Crystal Structure and Conformation of the Phosphotriester Adenosine 5’-O-(Diethyl phosphate). Possible Steric and Conformational Mechanisms for the Biochemical and Biological Effects Arising from Phosphate Alkylation

Phosphotriesterified oligonucleotides are often the major products resulting from the attack of mutagenic and carcinogenic alkylating agents on DNA and RNA. In order to elucidate the electronic and conformational perturbations arising from phosphate esterification, which may be the basis of its biochemical and biological effects, the X-ray structure of the triesterified nucleotide adenosine 5'-O-(diethyl phosphate) (C14H22N5O7P) was undertaken. The compound (FW = 403.33) crystallizes in the triclinic space group P1 (Z = 1) with unit cell parameters of a = 6.799 (1), b = 7.923 (1), c = 9.003 (1) Å, α = 86.86 (1), β = 77.98 (1), γ = 77.85 (1)°, V = 463 Å3, Dc = 1.444 g cm−3, and DM = 1.45 g cm−3. The structure was solved by heavy-atom methods and refined by the full-matrix least-squares technique to an R index of 0.039 (Rw = 0.051) using 1917 intensities. The D-ribofuranosyl ring is in a symmetrical twist conformation, C(2')-endo-C(1')-exo, with pseudorotational parameters P = 145.0 (2)° and Ƭm = 39.4 (2)°. The adenine base is anti (69.0 (3)°) about the C(1')-N(9) glycosyl bond, and the conformation about the exocyclic bond C(4')–C(5') is the preferred gauche+ (50.8 (3)°). Hydrogen bonding is centered about the ribosyl hydroxyls and the N(6) amino group of the base. The molecular packing is dominated by intermolecular base-alkyl stacking and alkyl-alkyl van der Waals interactions. The methyl group of one of the ethoxy groups is two-site disordered. Diethylation of the phosphate results in neutralization of the charge and geometric and conformational perturbations of the phosphodiester. All four P-O bonds are significantly shorter than those of the nonalkylated nucleotides. The three combinations of phosphodiester linkages display the (g−,t), (g+,g−), and (t,t) conformations which are different from the familiar (g−,g−) conformation of right-handed polynucleotide helices. The lack of preference of the alkylated sugar phosphate backbone for the (g−,g−) phosphodiester conformation would tend to destack the bases and promote alkyl-base stacking. This will lead to sugar phosphate backbone configurations which would provide a mechanism for the biochemical and biological effects induced by phosphate alkylation. © 1984, American Chemical Society. All rights reserved.

Duke Scholars

Author Richard Gerald Brennan Biochemistry