Ferrocene as a potential electrochemical reporting surrogate of abasic sites in DNA

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...

Interrogating Aptamer Chemical Space Through Modified Nucleotide Substitution Facilitated by Enzymatic DNA Synthesis

“…Preparation of (2‐azidopropyl)ferrocene [27] 12 precursor of triphosphate 3 was prepared according to the synthetic protocol outlined in Scheme 1. Briefly, commercially available ferrocene carboxaldehyde 7 was converted to the corresponding ferrocene unsaturated ester 8 by means of a Wittig‐Horner reaction [28] . The resulting ester 8 was then subjected to catalytic hydrogenation yielding saturated ester 9 [29] .…”

“…Briefly, commercially available ferrocene carboxaldehyde 7 was converted to the corresponding ferrocene unsaturated ester 8 by means of a Wittig-Horner reaction. [28] The resulting ester 8 was then subjected to catalytic hydrogenation yielding saturated ester 9. [29] Reduction with LiAlH 4 produced the corresponding alcohol 10 which was subjected to two consecutive S N 2-type of reactions yielding the desired azide building block 12.…”

Organometallic modification confers oligonucleotides new functionalities

“…The properties of some organometallic complexes make them useful as labels to facilitate imaging of oligonucleotides or elucidation of their secondary structures. The field is dominated by studies on ferrocene-labeled electrochemical probes and sensors [73][74][75][76][77] but recently luminescent organometallic labels 119,171 have also received attention.…”

“…67 Analogously, while a number of redox active organic compounds potentially useful as electrochemical labels have been reported, [68][69][70][71][72] ferrocene is by far the most widely employed moiety for this purpose. [73][74][75][76][77] Artificial ribonucleases bearing a transition metal ion at the catalytic core tend to be more active than their purely organic counterparts. [78][79][80][81][82][83] For converting DNA into a nanowire, coordination of an array of metal ions appears all but indispensable.…”

Enzymatic Synthesis of Vancomycin-Modified DNA

“…To form the connection between vancomycin and the aptamer we opted to use the copper(I)-catalyzed azide-alkyne cycloaddition (CuAAC) reaction, since this chemistry has previously been used to generate modified vancomycin derivatives [13]. In addition to this, nucleotides bearing a triazole-connecting linker arm are compatible with enzymatic DNA synthesis [43,44] and aptamer selection [45][46][47]. The synthesis of the vancomycin-bearing deoxyuridine triphosphate dU Van TP (Figure 2) involved synthesis of the previously reported azide-modified vancomycin [13] and CuAAC reaction with 5-ethynyl-dUTP (EdUTP) [48] under standard conditions (see Materials and Methods (Section 4.1) and Supplementary Materials for full synthetic details).…”