Stereochemistry of nucleic acids and their constituents. IV. Allowed and preferred conformations of nucleosides, nucleoside mono‐, di‐, tri‐, tetraphosphates, nucleic acids and polynucleotides

Abstract

AbstractA uniform notation and convention is suggested to describe the torsional angles in nucleic acids and their derivatives. The torsional angle χ, relating the stereochemistry of the base with respect to the sugar, shows more variation for the β‐purine glycosides than for the β‐pyrimidine glycosides. This variation is attributed to the fact that the β‐purine derivatives may form intramolecular O(5′)‐H…N(3) hydrogen bonding. The χ values for the α‐purine and α‐pyrimidine glycosides show preference for the –syn‐clinal (or anti) conformation. The mode of puckering of the sugar also influences the χ value. The various possible conformations for the furanose ring are described by the torsional angles τ0 τ1, τ2, τ3, τ4, about the five ring bonds. From an analysis of the torsional angles (ω, ϕ, ψ, ψ′, ϕ′, ω′) about the sugar phosphate bonds in the x‐ray structures of the known nucleosides, nucleotides, phosphodiesters, nucleic acids, and related compounds, and from a consideration of molecular models, it is found that the possible conformations for the backbone of helical nucleic acids is strikingly limited. Most importantly, the preferred conformation of the nucleotide unit in poly nucleotides and nucleic acids turns out to be the same as that found for the nucleotide in the crystal structure. It is observed that base “stacking” is a consequence of the restricted backbone conformation. The torsional angles are illustrated in the form of conformational “wheels”. Interrelation between the torsion angles about successive pairs of sugar‐phosphate bonds are presented in the form of conformational maps: ω,ϕ; ϕ,ψ; ψ.ψ′; ψ′,ϕ′; ϕ′,ω′; ω′,ω. The ω′,ω map shows the perferred conformations about the inter‐nucleotide bonds of right‐ and left‐handed helices and the possible conformations of phosphodiesters. The preferred conformation of the pyrophosphate and triphosphate is that in which the phosphate oxygens display a staggered arrangement when viewed along the P–P axis. A plausible structure and conformation for the ATPM2− backbound complex is presented. This structure differs from that proposed by SzentGyorgi in that the metal (only transition metals are considered here) is not bound to the NH2 nitrogen of adenine, but rather is simultaneously bound to N(7) of the ring and three phosphates (α, β, γ), or N(7) of the ring and two phosphates (β, γ). The remaining metal coordination may be satisfied by solvent–metal or enzyme–metal bonds.