Electrocatalytic DNA Oxidation

Reduced Graphene Oxide-Oligonucleotide Interfaces: Understanding Based on Electrochemical Oxidation of Guanines

Investigation into the interactions between biomolecules DNA/RNA and carbon nanomaterials is very important for applications in bioassays and bioanalysis. Graphene and graphene oxide (GO) have been successfully adopted by exploiting the binding affinity difference between single-stranded oligonucleotides (ssDNA) and double-stranded oligonucleotides (dsDNA) to graphene sheets. In this work, we describe the electrochemical DNA oxidation with [Ru(bpy)₃]²⁺ to understand the interaction between dsDNA (and corresponding ssDNA) and reduced graphene oxide (rGO). The electrochemical oxidation rate of guanine bases of ssDNA bound to rGO by electrochemically generated [Ru(bpy)₃]³⁺ was much slower than those unbound to rGO. Our study revealed that ssDNA constrained on rGO was significantly protected from the electron transfer to [Ru(bpy)₃]³⁺ because of π,π-stacking interaction between nucleobases and rGO. On the other hand, the oxidation rates of 11-, 20-, and 27-mer dsDNA bound to rGO increased relative to those of dsDNA alone, demonstrating that the guanine bases of dsDNA on the interaction with rGO became more accessible to [Ru(bpy)₃]³⁺. Our electrochemical data illustrated that dsDNA could be totally or partially dehybridized and bind to rGO to form ssDNA/rGO. Furthermore, absorption, circular dichroism spectra, and fluorescence measurements of ethidium bromide using ssDNA and dsDNA with rGO supported the dehybridization of dsDNA in the presence of rGO.

Metabolic toxicity screening using electrochemiluminescence arrays coupled with enzyme-DNA biocolloid reactors and liquid chromatography-mass spectrometry

New chemicals or drugs must be guaranteed safe before they can be marketed. Despite widespread use of bioassay panels for toxicity prediction, products that are toxic to a subset of the population often are not identified until clinical trials. This article reviews new array methodologies based on enzyme/DNA films that form and identify DNA-reactive metabolites that are indicators of potentially genotoxic species. This molecularly based methodology is designed in a rapid screening array that utilizes electrochemiluminescence (ECL) to detect metabolite-DNA reactions, as well as biocolloid reactors that provide the DNA adducts and metabolites for liquid chromatography-mass spectrometry (LC-MS) analysis. ECL arrays provide rapid toxicity screening, and the biocolloid reactor LC-MS approach provides a valuable follow-up on structure, identification, and formation rates of DNA adducts for toxicity hits from the ECL array screening. Specific examples using this strategy are discussed. Integration of high-throughput versions of these toxicity-screening methods with existing drug toxicity bioassays should allow for better human toxicity prediction as well as more informed decision making regarding new chemical and drug candidates.

Nature of guanine oxidation in RNA via the flash-quench technique versus direct oxidation by a metal oxo complex

Oxidation of RNA can be effected by two different techniques: a photochemical, electron-transfer method termed "flash-quench" and direct oxidation by metal oxo complexes. The flash-quench method produces selective oxidation using a metal photosensitizer, tris(bipyridyl)ruthenium(III) trichloride (Ru(bpy)(3)(3+)), and quencher, pentaamminechlorocobalt(III) chloride (Co(NH(3))(5)Cl(2+)). We have optimized the flash-quench technique for the following RNAs: tRNA(Phe), human ferritin iron-responsive element (IRE), and a mutated human ferritin IRE. We have also employed a chemical footprinting technique involving the oxoruthenium(IV) complex (Ru(tpy)(bpy)O(2+) (tpy = 2,2',2''-terpyridine; bpy = 2,2'-bipyridine)) to oxidize guanine. Comparison of the two methods shows that the flash-quench technique provides a visualization of nucleotide accessibility for a static conformation of RNA while the Ru(tpy)(bpy)O(2+) complex selectively oxidizes labile guanines and gives a visualization of a composite of multiple conformations of the RNA structure.

Unlabeled hairpin DNA probe for electrochemical detection of single-nucleotide mismatches based on MutS-DNA interactions

The paper described a label-free assay for the detection of single-nucleotide mismatches in which an unlabeled hairpin DNA probe and a MutS protein conjugate (His6-MutS-linker peptide-streptavidin binding peptide (HMLS)) are exploited for the detection of mismatches by electrochemical impedance spectroscopy (EIS). We demonstrate this method for eight single-nucleotide mismatches. Upon hybridization of the target strand with the hairpin DNA probe, the stem-loop structure is opened forming a duplex DNA. In duplexes containing a single nucleotide mismatch, the mismatch is present at the solvent exposed side, enabling more effective HMLS recognition and binding. The binding event is evaluated by EIS and analyzed with the help of Randles' equivalent circuits. The differences in the charge transfer resistance DeltaR(CT) before and after protein binding to the duplex DNA allows the unequivocal detection of all eight single-nucleotide mismatches. DeltaR(CT) allows the discrimination of a C-A mismatch with the concentration of the target strand as low as 100 pM.

Label-free electrochemical detection of adenosine based on electron transfer from guanine bases in an adenosine-sensitive aptamer

The selective recognition of adenosine with an adenosine-sensitive oligonucleotide is studied via the electrochemical oxidation of guanine bases of the aptamer in solution, leading to a label-free voltammetric aptasensor based on the difference in the oxidative electron transfer rate.

Electrochemical biosensor featuring a two-enzyme pathway and DNA for screening toxic reactive metabolites of arylamines

We demonstrate for the first time a biosensor featuring a sequential two-enzyme pathway suitable to screen potentially toxic reactive metabolites generated during metabolism.

Synergistic metabolic toxicity screening using microsome/DNA electrochemiluminescent arrays and nanoreactors

Platforms based on thin enzyme/DNA films were used in two-tier screening of chemicals for reactive metabolites capable of producing toxicity. Microsomes were used for the first time as sources of cytochrome (cyt) P450 enzymes in these devices. Initial rapid screening involved electrochemiluminescent (ECL) arrays featuring spots containing ruthenium poly(vinylpyridine), DNA, and rat liver microsomes or bicistronically expressed human cyt P450 2E1 (h2E1). Cyt P450 enzymes were activated via the NADPH/reductase cycle. When bioactivation of substrates in the films gives reactive metabolites, they are trapped by covalent attachment to DNA bases. The rate of increase in ECL with enzyme reaction time reflects relative DNA damage rates. "Toxic hits" uncovered by the array were studied in structural detail by using enzyme/DNA films on silica nanospheres as "nanoreactors" to provide nucleobase adducts from reactive metabolites. The utility of this synergistic approach was demonstrated by estimating relative DNA damage rates of three mutagenic N-nitroso compounds and styrene. Relative enzyme turnover rates for these compounds using ECL arrays and LC-UV-MS correlated well with TD 50 values for liver tumor formation in rats. Combining ECL array and nanoreactor/LC-MS technologies has the potential for rapid, high-throughput, cost-effective screening for reactive metabolites and provides chemical structure information that is complementary to conventional toxicity bioassays.

Photoelectrochemical sensor for the rapid detection of in situ DNA damage induced by enzyme-catalyzed fenton reaction

Photoelectrochemical sensors were developed for the rapid detection of oxidative DNA damage induced by Fe2+ and H2O2 generated in situ by the enzyme glucose oxidase. The sensor is a multilayer film prepared on a tin oxide nanoparticle electrode by layer-by-layer self-assembly and is composed of separate layers of a photoelectrochemical indicator, DNA, and glucose oxidase. The enzyme catalyzes the formation of H2O2 in the presence of glucose, which then reacts with Fe2+ and generates hydroxyl radicals by the Fenton reaction. The radicals attack DNA in the sensor film, mimicking metal toxicity pathways in vivo. The DNA damage is detected by monitoring the change of photocurrent of the indicator. In one sensor configuration, a DNA intercalator, Ru(bpy)2(dppz)2+ (bpy = 2,2'-bipyridine, dppz = dipyrido[3,2-a:2',3'-c]phenazine), was employed as the photoelectrochemical indicator. The damaged DNA on the sensor bound less Ru(bpy)2(dppz)2+ than the intact DNA, resulting in a drop in photocurrent. In another configuration, ruthenium tris(bipyridine) was used as the indicator and was immobilized on the electrode underneath the DNA layer. After oxidative damage, the DNA bases became more accessible to photoelectrochemical oxidation than the intact DNA, producing a rise in photocurrent. Both sensors displayed substantial photocurrent change after incubation in Fe2+/glucose in a time-dependent manner. And the detection limit of the first sensor was less than 50 microM. The results were verified independently by fluorescence and gel electrophoresis experiments. When fully integrated with cell-mimicking components, the photoelectrochemical DNA sensor has the potential to become a rapid, high-throughput, and inexpensive screening tool for chemical genotoxicity.

Electrochemical behavior of neomycin at DNA-modified gold electrodes

Deoxyribonucleic acid (DNA) modified gold electrodes are prepared by the dry adsorptive method and the electrochemical behavior of neomycin and the influence of Pb(II) are studied by cyclic voltammetry, chronocoulometry, differential pulse voltammetry. It is found that in 0.01M phosphate-buffered saline (PBS) buffer solutions (pH 7.3) at DNA/Au electrode neomycin exhibits an irreversible cathodic peak (E(p)=0.489V), which is more positive and less sensitive compared with that at bare gold electrodes (E(p)=0.423V). In the presence of Pb(II) the peak shifts toward positive with its height increasing. Moreover, the peak height is linear to neomycin concentration over the range of 0.15-57microM. The interaction of Pb(II)-neomycin complex with calf thymus DNA is also studied by calculating the binding constants (K) of the Pb(II)-neomycin complex to DNA and binding site size (s) from voltammetric data (1.0x10(7)M(-1) and 4bp, respectively).

Chemical-induced unfolding of cofactor-free protein monitored by electrochemistry

Protein folding has been studied extensively with an aim to better understanding of the relationship between protein sequence, structure, and function. A large variety of techniques have been developed and utilized to probe protein conformation and folding/unfolding transition. In this report, electrochemical monitoring of urea-induced unfolding of a large cofactor-free protein, bovine serum albumin (BSA), is described. Enhanced electrochemical oxidation of tyrosine and tryptophan in free amino acids and in BSA was achieved on an indium tin oxide electrode by using an electron mediator, Os(bpy)2dppz (bpy = 2,2'-bipyridine, dppz = dipyrido[3,2-a:2',3'-c]phenazine). The oxidation current was used as a signal reporter in the monitoring of urea-induced BSA denaturation. At high urea concentrations, the electrochemical signal increased by 3-fold relative to the native protein. The increase is attributed to the closer contact between the oxidizable residues in the unfolded BSA and Os(bpy)2dppz. The degree of unfolding assessed by electrochemistry correlates well with the established fluorescence technique in the range of 0-10 M urea. The method can be used to investigate the unfolding process of other cofactor-free proteins.

Self-assembled monolayers of thiol-end-labeled DNA at mercury electrodes

We show for the first time that thiol-end-labeled oligodeoxynucleotides form self-assembled monolayer (SAM) at Hg electrodes. Changes in voltammetric signals due to cytosine and Hg-S bond reduction indicated changes in positioning of the HS-(TTC)(7) molecules at the electrode with increasing HS-(TTC)7 concentration from lying flat with respect to SAMs, forming upright-standing molecules. This SAM behaved as an insulator not allowing electron transfer between [Ru(NH3)6]3+ and the electrode. Different adsorption modes of thiolated and thiol-free DNAs were observed.

Photoelectrochemical Oxidation of DNA by Ruthenium Tris(bipyridine) on a Tin Oxide Nanoparticle Electrode

Selective photoelectrochemical oxidation of DNA was achieved by ruthenium tris(bipyridine) immobilized on a tin oxide nanoparticle electrode. The metal complex was covalently attached to a protein, avidin, which adsorbed strongly on the tin oxide electrode by electrostatic interaction. Upon irradiation with 473-nm light, anodic photocurrent was generated in a blank electrolyte and was enhanced significantly after addition of poly(guanadylic acid) (poly-G) into the electrolyte. The current increased progressively with the nucleotide concentration, suggesting the enhancement effect was related to poly-G. The action spectrum indicates that the photocurrent was initiated by light absorption of the ruthenium compound immobilized on the electrode. Among the various polynucleotides examined, poly-G produced the largest photocurrent increase, followed by poly-A, single-stranded DNA, chemically damaged DNA, and double-stranded DNA, whereas poly-C and poly-U showed little effect. The combined experimental data support the hypothesis that the photoexcited Ru2+ species injects an electron into the semiconductor and produces Ru3+, which is then reduced back to Ru2+ by guanine and adenine bases in DNA, resulting in the recycling of the metal complex and enhanced photocurrent. The photoelectrochemical reaction can be employed as a new method for the detection of DNA damage.

Genotoxicity sensor response correlated with DNA nucleobase damage rates measured by LC-MS

Responses from "reagentless" DNA-based electrochemical toxicity sensors to DNA alkylating agents styrene oxide (SO), diepoxybutane (DEB), and methyl methanesulfonate (MMS) were compared to formation rates of total alkylated nucleobases in DNA measured by LC-UV-MS. Sensors utilized a catalytic metallopolymer in DNA films previously exposed to the damage agents. To achieve adequate sensitivity, LC-UV-MS analyses were done on DNA in solution reacted with the damage agents, and subsequently hydrolyzed to nucleosides with enzymes. Sensor response correlated well with nucleobase-adduct formation rates obtained by the molecule-specific analyses. Results confirm that the metallopolymer-DNA film sensors can be used to estimate relative DNA damage rates from nucleobase adduct-forming chemicals. Results from both methods correlated well with animal genotoxicity as estimated by TDL(o) values, the lowest dose producing carcinogenicity, in mice and rats. These sensors should be useful for rapid, inexpensive screening of moderately and severely genotoxic new chemicals.