Solvent effects on nucleotide conformation. I. A proton magnetic resonance study of the effect of electrolytes on uracil nucleotides and nucleosides in aqueous solution

Abstract

The pmr spectra of aqueous solutions of uracil, uridine, deoxyuridine, uridine 3'-monophosphate (3'-UMP), and uridine 5 '-monophosphate (5 '-UMP) have been studied as a function of electrolyte concentration. The addition of a "solvent-structure breaking" salt such as Mg(C104)2 or NaC104 to solutions of the nucleosides and nucleotides was found to result in significant upfield shifts of the uracil Hs resonance.

NMR spectroscopy of the ring nitrogen protons of uracil and substituted uracils; relevance to A ψ base pairing in the solution structure of transfer RNA

“…This may reflect the fact that monomer spectra represent predominantly anti conformations [9], which is the correct orientation for the AU pair, but incorrect for the AT pair in tRNA. Rotation of the NlH from its position above the ribose, as it is found in the anti conformation of pseudouridine, to the s:y position away from the ribose, would result in an upfield shift (due to the loss of the deshielding electric field effect produced by the ribose oxygen [10]. With this extra correction, the AT' versus AU0 difference is very nicely accounted for by the proposed s]M conformation of AT base pairs.…”

“…al. [9], this may reflect the opposing effects of a throughspace electric field effect from the hemiacetal oxygen [10], and a throughbond substituent effect. It is interesting to note that the C6H of a pseudouridine appears to lose the downfield effect, since this C6H resonance is observed 0.25 ppm upfield of the corresponding resonance in uracil.…”

Conformation and interaction of dinucleoside mono- and diphosphates. 2. Influence of the phosphodiester linkage (3'-5', 2'-5', and 5'-5') on the conformation of dinucleoside monophosphate

“…or by the change of relative position of the H-2' (C-2' in endo or exo). Most of the attention in the past has been focused on the latter situation, i.e., the change of C-2' or C-3' relative position (Hruska and Danyluk, 1968; Chan and Nelson, 1969;Bangerter and Chan, 1969;Prestegard and Chan, 1969).…”

Long-range Spin–Spin Coupling in Pyrimidine Nucleosides

“…The evidence that the anti conformations of U and dU are favored over syn in the solid state as well as in solution is not disputed (1)(2)(3)(4)(5)(6)(7)(8)(9)(10)(11). That syn conformations are not present to any detectable extent is generally agreed to be a consequence of unfavorable steric interactions (between the 2-keto oxygen and the endo ribose substituents) not present when the molecules are anti.…”