Tuning of Oxidation Potential of Ferrocene for Ratiometric Redox Labeling and Coding of Nucleotides and DNA

Abstract

Three sets of 7-deazaadeninea nd cytosine nucleosides and nucleoside triphosphates bearinge ither unsubstituted ferrocene, octamethylferrocenea nd ferrocenecarboxamide linked through an alkynet ether to position7or 5, respectively,w ere designed and synthesized.T he modified dN FcX TPsw ere good substrates for KOD XL DNA polymerase in primer extension and were used for enzymatic synthesis of redox-labelled DNA probes. Square-wave voltammetry showedt hat the octamethylferroceneo xidation potential was shifted to lower values, whilst the ferrocenecarboxamide was shifted to higherp otentials, as compared to ferrocene. Ta iled PEX products containing different ratios of Fc-labelled A( dA Fc )a nd FcPa-labelled C( dC FcPa )w eres ynthesized and hybridized with capture oligonucleotides immobilized on gold electrodes to study the electrochemistry of the redox-labelledD NA. Clearlyd istinguishable, fully orthogonal and ratiometric peaks were observed for the dA Fc and dC FcPa bases in DNA, demonstrating their potential for use in redox codingo fn ucleobases and for the direct electrochemical measuremento fthe relative ratio of nucleobases in an unknowns equence of DNA.

Enzymatic Construction of Artificial Base Pairs: The Effect of Metal Shielding

“…Despite displaying an exquisite fidelity of replication and a high propensity at distinguishing canonical nucleotides, DNA polymerases are highly tolerant to chemical alterations in the scaffold of nucleoside triphosphates. [35] This is particularly true for base-modified nucleotide analogues into which a variety of functional groups ranging from small residues [36] to large fragments including polymerases [37] or even antibodies [38] could be introduced into nucleic acids by polymerases. In the general context of identifying novel UBPs, the nucleotide candidate needs to be fully orthogonal to canonical DNA and has to be inserted opposite a templating modified nucleotide with an error rate not lower than 10 À 3 .…”

Covalent labeling of nucleic acids

“…196 In a recent report it was shown that differently substituted ferrocene labels could be incorporated into DNA using the above mentioned strategy. 197 Due to the orthogonality of the oxidizable labels it was possible to directly measure the relative abundance of two different nucleotides in a target sequence. 197 With future work, orthogonal labels for all four nuclebase may become available and provide a valuabe strategy for sequencing.…”

“…197 Due to the orthogonality of the oxidizable labels it was possible to directly measure the relative abundance of two different nucleotides in a target sequence. 197 With future work, orthogonal labels for all four nuclebase may become available and provide a valuabe strategy for sequencing.…”

Stereo‐Defined Ferrocenyl Glycol Nucleic Acid (Fc‐GNA) Constituents: Synthesis, Electrochemistry, Mechanism of Formation, and Anticancer Activity Studies

“…Conjugation of the redox-active ferrocenyl entity with nucleic acids and their constituents has been proved as an effective approach for bioanalytical applications. [32,33,[50][51][52][53][54] The Fc-XNA oligonucleotides [38] as well as some Fc-GNA [43,44,46] and Fc-PNA [35,55] constituents have also been studied by electrochemistry. To achieve complete spectroscopic characterization with electrochemical data, the compounds (R,R)-1, (S,R)-1, and (R,R)-2 were subjected to cyclic voltammetry (CV).…”