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Biomedical subjects

S Uesugi

Publications and source records attributed to S Uesugi.

At least 163 records · Page 9Linked to original sources
PubMed1985

Salt induced conformational transition between A and Z forms of r(CGCGCG) as revealed by a Raman spectroscopic study.

Solution conformation in different conditions of r(CGCGCG) has been studied by a Raman spectroscopic method. In NaCl solution, r (CGCGCG) takes only an A-form duplex in which guanosine and cytidine have C3'endo-anti conformation even at 5M salt concentration. In much higher ionic strength condition (5M NaCl plus 1M MgCl2 or 6M NaClO4), it undergoes a transition to a left-handed Z-form. The Raman spectrum of the Z-form RNA was found to be very similar to that of Z-form DNA, suggesting that Z-RNA involves a C3'endo-syn guanosine and an in between form of C2'endo-Cl'exo-anti cytidine.

Kinetics↗
PubMed1984

Synthesis and conformational studies of ribooligonucleotides which contain an alternating C-G sequence and show unusual circular dichroism spectra.

The poly [r(C-G)] duplex shows an unusually large negative CD band in the long wavelength region. In order to elucidate this phenomenon, r(C-G-C-G) and r(C-G-C-G-C-G) were synthesized by a phosphotriester method and their properties were examined by UV, CD, 1H and 31P NMR spectroscopy. These ribooligomers form self-duplexes at low temperature, the CD spectra of which show negative bands at around 290 nm and positive bands at around 265 nm. The results of 1H nuclear Overhauser effect experiments, 1H chemical shift-temperature profiles of base protons, and the sharp singlet observed for all H1' protons are consistent with a normal A-RNA structure but not with a Z-DNA like structure. The CD-temperature profiles and 31P NMR spectra support this conclusion. These results indicate that RNA duplexes with an alternating C-G sequence can give an unusually large negative CD band in the long wavelength region despite their right-handed helical structure.

Base Sequence↗
PubMed1984

Identification of oligonucleotide fragments produced in a strand scission reaction of the d(C-G-C-G-C-G) duplex by bleomycin.

To elucidate the mechanism of DNA strand scission by bleomycin, a d(C-G-C-G-C-G) duplex was treated with the bleomycin-iron ion complex in the presence of H2O2 and degradation products (1, 2, cytosine and deoxyguanosine 5'-phosphate) were identified. 1 and 2 contain a carboxymethyl group attached to the 3'-terminal phosphoryl group of d(C-Gp) and d(C-G-C-Gp), respectively. These compounds were identified by UV, 1H and 31P NMR spectroscopy and paper electrophoresis. 1 was synthesized from the protected dinucleotide and glycolic acid and the proton NMR spectrum was identical to that of 1 obtained as a degradation product. Thus the oligonucleotide fragments produced by the action of bleomycin on DNA were directly identified and cleavage of the C3'-C4' bond of the sugar residues was proved.

Bleomycin↗
PubMed1984

Conformation of ribooligonucleotide duplexes containing an alternating C-G sequence which show an unusual circular dichroism spectrum.

The poly[r(G-C)] duplex shows an unusually large negative band in the long wavelength region of the CD spectrum. In order to elucidate this phenomenon, r(C-G-C-G) and r(C-G-C-G-C-G) were synthesized chemically and their properties were examined by UV and CD, and 1H and 31P NMR spectroscopy. These ribooligomers form a self-complementary duplex at low temperature, the CD spectrum of which shows a negative band at around 290 nm and a positive band at around 265 nm with almost equal magnitudes. The proton resonances in the 1H NMR spectra of the oligo[r(C-G)] duplexes were assigned by nuclear Overhauser effect experiments. The chemical shift-temperature profiles of the base proton signals and the sharp singlets observed for all H1' protons are consistent with a normal A-RNA structure but not with a Z-DNA like structure. Moreover, a 500-MHz two-dimensional nuclear Overhauser effect experiment recorded for r(C-G-C-G-C-G) shows that all guanine bases adopt the normal anti-conformation. CD-temperature profiles and 31P NMR spectra of oligo[r(C-G)]s support this conclusion. These results indicate that duplexes of oligo- and polyribonucleotides containing alternating C-G sequences can give an unusually large negative CD band in the long wavelength region despite their right-handed helical structure.

Base Sequence↗
PubMed1984

Serological survey of hepatitis B virus (HBV) markers in out- and in-patients in a university hospital.

Of a total of 13,596 patients and 1,876 blood donors in a university hospital examined, 550 (4.1%) patients and 31 (1.7%) donors possessed hepatitis B surface antigen (HBsAg) in their blood. The higher incidence of HBsAg in the patient population than in the blood donors verified the view that medical personnel and hospitalized patients are at increased risk of acquiring HBV infection. To assess the actual hazard of the HBsAg-positive patients, we examined hepatitis Be antigen (HBeAg) and its antibody (anti-HBe) status of 228 HBsAg-positive patients and found that 39 (18%) were positive for HBeAg and 168 (74.5%) were positive for anti-HBe. This indicated that only one fifth of the HBsAg-positive patients should be drawn attention in terms of HBV transmission within a hospital.

Hepatitis B Antigens↗
PubMed1984

Synthesis and expression of RNase T1 gene.

In order to obtain knowledges about structure-function relationship of ribonuclease T1, we synthesized a structural gene for RNase T1 and several its modified genes. Using amino acid codons frequently used in Escherichia coli we designed genes consist of 328 X 2 bases. Synthesis of oligodeoxynucleotides with 9-20 base lengths was performed by 1% polystyrene supported triester approach and resulting 42 oligomers were joined together using T4 DNA ligase. The product was analyzed and utilyzed to construct expression vectors, which produced effectively fused proteins.

Amino Acid Sequence↗
PubMed1983

Poly(8-methyladenylic acid): a single-stranded regular structure with alternating syn-anti conformations.

Poly(8-methyladenylic acid) has been prepared by chemical synthesis of 8-methyladenosine 5'-diphosphate and enzymatic polymerization with polynucleotide phosphorylase. The polymer exhibits a large hypochromism and cooperative melting in neutral solution. The transition temperature is independent of salt concentration at moderate ionic strength and decreases slightly at high salt. The adenine ring vibration at 1626 cm-1 is independent of temperature. A high-resolution nuclear magnetic resonance spectrum is observed near the bottom of the melting range. The chemical shift of the H2 proton exhibits a large upfield shift in the ordered form, and the temperature profile of H2 is cooperative and congruent with the UV melting curve. The CH3 proton signal, in striking contrast to H2, is independent of temperature. These results support a regular, single-stranded helix in the ordered form, in contrast to both poly(adenylic acid) and poly(8-bromoadenylic acid). We suggest that the contrasting temperature dependence of the H2 and CH3 proton signals can be accounted for by regularly alternating syn and anti conformations of the 8-methyladenylic acid residues.

Magnetic Resonance Spectroscopy↗
PubMed1983

Raman diagnosis of nucleic acid structure: sugar-puckering and glycosidic conformation in the guanosine moiety.

Observations of Raman spectra of various nucleic acids indicate that the guanine ring breathing frequency is sensitive to the internal rotation angle around the glycosidic bond and to the conformation of the five-membered ring of the ribose residue that is directly connected with the guanine residue in question. It is found that 682 cm-1 for C2'-endo-anti, at 665 cm-1 for C3'-endo-anti, and at 625 cm-1 for C3'-endo-syn. A DNA octamer d(GpGpApApTpTpCpC) shows, in its aqueous solution, a broad Raman band at 680 cm-1 with a tail at 670 cm-1. This fact suggests that the guanosine residues in this oligomer take primarily C2'-endo-anti conformation but an appreciable amount of fluctuation of the ribose ring structure towards C3'-endo is involved.

Base Sequence↗
PubMed1983

Flexibility and rigidity of left-handed Z-DNA.

The local variation of torsional angles and helical parameters in Z-DNA was analyzed. The sugar phosphate backbone is fairly rigid but the angles at GpC linkage are more changeable than those at CpG linkage in order to form a variety of structures. The water channel at minor groove is important to stabilize and retain the novel Z-DNA helix.

DNA↗
PubMed1982

Synthesis and properties of ApU analogues containing 2'-halo-2'-deoxyadenosines. Effects of 2' substituents on oligonucleotide conformation.

Five A-U analogues containing deoxyadenosine or 2'-halo-2'-deoxyadenosines, which are known to have widely different C3'-endo conformer populations according to their electronegativities of the halogen substituents, dAfl-U, dAcl-U, dAbr-U, dAio-U, and dA-U, were synthesized chemically. Characterization of these dimers has been performed by UV absorption, circular dichroism, and proton nuclear magnetic resonance spectroscopy. The results show that the dimers containing 2'-halo-2'-deoxyadenosines have stacked conformations with a geometry similar to that of A-U and the degree of stacking decreases in the order dAfl-U greater than dAcl-U greater than dAbr-U greater than dAio-U. dAcl-U is assumed to have the same degree of stacking as A-U. dA-U takes a more stacked conformation than does dAio-U, but the mode of stacking is different from those of the other dimers. The effects of the 2' substituents on dimer conformation are discussed in terms of electronegativity, molecular size, and hydrophobicity.

Circular Dichroism↗
PubMed1982

Synthesis and properties of CpG analogues containing an 8-bromoguanosine residue. Evidence for Z-RNA duplex formation.

Three dinucleoside monophosphates containing 8-bromoguanosine (br8G), (2'-5')C-br8G, (3'-5')C-br8G, and dC-br8G, were synthesized and characterized by UV absorption, CD, and 1H NMR spectroscopy. The 1H NMR data show that all the br8G residues in these dimers take a syn glycosidic conformation. At low dimer strand concentration (5 X 10(-5) M), the UV hypochromicity data suggest that the degree of base stacking decreases in the following order, (2'-5')C-br8G greater than C-G approximately equal to dC-br8G greater than (3'-5')C-br8G. The CD data also suggest little stacking in (3'-5')C-br8G. At high dimer strand concentration (5 X 10(-3) M), only (3'-5')C-br8G shows duplex formation in 0.1 M NaCl. The duplex is assumed to take a left-handed helical structure similar to that of Z-DNA. The Tm of this duplex is surprisingly high for a dimer (about 35 and 45 degrees C at 5 X 10(-3) and 10(-2) M dimer strand concentration, respectively). The above results and the similarity between the CD spectra of (3'-5')C-br8G and poly(G-C) suggest the possible existence of Z-form structure in ribooligo- and ribopolynucleotides with alternating purine-pyrimidine sequences.

Circular Dichroism↗
PubMed1982

Deoxyoligonucleotide chain cleavage reactions by phenanthroline and bleomycin.

To elucidate the mechanisms of double-stranded DNA chain cleavage by 1,10-phenanthroline-Cu(I) and bleomycin-Fe(II) complexes in oxygen-dependent reactions, self-complementary deoxyoligonucleotides were treated with the complexes and the degradation products were characterized. The degradation products of d(C-G) by the phenanthroline complex were fully identified by UV, proton and carbon-13 NMR and paper electrophoresis. It is assumed that the DNA chain cleavage and concomitant base release are caused by oxidation of Cl' of the deoxyribose moiety. A duplex of d(ATACGCGTAT) was cleaved by both complexes. Bleomycin shows some sequence specificity but phenanthroline does not.

Base Sequence↗
PubMed1982

NMR studies of base-pairing in 15N-labeled ribotetranucleotide GGCUp.

95% N-15 enriched ribotetranucleotide GGCUp was prepared. Its aqueous solution gives three imino-proton resonances at 10.6, 12.0 and 13.6 ppm. The peak at 10.6 ppm split by N-15 into a doublet with coupling constant 90 Hz. On the preirradiation at this peak, the intensity of the 12.0 ppm peak decreased and the peak at 13.6 ppm remained unchanged. Therefore the 10.6 ppm peak was unambiguously assigned to the G imino proton and the 12.0 ppm peak to the U imino proton in the G:U base pair. By raising temperature the former two peaks coalesced at around 25 degrees C, while the signal of the G imino proton in the G:C pair was observed up to 35 degrees C. The G:U base pair seems to be disrupted first, then the break of the G:C pair is followed. Temperature dependences of the CH proton, N-15 and P-31 nuclei resonances were also measured.

Kinetics↗
PubMed1981

Left handed double helices: effect of sequence on the spatial configuration of high anti nucleic acids.

The conformational properties of purine-pyrimidine and pyrimidine-purine dinucleoside monophosphates in which the glycosidic torsion is fixed to congruent to 120 degree by the formation of a covalent link between the base and the sugar ring are explored by 1H NMR spectroscopy in order to obtain information about the spatial configuration of high anti nucleic acids. The intramolecular stack of the high anti dimers were found to be left handed, in contrast to that (right handed) for natural oligomers, which are low anti. Even though both the high anti pyrimidine-purine and purine-pyrimidine dimers have similar backbone torsion angles, they display widely different relative geometry between the bases; thus in the former there is extensive base-base overlap in the stack, and in the latter there is negligible intramolecular base-base overlap. In addition it was found that purine-pyrimidine systems form miniature double helices in which there is substantial interstrand purine-purine interaction; on the other hand the pyridine-purine high anti dinucleosides have no proclivity to form such base-paired complexes in solution. Mathematical polymerization of the conformation of the high anti purine-pyrimidine dinucleoside monophosphates generates a left handed helix for high anti polynucleotides. This also means that the double helix for high anti-nucleic acids containing purine-pyrimidine repeated units may also be left handed, as had been suggested [Sundaralingam, M., & Yathindra, N. (1977) Int. J. Quantum Chem., Quantum Biol. Symp. 4, 285]. It is suggested that the plasticity in the structure of genomic DNA is such that, if under certain conditions of interactions the sugar-base torsion of certain domains assume high anti values, that domain will become left handed, and this in turn can be a mechanism for the control of expression by genomic DNA.

Dinucleoside Phosphates↗