Crystallographic studies of nucleic acid components

The purpose of this study was to determine the three dimensional structures of several nucleic acid components by X-ray crystallographic techniques in order to examine the conformational details of these important metabolites. The study was conducted in two parts, the first part consisting of the determination of the structures of one natural and one synthetic nucleotide, and of one synthetic nucleoside. The second part of the study involved the synthesis of four modified pyrimidine bases believed to be involved in the mutations caused by hydroxylamine and bisulfite, and the determination of the crystal structures of these compounds. All data were collected on automated diffractometers using the 0-2e scan technique. All structures were solved using heavy-atom or direct methods.

Crystals of adenosine-5'-methylphosphonate hemihydrate are triclinic, space group P1, with a = 10.510(2), b = 9.419(2), c = 7.803(2)A, and α = 76.77(1), β = 97.24(2) and γ = 95.99(1)°. Full-matrix leastsquares refinement resulted in a final R factor of 0.029 for the 3339 significant data. The two independent molecules in the asymmetric unit are very similar in conformation, with unusual ribose conformations.

Crystals of disodium guanosine-5'-phosphate heptahydrate are orthorhombic, space group P2,2,2], with a = 22.267(2), . b = 21.360(2) and c = 9.035(1)A. Block-diagonal least-squares refinement resulted in a final R Factor of O.059. The aromatic bases of the nucleotide molecules are not stacked, but are packed in a "herringbone" pattern primarily stabilized by coordination of N(7) of the bases to a sodium ion.

Crystals of 4-thiopseudouridine are monoclinic, space group P21, with a = 15.434(2), b = 7.4381(5), c = 14.818(2)A and β = 110.45(1)°. The structure was solved by direct methods, but the determination was hampered by a high degree of pseudosymmetry in the crystal. The correct structure was chosen by refinement to a final R value of O.043 for the 3972 significant data.

Crystals of sodium 5,6-dihydrouracil-6-sulfonate monohydrate are monoclinic, space group P21/c, with a = 5.668(1), b = 11.026(2), c = 13.261(2)A and β = 94.62(2)°. The compound was obtained as a byproduct of the reaction of semicarbazide and bisulfite with cytosine. Full-matrix least-squares refinement resulted in a final R value of 0.032.

Crystals of sodium cytosine-5-methylene sulfonate trihydrate are monoclinic, space group P21/c, with a = 5.235(1), b = 22.843(5), c = 9.140(2)A and β = 90.93(1)°. This compound is the product of the reaction of bisulfite with 5-hydroxymethylcytosine. Full-matrix least-squares refinement resulted in a final R value of 0.038.

Crystals of sodium N4-hydroxy-5,6-dihydrocytosine-6-sulfonate monohydrate are monoclintc, space group P21/c, with a = 12.977(2), b = 8.384(2), c = 8.552(2)A and β = 106.89(1)°. Crystals of sodium 1-methyl-N4-hydroxy-5,6-dihydrocytosine-6-sulfonate tetrahydrate are monoclinic, space group P21/c, with a = 6.491(1), b = 11.129(2), c = 17.883(3)A and β = 93.50(1)°. In both structures, the N(4) hydroxy] group is located syn to the ring N(3) atom. This conformation would prevent such modified cytosine residues in a polynucleotide from participating in Watson-Crick base pairing.