3.6.1. Polishing and Cleaning 2663 3.6.2. Vacuum and Heat Treatments 2664 3.6.3. Carbon Electrode Activation 2665 3.7. Summary and Generalizations 2666 4. Advanced Carbon Electrode Materials 2666 4.1. Microfabricated Carbon Thin Films 2666 4.2. Boron-Doped Diamond for Electrochemistry 2668 4.3. Fibers and Nanotubes 2669 4.4. Carbon Composite Electrodes 2674 5. Carbon Surface Modification 2675 5.1. Diazonium Ion Reduction 2675 5.2. Thermal and Photochemical Modifications 2679 5.3. Amine and Carboxylate Oxidation 2680 5.4. Modification by “Click” Chemistry 2681 6. Synopsis and Outlook 2681 7. Acknowledgments 2682 8. References 2682

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Advanced carbon electrode materials for molecular electrochemistry.

Electrochemistry-based sensors offer sensitivity, selectivity and low cost for the detection of selected DNA sequences or mutated genes associated with human disease. DNA-based electrochemical sensors exploit a range of different chemistries, but all take advantage of nanoscale interactions between the target in solution, the recognition layer and a solid electrode surface. Numerous approaches to electrochemical detection have been developed, including direct electrochemistry of DNA, electrochemistry at polymer-modified electrodes, electrochemistry of DNA-specific redox reporters, electrochemical amplifications with nanoparticles, and electrochemical devices based on DNA-mediated charge transport chemistry.

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Electrochemical DNA sensors

A DNA array detection method is reported in which the binding of oligonucleotides functionalized with gold nanoparticles leads to conductivity changes associated with target-probe binding events. The binding events localize gold nanoparticles in an electrode gap; silver deposition facilitated by these nanoparticles bridges the gap and leads to readily measurable conductivity changes. An unusual salt concentration-dependent hybridization behavior associated with these nanoparticle probes was exploited to achieve selectivity without a thermal-stringency wash. Using this method, we have detected target DNA at concentrations as low as 500 femtomolar with a point mutation selectivity factor of approximately 100,000:1.

Array-based electrical detection of DNA with nanoparticle probes

Transition-Metal-Catalyzed C−S, C−Se, and C−Te Bond Formation via Cross-Coupling and Atom-Economic Addition Reactions

Bioorganometallic Chemistry of Ferrocene

Electron-transfer rates and electronic coupling factors for ferrocene groups attached to gold electrodes via oligo(phenylethynyl) “molecular wire” bridges of variable length and structure are reported. Attachment to gold was achieved via thiol groups at the end of the bridge opposite the ferrocene. Bridge structures were designed to promote strong coupling between gold and ferrocene, thereby promoting rapid electron transport over long distances. The effects of bridge length and of substituents on the phenyl rings in the bridge were addressed. Bridges containing between three and six phenylethynyl units were studied, and a “beta” value of 0.36 A-1 describing the exponential distance dependence of bridge-mediated electron-transfer rates was obtained. The effect on the rates of adding two propoxy groups onto one of the phenyl rings in the bridge was examined and found to be minimal. The standard electron-transfer rate constant of 350 s-1 obtained for the adsorbate with the longest bridge (six phenylethynyl ...

Electron Transfer at Electrodes through Conjugated “Molecular Wire” Bridges

Genotyping and gene-expression monitoring is critical to the study of the association between genetics and drug response (pharmacogenomics) and the association of sequence variation with heritable phenotypes. Recently, we developed an entirely electronic method for the detection of DNA hybridization events by the site-specific incorporation of ferrocenyl derivatives into DNA oligonucleotides. To perform rapid and accurate point mutation detection employing this methodology, two types of metal-containing signaling probes with varying redox potentials are required. In this report we describe a new ferrocene-containing phosphoramidite 9 that provides a range of detectable redox potentials. Using automated DNA/RNA synthesis techniques the two ferrocenyl complexes were inserted at various positions along oligonucleotide probes. Thermal stability analysis of these metal-containing DNA oligonucleotides indicates that incorporation of 9 resulted in no destabilization of the duplex. A mixture of oligonucleotides containing compounds 9 and I was analyzed by alternating current voltammetry (ACV) monitored at the 1st harmonic. The data demonstrate that the two ferrocenyl oligonucleotide derivatives can be distinguished electrochemically. A CMS-DNA array was prepared on an array of gold electrodes on a printed circuit board substrate with a self-assembled mixed monolayer, coupled to an electronic detection system. Experiments for the detection of a single-base match utilizing two signaling probes were carried out. The results demonstrate that rapid and accurate detection of a single-base mismatch can be achieved by using these dual-signaling probes on CMS-DNA chips.

Electronic Detection of Single-Base Mismatches in DNA with Ferrocene-Modified Probes

A series of phenylethynyl oligomers (I−V) possessing a ferrocene and thiol at each termini have been synthesized. These oligomers have been designed to overcome the inherent insolubility of this class of complexes by substitution at the phenyl groups with methyl and propoxy substituents. Several new reactions for preparing arenethiol-protected compounds are described. Interestingly, the generation of an arenethiol anion during base- or fluoride-catalyzed deprotection has been characterized.

Soluble Ferrocene Conjugates for Incorporation into Self-Assembled Monolayers.

The study of energy and electron-transfer processes through DNA duplexes and the development of DNA hybridization probes and electrochemical sensors have resulted in the incorporation of numerous transition-metal complexes into DNA oliognucleotides. These include ruthenium, osmium, iron, rhodium, and copper complexes. Ferrocene (Fc) and its derivatives are attractive electrochemical probes because of their stability and convenient synthetic chemistry. Fc-containing DNA oligonucleotides have been prepared by attaching ferrocenyl moieties to the 5‘ termini through either solid-phase synthesis using phosphoramidites or by reacting suitable ferrocenyl derivatives with end-functionalized oligonucleotides.

Uridine-Conjugated Ferrocene DNA Oligonucleotides: Unexpected Cyclization Reaction of the Uridine Base

The present invention is directed to methods and compositions for the use of self-assembled monolayers to electronically detect nucleic acids, particularly alterations such as nucleotide substitutions (mismatches) and single nucleotide polymorphisms (SNPs).

Changjun Yu

Papers

Electron Transfer at Electrodes through Conjugated “Molecular Wire” Bridges

Electronic Detection of Single-Base Mismatches in DNA with Ferrocene-Modified Probes

Soluble Ferrocene Conjugates for Incorporation into Self-Assembled Monolayers.

Uridine-Conjugated Ferrocene DNA Oligonucleotides: Unexpected Cyclization Reaction of the Uridine Base

Sequence determination of nucleic acids using electronic detection