Three sets of 7-deazaadenine and cytosine nucleosides and nucleoside triphosphates bearing either unsubstituted ferrocene, octamethylferrocene and ferrocenecarboxamide linked through an alkyne tether to position 7 or 5, respectively, were designed and synthesized. The modified dNFcX TPs were good substrates for KOD XL DNA polymerase in primer extension and were used for enzymatic synthesis of redox-labelled DNA probes. Square-wave voltammetry showed that the octamethylferrocene oxidation potential was shifted to lower values, whilst the ferrocenecarboxamide was shifted to higher potentials, as compared to ferrocene. Tailed PEX products containing different ratios of Fc-labelled A (dAFc ) and FcPa-labelled C (dCFcPa ) were synthesized and hybridized with capture oligonucleotides immobilized on gold electrodes to study the electrochemistry of the redox-labelled DNA. Clearly distinguishable, fully orthogonal and ratiometric peaks were observed for the dAFc and dCFcPa bases in DNA, demonstrating their potential for use in redox coding of nucleobases and for the direct electrochemical measurement of the relative ratio of nucleobases in an unknown sequence of DNA.

Central European Institute of Technology Masaryk University Kamenice 753 5 62500 Brno Czech Republic

Departament d'Enginyeria Química Universitat Rovira i Virgili 26 Països Catalans 43007 Tarragona Spain

Department of Organic Chemistry Faculty of Science Charles University Prague Hlavova 8 Prague 2 12843 Czech Republic

Institució Catalana de Recerca i Estudis Avançats Passeig Lluís Companys 23 08010 Barcelona Spain

Institute of Biophysics of the Czech Academy of Sciences Královopolská 135 61265 Brno Czech Republic

Institute of Organic Chemistry and Biochemistry Czech Academy of Sciences Flemingovo namesti 2 16610 Prague 6 Czech Republic

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