8-Methoxydeoxyguanosine as an Effective Precursor of 2-Aminoimidazolone, a Major Guanine Oxidation Product in One-Electron Oxidation of DNA

8-Methoxydeoxyguanosine as an Effective Precursor of 2-Aminoimidazolone, a Major Guanine Oxidation Product in One-Electron Oxidation of DN

Product Analysis of GG-Specific Photooxidation of DNA via Electron Transfer: 2-Aminoimidazolone as a Major Guanine Oxidation Product

Product Analysis of GG-Specific Photooxidation of DNA via Electron Transfer:  2-Aminoimidazolone as a Major Guanine Oxidation Produc

A Nucleobase that Releases Reporter Tags upon DNA Oxidation

We have developed a novel nucleosbase, edaG, that efficiently releases various reporter units upon one-electron oxidation. The edaG-selective degradation of ODNs was achieved by various mild oxidizing agents. The oxidant-dependent molecular releasing technique is quite useful not only for DNA-based drug releasing systems but also for the detection of long-range hole transport through DNA without time-consuming analysis

Synthesis of DNA Oligomers Containing Modified Uracil Possessing Electron-Accepting Benzophenone Chromophore

Synthesis of DNA Oligomers Containing Modified Uracil Possessing Electron-Accepting Benzophenone Chromophor

Design of a Hole-Trapping Nucleobase: Termination of DNA-Mediated Hole Transport at <i>N</i>²-Cyclopropyldeoxyguanosine

Design of a Hole-Trapping Nucleobase:  Termination of DNA-Mediated Hole Transport at N2-Cyclopropyldeoxyguanosin

Affinity Labeling of a Single Guanine Bulge

We have developed a conceptually new method for the selective labeling of duplex DNA containing a guanine bulge with a masked form of fluorescent 2-amino-1,8-naphthyridine. A naphthyridine derivative 2 tethering DNA-alkylating epoxide was synthesized from (S)-epichlorohydrin and naphthyridine derivative 1, which selectively binds to the guanine bulge duplex. HPLC analysis of the labeling reaction of bulge duplex d(GTT GTGTTG GA)/d(CAA CA A ACC T) (TGT/A_A) with 2 showed a formation of 2−TGT adduct for the guanine bulge. The reaction proceeded for the guanine bulge and a reduced efficiency for the cytosine bulge, but not at all for adenine and thymine bulges. The site of covalent bond formation in 2−TGT was unambiguously identified at the guanine two bases away from the bulge by the use of MALDI-TOF MS analysis of the oligomer fragments produced by strand scission. The labeling reaction was also observed for the guanine bulge flanking two G−C base pairs (CGC/G_G), producing a 2:1 adduct (2·2-CGC). Upon hydrolysis of 2−TGT and 2·2-CGC with concentrated hydrogen chloride, a release of fluorescent 2-aminonaphthyridine from the adduct was clearly detected, verifying a concept of an affinity labeling of the guanine bulge with a masked fluorescent chromophore. The affinity labeling targeting of the guanine bulge is a conceptually novel method for the postsynthetic labeling of DNA. Hybridization, to the target sequence, of a probe DNA possessing one extra guanine especially between two cytosines provides a unique site for the labeling by masked fluorophore 2. The technique may have broad application in genetic typing without using a conventional synthesis of fluorescent-labeled DNA oligomers

Site-Specific Discrimination of Cytosine and 5-Methylcytosine in Duplex DNA by Peptide Nucleic Acids

For site-specific discrimination of cytosine (C) and 5-methylcytosine (mC) in duplex DNA, we developed a new method using peptide nucleic acids (PNAs). The combination of a PNA-assisted DNA displacement complex and a fluorescein-labeled probe oligomer allowed the detection of mC at the defined sites in target DNA using a restriction enzyme. After treatment of the complex with a restriction enzyme, strong fluorescence emission was observed for the complex containing C at the target site, whereas the fluorescence intensity for the complex containing mC was extremely weak

Photochemistry of Benzophenone Immobilized in a Major Groove of DNA: Formation of Thermally Reversible Interstrand Cross-link

We here report a highly site and sequence selective formation of an interstrand cross-link of BPU-containing oligomer duplexes. The cross-link was found spontaneously reverted to original oligomers upon heating, providing a new method for the temporary connection of two DNA strands

Clear Distinction of Purine Bases on the Complementary Strand by a Fluorescence Change of a Novel Fluorescent Nucleoside

A new fluorescent nucleoside, benzopyridopyrimidine (BPP), which can sharply distinguish between A and G bases opposite BPP has been devised. The base-pairing degeneracy of BPP strongly contributes to the sharp fluorescence change that is dependent on the type of purine bases opposite BPP. The hybridization of an ODN probe containing BPP with a target DNA facilitates the judgment with the naked eye of the type of purine base located at a specific site on the target DNA. The BPP-containing ODN is a very effective probe for A/G SNP typing

Chemistry of Sequence-Dependent Remote Guanine Oxidation: Photoreaction of Duplex DNA Containing Cyanobenzophenone-Substituted Uridine

Chemistry of Sequence-Dependent Remote Guanine Oxidation:  Photoreaction of Duplex DNA Containing Cyanobenzophenone-Substituted Uridin