PubMed Health⌕ Search

Biomedical subjects

C Kojima

Publications and source records attributed to C Kojima.

At least 19 recordsLinked to original sources
PubMed1999

Structural effect of complete [Rp]-phosphorothioate and phosphorodithioate substitutions in the DNA strand of a model antisense inhibitor-target RNA complex.

Chemically modified DNA oligonucleotides have been crucial to the success of antisense therapeutics. Although such modifications are ubiquitous in the clinic, high-resolution structural studies of pharmaceutically relevant derivatives have been limited to only a few molecules. We have completed a high-resolution NMR structural study of three DNA.RNA hybrids with the sequence d(CCTATAATCC). r(GGAUUAUAGG). All hybrids contain an unmodified RNA strand, whereas the DNA strand of each hybrid contains one of three different sugar-phosphate backbone linkages at each nucleotide: (1) phosphate, (2) [Rp]-phosphorothioate, or (3) phosphorodithioate. The UV and NMR melting profiles revealed that the normal hybrid is more stable than the [Rp]-phosphorothioate, which in turn is more stable than the phosphorodithioate. Homonuclear two-dimensional nuclear Overhauser effect spectroscopy and double quantum-filtered correlation spectroscopy afforded nearly complete non-labile proton assignments. The three molecules show nearly equivalent chemical shifts, with the exception of H3' protons, which are shifted downfield in a manner that appears correlated with the degree of sulfur substitution at phosphate. All three hybrids exhibit unusually broad linewidths for deoxyribose protons H2' and H2".Distance restraints were calculated from NOE cross-peak intensities via a complete relaxation matrix approach using the program RANDMARDI. Detailed comparison of interproton distances from each hybrid indicates that the three molecules share a common structure, with neither strand in canonical A or B form. Correlation of R factors, calculated using the program CORMA with DNA H2'-base and H3'-base distances, revealed a relative increase in the population of B-type sugar conformations for deoxyriboses in the A+T-rich center of the hybrid sequence. It is widely known that the activity of enzymes which act upon DNA.RNA hybrid substrates (e.g. ribonuclease H) is impacted when the hybrids contain phosphorothioate or phosphorodithioate substitutions. The structural similarity of the three hybrids examined here suggests that factors other than global structure may mediate the activity of these enzymes.

Base Sequence↗
PubMed1999

Quantitative measurement of transverse and longitudinal cross-correlation between 13C-1H dipolar interaction and 13C chemical shift anisotropy: application to a 13C-labeled DNA duplex.

Measurement of both longitudinal and transverse relaxation interference (cross-correlation) between 13C chemical shift anisotropy and 13C-1H dipolar interactions is described. The ratio of the transverse to longitudinal cross-correlation rates readily yields the ratio of spectral densities J(0)/J(omegaC), independent of any structural attributes such as internuclear distance or chemical shift tensor. The spectral density at zero frequency J(0) is also independent of chemical exchange effects. With limited internal motions, the ratio also enables an accurate evaluation of the correlation time for overall molecular tumbling. Applicability of this approach to investigating dynamics has been demonstrated by measurements made at three temperatures using a DNA decamer duplex with purines randomly enriched to 15% in 13C.

Anisotropy↗
PubMed1998

Risk factors for recurrent and residual cholesteatoma in children determined by second stage operation.

OBJECTIVE: To clarify the risk factors for the development of recurrent and residual cholesteatoma in children. METHODS: We studied 84 ears of 83 children aged 10 years or younger who underwent a second stage operation 1 year after primary surgery with a canal wall reconstruction procedure, and analyzed the clinical risk factors for recurrent and residual cholesteatoma. RESULTS: Recurrent cholesteatoma was detected in 21 ears (25%) and residual cholesteatoma was noted in 35 (42%) of 84 ears. With respect to recurrent cholesteatoma, significant risk factors were determined to be male gender, pars flaccida type of cholesteatoma and the association of otitis media with effusion either in the side affected by cholesteatoma or on the opposite side. On the other hand, congenital type of cholesteatoma was a significant negative risk factor. With respect to residual cholesteatoma, the only risk factor was a posterosuperior type of cholesteatoma. Residual cholesteatoma was sometimes found even when the surgeon had declared complete removal of the cholesteatoma matrix at the time of primary surgery. CONCLUSIONS: High incidence of recurrent and residual cholesteatoma was noted at the second stage operation. Occurrence of recurrent cholesteatoma is closely related to eustachian tube dysfunction. Thin and highly proliferative cholesteatoma matrix in children may be responsible for high occurrence of residual cholesteatoma. Therefore, planned staged surgery is preferable to single stage surgery for the treatment of pediatric cholesteatoma.

Child↗
PubMed1998

DNA duplex dynamics: NMR relaxation studies of a decamer with uniformly 13C-labeled purine nucleotides.

Dynamics in a DNA decamer duplex, d(CATTTGCATC). d(GATGCAAATG), were investigated via a detailed 13C NMR relaxation study. Every 2'-deoxyadenosine and 2'-deoxyguanidine was chemically enriched with 15% 13C and 98% 15N isotopes. Six nuclear relaxation parameters [R(13Cz), R(1Hz), R(2(1)Hz13Cz), R(13Cx), R(2(1)Hz13Cx) and steady-state 13C¿1H¿ NOE] were measured at 600 MHz and three were measured at 500 MHz (1H frequency) for the CH spin systems of sugar 1', 3', and 4' as well as base 8 and 2 positions. A dependence of relaxation parameter values on chemical position was clearly observed; however, no sequence-specific variation was readily evident within our experimental error of approximately 5-10%, except for 3' and 5' termini. It was demonstrated that the random 15% 13C enrichment effectively suppressed both scalar and dipolar contributions of the neighboring carbons and protons on the relaxation parameters. To analyze dynamics via all observed relaxation parameters, full spectral density mapping (1992, J. W. Peng and G. Wagner, J. Magn. Reson. 98, 308) and the "model-free" approach (1982, Lipari and Szabo, J. Am. Chem. Soc. 104, 4546) were applied complementarily. A linear correlation between three spectral density values, J(omegaC), J(omegaH - omegaC), and J(omegaH + omegaC) was observed in plots containing all measured values, but not for the other spectral density terms including J(0). These linear correlations reflect the effect of overall motion and similar internal motions for each CH vector in the decamer. The correlations yielded two correlation times, 3-4 ns and 10-200 ps. One value, 3-4 ns, corresponds to the value of 3.3 ns obtained for the overall isotropic tumbling correlation time determined from analysis of 13C T1/T2 ratios. The possibility of overall anisotropic tumbling was examined, but statistical analysis showed no advantage over the assumption of simple isotropic tumbling. Lack of correlations entailing J(0) implies that a relatively slow chemical exchange contributes to yielding of effective Jeff(0) values. Based on spectral density mapping and the T1/T2 ratio analysis, three basic assumptions were initially employed (and subsequently justified) for the model-free calculation: isotropic overall tumbling, one internal motion, and the presence of chemical exchange terms. Except for terminal residues, the order parameter S2 and the corresponding fast internal motion correlation time were determined to be about 0.8 +/- 0.1 and 20 +/- 20 ps, respectively, for the various CH vectors. Only a few differences were observed between or within sugars and bases. The internal motion is very fast (ps-ns time scale) and its amplitude restricted; e.g., assuming a simple wobble-in-a-cone model, the internal motion is restricted to an angular amplitude of +/-22. 5 degrees for each of the 1', 3', 4', 2, and 8 positions in the purine nucleotides in the entire duplex.

Adenosine↗
PubMed1997

[Histopathological studies of temporal bones of patients with malignant melanoma].

Although malignant melanoma is known to metastasize to various sites including the temporal bones, there have been few studies on temporal bone histopathology in malignant melanoma. Here we describe the temporal bone histopathology of 5 patients (10 temporal bones) who died of malignant melanoma with multiple metastasis to many internal organs and bones. We investigated the temporal bone based on the following three points: 1) the presence of metastatic lesions in the temporal bone, 2) inner ear pathology, and 3) the distribution of melanin in the inner ear. Normal melanin distribution was also studied in 35 temporal bones of patients without malignant melanoma. Metastatic malignant melanoma was observed in 5 temporal bones from 3 patients, in two of whom the internal auditory canal was involved bilaterally by melanoma cell infiltration. In the remaining patient (one ear), metastatic melanoma was found along the dura mater of the posterior cranial fossa to the mastoid air cells. In the former two patients, the inner and outer hair cells as well as the stria vascularis showed degenerative changes to various extents. In particular, the inner ear changes were severe in the ear with the decongestion of the inner ear vessels. Melanin was found in the modiolus, stria vascularis, osseous spiral lamina, membranous labyrinth, and endolymphatic sac, as previously reported. The amount of melanin in the inner ear increased with age in the control patients, but was greater than in the controls, in all of the cases of malignant melanoma except one, in which metastatic lesions were present in the internal auditory canal with marked congestion of the inner ear vessels.

Adult↗
PubMed1997

[Transient hyperphosphatasemia observed in a boy with acute lymphoblastic leukemia].

A detailed time course of alkaline phosphatase (ALP; EC3.1.3.1) activity of transient hyperphosphatasemia (TH) in a 9-year-old boy with acute lymphoblastic leukemia (ALL) is described. The patient's serum ALP activity rose transiently to 49 times the upper limit of normal adult, without any evidences of hepatic and bone disease. The half-life of ALP activity was calculated about 10 days. We characterized ALP isoenzymes by usual electrophoresis using cellulose acetate membrane (Titan III iso-vis) and polyacrylamide disc gel (AlkPhor), and isoelectric focusing using polyacrylamide slab gel. The former two methods showed typical two bands (fast-alpha 2 and alpha 2 beta bands) and the latter one method revealed more basic bands of liver and bone, suggesting the extensive sialylation. The patient complained fever and diarrhea. Enterococcus faecium was detected from his stool. Etiologically, two more patients in the same ward showed TH in the same period. It suggested TH would be occurred by infectious states. Awareness of such benign forms of hyperphosphatasemia not related to malignancy will aid the physician in the differential diagnosis of elevated ALP activity.

Alkaline Phosphatase↗
PubMed1997

Structure model and physicochemical properties of the C-U mismatch pair in the double stranded RNA in solution.

Structure of the C-U mismatch pair was reported only in crystal but none in solution. Here we have studied the structure and physicochemical properties of the C-U mismatch pair in a double stranded RNA in solution. RNA oligomers r(CGACUCAGG) and r(CCUGCGUCG) form a double stranded structure with the C-U pair. The arrangement of the C-U pair derived from the model building based on nOe gives a similar structural feature to that in crystal. The modeling reveals that the amino-proton of cytidine and the keto-oxygen of uridine are located within hydrogen bonding distance, and the imino proton of uridine is exposed to bulk water. From the melting experiment which monitors chemical shifts of non-exchangeable protons, the melting of all the base-pairs including the C-U pair occurs simultaneously. This suggests the possibility where the C-U mismatch pair is stacked on the neighboring base-pairs in the double helix until the duplex is denatured to single strands.

Base Composition↗
PubMed1996

Solution Strucutres of DNA duplexes containing a DNA x RNA hybrid region, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) and d(GGAGA)r(UGAC) x d(GTCATCTCC).

The solution structures of two DNA duplexes containing a DNA*RNA hybrid region at different sites, d(GG)r(AGAU)d(GAC) x d(GTCATCTCC) (DHD, where D and H represent the DNA and DNA x RNA hybrid segments, respectively) and d(GGAGA)r(UGAC) x d(GTCATCTCC) (DDH), were determined by nuclear magnetic resonance spectroscopy to clarify the structural features of the D-H and H-D junctions. All proton-proton distances were derived from the NOESY spectra, with mixing times of 45 ms, and the restrained molecular dynamics were carried out starting from the typical A- and B-form conformations. Both duplexes were converged from the respective initial structures into structures with RMSD values of less than 1.0 angstrom. These structures were subjected to full relaxation matrix refinement to produce the final structures. In the case of the D-H junction, where the ribonucleotide was linked to the 3'-end of the DNA, the H2' and H2" signals of the deoxynucleotide overlapped completely, and the ribonucleotide had a H1'-H2' coupling constant larger than that of the normal C3'-endo sugar pucker. The dihedral angles, the pseudorotation phase angles, and the helical parameters changed at the H-D junction, but not at the D-H junction. A detailed comparison of the two duplexes revealed the structural heterogeneity between the DNA segment and the DNA x RNA hybrid region and the transitions at the junctions.

Base Sequence↗
PubMed1995

Existence of branched side chains in the cell wall mannan of pathogenic yeast, Candida albicans. Structure-antigenicity relationship between the cell wall mannans of Candida albicans and Candida parapsilosis.

Isolation of side chain oligosaccharides from mannans of Candida albicans NIH B-792 (serotype B) and Candida parapsilosis IFO 1396 strains has been conducted by acetolysis under mild conditions. Structural study of these oligosaccharides by 1H and 13C NMR and methylation analyses indicated the presence of novel branched side chains with the following structures in C. albicans mannan. [sequence: see text] It was observed that the H-1 proton chemical shifts of the second and the third mannose units from the reducing terminus in each oligosaccharide are shifted upfield by substitution with an alpha-linked mannose unit at position 6 of the 3-O-substituted mannose unit. An agglutination inhibition assay between factor 4 serum and cells of Candida stellatoidea IFO 1397 lacking the beta-1,2-linked mannose unit, with oligosaccharides obtained from these mannans, indicated that only the branched oligosaccharides were active. This finding suggests that the branched oligosaccharides correspond to the epitope of antigenic factor 4. The presence of the branched structure in other mannans was detected by the characteristic H-1-H-2-correlated cross-peak of the alpha-1,2-linked mannose unit connected with the 3,6-di-O-substituted one by two-dimensional homonuclear Hartmann-Hahn spectroscopy.

Acids↗
PubMed1995

Nuclear magnetic resonance study of complexes between CRP and its 22- and 28-base-pair operators.

The binding of the cAMP receptor protein (CRP) to the portion of the lac promoter comprising the core of the CRP recognition sequence has been investigated. The effect of the binding of CRP to the symmetrical 22- and 28-base-pair operators was investigated by 1H NMR. The binding of cAMP*CRP to the 22mer DNA did not bring about any changes in the chemical shift values of the imino proton resonances of the DNA, but did cause selective line broadening of the imino proton resonances of specific base pairs (TA 4, GC 5). These base pairs are contained in the motif 5'(TGTGA)3', which is thought to be the region crucial to interaction with the CRP. The binding of cAMP*CRP to the 28mer DNA brought about large changes in the imino proton resonances that seem to be induced by DNA bending. Therefore it seems likely that CRP requires DNA longer than a 22mer to bend it. We also used a C-terminal protease-digested CRP (CRPcy) in a DNA-binding experiment. The binding of cAMP*CRPcy to the 28mer DNA did not induce bending. These results indicate that the C-terminal region of CRP participates in DNA binding and is important for DNA bending.

Base Composition↗
PubMed1995

Binding affinities of isocarbacyclin methyl ester and its free acid to prostanoid receptors.

The binding affinities of isocarbacyclin methyl ester (CAS 88931-51-5, TEI-9090) and its free acid (CAS 88911-35-7, TEI-7165) to prostaglandin (PG) I2 receptors (IP receptors), PGE2 receptors (EP receptors) and thromboxane A2 receptors (TP receptors) were investigated. TEI-9090 exhibited low affinity for IP and EP receptors in mastocytoma P-815 cell membranes and no affinity for TP receptors in washed guinea-pig platelets. The IC50 values of TEI-9090 against [3H]iloprost (for IP receptors), [3H]PGE2 (for EP receptors) and [3H]SQ29,548 (for TP receptors) binding were 2803 +/- 327 nmol/l, 2509 +/- 1317 nmol/l and > 10000 nmol/l (n = 3), respectively. In contrast, TEI-7165 had high affinity for IP receptors (IC50 = 65.4 +/- 28.5 nmol/l, n = 3) but had moderate to low affinity for EP and TP receptors. The affinity of TEI-9090 for IP receptors was remarkably enhanced by pretreatment with rat serum as an esterase source. These findings suggest that TEI-9090 is converted to TEI-7165 by esterase, and that TEI-7165 exerts pharmacological effects through binding to IP receptors.

Animals↗
PubMed1994

Alpha 1-adrenoceptor subtypes mediating the regulation and modulation of Ca2+ sensitization in rabbit thoracic aorta.

Norepinephrine (10 microM), methoxamine (100 microM) and clonidine (100 microM) with guanosine 5'-triphosphate (GTP, 50 microM) or guanosine 5'-O-(3-thiotriphosphate) (GTP gamma-S, 10 microM) all significantly enhanced the contraction induced by 0.3 microM Ca2+ (pCa6.5) in beta-escin-skinned smooth muscle of rabbit thoracic aorta. The enhancement of Ca2+ contraction produced by norepinephrine was greater than that produced by methoxamine or clonidine. In beta-escin-skinned strips of chloroethylclonidine-pretreated smooth muscle, the enhancement of Ca2+ contraction produced by norepinephrine was significantly decreased, whereas the amplitude was the same as that produced by methoxamine or clonidine; this enhancement was inhibited by the selective alpha 1A-adrenoceptor antagonist WB 4101 (100 nM). The enhancement of Ca2+ contraction produced by methoxamine and clonidine was not affected by chloroethylclonidine pretreatment. The effects of methoxamine, clonidine and norepinephrine in the chloroethylclonidine-pretreated tissue were all inhibited by guanosine 5'-O-(2-thiodiphosphate) (GDP beta-S, 1 mM) and 1-(5-isoquinolinylsulfonyl)-methylpiperazine (H-7, 20 microM). Furthermore, the phosphorylation of myosin light chain produced by norepinephrine was greater than that produced by clonidine. These results suggest that both alpha 1-adrenoceptor subtypes (alpha 1A and alpha 1B) increase the Ca2+ sensitivity of contractile elements, and that the Ca2+ sensitization produced by alpha 1A-subtype receptors is mediated through G-protein and protein kinase C, and plays an important role in contraction of smooth muscle of rabbit thoracic aorta.

Animals↗
PubMed1994

Filtering methods for selection of singlet and doublet signals in NMR spectra of DNA oligomers.

The base proton (purine H8 and pyrimidine H6) resonances are key signals for the assignment of the proton resonances of DNA oligomers. They are classified into two groups, i.e., cytosine H6 signals, observed as doublets, and the other base proton signals, observed as singlets. Here we propose some experiments for distinguishing the cytosine H6 signals from the other base proton signals. Moreover, the ability of signal selection and the sensitivity as to signal detection were compared for all experiments, and the optimum conditions for spectral measurements were surveyed. Some of the experiments were employed as the NOESY detection pulse. Previously proposed experiments, such as HOENOE and HAL, were also used in the comparison.

Cytosine↗
PubMed1993

Structural study of a cell-wall mannan of Saccharomyces kluyveri IFO 1685 strain. Presence of a branched side chain and beta-1,2-linkage.

Acetolysis of the cell-wall mannan of Saccharomyces kluyveri under mild conditions, gave fragments with 1-6 mannose residues. The structures of mannopentaose and mannohexaose were determined to be [Formula; see text] respectively, by two-dimensional homonuclear Hartmann-Hahn spectroscopy and a sequential NMR assignment method that combines 1H-13C correlated spectroscopy, relayed coherence transfer spectroscopy, 1H-detected heteronuclear multiple-bond connectivity and methylation analysis. The H1 proton chemical shift of a neighboring alpha-1,2-linked mannose unit of the 3-O-substituted structure was shifted upfield by the addition of a mannose unit to the adjacent 3-O-substituted unit by an alpha-1,6 linkage. The characteristic H1--H2-correlated cross-peak of the alpha-1,3-linked mannose unit substituted by a beta-1,2 linkage, beta 1-->2Man alpha 1-->3, in the mannan of S. kluyveri, as also found by two-dimensional homonuclear Hartmann-Hahn spectroscopy in the mannan of Candida guilliermondii, a pathogenic yeast in man.

Carbohydrate Conformation↗
PubMed1993

Precise analyses of DNA structure by NMR.

Novel 1H NMR techniques were developed and applied to the analyses of the DNA structure. They distinguished the base proton signals of cytosine (uracil) from those of the other bases. Two dimensional experiments were also performed by using these techniques, and were found to be useful for signal assignments. Moreover, the (2'R)-[2'-2H]-labeled DNA 10-mer and 17-mer were synthesized to be used for the determination of precise structures. These stereoselective [2'-2H]-labeling made possible explicit stereospecific assignments and exact determination of the vicinal coupling constants, 3JHH, and thus the conformation of each deoxyribose ring was accurately determined.

Cytosine↗
PubMed1992

Characterization of alpha 1-adrenoceptor subtypes labeled by [3H]prazosin in single cells prepared from rabbit thoracic aorta.

alpha 1-Adrenoceptor agents with alpha 1-adrenoceptor subtypes sensitive and insensitive to inactivation by chloroethylclonidine were characterized in single cells prepared from rabbit thoracic aorta. WB 4101, 5-methylurapidil and spiperone interacted with high- and low-affinity sites labeled by [3H]prazosin. Chloroethylclonidine 10 microM pretreatment eliminated the low-affinity sites of displacement curves obtained with WB 4101 and 5-methylurapidil but had no effect on the high-affinity site for these agents. The treatment also reduced the site of the displacement curve obtained with spiperone but eliminated only the high-affinity site. Methoxamine and clonidine, alpha-adrenoceptor agonists, interacted with binding sites labeled by [3H]prazosin. The displacement curve for methoxamine was not affected by chloroethylclonidine 10 microM pretreatment, while that for clonidine was partially eliminated by the same type of pretreatment. These results suggest that, in single cells prepared from rabbit thoracic aorta: (1) WB 4101, 5-methylurapidil and spiperone interact with differing affinity at sites labeled by [3H]prazosin; (2) chloroethylclonidine-sensitive and -insensitive [3H]prazosin binding sites correspond to those with low- and high-affinity sites for WB 4101 and 5-methylurapidil, and a high- and low-affinity for spiperone, respectively; and (3) chloroethylclonidine treatment was shown to have no effect on the displacement curve of methoxamine but a partial effect on that of clonidine.

Animals↗
PubMed1992

Pharmacological characterization of contractile responses induced by alpha 1-agonists, norepinephrine and clonidine, by selective antagonists of their subtypes in rabbit thoracic aorta.

In the rabbit isolated thoracic aorta, WB 4101 and 5-methylurapidil dose-dependently shifted the concentration-response curves for norepinephrine to the right. Schild plots showed that the inhibition of responses for WB 4101 and 5-methylurapidil was biphasic, implying that norepinephrine acted through two receptor populations. Clonidine produced a concentration-dependent contraction in the isolated rabbit thoracic aorta. WB 4101 and 5-methylurapidil antagonized the contractions for clonidine, and the Schild plot to both antagonists against clonidine yielded a monophasic slope. Schild plots of the results obtained from the inhibition by WB 4101 and 5-methylurapidil for norepinephrine in strips pretreated with chloroethylclonidine yielded a straight line with a slope of unity. Specific binding of [3H]prazosin in the aortic membrane preparations was saturable. The Hill coefficient obtained from the inhibition curves for clonidine was significantly different from unity. Clonidine interacted with two binding sites labelled by [3H]prazosin, but the low affinity site was completely eliminated by pretreatment with 10 microM chloroethylclonidine. These results suggest that the subtype activated by norepinephrine is different from that activated by clonidine, and that norepinephrine-induced contraction through both alpha 1A- and alpha 1B-subtypes and clonidine through only the alpha 1A-subtype in the rabbit thoracic aorta.

Adrenergic alpha-Agonists↗