PubMed Health⌕ Search

Biomedical subjects

Etsuko Kawashima

Publications and source records attributed to Etsuko Kawashima.

11 recordsLinked to original sources
PubMed2005

N1-aminopropylagmatine, a new polyamine produced as a key intermediate in polyamine biosynthesis of an extreme thermophile, Thermus thermophilus.

In the extreme thermophile Thermus thermophilus, a disruption mutant of a gene homologous to speB (coding for agmatinase = agmatine ureohydrolase) accumulated N1-aminopropylagmatine (N8-amidino-1,8-diamino-4-azaoctane, N8-amidinospermidine), a new compound, whereas all other polyamines produced by the wild-type strain were absent from the cells. Double disruption of speB and speE (polyamine aminopropyltransferase) resulted in the disappearance of N1-aminopropylagmatine and the accumulation of agmatine. These results suggested the following. 1) N1-Aminopropylagmatine is produced from agmatine by the action of an enzyme coded by speE. 2) N1-Aminopropylagmatine is a metabolic intermediate in the biosynthesis of unique polyamines found in the thermophile. 3) N1-Aminopropylagmatine is a substrate of the SpeB homolog. They further suggest a new biosynthetic pathway in T. thermophilus, by which polyamines are formed from agmatine via N1-aminopropylagmatine. To confirm our speculation, we purified the expression product of the speB homolog and confirmed that the enzyme hydrolyzes N1-aminopropylagmatine to spermidine but does not act on agmatine.

Agmatine↗
PubMed2005

Stabilization of nucleic acids by unusual polyamines produced by an extreme thermophile, Thermus thermophilus.

Extreme thermophiles produce two types of unusual polyamine: long linear polyamines such as caldopentamine and caldohexamine, and branched polyamines such as quaternary ammonium compounds [e.g. tetrakis(3-aminopropyl)ammonium]. To clarify the physiological roles of long linear and branched polyamines in thermophiles, we synthesized them chemically and tested their effects on the stability of ds (double-stranded) and ss (single-stranded) DNAs and tRNA in response to thermal denaturation, as measured by differential scanning calorimetry. Linear polyamines stabilized dsDNA in proportion to the number of amino nitrogen atoms within their molecular structure. We used the empirical results to derive formulae that estimate the melting temperature of dsDNA in the presence of polyamines of a particular molecular composition. ssDNA and tRNA were stabilized more effectively by tetrakis(3-aminopropyl)ammonium than any of the other polyamines tested. We propose that long linear polyamines are effective to stabilize DNA, and tetrakis(3-aminopropyl)ammonium plays important roles in stabilizing RNAs in thermophile cells.

DNA, Bacterial↗
PubMed2004

New sequential-assignment routes of nucleic acid NMR signals using a [5'-(13)C]-labeled DNA dodecamer.

NMR signal assignments for DNA oligomers have been performed by the well-established sequential assignment procedures based on NOESY and COSY. The H4'/H5'/H5'' resonance region is congested and difficult to analyze without the use of isotope-labeled DNA oligomers. Here a DNA dodecamer constructed with 2'-deoxy[5'-(13)C]ribonucleotides, 5'-d(*C*G*C*G*A*A*T*T*C*G*CG)-3' (*N = [5'-(13)C]Nucleotide), was prepared in an effort to analyze the H4'/H5'/H5'' resonance region by 2D 1H-13C HMQC-NOESY. In the C5' and H1' resonance region, weak and strong cross peaks for C5'(i)-H1'(i) and C5'(i)-H1'(i-1), respectively, were found, thus enabling the sequential assignment within this region. A similar sequential assignment route was found between C5' and H2''. Proton pair distances evaluated from the canonical B-DNA as well as A-DNA indicated that these sequential-assignment routes on a 2D 1H-13C HMQC-NOESY spectrum work for most nucleic acid stem regions.

Carbon Isotopes↗
PubMed2003

6-(Levulinyloxymethyl)-3-methoxy-2-nitrobenzoyl and 2-(levulinyloxymethyl)-5-methoxy-4-nitrobenzoyl groups as novel base-labile groups for 5'-hydroxy protection in solid-phase oligonucleotide synthesis.

The 6-(levulinyloxymethyl)-3-methoxy-2-nitrobenzoyl (LMMoNBz) and 2-(levulinyloxymethyl)-5-methoxy-4-nitrobenzoyl (LMMpNBz) groups were developed as novel base-labile groups for 5'-hydroxy protection in solid-phase oligonucleotide synthesis. A comparative study of the utility of LMMoNBz, LMMpNBz, and 2-(levulinyloxymethyl)-5-nitrobenzoyl (LMNBz) groups is described.

Chromatography, High Pressure Liquid↗
PubMed2003

Design, synthesis and analysis of antiviral nucleosides bearing pyrrolepolyamide binding to nucleic acid (II): N2-pyrrolepolyamidopropylguanosine.

Synthesis of guanosine bearing pyrrolepolyamide (1) and analysis of DNA interaction with 1 were carried out. Compound 1 was synthesized by condensation of 2-N-beta-alanyl-3,5-TIPDS-guanosine with 1-methyl-4-[1-methyl-4-[1-methyl-4-(formylamino)pyrrole-2-carboxamido]pyrrole-2-carboxamido]pyrrole-2-carboxylic acid which was prepared from N-methylpyrrole. To investigate the interaction between 1 and DNA in Circular Dichroism spectra and Tm values, we used distamycin A and adenosine bearing pyrrolepolyamide (Apy), which has the high sequence-selectivity of DNA, as a contrast.

Antiviral Agents↗
PubMed2003

Synthesis of oligonucleoside phosphorodithioates by the H-phosphonothioate method using bis(2,6-dimethylphenyl)phosphorochloridate as a coupling agent.

The phosphorodithioate octamer [(TpS2)7T] was efficiently synthesized using bis(2,6-dimethylphenyl)phosphorochloridate as a coupling agent by the H-phosphonothioate method, which performed the sulfurization with elemental sulfur after completion of oligonucleoside H-phosphonothioate assembly, as the standard H-phosphonate method.

Chromatography, High Pressure Liquid↗
PubMed2002

Synthesis of [5'-13C]ribonucleosides and 2'-deoxy[5'-13C]ribonucleosides.

The present efficient synthesis of [5'-13C]ribonucleosides and 2'-deoxy[5'-13C]ribonucleosides is characterized by the synthesis of the D-[5-13C]ribose derivative as an intermediate via the Wittig reaction of 4-aldehydo-D-erythrose dialkyl acetals with Ph3P13CH3I-BuLi to introduce the 13C label at the 5-position of a pentose. This was followed by the highly diastereoselective osmium dihydroxylation for the preparation of 2,3-di-O-benzyl-D-[5-13C]ribose dialkyl acetal and the cyclization from D-[5-13C]ribose dialkyl acetal derivatives to the alkyl D-[5-13C]ribofuranoside derivative by the use of LiBF(4). The obtained D-[5-13C]ribose derivative was converted into [5'-13C]ribonucleosides and subsequently into the corresponding 2'-deoxynucleosides.

Carbon Isotopes↗
PubMed2002

Novel base-labile protecting groups for 5'-hydroxyl protection in the synthesis of oligonucleotides.

The 6-(levulinyloxymethyl)-3-methoxy-2-nitrobenzoyl (LMM0NBz) and 2-(levulinyloxy-methyl)-5-methoxy-4-nitrobenzoyl (LMMpNBz) groups were developed as novel base-labile protection for the 5'-hydroxyl group in solid-phase oligonucleotide synthesis. A comparative study on the utility of LMMoNBz, LMMpNBz, and 2-(levulinyloxymethyl)-5-nitrobenzoyl (LMNBz) groups for the synthesis of oligodeoxyribonucleotides, and the synthesis of oligoribonucleotides using the LMMoNBz group in combination with the acid-labile 1-ethoxyethylk (EE) group to protect the 2'-hydroxyl group, are described.

Hydroxyl Radical↗
PubMed2002

Stereoselective synthesis of [5'-2H1][5'-13C]nucleosides.

An approach to a synthesis of stereoselective 5'-monodeuterated nucleoside combined with 13C label is described. A preparation of (5R)-D-[5-(2)H1;5-(13)C]ribose derivative of 1,2:5,6-di-O-isopropyliden-alpha-D-allofranose was successfully achieved by a 13C Wittig reaction using Ph3P13CH3I-BuLi to 5-oxoribose derivative and subsequent transformation into D-[5-(13)C]ribose derivative with an AD reaction, selective acylation, oxidation with NaIO4, and a stereoselective deuteride transfer reaction from Alpine-Borane-d to 5-oxo-D-[5-(13)C]ribose derivative as the main reaction. (5'R)-[5'-(2)H1;5'-(13)C]nucleosides were synthesized in the established manner from this 5-(13)C/2H1-double-labeled ribose.

Nucleosides↗
PubMedDate not supplied

Novel base-labile protecting groups for 5'-hydroxy function in solid-phase oligonucleotide synthesis.

The 6-(levulinyloxymethyl)-3-methoxy-2-nitrobenzoyl (LMMoNBz) and 2-(levulinyloxymethyl)-5-methoxy-4-nitrobenzoyl (LMMpNBz) groups were developed as novel base-labile protection for the 5'-hydroxy function in solid-phase oligonucleotide synthesis. A comparative study of the LMMoNBz, LMMpNBz and 2-(levulinyloxymethyl)-5-nitrobenzoyl (LMNBz) protecting groups for oligonucleotide synthesis proved strong feasibility for the LMMoNBz group.

Chromatography, High Pressure Liquid↗