X-ray structure of cytidine-5'-O-dimethylphosphate. Novel stacking between the ribosyl O(2') hydroxyl oxygen atom and the base.


Journal Article

The anionic oxygen atoms of the phosphodiester backbone of RNA and DNA are particularly susceptible to esterification by many mutagenic and carcinogenic alkylating agents. To better understand the geometric, electronic and conformational properties of the alkylated sugar phosphate moiety, the X-ray structure of the phosphotriesterified nucleotide, cytidine-5'-O-dimethylphosphate (C11H18N3O8P), was undertaken. The compound crystallizes in the monoclinic space group P2, with unit cell parameters of a = 5.741(2), b = 11.625(1), c = 11.425(1)A, beta = 94.43(2) degrees. The structure was solved by direct methods and refined by block-diagonal least-squares technique to an R index of 0.034 (Rw = 0.046). The D-ribofuranosyl ring is in the 3T2 twist conformation (P = 13.1(2) degrees, tau m = 36.7(2) degrees) and the conformation about the C(1')-N(1) glycosyl bond is anti (XCN = 8.3(2) degrees). The four P-O bond lengths are significantly shorter than those of the nonalkylated nucleotides. The three sets of phosphodiester linkages, (omega 'A, omega A), (omega 'B, omega B) and (omega 'C, omega C), take the (g-,t), (t,g) and (g-,t) conformations, respectively. There is no base-base or alkyl-base stacking, however, a novel intermolecular stacking is found between the ribosyl O(2') hydroxyl oxygen atom and a neighboring pyrimidine ring. This hydroxyl-base stacking interaction may have implications in the stabilization of the tertiary and quarternary structure of ribonucleic acids and nucleic acid-protein complexes.

Full Text

Duke Authors

Cited Authors

  • Brennan, RG; Kondo, NS; Sundaralingam, M

Published Date

  • September 11, 1984

Published In

Volume / Issue

  • 12 / 17

Start / End Page

  • 6813 - 6825

PubMed ID

  • 6548306

Pubmed Central ID

  • 6548306

International Standard Serial Number (ISSN)

  • 0305-1048

Digital Object Identifier (DOI)

  • 10.1093/nar/12.17.6813


  • eng

Conference Location

  • England