DNA sensing by electrocatalysis with hemoglobin

Electrocatalysis offers a means of electrochemical signal amplification, yet in DNA-based sensors, electrocatalysis has required high-density DNA films and strict assembly and passivation conditions. Here, we describe the use of hemoglobin as a robust and effective electron sink for electrocatalysis in DNA sensing on low-density DNA films. Protein shielding of the heme redox center minimizes direct reduction at the electrode surface and permits assays on low-density DNA films. Electrocatalysis with methylene blue that is covalently tethered to the DNA by a flexible alkyl chain linkage allows for efficient interactions with both the base stack and hemoglobin. Consistent suppression of the redox signal upon incorporation of a single cytosine-adenine (CA) mismatch in the DNA oligomer demonstrates that both the unamplified and the electrocatalytically amplified redox signals are generated through DNA-mediated charge transport. Electrocatalysis with hemoglobin is robust: It is stable to pH and temperature variations. The utility and applicability of electrocatalysis with hemoglobin is demonstrated through restriction enzyme detection, and an enhancement in sensitivity permits femtomole DNA sampling

DNA Electrochemistry with Tethered Methylene Blue

Methylene blue (MB′), covalently attached to DNA through a flexible C_12 alkyl linker, provides a sensitive redox reporter in DNA electrochemistry measurements. Tethered, intercalated MB′ is reduced through DNA-mediated charge transport; the incorporation of a single base mismatch at position 3, 10, or 14 of a 17-mer causes an attenuation of the signal to 62 ± 3% of the well-matched DNA, irrespective of position in the duplex. The redox signal intensity for MB′–DNA is found to be least 3-fold larger than that of Nile blue (NB)–DNA, indicating that MB′ is even more strongly coupled to the π-stack. The signal attenuation due to an intervening mismatch does, however, depend on DNA film density and the backfilling agent used to passivate the surface. These results highlight two mechanisms for reduction of MB′ on the DNA-modified electrode: reduction mediated by the DNA base pair stack and direct surface reduction of MB′ at the electrode. These two mechanisms are distinguished by their rates of electron transfer that differ by 20-fold. The extent of direct reduction at the surface can be controlled by assembly and buffer conditions

Multiplexed Electrochemistry of DNA-Bound Metalloproteins

Here we describe a multiplexed electrochemical characterization of DNA-bound proteins containing [4Fe-4S] clusters. DNA-modified electrodes have become an essential tool for the characterization of the redox chemistry of DNA repair proteins containing redox cofactors, and multiplexing offers a means to probe different complex samples and substrates in parallel to elucidate this chemistry. Multiplexed analysis of endonuclease III (EndoIII), a DNA repair protein containing a [4Fe-4S] cluster known to be accessible via DNA-mediated charge transport, shows subtle differences in the electrochemical behavior as a function of DNA morphology. The peak splitting, signal broadness, sensitivity to π-stack perturbations, and kinetics were all characterized for the DNA-bound reduction of EndoIII on both closely and loosely packed DNA films. DNA-bound EndoIII is seen to have two different electron transfer pathways for reduction, either through the DNA base stack or through direct surface reduction; closely packed DNA films, where the protein has limited surface accessibility, produce electrochemical signals reflecting electron transfer that is DNA-mediated. Multiplexing furthermore permits the comparison of the electrochemistry of EndoIII mutants, including a new family of mutations altering the electrostatics surrounding the [4Fe-4S] cluster. While little change in the midpoint potential was found for this family of mutants, significant variations in the efficiency of DNA-mediated electron transfer were apparent. On the basis of the stability of these proteins, examined by circular dichroism, we propose that the electron transfer pathway can be perturbed not only by the removal of aromatic residues but also through changes in solvation near the cluster

Intraduplex DNA-Mediated Electrochemistry of Covalently Tethered Redox-Active Reporters

Intraduplex DNA-mediated reduction is established as a general mechanism for the reduction of distally bound stacked redox-active species covalently tethered to DNA through flexible alkane linkages. Methylene Blue (MB), Nile Blue (NB), and Anthraquinone (AQ) were covalently tethered to DNA with three different covalent linkages. Using these reporters DNA electrochemistry was shown to be both DNA-mediated and intra-, rather than inter-, duplex. Significantly, the charge transport pathway occurring through the DNA π-stack is established by using an intervening AC mismatch to break this path. The fact that the DNA-mediated reduction of MB occurs primarily via intraduplex intercalation is established through varying the proximity and integrity of the neighboring duplex DNA

Solid phase synthesis of functionalised SAM-forming alkanethiol-oligoethyleneglycols

We present an efficient solid phase synthesis methodology that provides easy access to a range of functionalised long-chain alkanethiol-oligoethyleneglycols that form well-defined self-assembled monolayers on gold and are compatible with pre- or post-assembly conjugation of (bio)molecules. We demonstrate the versatility of our synthetic route by synthesising LCAT-OEGs with a range of functional moieties, including peptides, electro-active redox groups, chemical handles for post-assembly conjugation of (bio)molecules, and demonstrate the application of our LCAT-OEG monolayers in immunosensing, where they show good biocompatibility with minimal biofouling

Probing molecular interactions with methylene blue derivatized self-assembled monolayers

The emergence of stratified and personalised medicine and the associated need for highly multiplexed detection strategies are driving the development of innovative sensor technology. Electronic immunosensor arrays capable of label-free and highly parallel monitoring of ligand binding have emerged as a particularly promising technology capable of meeting these new diagnostic challenges. In this study, we present an approach for interrogating molecular interactions electronically using redox active molecular monolayers. Specifically, we have synthesised self-assembled molecular monolayers assembled from long-chain alkanethiols (LCAT) incorporating oligoethyleneglycol (OEG) linkers that can be derivatized with a range of functional groups, including the redox active molecule methylene blue. Critically, we show that the electron transport properties of this redox-active monolayer are highly sensitive to the electrochemical environment, including the local concentration of protons and the electrostatic potential at the plane of electron transfer. Using a combination of cyclic voltammetry and QCM-D to study in detail the behaviour of the monolayer during functionalisation and analyte binding, we demonstrate that these redox properties can be exploited for the electrochemical sensing of molecular interactions (biotin–avidin in our case) on SAMs. Given the versatility of LCAT-OEG monolayers, in terms of linker lengths, choice of functional group, and ability to create mixed component layers and the straight-forward assembly of mixed SAMs of high quality, our electrochemical sensing approach forms an excellent and generic label-free platform for probing a wide range of molecular interactions