Mechanistic studies of Fc-PNA(⋅DNA) surface dynamics based on the kinetics of electron-transfer processes

Activationless Electron Transfer of Redox-DNA in Electrochemical Nanogaps

Our recent discovery of decreased reorganization energy in electrode-tethered redox-DNA systems prompts inquiries into the origin of this phenomenon and suggests its potential use to lower the activation energy of electrochemical reactions. Here, we show that the confinement of the DNA chain in a nanogap amplifies this effect to an extent to which it nearly abolishes the intrinsic activation energy of electron transfer. Employing electrochemical atomic force microscopy (AFM-SECM), we create sub-10 nm nanogaps between a planar electrode surface bearing end-anchored ferrocenylated DNA chains and an incoming microelectrode tip. The redox cycling of the DNA's ferrocenyl (Fc) moiety between the surface and the tip generates a measurable current at the scale of ∼10 molecules. Our experimental findings are rigorously interpreted through theoretical modeling and original molecular dynamics simulations (Q-Biol code). Several intriguing findings emerge from our investigation: (i) The electron transport resulting from DNA dynamics is many times faster than predicted by simple diffusion considerations. (ii) The current in the nanogap is solely governed by the electron transfer rate at the electrodes. (iii) This rate rapidly saturates as overpotentials applied to the nanogap electrodes increase, implying near-complete suppression of the reorganization energy for the oxidation/reduction of the Fc heads within confined DNA. Furthermore, evidence is presented that this may constitute a general, previously unforeseen, behavior of redox polymer chains in electrochemical nanogaps.

Electrochemical response of surface-attached redox DNA governed by low activation energy electron transfer kinetics

We demonstrate, using high scan rate cyclic voltammetry and molecular dynamics simulations, that the electrochemical response of electrode-attached redox DNA is governed by low reorganization energy electron transfer kinetics.

Metallic surface dynamics of genomic DNA and its nitrogenous bases: SERS assessment and theoretical considerations

The dynamics of genomic DNA and its nucleobases at a silver surface were explored using surface-enhanced Raman spectroscopy (SERS) and ab initio Verlet-type dynamics, respectively. The bands observed had full widths at half-maximum (FWHMs) in the wavenumber range 10-29 cm^-1. (Sub)picosecond molecular dynamics with global relaxation times of 0.37-1.06 ps were noted. Furthermore, the on-surface ab initio dynamics of the DNA bases were examined using DFT with a Verlet-type algorithm. The results attained for these ergodic dynamic systems describe real systems quite well and could therefore be correlated with corresponding experimental data.

Electron Transfer Processes in Ferrocene-Modified Poly(ethylene glycol) Monolayers on Electrodes

Electrochemistry is a powerful tool to study self-assembled monolayers. Here, we modified cystamine-functionalized electrodes with different lengths of linear poly(ethylene glycol) (PEG) polymers end-functionalized with a redox-active ferrocene (Fc) group. The electron transport properties of the Fc probes were studied using cyclic voltammetry. The Fc moiety attached to the shortest PEG (M_n = 250 Da) behaved as a surface-confined species, and the homogeneous electron transfer rate constants were determined. The electron transfer of the ferrocene group on the longer PEGs (M_n = 3.4, 5, and 10 kDa) was shown to be driven by diffusion. For low surface densities, where the polymer exists in the mushroom conformation, the diffusion coefficients (D) and rate constants were increasing with polymer length. In the loose brush conformation, where the polymers are close enough to interact with each other, the thickness of the layers (e) was unknown and a parameter D^1/2/e was determined. This parameter showed no dependence on surface density and an increase with polymer length.

Electrochemistry of Redox-Active Guest Molecules at β-Cyclodextrin-Functionalized Silicon Electrodes

Functionalization of silicon-based sensing devices with self-assembled receptor monolayers offers flexibility and specificity towards the requested analyte as well as the possibility of sensor reuse. As electrical sensor performance is determined by electron transfer, we functionalized H-terminated silicon substrates with β-cyclodextrin (β-CD) molecules to investigate the electronic coupling between these host monolayers and the substrate. A trivalent (one ferrocene and two adamantyl moieties), redox-active guest was bound to the β-CD surface with a coverage of about 10-11 mol/cm2 and an overall binding constant of 1.5⋅109 M-1. This packing density of the host monolayers on silicon is lower than that for similar β-CD monolayers on gold. The monolayers were comparable on low-doped p-type and highly doped p++ substrates regarding their packing density and the extent of oxide formation. Nonetheless, the electron transfer was more favorable on p++ substrates, as shown by the lower values of the peak splitting and peak widths in the cyclic voltammograms. These results show that the electron-transfer rate on the host monolayers is not only determined by the composition of the monolayer, but also by the doping level of the substrate.

Electron Transfer Mediated by Surface-Tethered Redox Groups in Nanofluidic Devices

Electrochemistry provides a powerful sensor transduction and amplification mechanism that is highly suited for use in integrated, massively parallelized assays. Here, the cyclic voltammetric detection of flexible, linear poly(ethylene glycol) polymers is demonstrated, which have been functionalized with redox-active ferrocene (Fc) moieties and surface-tethered inside a nanofluidic device consisting of two microscale electrodes separated by a gap of <100 nm. Diffusion of the surface-bound polymer chains in the aqueous electrolyte allows the redox groups to repeatedly shuttle electrons from one electrode to the other, resulting in a greatly amplified steady-state electrical current. Variation of the polymer length provides control over the current, as the activity per Fc moiety appears to depend on the extent to which the polymer layers of the opposing electrodes can interpenetrate each other and thus exchange electrons. These results outline the design rules for sensing devices that are based on changing the polymer length, flexibility, and/or diffusivity by binding an analyte to the polymer chain. Such a nanofluidic enabled configuration provides an amplified and highly sensitive alternative to other electrochemical detection mechanisms.

Influence of the Thiol Anchor on the Orientation of Surface-Grafted dsDNA Assemblies

The orientation of surface-grafted dsDNA assemblies relative to the surface depends strongly on the nature of the employed thiol anchor. This was shown by ssDNA capture probe strands of 20 bases grafted to a gold surface by three dithiane rings or a single mercaptohexyl group. The capture probe strands were hybridized to one end of complementary ssDNA strands (target) comprising 40, 60, or 80 bases (T₄₀ , T₆₀ , and T₈₀ ). At the other end of the targets a fluorophore-labeled reporter probe ssDNA strand of 20 bases was hybridized. To stiffen the DNA assemblies, the targets T₆₀ and T₈₀ were further hybridized to ssDNA patches of 20 or 40 bases. Whether the fluorescence intensity, and thus the distance between surface and fluorophore, increases or decreases with increasing target length depends on the thiol anchor. Attempts were made to heal the nicks that are present in the formed dsDNA assemblies by ligation. For enzymatic ligation, the presence of a phosphate at the 5'-end of the reporter probe and a patch is required, which may also influence the fluorescence intensity.

Modulation of charge transport across double-stranded DNA by the site-specific incorporation of copper bis-phenanthroline complexes

The site-specific incorporation of transition-metal complexes within DNA duplexes, followed by their immobilization on a gold surface, was studied by electrochemistry to characterize their ability to mediate charge. Cyclic voltammetry, square-wave voltammetry, and control experiments were carried out on fully matched and mismatched DNA strands that are mono- or bis-labeled with transition-metal complexes. These experiments are all consistent with the ability of the metal centers to act as a redox probe that is well coupled to the DNA π-stack, allowing DNA-mediated charge transport.

Nucleic-acid recognition interfaces: how the greater ability of RNA duplexes to bend towards the surface influences electrochemical sensor performance

Faster electron transfer kinetics were observed for redox labelled nucleic-acids duplexes containing RNA, suggesting a more flexibility, compared to DNA/DNA.

Preparation of metal-containing peptide nucleic acid bioconjugates on the solid phase

Peptide nucleic acids (PNAs) are a class of artificial DNA/RNA analogues that have unique physicochemical properties, which include a high chemical stability, resistance to nucleases and proteases, and higher mismatch sensitivity than DNA. PNAs were initially anticipated to be useful for application in antisense and antigene therapies; however, their poor cellular uptake has limited their use for such purposes in the "real world." Recently, it has been shown that the addition of metal complexes to these oligonucleotide analogues could open up new avenues for their utilization in various research fields. Such metallo-constructs have shown great promise, for a diverse range of applications, most notably in the biosensing area. In this book chapter, we report on the recent synthetic advances towards the preparation of these "(multi-)metallic PNAs" on the solid phase.

Di-heterometalation of thiol-functionalized peptide nucleic acids

As a proof-of-principle, two hetero-bimetallic PNA oligomers containing a ruthenium(II) polypyridyl and a cyclopentadienyl manganese tricarbonyl complex have been prepared by serial combination of solid-phase peptide coupling and in-solution thiol chemistry. Solid-phase N-terminus attachment of Ru(II)-polypyridyl carboxylic acid derivative, C1, onto the thiol-functionalized PNA backbone (H-a-a-g-t-c-t-g-c-linker-cys-NH 2) has been performed by standard peptide coupling method. As two parallel approaches, the strong affinity of thiols for maleimide and haloacetyl group has been exploited for subsequent post-SPPS addition of cymantrene-based organometallic cores, C2 and C3. Michael-like addition and thioether ligation of thiol functionalized PNA1 (H-gly-a-a-g-t-c-t-g-c-linker-cys-NH 2) and PNA2 (C1-a-a-g-t-c-t-g-c-linker-cys-NH 2) to cymantrene maleimide and chloroacetyl derivatives, C2 and C3, respectively, has been performed. The synthesized ruthenium(II)-cymantrenyl PNA oligomers have been characterized by mass spectrometry (ESI-MS) and IR spectroscopy. The distinct Mn-CO vibrational IR stretches, between 1,924-2,074 cm (-1) , have been used as markers to confirm the presence of cymantrenyl units in the PNA sequences and the purity of the HPLC-purified PNA thioethers assessed using LC-MS.

A ruthenocene-PNA bioconjugate--synthesis, characterization, cytotoxicity, and AAS-detected cellular uptake

Labeling of peptide nucleic acids (PNA) with metallocene complexes is explored herein for the modulation of the analytical characteristics, as well as biological properties of PNA. The synthesis of the first ruthenocene-PNA conjugate with a dodecamer, mixed-sequence PNA is described, and its properties are compared to a ferrocene-labeled analogue as well as an acetylated, metal-free derivative. The synthetic characteristics, chemical stability, analytical and thermodynamic properties, and the interaction with cDNA were investigated. Furthermore, the cytotoxicity of the PNA conjugates is determined on HeLa, HepG2, and PT45 cell lines. Finally, the cellular uptake of the metal-containing PNAs was quantified by high-resolution continuum source atomic absorption spectrometry (HR-CS AAS). An unexpectedly high cellular uptake to final concentrations of 4.2 mM was observed upon incubation with 50 μM solutions of the ruthenocene-PNA conjugate. The ruthenocene label was shown to be an excellent label in all respects, which is also more stable than its ferrocene analogue. Because of its high stability, low toxicity, and the lack of a natural background of ruthenium, it is an ideal choice for bioanalytical purposes and possible medicinal and biological applications like, e.g., the development of gene-targeted drugs.

Impact of single basepair mismatches on electron-transfer processes at Fc-PNA⋅DNA modified gold surfaces

Gold-surface grafted peptide nucleic acid (PNA) strands, which carry a redox-active ferrocene tag, present unique tools to electrochemically investigate their mechanical bending elasticity based on the kinetics of electron-transfer (ET) processes. A comparative study of the mechanical bending properties and the thermodynamic stability of a series of 12-mer Fc-PNA⋅DNA duplexes was carried out. A single basepair mismatch was integrated at all possible strand positions to provide nanoscopic insights into the physicochemical changes provoked by the presence of a single basepair mismatch with regard to its position within the strand. The ET processes at single mismatch Fc-PNA⋅DNA modified surfaces were found to proceed with increasing diffusion limitation and decreasing standard ET rate constants k(0) when the single basepair mismatch was dislocated along the strand towards its free-dangling Fc-modified end. The observed ET characteristics are considered to be due to a punctual increase in the strand elasticity at the mismatch position. The kinetic mismatch discrimination with respect to the fully-complementary duplex presents a basis for an electrochemical DNA sensing strategy based on the Fc-PNA⋅DNA bending dynamics for loosely packed monolayers. In a general sense, the strand elasticity presents a further physicochemical property which is affected by a single basepair mismatch which may possibly be used as a basis for future DNA sensing concepts for the specific detection of single basepair mismatches.