamics

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Investigation of self-association of molecules of desoxytetraribonucleoside triphosphates d(GpCpGpC) in solution by means of one-dimensional and two-dimensional1H NMR spectrometry

Cited by 1 publication

References 12 publications

Thermodynamic and Structural Properties of r(ACC) as Revealed by Ultraviolet Electronic Absorption, Circular Dichroism,¹H-NMR Spectroscopy and Monte Carlo Simulations

Thermodynamic and Structural Properties of r(ACC) as Revealed by Ultraviolet Electronic Absorption, Circular Dichroism,¹H-NMR Spectroscopy and Monte Carlo Simulations

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Investigation of self-association of molecules of desoxytetraribonucleoside triphosphates d(GpCpGpC) in solution by means of one-dimensional and two-dimensional1H NMR spectrometry

Cited by 1 publication

References 12 publications

Thermodynamic and Structural Properties of r(ACC) as Revealed by Ultraviolet Electronic Absorption, Circular Dichroism,1H-NMR Spectroscopy and Monte Carlo Simulations

Thermodynamic and Structural Properties of r(ACC) as Revealed by Ultraviolet Electronic Absorption, Circular Dichroism,1H-NMR Spectroscopy and Monte Carlo Simulations

Contact Info

Product

Resources

About

Thermodynamic and Structural Properties of r(ACC) as Revealed by Ultraviolet Electronic Absorption, Circular Dichroism,¹H-NMR Spectroscopy and Monte Carlo Simulations

Thermodynamic and Structural Properties of r(ACC) as Revealed by Ultraviolet Electronic Absorption, Circular Dichroism,¹H-NMR Spectroscopy and Monte Carlo Simulations