Electron Transport by Molecular Motion of redox-DNA Strands: Unexpectedly Slow Rotational Dynamics of 20-mer ds-DNA Chains End-Grafted onto Surfaces via C₆ Linkers

Abstract

The dynamics of electron transport within molecular layers of 3'-ferrocenylated 20-mer oligonucleotide, 5'-thiol end-grafted onto gold electrode surfaces via a six-carbon (C6) linker, is studied by cyclic voltammetry. Single-stranded Fc-DNA layers are observed to behave as diffusionless systems reflecting the rapid dynamics of the ssDNA strand. Following hybridization, the Fc-dsDNA-C6 layers give rise to a characteristic cyclic voltammetry behavior evidencing that the Fc head is animated by a purely diffusional motion, which is ascribed to free rotation of the rigid DNA duplex around its C6 anchoring linker. A model, describing the motion of the Fc head as resulting from hinge motion of the DNA duplex, is developed allowing the motional dynamics of the Fc-dsDNA-C6 chains to be quantified in terms of an apparent rotational diffusion coefficient, Dr. The value found for Dr is approximately 3-4 orders of magnitude slower than expected for free rotation of dsDNA in solution, pointing to a drastic motion-slowing role of the anchoring surface. Accessibility of the Fc head for the electron transfer at the electrode is also shown to modulate the apparent dsDNA dynamics. The dynamics of Fc-dsDNA-C 6 is found to be insensitive to the presence of a single mismatch in the middle of the strand, confirming that charge transport by dsDNA conduction (DNA CT) is not present for the systems studied here. However, electron transport by free hinge motion of the dsDNA chain is shown to be fast enough to, a priori, compete favorably with DNA CT.

Metal-containing peptide nucleic acid conjugates

“…This is especially true for short C 2 anchoring linkers. 183 In contrast, Fc-carrying DNA layers, which are attached to the electrode via longer C 6 anchoring linkers, allow free rotation of double-stranded layers.…”

Detection of Mismatched Duplexes by Synchronizing the Pulse Potential Frequency with the Dynamics of Ferrocene/Isoquinoline Conjugate‐Connected DNA Probes Immobilized onto Electrodes

“…In relation to this finding, Anne et al already reported, on the basis of fast cyclic voltammetry (CV) analyses, that charge-transport abilities of redox-modified, end-anchored DNA duplexes could be explained by the elastic bending of the duplexes toward the electrode surfaces. [25][26][27][28] Herein we present the relationship between the pulse potential frequencies of SWV and the anodic currents for the duplexes from the ferrocene/isoquinoline conjugate-connected probes, and declare that single-base-mismatched duplexes show enhanced bending elasticity compared with fully Keywords: bending elasticity · DNA · electrochemistry · single nucleotide polymorphisms · voltammetry Abstract: Cyclic voltammetry was performed at various scan rates for the duplexes from ferrocene/isoquinoline conjugate-connected DNA probes on gold electrodes. The relationship between the observed currents and the scan rates disclosed the enhanced bending elasticity of the mismatched duplexes compared with the fully matched duplexes.…”

Nucleotides and Nucleic Acids; Oligo- and Polynucleotides

“…If the linker is long and flexible then the signal acquired reflects the random motion of the oligonucleotide attached to the surface, whilst the electrochemical signal can be attenuated by bending of the duplex. 521 Charge transport does not require a contiguous backbone, as oligonucleotides with sticky ends are still able to transport charge over long distances despite the break in the phosphate backbone. 522 Charge transport is inhibited by low pH and by disruption of a duplex by a triple strand.…”