Probing DNA mismatched and bulged structures by using 19F NMR spectroscopy and oligodeoxynucleotides with an 19F-labeled nucleobase

In this study, DNA local structures with bulged bases and mismatched base pairs as well as ordinary full-matched base pairs by using (19)F NMR spectroscopy with (19)F-labeled oligodeoxynucleotides (ODNs) were monitored. The chemical shift change in the (19) F NMR spectra allowed discrimination of the DNA structures. Two types of ODNs possessing the bis(trifluoromethyl)benzene unit (F-unit) at specified uridines were prepared and hybridized with their complementary or noncomplementary strands to form matched, mismatched, or bulged duplexes. By using ODN F1, in which an F-unit was connected directly to a propargyl amine-substituted uridine, three local structures, that is, full-matched, G-U mismatch, and A-bulge could be analyzed, whereas other structures could not be discriminated. A molecular modeling study revealed that the F-unit in ODN F1 interacted little with the nucleobases and sugar backbone of the opposite strand because the linker length between the F-unit and the uridine base was too short. Therefore, the capacity of ODN F1 to discriminate the DNA local structures was limited. Thus, ODN F2 was designed to improve this system; aminobenzoic acid was inserted between the F-unit and uridine base so the F-unit could interact more closely with the opposite strand. Eventually, the G-bulge and T-U mismatch and the three aforementioned local structures could be discriminated by using ODN F2. In addition, the dissociation processes of these duplexes could be monitored concurrently by (19)F NMR spectroscopy.

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.

Chemical ligation of oligodeoxynucleotides by X-irradiation and its application to regulation of G-quadruplex formation

We demonstrated radiolytic ligation of oligodeoxynucleotides (ODNs) possessing disulfide bond and its application to regulation of DNA quadruplex formation. G-rich hexamer ODNs had poor ability to form quadruplex, while X-irradiation of the ODNs induced interstrand exchange reaction at disulfide bond to form ligated 12 mer ODNs, leading to the ready formation of quadruplex due to the entropic effect. Since complexation of the ligated ODNs with hemin in the presence of K(+) showed strong soret band absorption and also catalyzed the H(2)O(2)-mediated oxidation of luminol, it appears that the quadruplex formed from ligated ODNs showed a function similar to native DNA quadruplex.

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.

Synthesis and photooxidation of oligodeoxynucleotides containing 5-dimethylaminocytosine as an efficient hole-trapping site in the positive-charge transfer through DNA duplexes

We have designed and synthesized DNA duplexes containing 5-dimethylaminocytosine ((DMA)C) to investigate the effects of C(5)-substituted cytosine bases on the transfer and trapping of positive charge (holes) in DNA duplexes. Fluorescence quenching experiments revealed that a (DMA)C base is more readily one-electron oxidized into a radical cation intermediate as compared with other natural nucleobases. Upon photoirradiation of the duplexes containing (DMA)C, the photosensitizer-injected hole migrated through the DNA bases and was trapped efficiently at the (DMA)C sites, where an enhanced oxidative strand cleavage occurred by hot piperidine treatment. The (DMA)C radical cation formed by hole transfer may undergo specific hydration and subsequent addition of molecular oxygen, thereby leading to its decomposition followed by a predominant strand cleavage at the (DMA)C site. This remarkable property suggests that the modified cytosine (DMA)C can function as an efficient hole-trapping site in the positive-charge transfer in DNA duplexes.

Radiolytic Reduction Characteristics of Artificial Oligodeoxynucleotides Possessing 2-Oxoalkyl Group or Disulfide Bonds

A number of advances have been made in the development of modified oligodeoxynucleotides (ODNs), and chemical or physical properties of which are controlled by external stimuli. These intelligent ODNs are promising for the next generation of gene diagnostics and therapy. This paper focuses on the molecular design of artificial ODNs that are activated by X-irradiation and their applications to regulation of hybridization properties, conformation change, radiation-activated DNAzyme, and decoy molecules.

Radiolytic ligation of oligodeoxynucleotides possessing disulfide bond

Hypoxic X-radiolysis of diluted aqueous solutions was performed to generate hydrated electrons that induced one-electron reduction of oligodeoxynucleotides (ODNs) possessing a disulfide bond. Upon hypoxic irradiation, reductive ligation reaction between two types of ODNs occurred in the presence of a template ODN strand, resulting in the formation of a prescribed ODN in substantial amounts.

Radiolytic cyclization of stem-and-loop structured oligodeoxynucleotide with neighboring arrangement of α,ω-bis-disulfides

Upon X-ray irradiation of hypoxic aqueous solution, modified oligodeoxynucleotides (ODNs) bearing a pair of disulfides at both ends of the strand that forms a stem-and-loop structure with a neighboring arrangement of α,ω-bis-disulfides underwent efficient cyclization via an intramolecular exchange reaction at the disulfide moieties with a multiple turnover process. Mechanistic studies revealed that hydrogen atoms generated in the radiolysis of water are key active species initiating a chain reaction to produce cyclic ODN disulfides, in which addition of hydrogen atom results in dissociation of the original disulfide bond to generate a thiyl radical intermediate as the chain carrier for the succeeding disulfide exchange into cyclization. The properties were also assessed for the resultant cyclic ODN disulfide that has several favorable features for use in the transcriptional decoy strategy. The cyclic ODN disulfides produced by the present radiolytic method showed high thermal stability, resistance to nuclease, and high binding activity to a representative transcriptional factor of nuclear factor κB.

Radiolytic one-electron reductive cyclization of oligodeoxynucleotides possessing a disulfide bond

Radiolytic one-electron reduction of oligodeoxynucleotides (ODNs) possessing a disulfide bond induced strand exchange reaction in a hypoxia selective manner. In this study, we attempted to apply this radiolytic reaction to stem-and-loop structured ODNs. Hypoxic X-irradiation to an aqueous solution of stem-and-loop structured ODNs produced a cyclized DNA in good yield via an intrastrand ligation reaction.

Photoelectrochemical identification of 5-methylcytosine modification in DNA: combination of photosensitization and enzymatic cleavage

We present a novel photoelectrochemical approach for discriminating between cytosine and 5-methylcytosine in DNA when used in combination with enzymatic digestion. A photosensitizer-linked DNA duplex bearing 5-methylcytosine or cytosine at a given restriction site of the strand was immobilized on a gold electrode and digested with enzyme, and the photocurrent response was measured. We observed high photocurrent density that was selective for the methylated duplex.

Efficient photooxidative strand cleavage at 5-methylcytosine in DNA by sensitization with 9,10-anthraquinone-tethered oligonucleotides

Photoirradiation and subsequent hot piperidine treatment of the duplex consisting of 5-methylcytosine ((m)C)-containing DNA and 9,10-anthraquinone (AQ)-tethered complementary oligodeoxynucleotide led to selective oxidative strand cleavage at the target (m)C site, whereas no strand cleavage was observed for the duplex containing normal cytosine instead of (m)C. Incorporation of an AQ sensitizer into the interior of a strand induced an enhanced one-electron photooxidation, presumably because of a much larger intersystem crossing efficiency, leading to an efficient strand cleavage at the target (m)C site in DNA. Optimization of the photosensitizer could afford more strand cleavage at (m)C in DNA, thereby allowing for the more sensitive detection of the target (m)C on a sequencing gel.

Pathways of excess electron transfer in phenothiazine-tethered DNA containing single-base mismatches

The effects of local structural disorder on excess electron transfer (EET) in DNA were investigated by evaluating photoinduced electron transfer in phenothiazine (PTZ)-modified oligodeoxynucleotides bearing single-base mismatches. Unexpectedly, more efficient electron transfer was observed for the mismatched duplexes than for the complementary DNA, suggesting that distraction of hydrogen bond interaction at the mismatch site enables electron injection or hopping beyond the mismatch sites. It was also anticipated that water accessibility of the mismatched nucleobases could affect EET because protonation of the electron-captured pyrimidine intermediates became competitive to EET, especially at the mismatch sites.

DNA hairpins containing a diaminostilbene derivative as a photoinduced electron donor for probing the effects of single-base mismatches on excess electron transfer in DNA

To investigate the effects of local structural disorder induced by a single-base mismatch on excess electron transfer (EET) in DNA, a novel hairpin DNA containing diaminostilbene (DAS) as a photoinducible electron donor has been developed. It was clearly demonstrated that EET efficiency depends on the electron injection modes from the electron donors and redox properties of the mismatched bases.

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.

Radiation- and photo-induced activation of 5-fluorouracil prodrugs as a strategy for the selective treatment of solid tumors

5-Fluorouracil (5-FU) is used widely as an anticancer drug to treat solid cancers, such as colon, breast, rectal, and pancreatic cancers, although its clinical application is limited because 5-FU has gastrointestinal and hematological toxicity. Many groups are searching for prodrugs with functions that are tumor selective in their delivery and can be activated to improve the clinical utility of 5-FU as an important cancer chemotherapeutic agent. UV and ionizing radiation can cause chemical reactions in a localized area of the body, and these have been applied in the development of site-specific drug activation and sensitization. In this review, we describe recent progress in the development of novel 5-FU prodrugs that are activated site specifically by UV light and ionizing radiation in the tumor microenvironment. We also discuss the chemical mechanisms underlying this activation.

pH effect on the one-electron photooxidation of 5-methylcytosine with naphthoquinone sensitizer

The pH effect on the one-electron photooxidation of 5-methyl-2'-deoxycytidine (d(m)C) by sensitization with 1,4-naphthoquinone (NQ) was investigated. Upon photoirradiation of d(m)C in the presence of NQ under slightly acidic conditions such as pH 5.0, 5-formyl-2'- deoxycytidine (d(f)C) was formed efficiently, whereas similar NQ-photosensitized oxidation of d(m)C proceeded to lesser extent under neutral or basic conditions. Under slightly acidic conditions, dmC radical cation favors to undergo irreversible deprotonation at the C(5)-methyl group to form a methyl-centered radical, leading to a higher yield of the alkali-labile oxidation products including d(f)C. In contrast, the d(m)C radical cation competitively undergoes deprotonation at the exocyclic N(4)-amino group under neutral or basic conditions, resulting in a decreased yield of NQ-photosensitized oxidation products.

One-electron reductive template-directed ligation of oligodeoxynucleotides possessing a disulfide bond

Hypoxic X-radiolysis of diluted aqueous solutions was performed to generate hydrated electrons that induced one-electron reduction of oligodeoxynucleotides (ODNs) possessing a disulfide bond. Upon hypoxic irradiation of dinucleotides, two forms of dinucleotides were produced via intermolecular exchange of the disulfides and ligation that proceeded with a multiple turnover. In contrast to the efficient reaction induced by hypoxic irradiation, the reaction efficiency was dramatically decreased when irradiation was performed under aerobic conditions, presumably due to capturing reactive hydrated electrons by molecular oxygen. We subsequently applied these unique reaction characteristics to template-directed ligation. In the presence of a complementary template ODN, two ODNs possessing a disulfide bond produced a prescribed ODN with high regioselectivity via interstrand crossing upon hypoxic irradiation.

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.

Photoinduced excess electron injection into DNA duplexes containing mismatched base pairs

A series of DNA containing photoinduced electron donors and mismatched DNA base pairs have been prepared and applied for the chemical investigation of excess electron transfer (EET) in the duplex DNA. As the electron donors, phenothiazine (PTZ) with a flexible linker was tethered to the 5'-end or in the middle of the sequences, or diaminostilbene (DAS) was covalently linked to form a hairpin structure. The presence of mismatched base pair lowered EET efficiency in the DAS-capped DNA hairpins, on the other hand, efficient EET beyond the mismatch site was observed in the PTZ-conjugated DNA.

Photocurrent response after enzymatic treatment of DNA duplexes immobilized on gold electrodes: electrochemical discrimination of 5-methylcytosine modification in DNA

We demonstrate a photoelectrochemical approach to the detection of the methylation status of cytosine bases in DNA. We prepared anthraquinone (AQ) photosensitizer-tethered oligodeoxynucleotide (ODN) duplexes bearing 5-methylcytosine (mC) or the corresponding cytosine (C) at a restriction site of the ODN strand immobilized on gold electrodes, and measured their photocurrent responses arising from hole transport after enzymatic digestion. Treatment with HapII or HhaI of the duplexes bearing normal C led to strand cleavage, and the photosensitizer unit was eliminated from the ODN strand immobilized on the gold electrode, exclusively reducing the photocurrent density. With a similar treatment, the duplexes bearing mC showed higher photocurrent responses arising from hole transport through the duplex. This significant difference in the photocurrent response between mC and normal C residues in DNA on the gold electrodes is potentially applicable to the detection of mC modification in DNA.

Fluorometric identification of 5-methylcytosine modification in DNA: combination of photosensitized oxidation and invasive cleavage

An efficient fluorometric detection system of DNA methylation has been developed by a combination of a photooxidative DNA cleavage reaction with 2-methyl-1,4-naphthoquinone (NQ) chromophore and an invasive cleavage reaction with human Flap endonuclease-1. Enzymatic treatment of a mixture of photochemically fragmented target oligodeoxynucleotides (ODNs) at 5-methylcytosine mC) and hairpin-like probe oligomer possessing a fluorophore (F) and a quencher (D) resulted in a dramatic enhancement of fluorescence. In contrast, fluorescence emission for the ODN containing cytosine but not mC at the target sequence was extremely weak. In addition, by monitoring the fluorescence change, this system allows for the detection of mC in DNA at subfemtomole amounts. This system would provide a highly sensitive protocol for determining the methylation status in DNA by fluorescence emission.

Flavin-sensitized photoreduction of thymidine glycol

Photochemical reactivity of flavin adenine dinucleotide (FAD) and flavin mononucleotide (FMN) toward thymidine glycol (dTg) has been investigated. Fluorescence intensity of FAD was enhanced as increasing the concentration of dTg, suggesting that adenosine moiety of FAD interacts with dTg. However, photoreduction of dTg using reduced form of FAD gave repaired thymidine in almost the same yield as when reduced FMN was used alternatively, and thus such interaction seems to have no effect on the reduction. Oligodeoxynucleotides containing dTg were also photochemically repaired by reduced form of flavins in different yields depending on the sequence, which could be related to electron affinity of the nucleobases in DNA.

Regulation of DNA duplex formation by hypoxic irradiation: one-electron reduction characteristics of oligodeoxynucleotides possessing 2-oxoalkyl functional group

We synthesized oligodeoxynucleotides (ODN) possessing 2-oxoalkyl group on thymidine (d(oxo)T) to characterize the radiolytic reduction in aqueous solution. Corresponding unmodified ODNs were generated from ODNs containing d(oxo)T upon hypoxic irradiation. Enzymatic digestion of the duplex consisting of the hypoxically irradiated ODN containing d(oxo)T and its complementary strand resulted in an efficient cleavage, but no cleavage was observed when a control duplex was digested without irradiation.

Sensitive discrimination between cytosine and 5-methylcytosine in DNA by a modified invader method

We designed a detection system of 5-methylcytosine ((m)C) in DNA by a combination of photooxidative DNA cleavage reaction of 2-methyl-1,4-naphthoquinone chromophore with invader technology. Enzymatic treatment of a mixture of photochemically fragmented target oligodeoxynucleotides (ODNs) at (m)C and probe oligomer possessing a fluorophore and a quencher resulted in a dramatic enhancement of fluorescence. In contrast, fluorescence emission for the ODN containing C but not (m)C at the target sequence was extremely weak. We could detect (m)C in sub-femtomol DNA by monitoring the fluorescence change.

Drug release from functionalized oligodeoxynucleotide by photo-induced electron transfer

We synthesized a photoreactive hairpin-type oligodeoxynucleotide (P-ODN) possessing an o-nitrobenzyl chromophore and a triplet quencher of 1-aminonaphthalene. Photoirradiation of the hybrid of H-ODN with its complementary DNA led to release of drug in an efficient amount, while the photo-induced drug release was remarkably suppressed in the absence of complementary DNA.

The effect of triple helix forming on charge transport in DNA

The charge transport efficiency in DNA duplex could be regulated by thermal conversion between the formation and dissociation of partial triplex structure with a short strand oligonucleotide (ODN). Photoinduced long-distance one-electron oxidation in duplex ODNs with partial triplex structural region was examined at various temperatures to evaluate the charge transport efficiency. Under these conditions, the apparent charge transport was suppressed dramatically at 0 degrees C relative to 25 degrees C. These results strongly indicate that variation of temperatures could regulate the triplex formation and dissociation, resulting in the regulation of charge transport in DNA. Thus, triplex formation is expected to be a constituent of new well regulated biomaterial that will applicable to nano-scale electronic devices.

Detection of 5-methylcytosine in DNA by photo-functionalized oligodeoxynucleotides possessing 2-methyl-1,4-naphthoquinone chromophore

We developed a method for detection of 5-methylcytosine in DNA by photosensitized oxidation, using photo-functionalized oligodeoxynucleotides possessing 2-methyl-1,4-naphthoquinone chromophores (NQ) at the interior of the strand. The photooxidation and subsequent hot piperidine treatment of duplex consisting of the NQ-tethered oligodeoxynucleotide and its complementary strand bearing 5-methylcytosine residue led to selective DNA strand cleavage at the 5-methylcytosine residue, whereas no strand cleavage was detected for the control duplex with normal cytosine residue but not 5-methylcytosine.