Biomedical subjects

H Hiroaki

Publications and source records attributed to H Hiroaki.

27 records · Page 2Linked to original sources

PubMed1990

Studies on the structure and stabilizing factor of the CUUCGG hairpin RNA using chemically synthesized oligonucleotides.

A tridecaribonucleotide, r-UGAGCUUCGGCUC, and two analogues r(UGAGC)d(UUCG)r(GCUC) and r-UGAGCUUCIGCUC, which form a hairpin structure with a four-base-paired stem and a UUCG loop, were synthesized by the solid-phase phosphoramidite method. Properties of these three oligomers and d-TGAGCTTCGGCTC, the DNA analogue, were studied by UV, CD and NMR spectroscopy. The melting temperature (Tm) data suggest that the 2'-hydroxy1 groups and the 2-amino group of guanosine in the loop (9G) stabilize the CUUCGG hairpin which is known to have an unusually high Tm. NMR studies show that this 9G takes a syn conformation and the phosphodiester backbone has a turn at 9G-10G which is a junction of the stem and loop.

Base Sequence↗

PubMed1990

The role of a conserved guanosine residue in the hammerhead-type RNA enzyme.

We have designed a hammerhead-type RNA system which consists of three RNA fragments for normal and modified complexes which contain a non-cleavable substrate with 2'-O-methylcytidine and a guanosine-to-inosine replaced enzyme. Examination of the RNA-cleaving activity and conformational properties of the complexes suggests that the 2-amino group of a conserved guanosine residue in the loop region plays an important role for maintaining both the activity and loop conformation.

Base Sequence↗

PubMed1990

Base recognition mechanism of bleomycin: solution structure of d(GGGGAGCTCCCC)2 based on 1H-NMR and restrained molecular dynamics.

The self-complementary d(GGGGAGCTCCCC) dodecanucleotide cleavage by bleomycin occurs at G(4)pA(5) site rather than G(6)pC(7) site which is known as the preferential sequence. The molecular structure of this dodecamer is observed as the distorted B-DNA by the CD spectra and proton NMR measurements. Three-dimensional structures in solution evaluated by molecular dynamics calculations with inter proton distance restraints have the distorted form of the minor groove structure at G(6)pC(7) site. These evidences offer the recognition mechanism model of the DNA base sequence by bleomycin.

Base Sequence↗

PubMed1990

Identification of DNA degradation products by antitumor antibiotic, esperamicin.

Esperamicin A1 is a DNA-damaging agent characterized by a unique ten-membered ene-diyne core. We studied the detailed reaction mechanism by using synthetic DNA oligomers. The cleavage site and activity depend on the sequence of the oligomers. d(GGATCC) and d(GGTACC) were cleaved by the drug while d(CCATGG) and d(CCTAGG) were not cleaved under the present conditions. d(GGTACC) gave two major 5'-fragments. The result of partial nuclease digestion experiments suggests that these products are trimer and pentamer with a modified 3'-end.

Aminoglycosides↗

PubMed1990

Conformation and properties of hammerhead-type RNA enzymes.

We designed a hammerhead-type RNA enzyme system which consists of three ribooligonucleotide strands (1-3), synthesized these oligomers and their analogues, and examined conformation and properties of the RNA complexes. Imino proton NMR spectra of the complexes were measured and the signals were assigned by comparison with the spectra of some model duplexes. Examination of a complex containing a G----I mutation (Y = I) revealed that the 2-amino group of the third guanosine residue in the loop 1 (L1) plays an important role for maintaining both the activity and loop conformation.

Base Sequence↗

PubMed1989

A 2-deoxyribonolactone-containing nucleotide: isolation and characterization of the alkali-sensitive photoproduct of the trideoxyribonucleotide d(ApCpA).

It has been reported that ACA sequences in DNA are mutagenic hot spots in UV-induced mutagenesis and are sites of an alkali-sensitive lesion produced by UV irradiation. In order to characterize the UV-induced lesion of an ACA site, chemically synthesized trideoxyribonucleotide d(ApCpA) was irradiated with UV light and the alkali-sensitive photoproduct was isolated. The structure of this photoproduct was characterized as the trinucleotide containing 2-deoxyribonolactone at the internal residue by 2D DQF-COSY, FT-IR, FAB-MS, and chemical properties. It is known that this lesion is also produced by gamma-irradiation, neocarzinostatin, the 1,10-phenanthroline-copper complex, and hydrogen peroxide and is highly mutagenic because of its resistance to cleavage by certain apurinic/apyrimidinic (AP) endonucleases. Thus, 2-deoxyribonolactone may be one of the lethal DNA lesions induced by UV irradiation to organisms and one of the intermediates of UV-induced DNA strand breaks because the DNA strand is cleaved at this site with beta- and subsequent delta-elimination mechanisms.

Base Composition↗

PubMed1989

Novel 1H-31P heteronuclear coherence transfer spectroscopy based on spin locking MLEV-17 and its application to signal assignment for a short DNA fragment.

We have applied the MLEV-17 proton spin locking pulse to 1H-31P 2D heteronuclear correlation spectroscopy. Using this technique, long-range correlations between a proton and phosphorus that is up to 5 bonds distant are observed. Thus, the 3'-, 4'- and 5'-proton resonances can be traced 'sequentially' along the chain on the 2D NMR chart. Application of this technique to the complete assignment of the sugar proton and phosphorus resonances for d(ApGpA) is reported. This technique can also be used for convenient assignment of the phosphorus resonances of oligonucleotides as correlations between the 1'-proton and its 3'-side phosphorus are observed.

DNA↗

PubMed1989

Synthesis and properties of RNA with catalytic activity.

Ribooligonucleotides, which form the self-cleavage domain of a satellite RNA of tobacco ringspot virus, were synthesized by the solid-phase phosphoramidite method using o-nitrobenzyl groups for 2'-hydroxyl protection. The oligomers were obtained in quantities sufficient for NMR measurement. Specific cleavage at an expected site was observed when the three RNA fragments were mixed in the presence of magnesium ions.

Base Sequence↗

PubMed1989

NMR studies on DNA hairpin structures with a five nucleotide loop.

One- and two-dimensional NMR experiments have been undertaken to investigate the structure of DNA hairpins with a five nucleotide loop. Analysis of proton NMR spectra suggests that the four hairpin structures examined have some common structural features; B-type conformation in the stem region and the same stacking pattern, 5' (XXX-turn-XX) 3', in the loop region. The phosphorus NMR spectra suggest that the conformational changes in the loop region affect the backbone conformation of the stem duplex.

Base Sequence↗