Dynamics of Electron Transport by Elastic Bending of Short DNA Duplexes. Experimental Study and Quantitative Modeling of the Cyclic Voltammetric Behavior of 3‘-Ferrocenyl DNA End-Grafted on Gold

Abstract

The dynamics of electron transport within a molecular monolayer of 3'-ferrocenylated-(dT)(20) strands, 5'-thiol end-grafted onto gold electrode surfaces via a short C2-alkyl linker, is analyzed using cyclic voltammetry as the excitation/measurement technique. It is shown that the single-stranded DNA layer behaves as a diffusionless system, due to the high flexibility of the ss-DNA chain. Upon hybridization by the fully complementary (dA)(20) target, the DNA-modified gold electrode displays a highly unusual voltammetric behavior, the faradaic signal even ultimately switching off at a high enough potential scan rate. This remarkable extinction phenomenon is qualitatively and quantitatively justified by the model of elastic bending diffusion developed in the present work which describes the motion of the DNA-borne ferrocene moiety as resulting from the elastic bending of the duplex DNA toward and away from the electrode surface. Its use allows us to demonstrate that the dynamics of electron transport within the hybridized DNA layer is solely controlled by the intrinsic bending elasticity of ds-DNA. Fast scan rate cyclic voltammetry of end-grafted, redox-labeled DNA layers is shown to be an extremely efficient method to probe the bending dynamics of short-DNA fragments in the submillisecond time range. The persistence length of the end-anchored ds-DNA, a parameter quantifying the flexibility of the nanometer-long duplex, can then be straightforwardly and accurately determined from the voltammetry data.

Metal-containing peptide nucleic acid conjugates

“…Demaille, Anne and co-workers investigated the behaviour of Fc-carrying ssDNA and dsDNA layers. 181,182 In cyclic voltammetry, ssFc-DNA layers are described as diffusionless systems with high flexibility and rapid dynamics. After hybridisation, the voltammetric behaviour is explained by the so-called elastic bending diffusion model.…”

DNA probe modified with 3-iron bis(dicarbollide) for electrochemical determination of DNA sequence of Avian Influenza Virus H5N1

“…Such a change causes increase of distance between redox active label covalently attached to the probe from the surface of electrode. In consequence, the increase of electrons transfer resistance was observed (Anne et al 2006;Aoki et al, 2010;Farjami et al, 2011;Lai et al, 2006;Lubin et.al, 2009;Pavlovic et al, 2008;Yang et al, 2010). Such a system is called "on-off" mode of the electrochemical signal.…”

Electrochemical switching of the flavoprotein dodecin at gold surfaces modified by flavin-DNA hybrid linkers

“…50 This model is not in contradiction to the observation that single mismatches in the ds-DNA may affect the ET characteristics since the bending elasticity of ds-DNA should be highly sensitive to the base sequence, mismatch, or improper pairing. 50 The elastic bending diffusion model could help to understand why in this work ET was not observed when the Tarlov procedure was applied. In line with this model, the following explanation is suggested: after the formation of a dense and highly ordered monolayer, it should not be possible for the flavin redox centers to approach the electrode surface close enough for ET.…”

“…As a result of electrochemical studies on a ds-DNA monolayer of 20 base pairs equipped with a ferrocenyl head group, it has been suggested that ET occurs directly between the ferrocenyl head and the electrode without any contribution of the DNA base stack. 44,50 ET is only possible due to the elastic bending motion of DNA, and an elastic bending diffusion model has been developed. 50 This model is not in contradiction to the observation that single mismatches in the ds-DNA may affect the ET characteristics since the bending elasticity of ds-DNA should be highly sensitive to the base sequence, mismatch, or improper pairing.…”

“…44,50 ET is only possible due to the elastic bending motion of DNA, and an elastic bending diffusion model has been developed. 50 This model is not in contradiction to the observation that single mismatches in the ds-DNA may affect the ET characteristics since the bending elasticity of ds-DNA should be highly sensitive to the base sequence, mismatch, or improper pairing. 50 The elastic bending diffusion model could help to understand why in this work ET was not observed when the Tarlov procedure was applied.…”