title: Destabilizing effect of a fluorouracil extra base in a hybrid RNA duplex compared with bromo and chloro analogues.
abstract: In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-d(X)U (with X = F, Cl or Br) crystallizes as a double-stranded helix with four consecutive G-U and C-U mismatches. The deoxy chloro- and bromouracil derivatives are isomorphous, space group C2, unit-cell parameters a = 53.80, b = 19.40, c = 50.31 A, beta = 109.9 degrees, with the same infinite helix arrangement in the packing along the c axis with one extra DNA halogenouracil base included in the stacking. However, the fluorouracil derivative, with unit-cell parameters a = 53.75, b = 19.40, c = 45.84 A, beta = 105.7 degrees, is not isomorphous. The corresponding extra DNA base d(F)U of the second strand is ejected out of the helical stack, leading to a shortening of the c axis. The specific destabilization of the fluorouracil for the duplex building is analyzed in terms of the polarization effect of the halogen atom attached to the 3'-terminal base that modulates its interactions.
authors.affiliation: CSSB - Chimie Structurale Biomoléculaire (UPRES A7031 CNRS), UFR Biomédicale 74, Rue Marcel Cachin, 93017 Bobigny CEDEX, France.
authors.forename: W
authors.initials: W
authors.lastname: Cruse
authors.forename: P
authors.initials: P
authors.lastname: Saludjian
authors.forename: A
authors.initials: A
authors.lastname: Neuman
authors.forename: T
authors.initials: T
authors.lastname: Prangé
mesh_terms: D001966:Bromine / Q000737:chemistry; D002713:Chlorine / Q000737:chemistry; D003460:Crystallization; D018360:Crystallography, X-Ray; D005472:Fluorouracil / Q000737:chemistry*; D008958:Models, Molecular; D009690:Nucleic Acid Conformation; D009692:Nucleic Acid Heteroduplexes / Q000138:chemical synthesis / Q000737:chemistry*
chemical_list: D009692:Nucleic Acid Heteroduplexes; D002713:Chlorine; D001966:Bromine; D005472:Fluorouracil