What is the conformation of physiologically-active dinucleoside polyphosphates in solution? Conformational analysis of free dinucleoside polyphosphates by NMR and molecular dynamics simulations

Abstract

Dinucleoside polyphosphates, or dinucleotides (Np(n)N'; N, N' = A, U, G, C; n = 2-7), are naturally occurring ubiquitous physiologically active compounds. Despite the interest in dinucleotides, and the relevance of their conformation to their biological function, the conformation of dinucleotides has been insufficiently studied. Therefore, here we performed conformational analysis of a series of Np(n)N' Na(+) salts (N = A, G, U, C; N' = A, G, U, C; n = 2-5) by various NMR techniques. All studied dinucleotides, except for Up(4/5)U, formed intramolecular base stacking interactions in aqueous solutions as indicated by NMR. The conformation around the glycosidic angle in Np(n)N's was found to be anti/high anti and the preferred conformation around the C4'-C5', C5'-O5' bonds was found to be gauche-gauche (gg). The ribose moiety in Np(n)N's showed a small preference for the S conformation, but when attached to cytosine the ribose ring preferred the N conformation. However, no predominant conformation was observed for the ribose moiety in any of the dinucleotides. Molecular dynamics simulations of Ap(2)A and Ap(4)A Na(+) salts supported the experimental results. In addition, three modes of base-stacking were found for Ap(2/4)A: α-α, β-β and α-β, which exist in equilibrium, while none is dominant. We conclude that natural, free Np(n)N's (n = 2-5) at physiological pH exist mostly in a folded (stacked), rather than extended conformation, in several interconverting stacking modes. Intramolecular base stacking of Np(n)N's does not alter the conformation of each of the nucleotide moieties, which remains the same as that of the mononucleotides in solution.

CDP-Ethanolamine and CDP-Choline: one-pot synthesis and 31P NMR study

“…26 In our NMR experiments, the sample concentration was kept low enough to avoid intermolecular base stacking and to enable the detection of clear and sharp NMR signals. 27 We noticed that protons belonging to the nucleobase of CDP-Etn, when purified by HPLC under acidic conditions, display downfield shifts compared to those of the sodium salt of CDP-Etn (Dd = 0.15 ppm for H 5 , Dd = 0.23 ppm for H 6 ). This shift has been attributed to the protonation of cytosine at low pH.…”

Intramolecular Base Stacking of Dinucleoside Monophosphate Anions in Aqueous Solution

“…The relationships between the chemical properties of nucleobases and their stacking free energies in solution have been thoroughly studied both experimentally 3-11 and theoretically 12-22, 23 . In general, base stacking in nucleic acids is a net outcome of a delicate balance of steric, London and electrostatic forces among the bases and the solvent molecules that is subject to conformational constraints imposed by the phosphodiester linkage 24-26 .…”

Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy

“…9). Previous studies suggested that these compounds adopt non-face-to-back stacking motifs [160,161]. The long-wavelength couplet seen in the ECCD spectra of Ap 4 A and Ap 5 A (Fig.…”