research papers
In the presence of cobalt, rhodium or iridium hexammine salts, the RNA/DNA hybrid r-GCUUCGGC-dXU (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 Å, β = 109.9°, 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 Å, β = 105.7°, is not isomorphous. The corresponding extra DNA base dFU 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.
Supporting information
PDB references: r-GCUUCGGC-dClU, Rh(NH3), 1idw; r-GCUUCGGC-dBrU, Rh(NH3), 1iha; r-GCUUCGGC-dFU, Rh(NH3), 1id9; r-GCUUCGGC-dFU, Ir(NH3), 1icg