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) |
|---|---|
Division/Institute: |
08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP) |
UniBE Contributor: |
Zahn, Alain, Leumann, Christian |
Subjects: |
500 Science > 570 Life sciences; biology 500 Science > 540 Chemistry |
ISSN: |
0947-6539 |
Publisher: |
Wiley-VCH |
Language: |
English |
Submitter: |
Christian Leumann |
Date Deposited: |
26 May 2014 15:21 |
Last Modified: |
05 Dec 2022 14:34 |
PubMed ID: |
15714531 |
Uncontrolled Keywords: |
analysis, base, biphenyl, calorimetry, data, DNA, duplex, DUPLEXES, motif, Oligodeoxynucleotides, oligonucleotide stability, thermodynamic, titration |
BORIS DOI: |
10.7892/boris.53110 |
URI: |
https://boris.unibe.ch/id/eprint/53110 |
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