Preliminary studies for interaction of a cyclobutane thymine dimer region with its cognate antibody

A monoclonal antibody (TDM-2) specific to a UV-induced cyclobutane pyrimidine dimer has previously been established. We investigated here the structural requirements of antigen recognition by the antibody using chemically synthesized antigen analogs. TDM-2 bound to the cis-syn, but not the trans-syn thymine dimer, and recognized not only the cyclobutane ring but also the 5'- or 3'-side phosphate groups flanking the cyclobutane dimer site. The antibody showed strong binding to photodimer-containing single stranded DNA but indicated little binding to double stranded DNA.

Mechanistic studies on the neighboring base damage induced by KMnO4 oxidation of 8-oxoguanine in DNA

New types of DNA substrates containing an 8-oxoguanine residue (8-oxo-G) were prepared in order to examine the mechanisms for the neighboring base damage initiated by KMnO4 oxidation of the 8-oxo-G. The results obtained from the reactions suggested that the damage at remote sites in the single strands can be explained by an electronic interaction (redox reaction) between an oxidized 8-oxo-G species and the base (to be damaged), which are close each other in a loop structure. For the inefficient damage observed in duplex substrates, electron transfer through stacked bases might be involved.

A new Drosophila ultraviolet light-damaged DNA recognition endonuclease that selectively nicks a (6-4) photoproduct site

We have previously described the purification of an ultraviolet light (UV) damage-specific DNA-binding protein from Drosophila melanogaster, designated D-DDB P1 [Nucleic Acids Res., 23 (1995) 2600-2607]. Here, we obtained highly purified D-DDB P1 from Drosophila Kc cells, and we found that D-DDB P1 is also a nuclease. D-DDB P1 can selectively bind to pyrimidine (6-4) pyrimidone photoproducts, and in the presence of Mg++, D-DDB P1 can catalyze an incision immediately on the 3' and 5' sides of the (6-4) photoproduct site.

Stimulation of leukaemic cells from adult T-cell leukaemia patients with bacterial superantigens

Bacterial superantigens stimulate T cells in a manner that is restricted to the Vbeta of the T-cell receptor. We examined the ability of adult T-cell leukaemia (ATL) cells to respond to these superantigens. Mononuclear cells from 10 patients were cultured with staphylococcal enterotoxin A (SEA), staphylococcal enterotoxin B (SEB) or toxic shock syndrome toxin-1 (TSST-1), and their response was determined by MTT assay and 3H-thymidine incorporation assay. Cells from six patients showed a specific response to a single superantigen. In two cases the cells responded to TSST-1 and bore Vbeta2, the known target of TSST-1. In three cases the cells responded to SEA with one bearing Vbeta9, a target of SEA, and one bearing Vbeta16. In one case the cells responded to SEB. Most of the cells which proliferated in response to superantigens were determined genetically to be leukaemic. The response to TSST-1 was inhibited by anti-Vbeta2 antibody. The responding cells showed a strongly enhancement expression of interleukin-2 receptor. These findings indicate that leukaemic cells from a proportion of ATL patients have an ability to respond to T-cell receptor-dependent superantigens. This suggests that bacterial infection in such patients may contribute to the expansion of ATL cells.

Identification of specific amino acid residues of adenovirus 12 E1A involved in transformation and p300 binding

The early region 1A (E1A) gene of highly oncogenic adenovirus type 12 (Ad12) was analyzed for transforming activity and protein binding using specific mutations. The Ad12 E1A proteins were found to bind p300 protein mainly within the CR1 region, although mutations that affect both p300 binding and transformation were identified in both the CR1 and the N-terminal region. The most critical mutation dlf89 located in the CR1 region was further dissected by point mutations and the results identified 68S as the most critical for transformation and 67E as the most critical for p300 binding. Specific mutations that retain p300 binding but impair transcriptional repression of a viral enhancer were also identified in both the N-terminal and CR1 regions.

Specificities and rates of binding of anti-(6-4) photoproduct antibody fragments to synthetic thymine photoproducts

Pyrimidine (6-4) pyrimidone photoproducts are some of the major DNA photolesions induced by ultraviolet (UV) light. A monoclonal antibody (64M5) specific to a (6-4) photoproduct has been established and the corresponding single-chain antibody (64M5scFv) has been prepared. In this study, we characterized the ligand selectivities of 64M5 and 64M5scFv using synthetic octadeoxynucleotides containing either a central cis-syn cyclobutane thymine dimer (T[c,s]T), the (6-4) photoproduct of TpT (T[6-4]T), or its Dewar isomer (T[Dewar]T) by means of enzyme-linked immunosorbent assays (ELISA). Both 64M5 and 64M5scFv recognized T[6-4]T, but not the other photoproducts. We synthesized several biotinylated oligonucleotides of different lengths containing (T[6-4]T) to analyze the effects of the antigen size on the binding rates of an antigen binding fragment (64M5Fab) and 64M5scFv by means of surface plasmon resonance. The association rate constants for oligonucleotides of different sizes containing T[6-4]T as to 64M5Fab were found to be almost the same (1.9-5.6 x 10(5) M(-1) x s(-1)), while the dissociation rate constant for the largest oligonucleotide (d8mer, 8.0 x 10(-5) s(-1)) was significantly smaller than that for the d2mer (4.2 x 10(-2) s(-1)). These results indicate that 64M5Fab recognized the d2mer as the epitope and that the binding affinity for T[6-4]T depended on the flanking oligonucleotides. The dissociation rate constants for 64M5scFv as to the antigen analogs were almost the same as those for the various T[6-4]T-oligonucleotides as to 64M5Fab, suggesting that the conformations of these antibody binding regions are pretty similar to each other.

Design and anti-HIV-1 activity of hammerhead and hairpin ribozymes containing a stable loop

Three ribozymes, a hairpin ribozyme (HR112) and two hammerhead ribozymes (RZ115 and RZ119) containing a 5'C(UUCG)G3' loop were designed to cleave the U5 region in the long terminal repeat (LTR) of HIV-1 RNA. The t1/2 values of chemically synthesized substrates mediated by three ribozymes were measured. The transformed CEM cells possessing these three ribozyme-encoding genes were challenged with a HIV-1IIIB strain, and two of these three ribozymes, HR112 and RZ119, were shown to possess strong anti-HIV-1 activity.

Antigen structural requirements for recognition by a cyclobutane thymine dimer-specific monoclonal antibody

A monoclonal antibody (TDM-2) specific to a UV-induced cyclobutane pyrimidine dimer (T[cis-syn]T) has previously been established; however,the immunization had used UV-irradiated calf-thymus DNA containing a heterogeneous mixture of photoproduct sites. We investigated here the structural requirements of antigen recognition by the antibody using chemically synthesized antigen analogs. TDM-2 bound with cis-syn,but not trans-syn thymine dimer,and could bind strongly with four nucleotide analogs in which the cis-syn pyrimidine dimer was located in the center. Antigen analogs containing abasic linkers at the 5'- or 3'-side of the cis-syn cyclobutane pyrimidine dimer were synthesized and tested for binding to TDM-2. The results indicated that TDM-2 recognizes not only the cyclobutane ring but also both the 5'- and 3'-side nucleosides of the cyclobutane dimer. Furthermore,it was proved that either the 5'- or 3'-side phosphate group at a cyclobutane dimer site was absolutely required for the affinity to TDM-2. The antibody showed a strong binding to single stranded DNA but indicated little binding to double stranded DNA.

A new type of hairpin ribozyme consisting of three domains

We have constructed a new hairpin ribozyme with three stem-loop domains. In the ribozyme, another domain (domain I') was connected to the 3'-end of domain II of the parent hairpin ribozyme, and the new ribozyme can be trimmed after transcription from the DNA template using T7 RNA polymerase. Since a mutant ribozyme containing a substitution at the essential base in domain I' lacked the 3'-trimming reaction, the autoprocessing activity was proved to be derived from the catalytic reaction, similar to the wild-type ribozyme. Furthermore, the structure of the cleavage site from the self-trimming reaction was identified as a 2',3'-cyclic phosphate, which is the same as that of the wild-type. The processed ribozyme was designed to cleave an external substrate RNA derived from the mRNA of the human inducible nitric oxide synthase and was proved to cleave at the expected, unique site. The hairpin ribozyme containing the three-domains exhibited the 3'-self-trimming activity even in a runoff transcription reaction from the plasmid harboring the ribozyme gene with the three domains. The new type of hairpin ribozyme thus obtained has three stem-loop domains and is able to act as a catalytic RNA for both cis and trans cleavage. These ribozymes are of interest from the point of the structure-function relationship of the hairpin ribozyme and provide an important insight into over understanding of the role of the domain-domain interaction in the catalytic activity.

A recurrent translocation, t(16;21)(q24;q22), associated with acute myelogenous leukemia: identification by fluorescence in situ hybridization

Chromosome fluorescence in situ hybridization (FISH) analyses were performed on bone marrow cells in 3 adult patients with MDS or AML with a (16;21)(q24;q22) translocation. FISH analyses with AML1 probes at 21q22 proved in all 3 patients splitting of the AML1 gene at a region spanning exons 5 and 6 and the translocation of its 5' segment to distal 16q. Chromosome painting FISH analysis in patient 1 proved the translocation of the distal 21q segment to 16q, but it failed to prove the presumed translocation of the distal 16q segment to 21q, most likely because of its small size.

[Diffuse alveolar hemorrhage associated with idiopathic interstitial pneumonia syndrome after allogeneic bone marrow transplantation]

A 24-year-old male with myelodysplastic syndrome (refractory anemia) was treated with allogeneic bone marrow transplantation (BMT) from HLA-identical brother on September 9, 1994, after conditioning with busulfan and cyclophosphamide. From early in April 1995, the patient complained of cough and fever. Chest X-ray showed interstitial infiltrates involving hilar and lower lung fields. Although pulmonary infiltrates were resolved with methylprednisolone pulse therapy, on May 19, the patient rapidly deteriorated with dyspnea. Diffuse alveolar infiltrates appeared on chest X-ray and he died of respiratory failure. At autopsy, diffuse alveolar hemorrhage accompanied with thickening of the alveolar walls and interstitial infiltration of lymphocytes was demonstrated. There was no evidence of bleeding in other organs. This is a rare case of diffuse alveolar hemorrhage in the late stage of allogeneic BMT. This report should lead to an evaluation of this disease by the collection of similar cases.

Construction of hairpin ribozymes with a three-way junction

Hairpin ribozymes with high cleavage activities were designed. An extra sequence was introduced at the 3'-end of the hairpin ribozyme to increase the binding to the substrate RNA, as compared to the wild-type hairpin ribozyme. A three-way junction (TWJ) was formed between the newly designed ribozyme and the substrate RNA. The complex with a solid TWJ showed less RNA cleavage activity than the wild-type hairpin ribozyme. However, the ribozyme with a TWJ with five unpaired bases or propandiol phosphate linkers had higher cleavage activity than the parent ribozyme without the TWJ. When a cis-cleavage system, in which the 5'-end of the substrate RNA was conjugated to the 3'-end of the ribozyme, was employed, the complex with the TWJ containing unpaired bases was also cleaved faster than the complex with the solid TWJ. This suggested that these differences in the cleavage activities were derived from the confirmation, and this was proven by nondenaturing gel electrophoresis. The TWJ hairpin ribozyme containing unpaired bases is able to bind strongly with substrate RNAs and to cleave them efficiently. Since the three-way ribozyme presented here is more active than the wild-type ribozyme, this type of ribozyme can serve as a more efficient tool to control RNA activities in vitro and in vivo.

Hemolytic uremic syndrome following autologous peripheral blood stem cell transplantation in a patient with malignant lymphoma

Hemolytic uremic syndrome (HUS) has been reported in patients receiving bone marrow transplantation. However, only a few cases of HUS following autologous peripheral blood stem cell transplantation (PBSCT) have been reported. We present a case of HUS developing after autologous PBSCT in a 40-year-old man with non-Hodgkin's lymphoma. It appears that the chemotherapeutic agents administered during the conditioning regimen for PBSCT may have played an important role in the development of HUS in our patient. In the present case, the combination therapy of vincristine, methylprednisolone, and ticlopidine hydrochloride was effective.

Solution structure of an RNA.2'-O-methylated RNA hybrid duplex containing an RNA.DNA hybrid segment at the center

The solution structure of an RNA.2'-O-methylated RNA hybrid duplex containing an RNA.DNA hybrid segment at its center, (ggagaugac).(GmUmCmATCTCmCm), where lowercase letters, capital letters, and capital letters with the subscript m are RNA, DNA, and 2'-O-methylated RNA residues, respectively, was determined by observing the NMR spectra and performing the full relaxation matrix refinement. The 2'-O-methylation gives several characteristic features to oligoribonucleotides. In addition, this hybrid duplex is cleaved at a specific position by Escherichia coli ribonuclease HI, and so the role of the tertiary structure during the substrate recognition by the enzyme is of interest. The NOE connectivities among the proton resonances revealed that the duplex was a right handed helix. The 2'-O-methylated RNA segments had a typical C3'-endo conformation, and the 2'-O-methyl groups were directed to the minor groove of this duplex, taking the torsion angles phi (C1'-C2'-02'-CH3) that were all gauche(+). The DNA residues in the central RNA.DNA hybrid duplex formed the C3'-endo conformation, except for the middle thymine residue. No remarkable structural discontinuities were observed around the junction sites at either the 5'- or 3'-end of the DNA. The overall structure was close to the typical A-form duplex.

Behçet's disease associated with myelodysplastic syndromes. A case report and a review of the literature

BACKGROUND

Behçet's disease has rarely been reported in association with myelodysplastic syndromes (MDS). Increased production of reactive oxygen species (ROS) by neutrophils has a primary role in the pathogenesis of Behçet's disease. However, decreased production of ROS by neutrophils has frequently been reported in patients with MDS. The current study was undertaken to determine the role of ROS production in a patient with Behçet's disease and MDS.

METHODS

A patient with MDS with trisomy 8 who developed Behçet's disease is described and a review of the literature of patients with Behçet's disease in MDS is presented. The production of ROS by neutrophils was investigated by luminol-enhanced chemiluminescence (CL) assay.

RESULTS

Based on a review of the literature, 10 cases of Behçet's disease associated with MDS have been reported to date. Nine patients had undergone cytogenetic analysis of bone marrow cells, 7 of whom (78%) had trisomy 8. Neutrophils taken from the authors' patient during the active phase of Behçet's disease demonstrated an increased CL response. Moreover, serum from this patient increased the CL emission of neutrophils from healthy volunteers.

CONCLUSIONS

These data suggest that trisomy 8 predisposes to Behçet's disease in patients with MDS. Furthermore, an increased ROS production by neutrophils may be associated with the diverse clinical findings in this disease. In this study, neutrophils were activated directly by serum factors.

Flavin adenine dinucleotide as a chromophore of the Xenopus (6-4)photolyase

Two types of enzyme utilizing light from the blue and near-UV spectral range (320-520 nm) are known to have related primary structures: DNA photolyase, which repairs UV-induced DNA damage in a light-dependent manner, and the blue light photoreceptor of plants, which mediates light-dependent regulation of seedling development. Cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts [(6-4)photoproducts] are the two major photoproducts produced in DNA by UV irradiation. Two types of photolyases have been identified, one specific for CPDs (CPD photolyase) and another specific for (6-4)photoproducts [(6-4)photolyase]. (6-4)Photolyase activity was first found in Drosophila melanogaster and to date this gene has been cloned only from this organism. The deduced amino acid sequence of the cloned gene shows that (6-4)photolyase is a member of the CPD photolyase/blue light photoreceptor family. Both CPD photolyase and blue light photoreceptor are flavoproteins and bound flavin adenine dinucleotides (FADs) are essential for their catalytic activity. Here we report isolation of a Xenopus laevis(6-4)photolyase gene and show that the (6-4)photolyase binds non- covalently to stoichiometric amounts of FAD. This is the first indication of FAD as the chromophore of (6-4)photolyase.

Behçet's disease associated with myelodysplastic syndromes. A case report and a review of the literature

BACKGROUND

Behçet's disease has rarely been reported in association with myelodysplastic syndromes (MDS). Increased production of reactive oxygen species (ROS) by neutrophils has a primary role in the pathogenesis of Behçet's disease. However, decreased production of ROS by neutrophils has frequently been reported in patients with MDS. The current study was undertaken to determine the role of ROS production in a patient with Behçet's disease and MDS.

METHODS

A patient with MDS with trisomy 8 who developed Behçet's disease is described and a review of the literature of patients with Behçet's disease in MDS is presented. The production of ROS by neutrophils was investigated by luminol-enhanced chemiluminescence (CL) assay.

RESULTS

Based on a review of the literature, 10 cases of Behçet's disease associated with MDS have been reported to date. Nine patients had undergone cytogenetic analysis of bone marrow cells, 7 of whom (78%) had trisomy 8. Neutrophils taken from the authors' patient during the active phase of Behçet's disease demonstrated an increased CL response. Moreover, serum from this patient increased the CL emission of neutrophils from healthy volunteers.

CONCLUSIONS

These data suggest that trisomy 8 predisposes to Behçet's disease in patients with MDS. Furthermore, an increased ROS production by neutrophils may be associated with the diverse clinical findings in this disease. In this study, neutrophils were activated directly by serum factors.

Interaction of the basic protrusion of Escherichia coli ribonuclease HI with its substrate

In order to determine the actual distance between the active site and the substrate binding site, termed the basic protrusion, of Escherichia coli ribonuclease HI, synthetic oligonucleotide duplexes with gradually extended overhangs were used, in which the enzymatic cleavage was restricted to a single site with 2'-O-methylnucleosides. The affinity of the enzyme for each substrate was determined by kinetic analysis. It was found that the affinity increased markedly when one nucleotide was attached to the 3' end of the DNA strand of the nine-base-pair hybrid duplex and then increased slightly as the DNA strand was extended further, whereas elongation of the strand in the other direction caused no change. When a mutant enzyme, in which three lysine residues in the basic protrusion were altered to alanine, was used, no increase in the kcat/K(m) value was observed. The results indicate that, for the productive binding, the axis from the 3' to the 5' end of the RNA strand of the substrate duplex must be oriented in agreement with the direction from the active site to the basic protrusion of the enzyme. The distance between the active site and the basic protrusion in the enzyme-substrate complex was shorter than that anticipated in modeling studies. A dynamic structure refinement, referred to as the normal mode analysis, was carried out in order to simulate the fluctuations of the basic protrusion.

An epitope chimeric antigen for the hepatitis C virus serological screening test

The epitope chimeric antigen, CepCM, composed of the 9 selected major epitope regions (two in NS3, two each in the NS4 of two genotypes, two each in the core of two genotype, and one in the core in hepatitis C virus (HCV) polypeptide), was expressed as a fusion protein of the trpE peptide in E. coli. An ELISA test using this antigen produced the same judgements with most of the panel sera as a second generation HCV screening kit. Though discrepancies were found in twelve samples (5% of the samples), further analysis revealed that eleven samples were indeterminate sera as judged by an immunoblot test. The reactivity found in several seroconversion series sera suggested that CepCM has superior reactivity to HCV infected sera than some second generation kits. These data indicated that an epitope chimeric antigen with a man-made sequence will be a excellent tool for a diagnostic test kit.

Constructing an efficient trans-acting genomic HDV ribozyme

We have engineered a genomic HDV ribozyme to construct several trans-acting ribozymes for use in trans to cleave target RNAs. Among the 10 different combinations attempted, only HDV88-Trans had cleavage activity on the 13-nucleotide substrate, R13, in vitro. To improve the cleavage efficiency, at least in vitro, of the HDV88-Trans ribozyme (kclv = 0.022 min(-1)), we have constructed several variants that differ in forming stem II (length) in the pseudoknot secondary structure model. When cleavage rate constants were analyzed and compared among variants of HDV88-Trans, HDV88-Trans-4 yielded kclv = 1.7 min(-1). HDV88-Trans-4 thus represents the highest active genomic HDV ribozyme that functions in trans thus far constructed, and has activity under physiological conditions (pH 7.1 at 37 degrees C with 1 mM of MgCl2).

Enhanced folding of hairpin ribozymes with replaced domains

Reversely joined ribozymes (Komatsu et al., 1995) have been proven to be active. Here we describe the construction of hairpin ribozymes with separated domains, but containing complementary arms for association of the two domains. Linker nucleotides were inserted between the arms and domains. These ribozymes were active under the standard conditions (12 mM MgCl2), depending on the length of the linker. When the complementary arms were covalently joined through a stable loop, these ribozymes showed cleavage activities. However, the K(m) value of the stem-loop ribozymes was found to be larger than that of the parent ribozyme, which can adopt both linear and bent conformations. Kinetic analyses of these modified hairpin ribozymes suggest a higher turnover of the hairpin ribozyme as compared to other small ribozymes. The present ribozymes provide insight into the nature of the domain interaction and are suitable for physicochemical studies on the tertiary structure of the hairpin ribozyme.

3-Amino-1,4-dimethyl-5H-pyrido[4,3-b]indole (Trp-P-1) inhibits the binding activity of T4 endonuclease V to UV-damaged DNA

3-Amino-1,4-dimethyl-5H-pyrido[4,3-b]indole (Trp-P-1) is a mutagen/carcinogen derived from cooked foods which enhances the induction of mutations and chromosome aberrations by UV without microsomal activation. These co-mutagenic effects are considered to arise from inhibition of DNA excision repair at the incision step. However, the inhibition mechanism has not been clarified. In this study we show, using agarose gel electrophoresis, that Trp-P-1 inhibits incision by T4 endonuclease V, which cleaves DNA at the site of cyclobutane dimers. Trp-P-1 also inhibits the binding of this enzyme to UV-damaged DNA in a gel shift assay. In addition, the results of DNA unwinding assay with topoisomerase I suggest that Trp-P-1 intercalates into DNA molecules. The known intercalators ethidium bromide and acriflavine demonstrate similar effects in these experiments. However, 2-amino-1-methyl-6-phenylimidazo[4,5-b]pyridine (PhIP), which showed no co-mutagenic effects in our previous study, does not demonstrate such effects. These results suggest that Trp-P-1 changes DNA conformation by intercalation, causing inhibition of binding of repair enzymes to UV-damaged DNA, and this in turn leads to inhibition of DNA excision repair and to co-mutagenic effects.

[Prevention of infections in a case with myelodysplastic syndrome by an intermittent subcutaneous administration of G-CSF]

An 83-year-old male was admitted to our hospital because of pancytopenia and low grade fever on April 19, 1993. On admission, hematological data were as follows: WBC 1,000/microliters with 19% neutrophils, RBC 367 x 10(4)/microliters, Hb 9.5 g/dl and platelets 6.7 x 10(4)/microliters. Bone marrow examination revealed 6.6% myeloblasts and 33.5% erythroblasts. Morphological abnormalities included hypersegmentation, degranulation and pseudo-Pelger's nuclear anomaly in neutrophils. Based on these findings the diagnosis of refractory anemia with excess of blasts (RAEB) of the myelodysplastic syndrome (MDS) was made and therapy with low dose Cytarabine (Ara-C) was initiated in April 1993. The patient had two episodes of severe pneumonia in June and July. Therefore, 75 micrograms/day of G-CSF was given in addition to antibiotic therapy for the second episode of infection in July. Thereafter the severe infection subsided, and G-CSF administration was switched to an intermittent schedule (75 micrograms twice a week) since September. Cytarabine ocfosfate (100 mg/day) was added for 10-14 days at interval 1-2 months from October,1993. He has been well with no episode of infection for more than two year. One major concern regarding the clinical application of G-CSF in MDS patients is related to the possible stimulation of leukemic cell proliferation. Frequent hematological monitoring is necessary in patients with RAEB who are prone to develop acute myeloid leukemia. However, we administered G-CSF at a relatively low dose twice a week for over two year and could successfully prevent infections without inducing the leukemic changes.

Triplex-mediated cleavage of DNA by 1,10-phenanthroline-linked 2'-O-methyl RNA

We have previously reported that 2'-O-methyl RNAs are efficient probes for duplex DNA. Here we describe the design, synthesis, and DNA cleaving activity of 1,10-phenanthroline (OP)-linked 2'-O-methyl RNA (OP-m). Although a local triple helix was formed, both with OP-m and a control OP-linked DNA at the target sequence of the duplex DNA, the promoter region of the human thrombomodulin gene, the cleavage efficiencies on both strands were not proportional when OP-M was used as a cleavage agent. These results may reflect the structural differences of the respective triple helices and the duplex-triplex junction, formed from the two types of triplex-forming oligonucleotides, 2'-O-methyl RNA and DNA. Since the OP-ms were found to work as preferential purine-strand cutters for duplex DNA, they would be useful as unique tools for genome analysis.