Pentafluorophenyl–Phenyl Interactions in Biphenyl‐DNA

We prepared and investigated oligonucleotide duplexes of the sequence d(GATGAC( X ) n GCTAG)⋅d(CTAGC( Y ) n GTCATC), in which X and Y designate biphenyl‐ (bph) and pentafluorobiphenyl‐ ( 5F bph) C ‐nucleotides, respectively, and n varies from 0–4. These hydrophobic base substitutes are expected to adopt a zipperlike, interstrand stacking motif, in which not only bph/bph or 5F bph/ 5F bph homo pairs, but also 5F bph/bph mixed pairs can be formed. By performing UV‐melting curve analysis we found that incorporation of a single 5F bph/ 5F bph pair leads to a duplex that is essentially as stable as the unmodified duplex ( n =0), and 2.4 K more stable than the duplex with the nonfluorinated bph/bph pair. The T m of the mixed bph/ 5F bph pair was in between the T m values of the respective homo pairs. Additional, unnatural aromatic pairs increased the T m by +3.0–4.4 K/couple, irrespective of the nature of the aromatic residue. A thermodynamic analysis using isothermal titration calorimetry (ITC) of a series of duplexes with n =3 revealed lower (less negative) duplex formation enthalpies (Δ H ) in the 5F bph/ 5F bph case than in the bph/bph case, and confirmed the higher thermodynamic stability (Δ G ) of the fluorinated duplex, suggesting it to be of entropic origin. Our data are compatible with a model in which the stacking of 5F bph versus bph is dominated by dehydration of the aromatic units upon duplex formation. They do not support a model in which van der Waals dispersive forces (induced dipoles) or electrostatic (quadrupole) interactions play a dominant role.