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Tamura T, Furukawa T, Komatsu Y, Ohtsuka E, Inoue H. Toward artificial ribonucleases: design and synthesis of 2'-O-methyloligonucleotides with a terpyridine-copper(II) complex. NUCLEIC ACIDS SYMPOSIUM SERIES 2000:109-10. [PMID: 10780403 DOI: 10.1093/nass/42.1.109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
In order to construct an antisense 2'-O-methyloligonucleotide with an internal terpyridine-Cu(II) complex, a novel synthon was synthesized. This synthon was a 2'-deoxy-uridine-3'-phosphoramidite derivative with a terpyridine group at the 5'-O and a dimethoxytritylated hydroxypropyl group at the C-5. The antisense agent cleaved the RNA site-specifically and in a moderate yield.
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27
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Ogata M, Saito K, Ohtsuka E, Kikuchi H, Nasu M. [Leukocytopenia and thrombocytopenia preceded by human parvovirus B19 infection: report of three adult cases]. [RINSHO KETSUEKI] THE JAPANESE JOURNAL OF CLINICAL HEMATOLOGY 2000; 41:596-600. [PMID: 11020984] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/17/2023]
Abstract
In Saiki City, Oita, Japan, erythema infectiosum in children has been prevalent from June, 1999 to the time of writing (January, 2000). We present three adult cases of parvovirus B19-associated leukocytopenia and thrombocytopenia that developed during this epidemic. Between June and November, 1999, a 32-year-old woman, a 38-year-old woman, and a 63-year-old man were referred to our hospital for treatment of leukocytopenia and thrombocytopenia. All complained of common cold-like symptoms. Their WBC counts (percentage of neutrophils) were 1,000/microliter (70%), 1,900/microliter (40%) and 1,680/microliter (40%), their hemoglobin levels 9.4 g/dl, 9.8 g/dl and 14.9 g/dl, and their platelet counts 10.8 x 10(4)/microliter, 6.9 x 10(4)/microliter and 4.5 x 10(4)/microliter, respectively. The diagnosis of parvovirus B19 infection was documented by the presence of B19-specific IgM antibodies or serum positivity for viral DNA. In two cases, the leukocytopenia and thrombocytopenia resolved gradually. In the other case, leukocytopenia, thrombocytopenia and B19 infection persisted for more than two months. These cases suggest that parvovirus B19 may be a common cause of leukocytopenia and thrombocytopenia even in adult patients without hematological disorders (erythropoietic stress), and that testing for parvovirus infection is justified in such patients, even if anemia is slight, especially when erythema infectiosum is prevalent.
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Komatsu Y, Yamashita S, Kazama N, Nobuoka K, Ohtsuka E. Construction of new ribozymes requiring short regulator oligonucleotides as a cofactor. J Mol Biol 2000; 299:1231-43. [PMID: 10873448 DOI: 10.1006/jmbi.2000.3825] [Citation(s) in RCA: 38] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
A hairpin loop and an oligonucleotide bound to the loop form one-half of the pseudoknot structure. We have designed an allosteric hammerhead ribozyme, which is activated by the introduction of this motif by using a short complementary oligonucleotide as a cofactor. Stem II of the hammerhead ribozyme was substituted with a non-self-complementary loop sequence (loop II) to abolish the cleavage activity. The new ribozyme had almost no cleavage activity of the target RNA. However, it exhibited the cleavage activity in the presence of a cofactor oligoribonucleotide, which is complementary to loop II of the ribozyme. The activity is assumed to be derived from the formation of a pseudo-stem structure between the cofactor oligonucleotide and loop II. The structure including the loop may be similar to the pseudo-half-knot structure. The activation efficiencies of the cofactor oligonucleotides were decreased as the lengths of the oligonucleotides increased, and the ribozyme with a longer loop II was more active than that with a short loop II. Oligoribonucleotides with 3'-dangling purine bases served as efficient cofactors of the ribozyme, and a 2'-O-methyloligonucleotide enhanced the cleavage activity of the ribozyme most efficiently, by as much as about 750-fold as compared with that in the absence of the oligonucleotide. Cofactor oligonucleotides with a cytidine base at the 3'-end also activated a ribozyme with the G10.1.G11.1 mutation, which eliminates the cleavage activity in the wild-type. The binding sites of the oligonucleotide were identified by photo-crosslinking experiments and were found to be the predicted sites in the loop. This is the first report of a design aimed at positively controlling the activity of ribozymes by employing a structural motif. This method can be applied to control the activities of other functional RNAs with hairpin loops.
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29
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Yokoyama H, Mizutani R, Satow Y, Komatsu Y, Ohtsuka E, Nikaido O. Crystal structure of the 64M-2 antibody Fab fragment in complex with a DNA dT(6-4)T photoproduct formed by ultraviolet radiation. J Mol Biol 2000; 299:711-23. [PMID: 10835279 DOI: 10.1006/jmbi.2000.3772] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
DNA photoproducts with (6-4) pyrimidine-pyrimidone adducts formed by ultraviolet radiation are implicated in mutagenesis and cancer, particularly skin cancer. The crystal structure of the Fab fragment of the murine 64M-2 antibody specific to DNA T(6-4)T photoproducts is determined as a complex with dT(6-4)T, a (6-4) pyrimidine-pyrimidone photodimer of dTpT, at 2.4 A resolution to a crystallographic R-factor of 0.199 and an R(free) value of 0.279. The 64M-2 Fab molecule is in an extended arrangement with an elbow angle of 174 degrees, and its five complementarity-determining regions, except L2, are involved in the ligand binding. The bound dT(6-4)T ligand adopting a ring structure with (6-4) linked 5' thymine-3' pyrimidone bases is fully accommodated in an antigen-binding pocket of about 15 Ax10 A. The 5'-thymine and 3'-pyrimidone bases are in half-chair and planar conformations, respectively, and are nearly perpendicular to each other. The 5'-thymine base is hydrogen-bonded to Arg95H and Ser96H, and is in van der Waals contact with Tyr100iH. The 3'-pyrimidone base is hydrogen-bonded to His35H, and is in contact with Trp33H. Three water molecules are located at the interface between the bases and the Fab residues. Hydrogen bonds involving these water molecules also contribute to Fab recognition of the dT(6-4)T bases. The sugar-phosphate backbone connecting the bases is surrounded by residues His27dL, Tyr32L, Ser92L, Trp33H, and Ser58H, but is not hydrogen-bonded to these residues.
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MESH Headings
- Animals
- Antibodies, Antinuclear/chemistry
- Antibodies, Antinuclear/immunology
- Antibody Specificity
- Binding Sites, Antibody
- Cattle
- Crystallography, X-Ray
- DNA/chemistry
- DNA/genetics
- DNA/immunology
- DNA/radiation effects
- DNA Damage/genetics
- DNA Damage/immunology
- DNA Damage/radiation effects
- DNA, Single-Stranded/chemistry
- DNA, Single-Stranded/genetics
- DNA, Single-Stranded/immunology
- DNA, Single-Stranded/radiation effects
- Epitopes/chemistry
- Epitopes/genetics
- Epitopes/immunology
- Epitopes/radiation effects
- Hydrogen Bonding
- Immunoglobulin Fab Fragments/chemistry
- Immunoglobulin Fab Fragments/immunology
- Immunoglobulin Variable Region/chemistry
- Immunoglobulin Variable Region/immunology
- Mice
- Mice, Inbred BALB C
- Models, Molecular
- Molecular Sequence Data
- Nucleic Acid Conformation/radiation effects
- Nucleotides/chemistry
- Nucleotides/genetics
- Nucleotides/immunology
- Protein Conformation
- Pyrimidine Dimers/chemistry
- Pyrimidine Dimers/genetics
- Pyrimidine Dimers/immunology
- Pyrimidine Dimers/radiation effects
- Static Electricity
- Ultraviolet Rays
- Water/metabolism
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30
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Komatsu Y, Kanzaki I, Shirai M, Kumagai I, Yamashita S, Ohtsuka E. Functional domain-assembly in hairpin ribozymes. J Biochem 2000; 127:531-6. [PMID: 10739942 DOI: 10.1093/oxfordjournals.jbchem.a022637] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Functional structures of hairpin ribozymes have been investigated by constructing various chemically modified molecules. Domain-exchange and linker insertion experiments were performed to find active conformations of the RNA enzyme showing cleavage activity. Our experiments and other evidence suggest that the active structure has a bent conformation, and that domain-interactions are essential for the cleavage activity.
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31
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Torizawa T, Yamamoto N, Suzuki T, Nobuoka K, Komatsu Y, Morioka H, Nikaido O, Ohtsuka E, Kato K, Shimada I. DNA binding mode of the Fab fragment of a monoclonal antibody specific for cyclobutane pyrimidine dimer. Nucleic Acids Res 2000; 28:944-51. [PMID: 10648787 PMCID: PMC102577 DOI: 10.1093/nar/28.4.944] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Monoclonal antibodies specific for the cyclobutane pyrimidine dimer (CPD) are widely used for detection and quantification of DNA photolesions. However, the mechanisms of antigen binding by anti-CPD antibodies are little understood. Here we report NMR analyses of antigen recognition by TDM-2, which is a mouse monoclonal antibody specific for the cis - syn -cyclobutane thymine dimer (T[ c, s ]T). (31)P NMR and surface plasmon resonance data indicated that the epitope recognized by TDM-2 comprises hexadeoxynucleotides centered on the CPD. Chemical shift perturbations observed for TDM-2 Fab upon binding to d(T[ c, s ]T) and d(TAT[ c, s ]TAT) were examined in order to identify the binding sites for these antigen analogs. It was revealed that d(T[ c, s ]T) binds to the central part of the antibody-combining site, while the CPD-flanking nucleotides bind to the positively charged area of the V(H)domain via electrostatic interactions. By applying a novel NMR method utilizing a pair of spin-labeled DNA analogs, the orientation of DNA with respect to the antigen-binding site was determined: CPD-containing oligonucleotides bind to TDM-2 in a crooked form, draping the 3'-side of the nucleotides onto the H1 and H3 segments, with the 5'-side on the H2 and L3 segments. These data provide valuable information for antibody engineering of TDM-2.
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32
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Komatsu Y, Kumagai I, Ohtsuka E. Investigation of the recognition of an important uridine in an internal loop of a hairpin ribozyme prepared using post-synthetically modified oligonucleotides. Nucleic Acids Res 1999; 27:4314-23. [PMID: 10536137 PMCID: PMC148711 DOI: 10.1093/nar/27.22.4314] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
We introduced 4-thio- ((4S)U), 2-thio- ((2S)U), 4- O -methyluridine ((4Me)U) and cytidine substitutions for U+2, which is an important base for cleavage in a substrate RNA. Oligonucleotides containing 4-thio- and 4- O -methyluridine were prepared by a new convenient post-synthetic modification method using a 4- O - p -nitrophenyl-uridine derivative. A hairpin ribozyme cleaved the substrate RNA with either C+2, (4S)U+2 or (4Me)U+2 at approximately 14-, 6- and 4-fold lower rates, respectively, than that of the natural substrate. In contrast, the substrate with a (2S)U+2 was cleaved with the same activity as the natural substrate. These results suggest that the O4 of U+2 is involved in hydrogen bonding at loop A, but the O2 of U+2 is not recognized by the active residues. Circular dichroism data of the ribozymes containing (4S)U+2 and (2S)U+2, as well as the susceptibility of the thiocarbonyl group to hydrogen peroxide, suggest that a conformational change of U+2 occurs during the domain docking in the cleavage reaction. We propose here the conformational change of U+2 from the ground state to the active molecule during the reaction.
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33
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Kobayashi H, Kato J, Morioka H, Stewart JD, Ohtsuka E. Tryptophan H33 plays an important role in pyrimidine (6-4) pyrimidone photoproduct binding by a high-affinity antibody. PROTEIN ENGINEERING 1999; 12:879-84. [PMID: 10556249 DOI: 10.1093/protein/12.10.879] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The importance of Trp H33 in antibody recognition of DNA containing a central pyrimidine (6-4) pyrimidone photoproduct was investigated. This residue was replaced by Tyr, Phe and Ala and the binding abilities of these mutants were determined by surface plasmon resonance and fluorescence spectroscopy. Conservative substitution of Trp H33 by Tyr or Phe resulted in moderate losses of binding affinity; however, replacement by Ala had a significantly larger impact. The fluorescence properties of DNA containing a (6-4) photoproduct were strongly affected by the identity of the H33 residue. DNA binding by both the wild-type and the W-H33-Y mutant was accompanied by a small degree of fluorescence quenching; by contrast, binding by the W-H33-F and W-H33-A mutants produced large fluorescence increases. Taken together, these variations in binding and fluorescence properties with the identity of the H33 residue are consistent with a role in photoproduct recognition by Trp H33 in the high-affinity antibody 64M5.
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34
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Ohno E, Ohtsuka E, Saburi Y, Ono K, Kikuchi H, Nasu M. Reactive oxygen species production of neutrophils in patients with acute promyelocytic leukemia during treatment with all-trans retinoic acid. Am J Hematol 1999; 62:120-1. [PMID: 10577282 DOI: 10.1002/(sici)1096-8652(199910)62:2<120::aid-ajh12>3.0.co;2-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
We measured N-formyl-methionyl-leucyl-phenylalanine-induced reactive oxygen species production by neutrophils from three patients with acute promyelocytic leukemia during treatment with all-trans retinoic acid using a luminol-enhanced chemiluminescence assay. The maximum level of reactive oxygen species production during all-trans retinoic acid treatment was 58.8 +/- 2.3 x 10(4) (mean +/- SEM) counted photons per seconds (cps), which was significantly higher (p<0.0001) than that of neutrophils from health volunteers (13.3 +/- 2.3 x 10(4) cps).
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35
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Abstract
Syntheses of nucleic acids are of importance not only in the natural product chemistry but also in the molecular recognition study in biology. This review describes syntheses of RNA and DNA, which were found to be related each other. Deoxyinosine probes were developed for cloning genes with degenerated codons. Synthetic genes for c-Ha-ras and T4 endonuclease V provided new approaches in recognition of nucleic acids by proteins. Antibodies specific for photo-damaged pyrimidines in DNA have been studied by cloning and mutating their genes.
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36
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Shibata N, Ohnuma T, Takahashi T, Ohtsuka E, Ueki A, Arai H. Genetic association between alpha-2 macroglobulin and Japanese sporadic Alzheimer's disease. Neurosci Lett 1999; 271:132-4. [PMID: 10477120 DOI: 10.1016/s0304-3940(99)00541-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Alpha-2 macroglobulin (encoded by the gene A2M) is a serum pan-protease inhibitor that may be related with the pathogenesis of Alzheimer's disease (AD) because of its ability to mediate amyloid beta degradation. Recently, several groups have reported that the five-nucleotides deletion in A2M gene at the 5' splice site of exon 18 might increase risk for AD. In the present study, therefore, this mutation was studied in 69 healthy controls and 55 sporadic AD cases by polymerase chain reaction- restriction fragment length polymorphism method. The allelic frequencies with the deletion (A2M-2) are 9.4 and 6.4% in the control and AD groups, respectively. There is no significant difference in the A2M-2 frequencies between the controls and sporadic AD cases. This is the first report to study the frequencies of A2M-2 in Japanese AD cases, suggesting its no genetic association with sporadic AD.
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37
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Torizawa T, Kato K, Kato J, Kobayashi H, Komatsu Y, Morioka H, Nikaido O, Ohtsuka E, Shimada I. Conformational multiplicity of the antibody combining site of a monoclonal antibody specific for a (6-4) photoproduct. J Mol Biol 1999; 290:731-40. [PMID: 10395826 DOI: 10.1006/jmbi.1999.2926] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The antigen binding site of monoclonal antibody 64M5, which possesses a high degree of affinity for DNA containing pyrimidine (6-4) pyrimidone photoproducts, were investigated by use of stable-isotope-assisted NMR spectroscopy. A variety of 64M5 Fab fragments specifically labeled with 13C and 15N at backbone amide groups were prepared. Extensive assignments of amide resonances originating from the variable region of 64M5 were made by using 2D-HN(CO) measurements along with recombination of the heavy and light chains of 64M5. On the basis of chemical shift changes of the amide resonances caused upon addition of d(T[6-4]T) and d(GTAT[6-4]TATG), the binding sites of 64M5 Fab for the (6-4) photodimer and for the oligodeoxynucleotides flanking it were identified. It was revealed that the L1 and L3 segments, which are responsible for the binding to (6-4) photodimer, exhibit conformational multiplicities in the absence of antigens, and take different conformations between the d(T[6-4]T) and d(GTAT[6-4]TATG)-bound forms. On the basis of spectral comparison with another Fab fragment with a similarity in the amino acid sequence of the VL domain of 64M5, we suggest that the conformational multiplicities observed in the present study is caused by a substitution of an amino acid residue at the position of a key residue in L3 canonical structure, which leads to a preferable effect on the antigen binding, and by a specific combination of L1 and L3 canonical structures.
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38
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Monden Y, Arai T, Asano M, Ohtsuka E, Aburatani H, Nishimura S. Human MMH (OGG1) type 1a protein is a major enzyme for repair of 8-hydroxyguanine lesions in human cells. Biochem Biophys Res Commun 1999; 258:605-10. [PMID: 10329432 DOI: 10.1006/bbrc.1999.0649] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
8-Hydroxyguanine (8-OH-G) is the site of a frequent mutagenic lesion of DNA, produced by oxidative damage. MutM of E. coli and OGG1 of Saccharomyces cervisiae are known to possess 8-OH-G glycosylase activity and apurinic (AP) site lyase activity to repair 8-OH-G lesions. Recently, cDNA clones of human OGG1 homologues (hMMH) of four isoforms (type 1a, type 1b, type 1c, and type 2) were isolated. However, it is unknown whether expression of endogenous hMMH proteins actually occurs in mammalian cells. Here using hMMH type 1a-specific antibody and cells overexpressing tag-fused hMMH type 1a, we show the expression of hMMH type 1a protein in many types of human cells and show that endogenous hMMH type 1a protein has 8-OH-G glycosylase/AP lyase activity. Furthermore, we show that upon depletion of hMMH type 1a protein in a whole cell extract by its antibody, most of the AP lyase activity is lost, indicating that hMMH type 1a protein is a major enzyme for repair of 8-OH-G lesions in human cells.
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39
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Kobayashi H, Sato K, Komatsu Y, Morioka H, Stewart JD, Tsurimoto T, Ohtsuka E. Effects of a high-affinity antibody fragment on DNA polymerase reactions near a (6-4) photoproduct site. Photochem Photobiol 1999; 69:226-30. [PMID: 10048314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/11/2023]
Abstract
Pyrimidine (6-4) pyrimidone photodimers are major photoproducts that have mutagenic and carcinogenic consequences. One major reason for these biological effects of (6-4) photoproducts may be base mispairing/DNA replication errors due to hydrogen bonding to bases opposite these damaged sites. We synthesized a modified 41-mer DNA containing a (6-4) photoproduct using a preformed building block, then employed it as a template for primer extension reactions catalyzed by Klenow fragment and DNA polymerases alpha, beta and delta (pol alpha, pol beta and pol delta). None of these DNA polymerases were able to bypass the (6-4) photoproduct and elongation terminated at or near the 3'-pyrimidone of the photoproduct, depending on the dNTP concentration. When a single-chain Fv (scFv) with high affinity for the (6-4) photoproduct was included in the polymerization reaction, DNA synthesis was inhibited at base positions four, six, eight or eight nucleotides prior to the 3'-pyrimidone by Klenow fragment, pol alpha, pol beta or pol delta, respectively. These results suggest that the scFv can bind to the template DNA containing a (6-4) photoproduct and inhibit extension reactions by polymerases.
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40
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Kobayashi H, Morioka H, Tobisawa K, Torizawa T, Kato K, Shimada I, Nikaido O, Stewart JD, Ohtsuka E. Probing the interaction between a high-affinity single-chain Fv and a pyrimidine (6-4) pyrimidone photodimer by site-directed mutagenesis. Biochemistry 1999; 38:532-9. [PMID: 9888792 DOI: 10.1021/bi9809167] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have used site-directed mutagenesis to uncover the origin of the binding affinity differences exhibited by a series of monoclonal antibodies that recognize pyrimidine (6-4) pyrimidone photoproducts in the context of single- or double-stranded DNA. In this study, we have focused on two antibodies-64M3 and 64M5-that share the same binding specificity but differ in their affinities. We used single-chain Fv (scFv) derivatives for these studies since they can be easily expressed in Escherichia coli. To facilitate this, we also developed a simple, on-column refolding procedure for scFvs that is rapid and does not require high dilution. We took several precautions to ensure that the scFvs faithfully reflected the behavior of the parent monoclonal antibodies. Results obtained from chimeric scFvs constructed from 64M3 and 64M5 suggested that the higher affinity of the 64M5 antibody was mainly due to its VL region. Loop-grafting studies in which VH CDR loops of 64M3 were individually transplanted into 64M5 were consistent with this hypothesis. Since the VL sequences of 64M3 and 64M5 differ at only three positions (L30, L50, and L90), alanine-scanning mutagenesis was used to assess the importance of these three residues in DNA binding by 64M5. These studies highlighted the importance of all three VL CDR loops; furthermore, they suggested that photoproduct binding involved conformational changes within the VL region.
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41
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Hori T, Kikuchi H, Ohtsuka E, Ono K, Saburi Y, Nasu M. A rapid method for determination of the relative copy number of HTLV-I proviral genome in HTLV-I carriers and adult T-cell leukemia patients by polymerase chain reaction. HAEMATOLOGIA 1999; 29:265-76. [PMID: 10438066] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 04/13/2023]
Abstract
Ten adult T-cell leukemia (ATL) patients and 11 asymptomatic human T-cell leukemia virus type I (HTLV-I) carriers were examined by polymerase chain reaction (PCR) assay with a reduced sensitivity to evaluate its utility in detecting the relative copy number of the HTLV-I genome in clinical samples. Differences in the intensities of the PCR products were observed between the acute type ATL patients and ATL patients in remission or carriers. Intense bands were found in all acute type ATL patients (6/6, 100%), while specific bands were seen in only 2 carriers (2/11, 18.2%). The bands found in one of the two patients in remission were weak. One patient, who had acute type ATL, had achieved a remission but later relapsed. Using this technique, we examined the differences in the intensities of the bands of the PCR products in a patient with acute type ATL who had achieved remission but later relapsed. Thus, this technique may be of clinical importance in diagnosing acute ATL and assessing the effect of therapy.
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Ikewaki J, Ohtsuka E, Uno N, Ogata M, Kikuchi H, Nasu M, Yokoyama S. [Lymphoma associated hemophagocytic syndrome with plasmacytosis in the bone marrow and hypergammaglobulinemia]. [RINSHO KETSUEKI] THE JAPANESE JOURNAL OF CLINICAL HEMATOLOGY 1998; 39:1175-9. [PMID: 10028850] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 02/10/2023]
Abstract
A 72-year-old woman was admitted to our hospital because of fever, anemia and thrombocytopenia in March 1997. Laboratory findings showed elevated serum LDH levels and polyclonal gammopathy. Bone marrow aspiration samples revealed hemophagocytosis and plasmacytosis. Although serum interleukin-6 was elevated, serum interferon-lambda and tumor necrosis factor-alpha were below detectable limits. Magnetic resonance images disclosed a tumor in the patient's pelvic cavity. The tumor was resected and diagnosed as non-Hodgkin's lymphoma. The patient was treated with combination chemotherapy and has remained in complete remission. Also, histiocyte and plasma cell counts in the bone marrow fell significantly and the serum interleukin-6 level returned to the normal range. We reasoned that lymphoma cells may have induced plasmacytosis in the bone marrow and polyclonal gammopathy accompanied by hemophagocytic syndrome.
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43
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Ogata M, Ogata Y, Kohno K, Uno N, Ohno E, Ohtsuka E, Saburi Y, Kamberi P, Nasu M, Kikuchi H. Eosinophilia associated with adult T-cell leukemia: role of interleukin 5 and granulocyte-macrophage colony-stimulating factor. Am J Hematol 1998; 59:242-5. [PMID: 9798664 DOI: 10.1002/(sici)1096-8652(199811)59:3<242::aid-ajh11>3.0.co;2-o] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
To clarify the mechanism of eosinophilia in adult T-cell leukemia (ATL), we studied three ATL patients having marked eosinophilia. Eosinophil-predominant colony-stimulating activity was detected in the serum of one patient and in the conditioned media (CM) from cultured ATL cells from two patients. Soluble interleukin 5 (IL-5), but no interleukin 3 (IL-3) and granulocyte-macrophage colony-stimulating factor (GM-CSF), was detected in sera from all patients. On the other hand, GM-CSF was produced in vitro by ATL cells from all cases, whereas detectable IL-3 and IL-5 was produced by cells from only one, suggesting that in the other two cases, the serum IL-5 was produced by the normal reacting lymphocytes. The fact that no patient showed marked neutrophilia supports the possibility that IL-5 may have a leading role in the development of eosinophilia, with GM-CSF produced by ATL cells playing a complementary role.
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44
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Kobayashi H, Morioka H, Nikaido O, Stewart JD, Ohtsuka E. The role of surface lysines in pyrimidine (6-4) pyrimidone photoproduct binding by a high-affinity antibody. PROTEIN ENGINEERING 1998; 11:1089-92. [PMID: 9876931 DOI: 10.1093/protein/11.11.1089] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
The roles of four VH surface lysine side-chains in antibody recognition of DNA containing a central pyrimidine (6-4) pyrimidone photoproduct was investigated. Three of the four lysines (at positions H62, H64 and H66) are strongly conserved; however, the presence of lysine at position H68 was highly unusual. Each lysine was replaced individually by alanine; in addition, a quadruple mutant was also created. Studies of the binding kinetics revealed that these lysine residues mainly influenced the association phase. Our results suggest that these side chains help to guide the DNA polyanion to the antigen binding pocket by electrostatic effects.
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Komatsu Y, Shirai M, Ohtsuka E. Modification and application of self-trimming hairpin ribozymes to targeting a transcribed RNA in vitro. J Biochem 1998; 124:986-91. [PMID: 9792923 DOI: 10.1093/oxfordjournals.jbchem.a022217] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The three-domain hairpin ribozyme was improved by increasing the number of linker bases connecting domain I' with domain II from six to seven, and a new ribozyme was designed to release a trans-acting ribozyme that is able to bind with target RNAs by three hybridizing arms. The trans-cleavage activities of the trimmed ribozyme were used to cleave a long target RNA, with 85 bases transcribed from a synthetic gene encoding induced nitric oxide synthase (iNOS). Although the ribozyme with three-hybridizing arms did not efficiently cleave the long target RNA, the overall activity, from self-trimming to the trans-cleavage reaction of the target RNA, was higher than that of the ribozyme with two hybridizing arms.
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Koizume S, Inoue H, Kamiya H, Ohtsuka E. Neighboring base damage induced by permanganate oxidation of 8-oxoguanine in DNA. Nucleic Acids Res 1998; 26:3599-607. [PMID: 9671825 PMCID: PMC147747 DOI: 10.1093/nar/26.15.3599] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We found that single-stranded DNA oligomers containing a 7, 8-dihydro-8-oxoguanine (8-oxo-G) residue have high reactivity toward KMnO4; the oxidation of 8-oxo-G induces damage to the neighboring nucleotide residues. This paper describes the novel reaction in detail, including experiments that demonstrate the mechanism involved in the induction of DNA damage. The results using DNAs of various base compositions indicated that damaged G, T and C (but not A) sites caused strand scissions after hot piperidine treatment and that the damage around the 8-oxo-G occurred at G sites in both single and double strands with high frequency. The latter substrates were less sensitive to damage. Further, kinetic studies of the KMnO4reaction of single-stranded oligomers suggested that thereactivity of the DNA bases at the site 5'-adjacent to the 8-oxo-G was in the order G >A >T, C. This preference correlates with the electron donating abilities of the bases. In addition, we found that the DNA damage at the G site, which was connected with the 8-oxo-G by a long abasic chain, was inhibited in the above order by the addition of dG, dA or dC. On the other hand, the damage reactions proceeded even after the addition of scavengers for active oxygen species. This study suggests the involvement of a redox process in the unique DNA damage initiated by the oxidation of the 8-oxo-G.
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Ohtsuka E, Uno N, Ogata M, Ohno E, Hirota K, Tezono K, Tokimatsu I, Kikuchi H, Nasu M. [Prevention of cytomegalovirus pneumonia in patients with adult T-cell leukemia by nested PCR monitoring]. Gan To Kagaku Ryoho 1998; 25:1609-11. [PMID: 9725057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
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Torizawa T, Kato K, Kimura Y, Asada T, Kobayashi H, Komatsu Y, Morioka H, Nikaido O, Ohtsuka E, Shimada I. 31P NMR study of the interactions between oligodeoxynucleotides containing (6-4) photoproduct and Fab fragments of monoclonal antibodies specific for (6-4) photoproduct. FEBS Lett 1998; 429:157-61. [PMID: 9650581 DOI: 10.1016/s0014-5793(98)00582-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
A 31P nuclear magnetic resonance (NMR) study of the interactions between oligonucleotides containing the (6-4) photoproduct and the Fab fragments of monoclonal antibodies (64M3 and 64M5) recognizing the (6-4) photoproduct is reported. The 31P chemical shift data indicate that backbone conformation of (64) adduct is affected by the presence of flanking oligodeoxynucleotides, and (6-4) adducts with different backbone conformations are accommodated in the antigen binding sites of these antibodies. It was also revealed that epitopes for these antibodies consist of not only the (6-4) adduct but the flanking di- or tri-deoxynucleotides on both the 5' and 3' sides as well.
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Morioka H, Miura H, Kobayashi H, Koizumi T, Fujii K, Asano K, Matsunaga T, Nikaido O, Stewart JD, Ohtsuka E. Antibodies specific for (6-4) DNA photoproducts: cloning, antibody modeling and construction of a single-chain Fv derivative. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1385:17-32. [PMID: 9630483 DOI: 10.1016/s0167-4838(98)00029-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We have investigated a series of four monoclonal antibodies that specifically recognize pyrimidine (6-4) pyrimidone photoproducts. One of these antibodies (64M4), bound all four possible pyrimidine-pyrimidone photoadducts with equal affinities whereas the others (64M2, 64M3 and 64M5) were selective for TC and TT sequences. In addition, 64M5 had the highest binding affinity for photodamaged DNA of the four [T. Mori et al., Photochem. Photobiol. 54 (1991) 225-232]. To help understand the differences between these antibodies, we have cloned and sequenced the variable region genes from all four. Comparing these sequences revealed that all four were highly similar to one another, although there were some differences in potential antigen-contact regions. To assess the influences of these sequence differences at the structural level, computer models were constructed for all four antibodies. Most of the sequence differences occurred in potential antigen contact regions, suggesting specific positions that might account for the observed differences in binding affinities and selectivities. A single-chain Fv derivative of 64M5 was therefore constructed and characterized to provide an experimental system in which structure-function relationships can be tested. This derivative could be isolated from Escherichia coli using two chromatographic steps and possessed the same binding specificity as the parent monoclonal antibody.
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Oku T, Ikeda S, Sasaki H, Fukuda K, Morioka H, Ohtsuka E, Yoshikawa H, Tsurimoto T. Functional sites of human PCNA which interact with p21 (Cip1/Waf1), DNA polymerase delta and replication factor C. Genes Cells 1998; 3:357-69. [PMID: 9734782 DOI: 10.1046/j.1365-2443.1998.00199.x] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND PCNA, an eukaryotic DNA sliding clamp interacts with replication factors and the cell cycle protein, p21(Cip1/Waf1) and functions as a molecular switch for DNA elongation. To understand how DNA replication is regulated through PCNA, elucidation of the precise mechanisms of these protein interactions is necessary. RESULTS Loop-region mutants in which human PCNA sequences were substituted with the corresponding Saccharomyces cerevisiae PCNA regions were prepared. Analysis of their functions, along with previously prepared alanine scanning mutants, demonstrated that some loops interact with DNA polymerase delta (pol delta) and replication factor C (RFC). The p21 binding sites of PCNA, mapped by affinity measurement of the mutant forms, found to be located within a distinct structure of the PCNA monomer, overlap with RFC- and pol delta-interaction sites. Competition between p21 and pol delta or RFC for binding to PCNA results in efficient inhibition of its stimulation of pol delta DNA synthesis and RFC ATPase but not of PCNA loading on DNA by RFC. CONCLUSIONS Semi-saturated amounts of p21 selectively block formation of the active pol delta complex but not the RFC-PCNA complex at 3'-ends of DNA primers. This differential effect may explain the specific inhibition of DNA replication by p21.
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