Facile Synthesis and Detailed Characterization of a New Ferrocenyl Uracil Peptide Nucleic Acid Monomer

A new ferrocenyl uracil peptide nucleic acid (PNA) monomer, tert-butyl-2-(N-(2-(((9H-floren-9-yl)methoxy)carbonylamino)ethyl)-2-(5-(N-ferrocenylmethylbenzamido)-2,4-dioxo-3,4-dihydropyrimidin-1(2H)-yl)acetamido)acetate (1), has been successfully prepared in good yield by a procedure involving
the one-pot reaction of the key synthon, 5-(ferrocenylmethylamino)pyrimidine-2,4(1H,3H)-dione (4), itself
prepared from the reaction of (ferrocenylmethyl)trimethylammonium iodide and 5-aminouracil, with
benzoyl chloride followed by ethyl bromoacetate. After hydrolysis of the ester, the acid was coupled
with a protected PNA backbone to generate 1. NMR spectroscopy showed that 1 hydrogen bonds
9-ethyladenine (EA) in a 1:1 mixture of CD3CN:CDCl3 with an association constant Ka of 70 M-1 at 30
°C. This value is comparable with those observed for model receptors and shows that the ferrocenyl
moiety of 1 does not hinder the hydrogen bonding of our new PNA monomer to the complementary
DNA base or if it does, not significantly. 1 is oxidized to 1+ with a reversible potential of +538 mV vs
the DMFc0/+ (decamethylferrocene) couple under voltammetric conditions in a 1:1 mixture of CH3CN:CHCl3 (0.1 M Bu4NPF6). For this reversible process, a slightly larger diffusion coefficient of 4.2 × 10-6
cm2·s-1 than usually found for these compounds was determined from these electrochemical studies,
which should be analytically useful as it will readily afford submicromolar voltammetric detection limits.