To qualify DNA data, we have developed a statistical method of deciding whether the DNA data has an acceptable accuracy in sequencing process. The method is to test the probability of sequencing errors, based on partial re-sequencing. The method was successfully applied to a yeast mitochondrial DNA which is previously sequenced (1). The analysis indicates that the entire sequence...
Conformational change in individual giant DNAs from pig liver is studied by use of fluorescence microscopy. With the addition of spermidine (a trivalent amine), each DNA chains undergo abrupt transition from an elongated coiled state into a folded compact state. It is found that the all-or-none characteristics in the folding transition for the mammalian DNA is similar to that in...
We attempted the rapid detection method of Legionella pneumophila by the asymmetric PCR and the fluorescence polarization. Eleven extracted DNAs from L. pneumophila serogroup 1 ∼ 6, L bozemanii, L dumoffii, L. gormanii, L micdadei, and Pseudomonas aeruginosa were amplified by asymmetric PCR, and the polarization of those products were measured. Only the polarization of L...
Benzimidazole compounds (Fig. 1) have been synthesized to study their DNA-bind-ing properties. Results obtained with spectroscopy and viscosity measurements indicate that the binding mode varies from intercalation to groove-binding, depending on the number of benzimidazole rings (conformation and size of compounds).
The crystal structure of DNA dodecamer with the sequence of d(CGCAAATTXGCG), where X is 2′-deoxy-N4-methoxycytidine, has been determined by X-ray analysis. The dodecamers form a double helix with B-form conformation. The electron density indicates that the two modified cytosine bases respectively make a pair with the adenine bases on the opposite strand in a manner of Watson...
A novel 2′-thio-2′-deoxyuridine derivative bearing a reactive ester at 2′-position was synthesized and incorporated into oligodeoxyribonucleotides (ODNs) for the post-synthetic modification of ODNs. This ODNs was reacted with several amines to give ODNs having a functional group at 2′-position.
To construct nuclease-resistant oligonucleotides, we designed novel carbocyclic L-nucleoside analogues (1-4) whose glycosyl conformation is fixed at χ ≈ 180° by an oxygen-bridge between the base and the cyclopentane ring. We have already achieved the racemic synthesis of these analogues. In this study, we succeeded in synthesizing an optically active form of these analogues. The...
We have previouly demonstrated that the ODNs with 2-amino-6-(2-phenylsulfoxyethyl)purine nucleoside derivative were capable of efficient interstrand cross-linking with cytidine selectively. In this new strategy, less reactive precursor was auto-activated within a duplex to generate 2-amino-6-vinylpurine derivative. However, it turned out that 2-amino-6-(2-phenylsulfinyl...
Peplomycin-mediated degradation of parallel-stranded (ps) duplex was investigated. It was found that Co- and Fe- peplomydns degraded ps DNA duplex by 4′-hydrogen abstraction at 5′-GPy (pyrimidine) site in a similar manner to that of antiparallel B-DNA. While the orientation of two strands of ps and B-form DNA duplexes are reversed, peplomycin metal complex can bind to ps DNA...
We report a novel non-enzymatic template-directed reversible photoligation of oligodeoxyribonucleotides (ODNs). In this photoligation system, a modified ODN containing 5-vinyldeoxyuridine at 5′-end reacts by photoirradiation at 366 nm with cytosine and thymine at the 3′-end of another ODN in the presence of a complementary template to yield a ligated ODN quantitatively. The...
We report the preparation of a deoxyribooligonucleotide containing a new thymine (6-4) photoproduct analog. The (6-4) photoproduct is one of the major forms of DNA lesions, and leads to mutation in DNA. An antibody (64M5) that binds the (6-4) photoproduct has been described. To investigate the interaction of the photoproduct with the 64M5 antibody, we prepared a (6-4...
Recently we found that KMnO4 oxidation of DNA oligomers containing a 7,8-dihydro-8-oxoguanine (8-oxo-G) residue induces damage to the neighboring base residues; other modified bases, 7,8-dihydro-8-oxoadenine (8-oxo-A) and 5-hydroxyuracil (5-oh-U), show similar behavior in DNA. The present study indicated that the ability to induce damage, which could also occur by the oxidation...
Synthesis of oligonucleotide 26-mers including single 5-formyl-2′-deoxy-uridine (1) or 5-formyl-2′-O-methyl-uridine (2) in place of thymidine at the κB site has been accomplished. One of the 26-mers with 1 was critically discriminated by the NFκB p50 homodimer in binding.
Syntheses of N-Fmoc δ-amino acids with an ether linkage in the main chain and six different nucleobases on the side chain, Fmoc-NH-C*H(CH2-CH2-B)-CH2-O-CH2-COOH (B = N6-benzoyladenine, thymine, uracil, N4-benzoylcytosine, guanine, and N2-isobutyryl-guanine) are described. The δ-amino acids were prepared through 8-12 step synthesis starting from L-homoserine and could be linked...
PNAs are DNA analogues in which the nucleic acid's backbone is replaced by a chiral or achiral pseudopeptide backbone and nucleobases are attached to the backbone by methylene carbonyl linkers. The easy to modify PNA structure gives the possibility to obtain monomers, and subsequently oligomers, with improved properties. We have synthesised several new PNA monomers, starting from...
Novel nucleotide analogues 1-6 were prepared as “multi-substrate”analogue inhibitors for purine nucleoside phosphorylases (PNPs). The cyclopropane and the tetrahydrofuran moieties of the alkyl spacer connecting a nucleobase and difluoromethylene phosphonic acid were found to be effective for good inhibition of PNPs.
Several nucleosides have been prepared as a possible inhibitor of human S-adenosyl-L-homocysteine (SAH) hydrolase for the development of anti-viral agents. Recently, SAH hydrolase has been considered as an attractive target for parasite chemotherapy for malaria. We report synthesis of several nucleosides including carbocyclic nucleosides and their inhibitory activities against...
A carbocyclic cyclopropane fused nucleoside, 9-(c-4-hydroxy- methylbicyclo[3.1.0]hex-r-2-yl)-9H-adenine, has been efficiently synthesized from 2-azabicyclo-[2.2.1]hex-5-en-3-one(ABH) in 6 steps, namely cyclopropanation, reductive amide cleavage (RAC) reaction and adenine ring construction.
A first total synthesis of the nucleoside antibiotic herbicidin B (1) was achieved in which a novel aldol-type C-glycosidation reaction promoted by samarium diiodide (Sml2) was used as a key step. Construction of the desired stereochemistry of the tricyclic-sugar moiety was successfully achieved by conformational restriction strategy based on repulsion between adjacent bulky...
A series of the oxanosine and carbocyclic oxanosine derivatives were synthesized to evaluate for their anti-HIV activity. Compound 1, 7 and 9 showed weak anti-HIV activities.
The chemical syntheses of genes encoding human c-Ha-ras and T4 endonuclease V are described. These genes have been used for studies of mutagenesis by damaged bases and recognition of nucleic acids by proteins. The modes of interaction of photo-damaged DNA and cognate antibodies have also been investigated by biochemical and physicochemical approaches.
This paper reports the synthesis of nucleotide antibiotics having N-acyl phosphoramidate linkages. The key reaction, the construction of the N-acyl phosphoramidate linkage was achieved by the reaction of nucleoside 5′-phosphoramidite derivatives with carboxamide derivatives in the presence of 5-(3,5-dinitrophenyl)-l/H-tetrazole as a very effective activator. By use of this...
An efficient synthesis of cyclic IDP-carbocyclic-ribose, as a stable mimic for cyclic ADP-ribose, was achieved. 8-Bromo-N1-carbocyclic-ribosylinosine derivative 10, prepared from N1-(2,4-dinitrophenyl)inosine derivative 5 and an optically active carbocyclic amine 6, was converted to 8-bromo-N1-carbocyclic-ribosylinosine bisphosphate derivative 15. Treatment of 15 with I2 in the...
PNAs are relatively novel DNA analogues, intensively studied due to their potential as gene-targeted drugs with antigene and antisense properties. In 1996 we elaborated a new method of synthesis of PNA monomer backbones based on the Mitsunobu reaction with N-tosyl-protected (Tos) amino acid esters as acidic components of the reaction. Since the method used for the Tos group...
2′-Deoxyoxanosine (dOxo) is a novel DNA lesion produced from 2′-deoxyguanosine by the reaction with nitrous acid or nitric oxide. We found that dOxo reacted with glycine under physiological conditions. The product was identified by spectrometric data as an adduct between the six membered ring of dOxo and an amino group of glycine. The adduct was more stable than dOxo under...