Ferrocene as an electrochemical reporting surrogate of abasic sites in DNA

29 July 2022, Version 2
This content is a preprint and has not undergone peer review at the time of posting.

Abstract

Methods for the real-time monitoring of the substrate acceptance of modified nucleotides by DNA polymerases are in high demand. In a step towards this aim, we have incorporated ferrocene-based abasic nucleotides into DNA templates and evaluated their compatibility with enzymatic synthesis of unmodified and modified DNA. All canonical nucleotides can be incorporated opposite ferrocene sites with a strong preference for purines. DNA polymerases with lesion-bypass capacity such as Dpo4 permit to resume DNA synthesis beyond the site of incorporation. Modified purine nucleotides can readily be incorporated opposite ferrocene basic site analogs, while pyrimidine nucleotides decorated with simple side-chains are also readily tolerated. These findings open up directions for the design of electrochemical sensing devices for the monitoring of enzymatic synthesis of modified DNA.

Keywords

Ferrocene
DNA polymerases
Modified nucleic acids
Nucleoside triphosphates
abasic nucleoside analogues
Primer extension reactions

Supplementary materials

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Description
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Supporting Information
Description
Synthetic details, additional gel images, and characterization of compounds and modified oligonucleotides
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