Studies of DNA Damage Inhibition by Dietary Antioxidants Using Metallopolyion/DNA Sensors

Voltammetric sensors featuring thin‐films containing osmium and ruthenium metallopolymers were evaluated to monitor the influence of antioxidants on DNA damage reactions. In the first example, apigenin, chrysin, and ascorbic acid were shown to inhibit oxidation of DNA by hydroxyl radicals generated with Fenton's reagent. A second example involved films of DNA with myoglobin (Mb) as an enzyme mimic which was used to convert styrene to styrene oxide. Here, the Ru peak of the sensor served as a marker of DNA damage from adduct formation between nucleobases and styrene oxide. There was no influence of the antioxidants on the reaction of styrene oxide itself with DNA films, but significant damage protection was afforded by micromolar amounts of antioxidants when styrene oxide was generated by Mb in the sensor films. This suggests that protection ensued from action of the antioxidants at the enzyme conversion level, probably by reduction of the active ferryloxy intermediate of the protein. Results demonstrate the usefulness of the thin metallopolyion/DNA film sensors in investigations of DNA damage inhibition.     

Comparison of Different Strategies on DNA Chip Fabrication and DNA‐Sensing: Optical and Electrochemical Approaches

New strategies for the construction of DNA chips and the detection of DNA hybridization will be discussed in this review. The focus will be on the use of polypyrrole as a linker between a substrate and oligonucleotide probes. The modification step is based on the electrochemical copolymerization of pyrrole and oligonucleotides bearing a pyrrole group on its 5′ end. This strategy was employed for the immobilization of oligonucleotides on millimeter‐sized electrodes, microelectrode arrays, as well as for the local structuring of homogeneous gold surfaces. Our approaches for the localized patterning of gold surfaces will be also discussed. Localized immobilization was achieved by using an electrospotting technique, where a micropipette served as an electrochemical cell where spot sizes with 800 μm diameters were fabricated. The use of a microcell using a Teflon covered metal needle with a cavity of 100 μm resulted in immobilized probe spots of 300 μm. Scanning electrochemical microscopy (SECM) was also used, and surface modifications of 100 μm were obtained depending on the experimental conditions. Different detection methods were employed for the reading of the hybridization event: fluorescence imaging, surface plasmon resonance imaging (SPRI), photocurrent measurements, and voltamperometric measurements using intercalators. Their advantages concerning the various immobilization strategies will also be discussed.     

Discovery of Small‐Molecule Interleukin‐2 Inhibitors from a DNA‐Encoded Chemical Library

Libraries of chemical compounds individually coupled to encoding DNA tags (DNA‐encoded chemical libraries) hold promise to facilitate exceptionally efficient ligand discovery. We constructed a high‐quality DNA‐encoded chemical library comprising 30 000 drug‐like compounds; this was screened in 170 different affinity capture experiments. High‐throughput sequencing allowed the evaluation of 120 million DNA codes for a systematic analysis of selection strategies and statistically robust identification of binding molecules. Selections performed against the tumor‐associated antigen carbonic anhydrase IX (CA IX) and the pro‐inflammatory cytokine interleukin‐2 (IL‐2) yielded potent inhibitors with exquisite target specificity. The binding mode of the revealed pharmacophore against IL‐2 was confirmed by molecular docking. Our findings suggest that DNA‐encoded chemical libraries allow the facile identification of drug‐like ligands principally to any protein of choice, including molecules capable of disrupting high‐affinity protein–protein interactions.     

Direct Detection of DNA and DNA‐Ligand Interaction by Impedance Spectroscopy

In this work we present an impedimetric detection system for DNA‐ligand interactions. The sensor system consists of thiol‐modified single‐stranded DNA chemisorbed to gold. Impedance measurements in the presence of the redox system ferri‐/ferrocyanide show an increase in charge transfer resistance (R_ct) after hybridisation of a complementary target. Different amounts of capture strands, used for gold electrode modification, result in surface coverages between 3 and 15 pmol/cm² ssDNA. The relative change in R_ct upon hybridisation increases with increasing amount of capture probe on the electrode from 1.5‐ to 4.5‐fold. Impedimetric detection of binding events of a metal‐intercalator ([Ru(phen)₃]²⁺) and a groove binder (spermine) to double‐stranded DNA is demonstrated. Binding of [Ru(phen)₃]²⁺ and spermine exhibits a decrease in charge transfer resistance. Here, the ligand’s interaction leads to electrostatic shielding of the negatively charged DNA backbone. The impedance changes have been evaluated in dependence on the concentration of both DNA binders. Furthermore, the association of a single‐stranded binding protein (SSBP) is found to cause an increase in charge transfer resistance only when incubated with single‐stranded DNA. The specific binding of an anti‐dsDNA antibody to the dsDNA‐modified electrode surface decreases in contrast the interfacial impedance.     

DNA‐Accelerated Catalysis of Carbene‐Transfer Reactions by a DNA/Cationic Iron Porphyrin Hybrid

A novel DNA‐based hybrid catalyst comprised of salmon testes DNA and an iron(III) complex of a cationic meso‐tetrakis(N‐alkylpyridyl)porphyrin was developed. When the N‐methyl substituents were placed at the ortho position with respect to the porphyrin ring, high reactivity in catalytic carbene‐transfer reactions was observed under mild conditions, as demonstrated in the catalytic enantioselective cyclopropanation of styrene derivatives with ethyl diazoacetate (EDA) as the carbene precursor. A remarkable feature of this catalytic system is the large DNA‐induced rate acceleration observed in this reaction and the related dimerization of EDA. It is proposed that high effective molarity of all components of the reaction in or near the DNA is one of the key contributors to this unique reactivity. This study demonstrates that the concept of DNA‐based asymmetric catalysis can be expanded into the realm of organometallic chemistry.     

Direct DNA Hybridization on the Single‐Walled Carbon Nanotubes Modified Sensors Detected by Voltammetry and Electrochemical Impedance Spectroscopy

Carboxylic acid functionalized single‐walled carbon nanotubes modified graphite sensors (SWCNT‐PGEs) were developed for electrochemical monitoring of direct DNA hybridization related to specific sequence of Hepatitis B virus, which substantially enhance the electrochemical transduction resulting from guanine oxidation signal comparison to bare PGEs. The performance characteristics of DNA hybridization on disposable CNT‐PGE were explored measuring the guanine signal in terms of optimum analytical conditions; probe and target concentration, hybridization time, and selectivity. The voltammetric results were also complemented with electrochemical impedance spectroscopy (EIS), that was used to characterize the successful construction of carbon nanotubes modification onto the surface of PGEs.     

A Kinetic and Structural Investigation of DNA‐Based Asymmetric Catalysis Using First‐Generation Ligands

The recently developed concept of DNA‐based asymmetric catalysis involves the transfer of chirality from the DNA double helix in reactions using a noncovalently bound catalyst. To date, two generations of DNA‐based catalysts have been reported that differ in the design of the ligand for the metal. Herein we present a study of the first generation of DNA‐based catalysts, which contain ligands comprising a metal‐binding domain linked through a spacer to a 9‐aminoacridine moiety. Particular emphasis has been placed on determining the effect of DNA on the structure of the Cu^II complex and the catalyzed Diels–Alder reaction. The most important findings are that the role of DNA is limited to being a chiral scaffold; no rate acceleration was observed in the presence of DNA. Furthermore, the optimal DNA sequence for obtaining high enantioselectivities proved to contain alternating GC nucleotides. Finally, DNA has been shown to interact with the Cu^II complex to give a chiral structure. Comparison with the second generation of DNA‐based catalysts, which bear bipyridine‐type ligands, revealed marked differences, which are believed to be related to the DNA microenvironment in which the catalyst resides and where the reaction takes place.     

Structural Identification of DNA Adducts Derived from 3‐Nitrobenzanthrone,a Potent Carcinogen Present in the Atmosphere

3‐Nitrobenzanthrone is a powerful bacterial mutagen and carcinogen to mammals. To obtain precise information on DNA‐adduct formation by 3‐nitrobenzanthrone, a number of DNA adducts, including N‐(2′‐deoxyguanosin‐8‐yl)‐3‐aminobenzanthrone ( 13 a ), 2‐(2′‐deoxyguanosin‐N²‐yl)‐3‐aminobenzanthrone ( 14 a ), N‐(2′‐deoxyadenosin‐8‐yl)‐3‐aminobenzanthrone ( 15 a ), 2‐(2′‐deoxyadenosin‐N⁶‐yl)‐3‐aminobenzanthrone ( 16 a ), and their N‐acetylated counterparts 13 b , 14 b , 15 b , and 16 b were synthesized by palladium‐catalyzed aryl amination of the corresponding nucleoside and bromobenzanthrone derivatives. Among these DNA adducts, DNA adducts 13 a , 13 b , 14 a , 14 b , and 16 a were identified in the reaction mixture of nucleosides (2′‐deoxyguanosine, 2′‐deoxyadenosine, or DNA) with N‐acetoxy‐3‐aminobenzanthrone or N‐acetyl‐N‐acetoxy‐3‐aminobenzanthrone, both of which are recognized as activated metabolites of 3‐nitrobenzanthrone. The formation of these multiple DNA adducts may help explain the potent mutacarcinogenicity of 3‐nitrobenzanthrone.     

Elucidation of the Dexter‐Type Energy Transfer in DNA by Thymine–Thymine Dimer Formation Using Photosensitizers as Artificial Nucleosides

C‐nucleosides of 4‐methylbenzophenone, 4‐methoxybenzophenone, and 2′‐methoxyacetophenone were synthetically incorporated as internal photosensitizers into DNA double strands. This structurally new approach makes it possible to study the distance dependence of thymidine dimer formation because the site of photoinduced triplet energy transfer injection is clearly defined. The counterstrands to these modified strands lacked the phosphodiester bond between the two adjacent thymidines that are supposed to react with each other. Their dimerization could be evidenced by gel electrophoresis because the covalent connection by cyclobutane formation between the two thymidines changes the mobility. A shallow exponential distance dependence for the formation of thymidine dimers over up to 10 A‐T base pairs was observed that agrees with a Dexter‐type triplet–triplet energy transfer mechanism. Concomitantly, a significant amount of photoinduced DNA crosslinking was observed.     

Toluene Dioxygenase‐Catalyzed Synthesis of cis‐Dihydrodiol Metabolites from 2‐Substituted Naphthalene Substrates: Assignments of Absolute Configurations and Conformations from Circular Dichroism and Optical Rotation Measurements

cis‐Dihydrodiol metabolites have been isolated from naphthalene and six 2‐substituted naphthalene substrates. Their structures and absolute configurations have been determined by a combination of calculated (TDDFT) and experimentally based circular dichroism (CD) and optical rotation (OR) methods. The “inverse” styrene helicity rule is shown to be incorrect for the interpretation of the CD spectra of cis‐dihydrodiols. A striking conclusion is that CD spectra correlate directly with the helicity of the styrene chromophore: that is, the sign of the long‐wavelength Cotton effect is identical with the sign of styrene torsion angle, whereas the OR sign is dependent on the absolute configuration of the allylic carbon atom. The results demonstrate that a predictive model previously used for the determination of preferred regio‐ and stereoselectivity associated with TDO‐catalyzed cis‐dihydroxylation of substituted benzene substrates can now be successfully extended to substituted naphthalene substrates.     

Voltammetric Studies on the Recognition of a Copper Complex to Single‐ and Double‐Stranded DNA and Its Application in Gene Biosensor

A mixed‐ligands copper complex [Cu(phendione)(DAP)]SO₄ (phendione=1,10‐phenanthroline‐5,6‐dione, DAP=2,3‐diaminophenazine) was synthesized. Cyclic voltammetry showed that the complex underwent an obvious decrease of redox peak currents and positive shift of formal potential after interaction with double‐stranded DNA (dsDNA), suggesting that the copper complex behaved as a typical metallointercalator for dsDNA, The recognition properties of the copper complex to single‐stranded DNA (ssDNA) and dsDNA were assessed using surface‐based electrochemical methods and the results suggested that the complex had obviously different redox signals at ssDNA and dsDNA modified electrodes. The copper complex was further used as an electroactive indicator for the detection of cauliflower mosaic virus (CaMV) 35S promoter gene.     

DNA‐Encoded Tuning of Geometric and Plasmonic Properties of Nanoparticles Growing from Gold Nanorod Seeds

Systematically controlling the morphology of nanoparticles, especially those growing from gold nanorod (AuNR) seeds, are underexplored; however, the AuNR and its related morphologies have shown promises in many applications. Herein we report the use of programmable DNA sequences to control AuNR overgrowth, resulting in gold nanoparticles varying from nanodumbbell to nanooctahedron, as well as shapes in between, with high yield and reproducibility. Kinetic studies revealed two representative pathways for the shape control evolving into distinct nanostructures. Furthermore, the geometric and plasmonic properties of the gold nanoparticles could be precisely controlled by adjusting the base compositions of DNA sequences or by introducing phosphorothioate modifications in the DNA. As a result, the surface plasmon resonance (SPR) peaks of the nanoparticles can be fine‐tuned in a wide range, from visible to second near‐infrared (NIR‐II) region beyond 1000 nm.