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Gemcitabine, Pyrrologemcitabine and 2'-Fluoro- 2'-Deoxycytidines: Synthesis, Physical Properties and Impact of Sugar Fluorination on Silver Ion Mediated Base Pairing.

The stability of silver mediated "dC-dC" base pairs relies not only on the structure of the nucleobase but also is sensitive to structural modification on the sugar moiety. 2'-Fluorinated 2'-deoxycytidines with fluorine atoms in the arabino (up) and the ribo (down) configuration, as well as with geminal fluorine substitution (anticancer drug gemcitabine) and the novel fluorescent phenylpyrrolo-gemcitabine (phPyrGem) were synthesized. All nucleosides display the recognition face of naturally occurring 2'-deoxycytidine. Nucleosides were converted into phosphoramidites and incorporated in 12-mer oligonucleotides by solid-phase synthesis. Addition of silver ions to DNA duplexes with a fluorine modified "dC-dC" pair near central position led to significant duplex stabilization. The stability increase was higher for duplexes with fluorinated sugar residues than those with the unchanged 2'-deoxyribose moiety. Similar observations were made on "dC-dT" pairs and to a minor extend on the "dC-dA" pairs. The increase of silver ion mediated base pair stability was reversed by annulation of a pyrrole ring to the cytosine moiety as shown for 2'-fluorinated phPyrGem compared to phenylpyrrolo-dC (phPyrdC). The phenomenon results from stereoelectronic effects induced by fluoro substitution which are transmitted from the sugar moiety to the silver ion mediated base pairs. This depends on the number of fluorine substituents, their configuration and the structure of the nucleobase.

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