Pentafluorophenyl phenyl interaction in biphenyl DNA

Zahn, Alain; Brotschi, Christine; Leumann, Christian J. (2005). Pentafluorophenyl phenyl interaction in biphenyl DNA. Chemistry - a European journal, 11(7), pp. 2125-2129. Wiley-VCH

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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 (DeltaH) in the (5F)bph/(5F)bph case than in the bph/bph case, and confirmed the higher thermodynamic stability (DeltaG) 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

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Departement of Chemistry and Biochemistry

UniBE Contributor:

Zahn, Alain and Leumann, Christian


500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry








Christian Leumann

Date Deposited:

26 May 2014 15:21

Last Modified:

11 Dec 2014 13:13

PubMed ID:


Uncontrolled Keywords:

analysis, base, biphenyl, calorimetry, data, DNA, duplex, DUPLEXES, motif, Oligodeoxynucleotides, oligonucleotide stability, thermodynamic, titration




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