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An integrated view of the activities of defibrotide.

Defibrotide is a polydeoxyribonucleotide sodium salt extracted from mammalian organs. Its mean molecular weight is 15,000-30,000 daltons. Defibrotide contains aptamers, i.e., single-stranded polynucleotides with a well-defined base sequence and composition (5'-GGTTGG-ATT-GGTTGG-3' and 5'-GGTTGG-ATC-GGTTGG-3') that bind thrombin. For the time being, these aptamers are the only ones that have been identified in defibrotide, but there may also be other aptamers that bind proteins other than thrombin. Defibrotide has no anticoagulant activity, but in some other aspects it probably parallels heparin. Heparin is a sulfated polysaccharide sodium salt with a mean molecular weight ranging from 5,000 to 40,000 daltons extracted from mammalian organs. It contains disaccharide sequences of well-defined structure and frequency. Heparin binds an array of proteins, enzymes, and growth factors and shows inhibitory or stimulatory or protective activity. Defibrotide has a spectrum of interesting pharmacological properties that make this drug very useful for the treatment of arterial and venous thrombotic diseases. In fact, defibrotide has profibrinolytic, antithrombotic-thrombolytic, anti-ischemic, and antiatherosclerotic activity and protective activity in shock. What have all the above activities to do with a single drug? The explanation is that atherosclerosis, myocardial, renal, and liver ischemia, hemorrhagic and septic shock, and shock induced by occlusion of splanchnic artery and thrombosis are different facets of the same entity: the polyhedric inflammatory process.

Fibrinolytic Agents↗

Treatment of severe veno-occlusive disease with defibrotide: compassionate use results in response without significant toxicity in a high-risk population.

Hepatic veno-occlusive disease (VOD) is the most common of the regimen-related toxicities accompanying stem cell transplantation (SCT). Despite aggressive therapies, including the combination of tissue plasminogen activator (t-PA) and heparin, severe VOD is almost uniformly fatal. Defibrotide (DF) is a polydeoxyribonucleotide with activity in several vascular disorders and, unlike t-PA and heparin, produces no systemic anticoagulant effects. Nineteen patients who developed severe VOD after SCT were treated with DF on a compassionate-use basis. Patients had clinically established VOD and met risk criteria predicting progression and fatality. At the initiation of DF, all 19 patients had evidence of multiorgan dysfunction; median bilirubin was 22.3 mg/dL, 12 patients had renal insufficiency (5 dialysis dependent), 14 required oxygen supplementation, and encephalopathy was present in 8 patients. Beginning a median of 6 days after diagnosis of VOD, DF was administered intravenously in doses ranging from 5 to 60 mg/kg/d for a planned minimum course of 14 days. In no case was DF discontinued for attributable toxicity. No severe hemorrhage related to DF administration was observed. Resolution of VOD (bilirubin <2 mg/dL with improvement in other symptoms and signs) was seen in 8 patients (42%). Six of 8 responders survived past day +100, contrasted with the 2% predicted survival reported in comparable patients. The observed response rate, survival to day +100, and absence of significant DF treatment-associated toxicity are compelling and warrant further evaluation.

Adolescent↗

Effect of deoxyribonuclease on adriamycin-polynucleotide complexes.

Recent interest in the use of adriamycin-DNA complex as an approach to improve the therapeutic effectiveness and to reduce toxicity of adriamycin for cancer chemotherapy requires an in-depth understanding of the physicochemical and biochemical properties of such complexes. The interactions of adriamycin with single-strand polydeoxyribonucleotides, double-strand DNA, and double-strand ribodeoxyribopolynucleotide hybrids were therfore investigated. Association constants (Kapp) of adriamycin and polynucleotides were obtained. These data showed that the inherent variable in such complex lies in the composition of the polynucleotides. Alternate deoxyguanylate (dG)-deoxycytidylate (dC) sequence binds 7-fold better than alternate deoxyadenylate (dA)-deoxythymidylate (dT) sequence. Comparative studies of the hydrolysis of DNA duplexes by deoxyribonucleases I and II with and without adriamycin were also carried out. The rate of hydrolysis decreased in the order poly(dA-dT) greater than calf thymus DNA greater than poly(dG-dC) greater than poly(dA)-poly(dT) greater than poly(dG)-poly(dC) for DNase I and poly(dA)-dT) greater than calf thymus DNA greater than poly(dG-dC) greater than poly(dA)-poly(dT) greater than poly(dG)-poly(dC) for DNase II. Intercalation of adriamycin to deoxyribopolynucleotide duplex resulted in inhibition of DNase II two to three times more than tat of DNase I. On the other hand, intercalation of adriamycin to homodeoxypolynucleotide duplex poly(dA)-poly(dT) and poly(dG)-poly(dC) enhanced the DNase I hydrolysis. If DNase I activity could be related to serum DNase and DNase II related to tumor lyososomal DNase as in the endocytosis mechanism proposed by Trouet et al. (Cancer Chemotherapy Rept., 59: 260, 1975), the best adriamycin carrier suggested by this investigation could be poly(dA)-poly(dT) and poly(dG-dC). It is also suggested in this study that adriamycin-RNA-DNA hybrid could be of interest as an antiviral agent by a similar release mechanism via RNase H, an enzyme associated with viral reverse transcriptase.

Animals↗

Structural principles of B-DNA grooves hydration in fibers as revealed by Monte Carlo simulations and X-ray diffraction.

Being interested in possible effects of sequence-dependent hydration of B-DNA with mixed sequence in fibers, we performed a series of Monte Carlo calculations of hydration of polydeoxyribonucleotides in B form, considering all sequences with dinucleotide repeat. The computational results allow the ten base-stacking types to be classified in accordance with their primary hydration in the minor groove. As a rule, the minor groove is occupied by two water molecules per base pair in the depth of the groove, which are located nearly midway between the planes of successive base pairs and symmetrically according to the dyad there. The primary hydration of the major groove depends on the type of the given base pair. The coordinates of 3 water molecules per base pair in the depth of the major groove are determined by the type of this pair together with its position and orientation in the helix, and are practically independent on the adjacent base pairs. A/T-homopolymer tracts do not fit into this hydration pattern; the base pair edges are hydrated autonomously in both grooves. Analysis of the Li-B-DNA x-ray diffraction intensities reveals those two water positions in the minor groove. In the major groove, no electronic density peaks in sufficient distance from the base edges were found, thus confirming the absence of any helical invariance of primary hydration in this region. With the help of the rules proposed in this paper it is possible to position the water molecules of the first hydration shell in the grooves of canonical B-DNA for any given sequence.

Chemical Phenomena↗

Determination of some nuclear deoxyribonucleases in X-irradiated rat thymocytes.

The spectrum of nuclear nucleases in control and irradiated (4 Gy) thymocytes has been investigated. Using the method of SDS electrophoresis of nuclear proteins in 3H-DNA-polyacrylamide gels a number of polypeptides of MW. 35, 32, 17.7, 17.2 and 16.4 kDa possessing nuclease activity were found. The 35 kDa enzyme is only active in the presence of Ca2+ and Mg2+ ions. In response to cycloheximide injection (3 mg/100 g body weight) and irradiation, we did not detect the 35 kDa nuclease activity. Nucleases of 32, 17.7, 17.2 and 16.4 kDa are active in the presence of Ca2+ ions. The activities of these nucleases increases 60 min after irradiation. These nucleases were also found in the fraction of polydeoxyribonucleotide (PDN).

Animals↗

Biochemical characterization and visualization of plasma membrane-DNA-protein complexes from Bacillus subtilis.

Subcellular fractions containing plasma membranes with bound DNA and associated proteins were isolated from two different cultures of Bacillus subtilis 168 growing exponentially at different rates. Differences in the contents of individual between the dissociated complexes, established electrophoretically, can be explained by dynamic binding of the proteins to DNA, resulting in a control of DNA, resulting in a control of DNA replication. Electron microphotographs of isolated complexes display, in addition to unit membranes, associated filamentous structures in different arragement. Patterns obtained after treating the complexes with nucleases suggest a polydeoxyribonucleotide character of the filamentous structures.

Bacillus subtilis↗

Reactivity of pyrimidine nucleosides under the conditions of the pyrimidine sequencing reactions of Maxam and Gilbert.

Several pyrimidine nucleosides and polydeoxyribonucleotides have been examined with respect to their ultraviolet absorption spectra and the kinetics of their decomposition under the conditions used in the C- and (C + T)-specific treatments of the sequencing procedure of Maxam and Gilbert. In hydrazine-water (56:44, v/v), at 20 degrees C, thymidine was found to be virtually fully ionized. Under these conditions, the susceptibility to hydrazinolysis decreased in the order N3-methylthymidine greater than uridine approximately equal to deoxyuridine greater than deoxycytidine approximately equal to polydeoxycytidylate greater than polythymidylate much greater than thymidine greater than 5-methyldeoxycytidine. Addition of sodium chloride to 1.5 M slightly accelerated hydrazinolysis of those nucleosides bearing nonionizable heterocyclic moieties and retarded hydrazinolysis severalfold for those nucleosides containing an ionizable aglycone (thymidine, deoxyuridine, uridine). It is concluded that the nucleosides of this latter class react with hydrazine largely or exclusively in their nonionized form and that the main effect of added salt is increased ionization of the heterocycles, resulting in a decreased population of nonionized nucleosides.

Base Sequence↗

A 5'----3' exoribonuclease of Saccharomyces cerevisiae: size and novel substrate specificity.

The purification scheme for a 5'----3' exoribonuclease of Saccharomyces cerevisiae has been modified to facilitate purification of larger amounts of enzyme and further extended to yield highly purified enzyme by use of poly(A)-agarose chromatography. As determined by either sodium dodecyl sulfate-polyacrylamide gel electrophoresis or physical characterization, the enzyme has a molecular weight of about 160,000. Further studies of its substrate specificity show that poly(C) and poly(U) preparations require 5' phosphorylation for activity and that poly(A) with a 5'-triphosphate end group is hydrolyzed at only 12% of the rate of poly(A) with a 5'-monophosphate end group. DNA is not hydrolyzed, but synthetic polydeoxyribonucleotides are strong competitive inhibitors of the hydrolysis of noncomplementary ribopolymers. Poly(A).poly(U) and poly(A).poly(dT) are hydrolyzed at 60 and 50%, respectively, of the rate of poly(A) at 37 degrees C. The RNase H activity of the enzyme can also be demonstrated using an RNA X M13 DNA hybrid as a substrate. When poly(dT).poly(dA) with a 5'-terminal poly(A) segment on the poly(dA) is used as a substrate, the enzyme hydrolyzes the poly(A) "tail," removing the last ribonucleotide, but does not hydrolyze the poly(dA).

Exoribonucleases↗

A DNA glycosylase for oxidized thymine residues in Drosophila melanogaster.

A DNA glycosylase activity which excises fragmented thymine residues has been identified in cell extracts from Drosophila melanogaster embryos. The enzyme has an apparent Mr = 40,000, acts preferentially on double-stranded polydeoxyribonucleotide substrate and requires no co-factors. The DNA glycosylase presumably acts in excision-repair of pyrimidines damaged by hydroxyl radicals and other oxidizing species. This is the first identification of a DNA glycosylase in Drosophila cells.

Animals↗

Studies on the interaction between steffimycins and DNA.

The complexes formed between steffimycins and DNA were studied using various physicochemical techniques. The binding process has been followed spectrophotometrically or fluorimetrically. The binding parameters n and K, evaluated according to McGhee and Von Hippel, show a good affinity of these antibiotics for the macromolecule. Flow dichroism measurements showed that in the complex with DNA, the antracycline moiety of the steffimycins is intercalated between two base pairs of the macromolecule. The binding experiments with various polydeoxyribonucleotides and with various DNA samples, having different base pair compositions, suggest that an alternate sequence of A-T, such as that of poly[d(A-T)] . poly[d(A-T)], represents a good receptor site for the binding of steffimycins to DNA. The lack of in vivo activity of these antibiotics is discussed.

Anthracyclines↗

Oligotide attenuates leukocyte-endothelial cell interaction via P-selectin in the rat mesenteric vascular bed.

A novel single stranded polydeoxyribonucleotide (oligotide) was studied for its ability to modulate leukocyte-endothelial cell interaction, by means of intravital microscopy in the rat mesenteric microvasculature. Superfusion of the rat mesentery with 50 microM NG-nitro-L-arginine methyl ester (L-NAME), caused a significant, time-dependent increase in leukocyte rolling and adherence compared to control rats superfused with Krebs-Henseleit solution. However, oligotide (15 mg/kg i.v.) consistently reduced the L-NAME-induced leukocyte rolling (62 +/- 14 vs. 23 +/- 3 cells/min; P < 0.02) and adherence (11 +/- 2 vs. 4 +/- 1 cells/100 microns length of venule P < 0.01), without altering systemic blood pressure or mesenteric venular shear rate. Moreover, immunohistochemical localization of P-selectin expression on mesenteric venules was significantly increased (P < 0.01) after exposure to L-NAME, which was significantly attenuated by oligotide (P < 0.05). Similar results were also obtained by flow cytometric analysis performed on rat platelets. Stimulation of rat platelets with L-NAME significantly (P < 0.05) increased the fluorescence intensity of P-selectin, while the concomitant treatment of isolated rat platelets with L-NAME plus oligotide significantly (P < 0.005) attenuated P-selectin fluorescence intensity. Our data demonstrate that in vivo administration of oligotide can reduce leukocyte rolling and adherence in the mesenteric rat microvasculature by attenuating P-selectin expression, and confirming the key role of nitric oxide as an important regulator of leukocyte-endothelial cell interaction.

Animals↗

Yeast ribonuclease H(70) cleaves RNA-DNA junctions.

A specific substrate, M13 DNA:RNA-[32P]DNA, was synthesized to investigate the mode of cleavage of enzymes with RNase H activity. RNase H(70) from Saccharomyces cerevisiae hydrolyzes the phosphodiester bond at the RNA-DNA junction of this substrate, thereby producing a 5'-monophosphate-terminated polydeoxyribonucleotide and 3'-hydroxyl-terminated oligoribonucleotides.

DNA↗

In vivo promoter activity of the synthetic Pribnow box.

The synthetic polydeoxyribonucleotides TGCA(TTATAATGCA)1-4, containing the consensus Pribnow box, were inserted upstream of the promoterless gal operon in a specially constructed plasmid. Using the MacConkey agar indicator technique it has been shown that these inserts are able to induce an efficient in vivo expression of the gal operon.

Base Sequence↗

Preliminary characterization of the temperature-sensitive defect in DNA replication in a mutant mouse L cell.

Temperature-sensitive ts A1S9 mouse L cells synthesize DNA apparently normally for 6-8 hr upon incubation at 38.5 degrees C. Thereafter, these cells are able to perform limited polydeoxyribonucleotide chain synthesis at the high temperature, but are unable to convert newly replicated small single-strand segments of DNA (of the order of molecular weight 10(6) daltons) to large molecular weight chromosomal DNA. Data obtained are compatible with a model which suggests that ts A1S9 cells are able to carry out most individual reactions of DNA synthesis at the high temperature, but are temperature-sensitive in a protein which participates in the joining of small DNA segments to make chromosomal DNA strands. When cells are reincubated at a permissive temperature, after the temperature-sensitive lesion has been established, they recover the latter capability several hours before they are able once again to synthesize DNA at normal rates.

Centrifugation, Density Gradient↗

Generation of hybridoma antibodies to double-stranded DNA from non-autoimmune BALB/c strain: studies on anti-idiotype.

A hybridoma obtained between normal spleen cells from BALB/c mice (a non-autoimmune strain) and SP2-O-Ag 14 myeloma cell line was designated as HB2. These hybrid cells produced an IgM kappa-anti-ds-DNA antibody, but their specificity was limited to some polydeoxyribonucleotides such as natural ds-DNA from calf thymus, poly dG-poly dC, poly d(GC) and poly d(GC)-poly d(GC). In contrast, poly dA-poly dT, poly d(AT) were not recognized. The configuration of the nucleic acid helix plays a small role if any, in the building of the epitopes recognized by the hybridoma HB2 antibodies, while the presence of G and C appeared to be essential. These epitopes could not be found on ss- and ds-polyribonucleotides. B cells able to produce anti-ds-DNA antibodies are therefore present in non-autoimmune BALB/c mice, but not enough to produce the corresponding antibodies at a detectable level in the serum. Following immunization of BALB/c mice with hybridoma HB2 monoclonal antibodies, anti-idiotype antibodies were obtained which also recognized idiotopes present in the serum from both murine MRL/1 and human systemic lupus erythematosus (SLE).

Animals↗

Purification and properties of the exocellular beta-lactamase of Actinomadura strain R39.

The exocellular beta-lactamase (penicillin amido-beta-lactamhydrolase, EC 3.5.2.6) of Actinomadura R39 consists of one single polypeptide chain of molecular weight about 15 200. It exhibits a highly asymmetrical shape, has a low isoelectric point (at pH 5.0) and contains about 9.3% (w/w) of a polydeoxyribonucleotide with which it forms a rather stable complex. Removal of a substantial amount of this deoxyribonucleotide by treatment with DNAase I has no effect on the enzyme activity. The beta-lactamase has a wide spectrum of activity. Penicillins and delta 3-cephalosporins can be either good or poor substrates. Oxacillin, which is a poor substrate of most beta-lactamases from Gram-positive bacteria, is a good substrate of the beta-lactamase of Actinomadura R39. Its best substrate, however, is nitrocefin (kcat/Km: 2300 000 M-1.s-1; catalytic centre activity: 210 s-1). The kcat/Km values observed with some penicillins and delta 3-cephalosporins are similar to the values of the bimolecular rate constants that govern the formation of the acyl-enzyme intermediates between these antibiotics and the serine D-alanyl-D-alanine peptidase that is also secreted by the same strain Actinomadura R39. Such a relationship, however, is not observed with all the beta-lactam compounds tested.

Amino Acids↗

Daunorubicin and doxorubicin, anthracycline antibiotics, a physicochemical and biological review.

Daunorubicin and doxorubicin, two antibiotics belonging to the anthracycline group, are widely used in human cancer chemotherapy. Their activity has been attributed mainly to their intercalation between the base pairs of native DNA. Complex formation between daunorubicin or doxorubicin with polydeoxyribonucleotides and DNAs of various base composition or chromatins has been investigated by numerous techniques. Many authors have tried to correlate biological and therapeutic activities with the affinity of the drugs for DNA or some specific sequences of DNA. In vivo these anthracycline drugs cause DNA damage such as fragmentation and single-strand breaks. The mechanism of action of anthracyclines involves the inhibition of RNA and DNA syntheses. There exists two limiting factors in the use of anthracyclines as antitumoral agents: a chronic or acute cardiotoxicity and a spontaneous or acquired resistance. In both cases, there is probably an action at the membrane level. It has to be noted that daunorubicin and doxorubicin have a particular affinity for phospholipids and that the development of resistance is linked to some membrane alterations.

Animals↗