Biological and Medicinal Chemistry

Ferrocene as an electrochemical reporting surrogate of abasic sites in DNA

Authors

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.

Version notes

Small error in Figure 6 was corrected

Content

Thumbnail image of Manuscript.pdf

Supplementary material

Thumbnail image of SupportingInformation.pdf
Supporting Information
Synthetic details, additional gel images, and characterization of compounds and modified oligonucleotides