Site-specific DNA oxidation by a dinuclear copper complex containing a photoisomerizable azobenzene ligand

A dinuclear copper complex possessing an azobenzene backbone (Cu^[II]_[2]1) was synthesized and its affinity towards DNA was investigated and found to be dependent on the trans–cis isomeric forms. Upon exposure to UV light at 365 nm the trans form of the complex (Cu^[II]_[2]trans-1) underwent photoisomerization into the cis-isomer (Cu^[II]_[2]cis-1), which reverted to the original trans-form on exposure to visible light at 420 nm. Both thetrans and cis isomers exhibited moderate DNA cleavage activity toward plasmid duplex DNA in the presence of a reducing agent 3-mercaptopropionic acid (MPA) suggesting that the Cu^[I] species could activate molecular oxygen to form a reactive oxygen species in situ. Interestingly, the isomeric copper complexes showed different site-specificities in the oxidation of an oligodeoxynucleotide having single-strand–double-helix junctions in the sequence. The trans isomer Cu^[I]_[2]trans-1 induced oxidation at the consecutive deoxyguanosine site (GG) near the junction; on the other hand, such site-specificity was not observed in the case of Cu^[I]_[2]cis-1

(13)C-labeled indolequinone-DTPA-Gd conjugate for NMR probing cytochrome:P450 reductase-mediated one-electron reduction.

We designed and synthesized a new class of (13)C-labeled NMR probe, (13)C-IQ-Gd, to monitor one-electron reductions by cytochrome:P450 (CYP450) reductase under hypoxic conditions. (13)C-IQ-Gd consisted of a Gd(3+)-diethylene triamine pentaacetic acid (DTPA) complex unit and an indolequinone ((13)C-IQ) unit bearing a (13)C-labeled methoxy group. The (13)C NMR signal of (13)C-IQ-Gd was suppressed because of the intramolecular paramagnetic effect of Gd(3+), whereas enzymatic reduction mediated by CYP450 reductase under hypoxic conditions yielded an intensed (13)C NMR signal due to enzymatic activation of the IQ unit followed by release of the DTPA-Gd unit from (13)C-IQ-Gd. This (13)C NMR spectral change allowed the monitoring of CYP450 reducatase-mediated one-electron reduction

Reversible modification of oligodeoxynucleotides: click reaction at phosphate group and alkali treatment

We characterized click reaction between oligodeoxynucleotides (ODNs) possessing acetylene groups at the phosphate unit and azide compounds. Cu(I)-catalyzed cycloaddition proceeded efficiently to form the corresponding functional ODNs. The resulting ODNs could be converted into ordinary ODNs by treatment with aqueous methylamine. The present method successfully achieved a reversible modification of ODNs

Aggregate formation and radiolytic degradation of amphiphilic DNA block copolymer possessing disulfide bond.

We have designed a novel aggregate of DNA block copolymer (DBC) that is sensitive to hypoxic X-irradiation. The DBC consists of tetrahydropyrane-protected 2-hydroxyethyl methacrylate as a hydrophobic unit and oligodeoxynucleotides as a hydrophilic unit, which are linked to a radiation-sensitive disulfide bond. The DBC self-assembled efficiently to form aggregates that encapsulated small molecules such as nile red and pyrene. Hypoxic X-irradiation could then induce reductive degradation of the DBC aggregates via an exchange reaction of the disulfide bond to release guest molecules

Stepwise regulation of hole transport in DNA by control of triplex formation.

A functionality for regulating hole transport efficiency is a prerequisite for the utilization of DNA duplexes as nanodevices. Herein, we report the regulation of hole transport in anthraquinone-tethered DNA with dual triplex forming sites. Long-range photooxidation experiments showed that hole transport was effectively suppressed by the formation of triplex at low temperature, while it was recovered by dissociation to the duplex at higher temperature. Variation of temperature induced the formation and dissociation of the third strand at each triplex region individually, leading to the stepwise regulation of hole transport in DNA

Monitoring of duplex and triplex formation by 19F NMR using oligodeoxynucleotides possessing 5-fluorodeoxyuridine unit as 19F signal transmitter.

We prepared oligodeoxynucleotides (ODNs) possessing a 5-fluorodeoxyuridine (5-FU) unit as a 19F-signal transmitter, and characterized their structures including single strand, duplex, and triplex using 19F NMR. The change in chemical shift induced by incorporation of 5-FU into the ODNs and the formation of higher order structures allowed monitoring of structural changes. Data from UV melting experiments and CD spectra were consistent with the spectral changes in the NMR studies. These 19F-labeled ODNs may be promising molecular probes for the identification of DNA structures in complicated biological conditions

A pulse radiolysis study on the reactions of hydroxyl radical and sulfate radical anion with guanidine derivatives in aqueous solution

The reactions of hydroxyl radical (OH) with guanidine, 1, 1-dimethylguanidine, and 1-ethylguanidine have been investigated by the method of pulse radiolysis. The characteristic absorption observed in the OH reaction with guanidine under basic conditions was assigned to a nitrogen-centered radical. On the other hand, reducing carbon-centered radicals were generated in the OH reaction with 1, 1-dimethylguanidine and 1-ethylguanidine over a pH range of 7–13, which may suggest that the primarily formed nitrogen-centered radicals at a high pH are converted into carbon-centered radicals by hydrogen atom shift. Similar transient species were also observed in the reaction of sulfate radical anion with the guanidine derivatives

Photoelectrochemical evaluation of pH effect on hole transport through triplex-forming DNA immobilized on a gold electrode

We characterized pH effect on hole transport through DNA duplexes possessing a partial triplex-forming region. Direct electrochemical measurement of the current response of photosensitizer-tethered DNA immobilized on a gold electrode revealed that the partial triplex formation under acidic conditions suppressed photocurrent due to hole transport, while dissociation of the triplex into the duplex as occurred upon increasing pH values recovered the photocurrent efficiency. Reversible conversion between duplex and triplex induced upon cyclic alternation of pH values resulted in a rise and fall of photocurrent responses, indicating that pH change may feature in the switching function of hole transport in DNA. These electrochemical behaviors could be correlated to the results obtained in long-range photo-oxidative DNA cleavage experiments, in which DNA cleavage at the hole trapping site beyond the triplex region was significantly suppressed under triplex-forming acidic conditions

Radiolytic one-electron reduction characteristics of tyrosine derivative caged by 2-oxopropyl group

We employed X-irradiation to activate a caged amino acid with a 2-oxoalkyl group. We designed and synthesized tyrosine derivative caged by a 2-oxoalkyl group (Tyr(Oxo)) to evaluate its radiolytic one-electron reduction characteristics in aqueous solution. Upon hypoxic X-irradiation, Tyr(Oxo) released a 2-oxopropyl group to form the corresponding uncaged tyrosine. In addition, radiolysis of dipeptides containing Tyr(Oxo) revealed that the efficiency of radiolytic removal of 2-oxopropyl group increased significantly by the presence of neighboring aromatic amino acids