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PubMed2001

Type-1 ribosome-inactivating protein from iris (Iris hollandica var. Professor Blaauw) binds specific genomic DNA fragments.

The capacity of IRIP, a type-1 ribosome-inactivating protein (RIP) isolated from the bulbs of Iris hollandica, to bind specific DNA sequences from a mixture of approx. 200 bp (average length) fragments of total genomic DNA from Iris genome was studied. Fragments that were preferentially bound by IRIP were enriched by several cycles of affinity binding and PCR, and were cloned and sequenced. The selected DNA fragments do not share conserved sequences, indicating that IRIP does not bind DNA fragments in a strictly sequence-specific manner. According to sequence analysis, most IRIP-bound fragments contain one or more possible free energy-stable hairpin structure(s) in their secondary structure, which may be the basis for recognition between IRIP and these DNA fragments. Some, but not all, DNA fragments moderately lower the RNA N-glycosidase activity of IRIP towards rabbit reticulocyte lysate ribosomes. IRIP does not remove adenines from the binding fragments, which implies that it does not act as a polynucleotide:adenosine glycosidase towards these DNA fragments. The selective binding of IRIP to conspecific DNA fragments is also discussed in view of the novel concept that RIPs may act as DNA-binding proteins with a regulatory activity on gene expression.

Blotting, Southern↗
PubMed1981

Kinetic and equilibrium metal-ion-binding behaviour reflected in a metal-ion-dependent antigenic determinant in bovine prothrombin. Comparison with bovine prothrombin fragment 1.

Rabbit anti-(bovine prothrombin fragment 1) antibodies were fractionated by using fragment-1 affinity chromatography in the absence of metal ions, and showed an absolute requirement for the presence of metal ions in their interactions with bovine fragment 1 or prothrombin. These antibodies were employed to evaluate both the rate constants for a protein conformation change and the equilibrium metal-ion binding to isolated bovine fragment 1 and intact prothrombin. The close similarity of the rates obtained for the conformation change in fragment 1 and those observed in prothrombin indicated that the same process is involved in both proteins and that the non-fragment-1 region of the prothrombin has essentially no effect on this process in the fragment-1 region. Equilibrium metal-ion-binding studies indicate that the details of the metal-ion-binding process in fragment 1 and prothrombin are essentially the same. We conclude that the metal-ion-binding behaviour of the fragment-1 domain of intact prothrombin is identical with that of isolated fragment 1.

Animals↗
PubMed1981

Characterization of the inhibition of fibrin assembly by fibrinogen fragment D.

Fragment D (Mr 100 000) prepared from a terminal plasmin digest of fibrinogen was isolated and used to study its effect on fibrin formation. Increasing amounts of fragment D added to a solution of fibrinogen and thrombin decrease the rigidity of the resultant gel (10% of control at 2 mol of fragment D/mol of fibrinogen). Half-maximal inhibition is achieved at 1 mol of fragment D/mol of fibrinogen for non-cross-linked clots and at 1/2 mol of fragment D/mol of fibrinogen for cross-linked clots. "Clottability' decreases concomitantly with the rigidity. Only small amounts of fragment D (less than 10% for non-cross-linked gels) are incorporated into the gel. Light-scattering shows an increase in the final fibre thickness at fragment D concentrations up to 2 mol of fragment D/mol of fibrinogen, from 60 molecules/cross-section for the control to 120 molecules/cross-section. Higher fragment D concentrations lead to a decrease in the final fibre thickness. The limit fibre thickness is 8 nm, with a length of 80 nm, which is equivalent to a fibrin trimer. On the basis of results of synthetic-substrate and fibrinopeptide-release assays, it is clear that thrombin inactivation is not responsible for this effect. These data suggest that fragment D may inhibit fibrin formation by blocking the bimolecular polymerization of activated fibrin monomer molecules to form protofibrils, although additional effects on subsequent assembly steps may also be involved.

Blood Coagulation↗
PubMed2001

Meiotic and mitotic instability of two EMS-produced centric fragments in the haplodiploid wasp Nasonia vitripennis.

Terminal deletions that result in chromosomal fragments with centromeres (centric fragments) are relatively easy to generate and study in the haplodiploid insect Nasonia. We investigated the transmission stability of two chromosomal fragments generated by chemical mutagenesis. Visible mutations at the R locus (peach-233 and St-DR) and a linked body-colour mutant (purple) were used to track transmission of the centric fragments (which lack the purple locus and are wild-type at the R locus). Transmission rates in meiotic oogenesis were low (medians 0.15-0.18) and comparable to previous data on centric fragments in this species. The homologous chromosome genetic background strongly affected meiotic stability of one centric fragment (CF2) but not the other (CF1). Specifically, in peach/scarlet R locus heterozygous females, CF2 showed a normal segregation proportion with the chromosome bearing the scarlet allele (0.16), but near complete failure to segregate with peach (0.0002). Data show that this is due to loss of CF2 in eggs receiving peach, rather than to preferential segregation of CF2 with scarlet or mortality of CF2-bearing males. CF1 shows typical segregation ratios with both chromosomes. We hypothesize that deletions (or rearrangements) associated with the peach-233 mutant inhibit proper pairing and segregation of CF2. Consistent with the model, CF2 did segregate with chromosomes that had undergone recombination between peach and purple (a body-colour mutation 10 cM from peach), indicating that the domains inhibiting segregation are closely linked to peach. Mitotic instability also differed between the two fragments; reduced mitotic stability may relate to absence of telomeres on these centric fragments. Given the relative ease of generating and tracking terminal deletions in Nasonia, we propose this as a good system for studying mitotic and meiotic stability of centric fragments. Finally, results are discussed in relation to the evolution of B chromosomes from centric fragments.

Animals↗
PubMedDate not supplied

Use of electrocautery probes in arthroscopic removal of apical sesamoid fracture fragments in 18 Standardbred horses.

OBJECTIVE: To develop a technique for arthroscopic excision of apical sesamoid fracture fragments using electrocautery probes. ANIMALS OR SAMPLE POPULATION: A total of 18 Standardbred horses. METHODS: Arthroscopic removal of apical sesamoid fracture fragments using both hook and loop electrocautery probes was performed on 18 Standardbred horses. The fracture fragments were approached using either an ipsilateral (3) or contralateral (15) arthroscopic triangulation technique. Distension of the metacarpo- (metatarso)-phalangeal joints was achieved using a 1.5% glycine solution. Under arthroscopic guidance, both the suspensory and intersesamoidean ligament attachments to the abaxial and the axial margins of the apical fragment were transected using a hook electrocautery probe. Subsequently, the palmar (plantar) soft tissue attachments to the apical fragment were transected with a loop electrocautery probe. Once freed of soft tissue attachments, the apical fragment was removed with Ferris-Smith intervertebral disc rongeur. The arthroscopic portals were closed in a routine manner. RESULTS: Horse ages ranged from 2 to 8 years (median, 2.5 years). Eighteen apical sesamoid fracture fragments were removed from the left (8) and right (8) hind limbs and the left (1) and right (1) forelimbs. Apical fragments occured in 15 lateral and 3 medial proximal sesamoid bones. No major complications occurred during or after surgery. The electrocautery probes permitted an easy and precise dissection of all soft tissue attachments to the apical sesamoid fracture fragments in all horses. Follow-up time was 7 to 44 months (median, 26 months); 10 of 14 horses returned to racing. Seven of nine horses that raced before surgery raced again and three of five that had not raced before surgery, raced afterwards. CONCLUSION: Arthroscopic excision of apical sesamoid fracture fragments can be accomplished arthroscopically using electrocautery probes. CLINICAL RELEVANCE: Arthroscopic electrosurgery is an efficient and safe alternative for intra-articular dissection in horses.

Animals↗
PubMed2005

Fragmentation dynamics of condensed phase thymine by low-energy (10-200 eV) heavy-ion impact.

We report measurements of the formation and desorption of ionic fragments induced by very low-energy (10-200 eV) Ar(+) irradiation of thymine (T) films, deposited on a polycrystalline Pt substrate. A multitude of dissociation channels is observed, among which the major cation species are identified as HNCH(+), HNC(3)H(4) (+), C(3)H(3) (+), OCNH(2) (+), [T-OCN](+), [T-OCNH(2)](+), [T-O](+), and [T+H](+) and the major anions as H(-), O(-), CN(-),and OCN(-). Cation fragment desorption appears at much lower threshold energies (near 15 eV) than anion fragment desorption, where the latter depends strongly on the film thickness. It is proposed that anion fragment formation and desorption results from projectile impact-induced excitation of either (1) a neutral thymine molecule, followed by fragmentation and charge exchange between the energetic neutral fragment and the substrate (or film) and/or (2) a deprotonated monoanionic thymine molecule to a dissociative state, followed by a unimolecular fragmentation of the excited thymine anion. The H(-) and O(-) fragment formations may have a further contribution from dipolar dissociation, e.g., formation of electronically excited neutral thymine, followed by dissociation into O(-)+[T-O](+), due to their reduced sensitivity to the film thickness. Positive-ion fragment desorption exhibits no significant dependence on film thickness before the emergence of surface charging, and originates from a kinetically assisted charge-transfer excitation. The results suggest that the potential energy of the incident ion plays a significant role in lowering the threshold energy of kinetic fragmentation of thymine. Measurements of the time-dependent film degradation yields for 100-eV Ar(+) suggest a quantum efficiency for degradation of about six thymine molecules per incident ion.

Cations↗
PubMed2006

Modelization of the fragmentation dynamics of krypton clusters (Kr(n),n=2-11) following electron impact ionization.

We present the first prediction for the fragmentation dynamics following electron impact ionization of neutral krypton clusters from 2 to 11 atoms. Fragment proportions and parent ion lifetimes are deduced from a molecular dynamics with quantum transitions study in which the nuclei are treated classically and the transitions between electronic states quantum mechanically. The potential-energy surfaces are derived from a diatomics-in-molecules model to which induced dipole-induced dipole and spin-orbit interactions are added. The results show surprisingly fast and extensive fragmentation for clusters of such a heavy atom, although not as extensive as in the case of neon clusters studied previously [D. Bonhommeau et al., J. Chem. Phys. 123, 54316 (2005)]. The parent ion lifetimes range from 2.8 to 0.7 ps, and the most abundant fragment is Kr(2) (+) for all studied sizes, followed by Kr(+) for sizes smaller than 7 atoms and by Kr(3) (+) for larger sizes. Trimer and larger fragments are found to originate from the lower electronic states of parent ions. The comparison with preliminary results from experiments on size-selected neutral clusters conducted by Steinbach et al. (private communication) reveal a good agreement on the extensive character of the fragmentation. It is checked that the additional internal energy brought by the helium scattering technique used for size selection does not affect the fragment proportions. In addition, the existence of long-lived trajectories is revealed, and they are found to be more and more important for larger cluster sizes and to favor the stabilization of larger fragments. The implications of this work for microsecond-scale dynamics of ionized rare-gas clusters are discussed. In particular, given the extent of fragmentation of the parent clusters and the fast kinetics of the whole process, the small cluster ions that exhibit a monomer loss in the microsecond time window must originate from much larger neutral precursors. The decay rate of the II(12)(u) state of the ionic dimer Kr(2) (+) by spin-orbit coupling is found to be of the order of 3 ps, in contrast to the expected tens of microseconds, but only reasonably faster than the corresponding state of HeNe(+). Finally, the spin-orbit interaction strongly affects both the Kr(+)Kr(2) (+) ratio and some of the characteristic times of the dynamics, especially for smaller sizes, but not the overall dependence of the fragment proportions as a function of cluster size.

Journal Article↗
PubMed2006

Fragmentation dynamics of argon clusters (Ar(n), n = 2 to 11) following electron-impact ionization: modeling and comparison with experiment.

The fragmentation dynamics of argon clusters ionized by electron impact is investigated for initial cluster sizes up to n = 11 atoms. The dynamics of the argon atoms is modeled using a mixed quantum-classical method in which the nuclei are treated classically and the transitions between electronic states quantum mechanically. The potential-energy surfaces are derived from a diatomics-in-molecules model with the addition of the induced dipole-induced dipole and spin-orbit interactions. The results show extensive and fast fragmentation. The dimer is the most abundant ionic fragment, with a proportion increasing from 66% for n = 2 to a maximum of 95% for n = 6 and then decreasing down to 67% for n = 11. The next abundant fragment is the monomer for n < 7 and the trimer otherwise. The parent ion dissociation lifetimes are all in the range of 1 ps. Long-lived trajectories appear for initial cluster sizes of seven and higher, and favor the formation of the larger fragments (trimers and tetramers). Our results show quantitative agreement with available experimental results concerning the extensive character of the fragmentation: Ar+ and Ar2(+) are the only ionic fragments for sizes up to five atoms; their overall proportion is in quantitative agreement for all the studied sizes; Ar2(+) is the main fragment for all sizes; stable Ar3(+) fragments only appear for n > or = 5, and their proportion increases smoothly with cluster size from there. However, the individual ionic monomer and dimer fragment proportions differ. The experimental ones exhibit oscillations with initial cluster size, with a slight tendency to decrease on average for the monomer. In contrast our results show a monotonic, systematic evolution, similar to what was found in our earlier studies on neon and krypton clusters. Several hypotheses are discussed in order to find the origin of this discrepancy. Finally, the metastable II(1/2)u and II(1/2)g states of Ar2(+) are found to decay with a lifetime of 3.5 and 0.1 ps, respectively, due to spin-orbit coupling. The difference with the commonly accepted microsecond range value for rare-gas dimer ions could originate from the role of autoionizing states in the formation of the parent ions.

Journal Article↗
PubMed2002

Disappearance of insectivorous birds from tropical forest fragments.

Determining the impact of forest disturbance and fragmentation on tropical biotas is a central goal of conservation biology. Among tropical forest birds, understory insectivores are particularly sensitive to habitat disturbance and fragmentation, despite their relatively small sizes and freedom from hunting pressure. Why these birds are especially vulnerable to fragmentation is not known. Our data indicate that the best determinant of the persistence of understory insectivorous birds in small fragments is the ability to disperse through deforested countryside habitats. This finding contradicts our initial hypothesis that the decline of insectivorous birds in forest fragments is caused by impoverished invertebrate prey base in fragments. Although we observed significantly fewer insectivorous birds in smaller fragments, extensive sampling of invertebrate communities (106,082 individuals) and avian diets (of 735 birds) revealed no important differences between large and small fragments. Neither habitat specificity nor drier fragment microclimates seemed critical. Bird species that were less affected by forest fragmentation were, in general, those that used the deforested countryside more, and we suggest that the key to their conservation will be found there.

Animals↗
PubMed1982

Junction between Z and B conformations in a DNA restriction fragment: evaluation by Raman spectroscopy.

Raman vibrational spectra were obtained from two DNA restriction fragments and the DNA polymer (dG-dC)n . (dG-dC)n in 0.01 and 4.5 M NaCl. One fragment contained 95 base pairs (bp) of the Escherichia coli lactose operator-promoter region (95-bp fragment). The other fragment consisted of the 95-bp region flanked by 26 and 32 bp of dC-dG sequences and BamHI ends (157-bp fragment). In 0.01 M NaCl all three DNAs have Raman spectra characteristic of a right-handed B conformation. The high salt spectrum of the 95-bp fragment is also characteristic of a B conformation. However, the spectrum of the 157-bp fragment in 4.5 M NaCl shows major intensity changes from the 0.01 M NaCl spectrum. These changes are also observed in the high salt spectra of (dG-dC)n . (dG-dC)n and are correlated with the presence of a left-handed Z conformation. Comparisons between the high salt Raman spectra of the 157-bp fragment and spectra calculated from (dG-dC)n . (dG-dC)n and the 95-bp fragment indicated that essentially all of the dC-dG regions in the 157-bp fragment are in the Z conformation and a large part (approximately 80%) of the 95-bp region no longer has a B-type backbone vibration. However, this non-B-DNA-like character of the central region is not indicated by base vibrations.

Base Composition↗
PubMed2003

Evidence for the proteolytic processing of dentin matrix protein 1. Identification and characterization of processed fragments and cleavage sites.

Full-length cDNA coding for dentin matrix protein 1 (DMP1) has been cloned and sequenced, but the corresponding complete protein has not been isolated. In searching for naturally occurring DMP1, we recently discovered that the extracellular matrix of bone contains fragments originating from DMP1. Shortened forms of DMP1, termed 37K and 57K fragments, were treated with alkaline phosphatase and then digested with trypsin. The resultant peptides were purified by a two-dimensional method: size exclusion followed by reversed-phase high performance liquid chromatography. Purified peptides were sequenced by Edman degradation and mass spectrometry, and the sequences compared with the DMP1 sequence predicted from cDNA. Extensive sequencing of tryptic peptides revealed that the 37K fragments originated from the NH2-terminal region, and the 57K fragments were from the COOH-terminal part of DMP1. Phosphate analysis indicated that the 37K fragments contained 12 phosphates, and the 57K fragments had 41. From 37K fragments, two peptides lacked a COOH-terminal lysine or arginine; instead they ended at Phe173 and Ser180 and were thus COOH termini of 37K fragments. Two peptides were from the NH2 termini of 57K fragments, starting at Asp218 and Asp222. These findings indicated that DMP1 is proteolytically cleaved at four bonds, Phe173-Asp174, Ser180-Asp181, Ser217-Asp218, and Gln221-Asp222, forming eight fragments. The uniformity of cleavages at the NH2-terminal peptide bonds of aspartyl residues suggests that a single proteinase is involved. Based on its reported specificity, we hypothesize that these scissions are catalyzed by PHEX protein. We envision that the proteolytic processing of DMP1 plays a crucial role during osteogenesis and dentinogenesis.

Alkaline Phosphatase↗
PubMed1968

Catabolic origin of a Bence Jones protein fragment.

Gel filtration analysis of the urinary proteins of some patients with myeloma has shown the presence of "fragments" of Bence Jones proteins which correspond to the variable half of these proteins. Experiments have been carried out to establish the origin of a "fragment" observed in a patient who excreted a large amount of this protein. Labeled homologous Bence Jones protein has been injected into this and other control patients. Excretion of labeled "fragment" has been observed in all. Analysis by peptide mapping and radio-autography of this labeled "fragment" isolated from the urine showed that the invariable half of the Bence Jones protein was not excreted; it seemed thus likely that the invariable half was metabolized to small peptides and free amino acids. A labeled Bence Jones protein which was excreted without any accompanying "fragment" was injected into the patient who excreted large amounts of "fragment." No excretion of labeled "fragment" was observed. It was thus concluded that the property of being degraded to "fragment" is characteristic of some "fragile" Bence Jones proteins and is not determined by the patient. Incubation with serum or urine of the "fragile" Bence Jones protein failed to produce any "fragment." "Fragments" of Bence Jones proteins are thus most likely formed during excretion of these proteins through the kidney and are products of the catabolism of Bence Jones proteins.

Autoradiography↗
PubMed1986

Identification of a restriction fragment length polymorphism by a CR1 cDNA that correlates with the number of CR1 on erythrocytes.

A genetic basis for the regulation of the number of CR1 on E of different normal individuals was investigated by probing Southern blots of their genomic DNA with a 0.75-kb fragment of CR1 cDNA. Using Hind III, we observed a RFLP involving fragments of 7.4 kb and 6.9 kb that correlated with the number of CR1 on E. 32 individuals having only the 7.4-kb restriction fragment had a mean of 661 +/- 33 (SEM) CR1/E, 11 donors having both restriction fragments had a mean of 455 +/- 52 CR1/E, and 7 individuals having only the 6.9-kb fragment had a mean of 156 +/- 13 CR1/E, all means being significantly different (p less than 0.005). Cosegregation in a normal family of the Hind III restriction fragments with the S, F, and F' structural allotypes of CR1 confirmed that the regulatory element identified by these fragments is linked to the CR1 gene. Moreover, an analysis of the relative expression on E of these structural allotypes in association with either the 7.4-kb Hind III fragment or the 6.9-kb fragment showed that this regulatory element is cis-acting. In contrast, quantitation of CR1 of B lymphocytes and neutrophils revealed no differences in total CR1 expression between individuals homozygous for the 7.4-kb and 6.9-kb Hind III fragments. Thus, we have identified a genomic polymorphism that is linked to the CR1 gene and is associated with a cis-acting regulatory element for the expression of CR1 on E.

DNA↗
PubMed2006

Can neutral theory predict the responses of Amazonian tree communities to forest fragmentation?

We use Hubbell's neutral theory to predict the impact of habitat fragmentation on Amazonian tree communities. For forest fragments isolated for about two decades, we generate neutral predictions for local species extinction, changes in species composition within fragments, and increases in the probability that any two trees within a fragment are conspecific. We tested these predictions using fragment and intact forest data from the Biological Dynamics of Forest Fragments Project in central Amazonia. To simulate complete demographic isolation, we excluded immigrants--species absent from a fragment or intact forest plot in the initial census but present in its last census--from our tests. The neutral theory correctly predicted the rate of species extinction from different plots as a function of the diversity and mortality rate of trees in each plot. However, the rate of change in species composition was much faster than predicted in fragments, indicating that different tree species respond differently to environmental changes. This violates the key assumption of neutral theory. When immigrants were included in our calculations, they increased the disparity between predicted and observed changes in fragments. Overall, neutral theory accurately predicted the pace of local extinctions in fragments but consistently underestimated changes in species composition.

Conservation of Natural Resources↗
PubMed1998

Cytarabine-induced destabilization of a model Okazaki fragment.

Cytarabine is a potent anticancer drug that interferes with elongation of the lagging strand at the replication fork during DNA synthesis. The effects of cytarabine substitution on the structural and thermodynamic properties of a model Okazaki fragment were investigated using UV hyperchromicity and 1H NMR spectroscopy to determine how cytarabine alters the physicochemical properties of Okazaki fragments that are intermediates during DNA replication. Two model Okazaki fragments were prepared corresponding to a primary initiation site for DNA replication in the SV40 viral genome. One model Okazaki fragment consisted of five ribo- and seven deoxyribonucleotides on the hybrid strand, together with its complementary (DNA) strand. The second model Okazaki fragment was identical to the first with the exception of cytarabine substitution for deoxycytidine at the third DNA nucleotide of the hybrid strand. Thermodynamic parameters for the duplex to single strand transition for each model Okazaki fragment were calculated from the concentration dependence of the T m at 260 nm. Cytarabine significantly decreased the stability of this model Okazaki fragment, decreasing the melting temperature from 46.8 to 42.4 degrees C at a concentration of 1.33 x 10(-5) M. The free energy for the duplex to single strand transition was 1.2 kcal/mol less favorable for the cytarabine-substituted Okazaki fragment relative to the control at 37 degrees C. Analysis of the temperature dependence of the imino1H resonances for the two duplexes demonstrated that cytarabine specifically destabilized the DNA:DNA duplex portion of the model Okazaki fragment. These results are consistent with inhibition of lagging strand DNA synthesis by cytarabine substitution resulting from destabilization of the DNA:DNA duplex portion of Okazaki fragments in vivo .

Antimetabolites, Antineoplastic↗
PubMed1982

Discrete subgenomic DNA fragments in incomplete particles of adenovirus type 2.

Discrete subgenomic DNA fragments were found in three out of thirty-two preparations of adenovirus type 2 incomplete particles grown in human Hep-2 cells and examined over the course of 1 year. One preparation contained three fragments corresponding to 5, 14 and 19% of the genome, another contained a 37% fragment and the third a 40% fragment. Each fragment hybridized exclusively to the left end of the genome. Digestion of the nick-translated 37% fragment with HindIII confirmed that it contained the left 37.3% of the genome. Synthesis of these fragments was not dependent on high input multiplicity of infection. Comparable fragments were not found in unpackaged DNA from the corresponding infected cells. This is consistent with the hypothesis that such fragments are generated during virus assembly or, alternatively, may reflect the very small proportion of these fragments relative to the pool of unpackaged DNA within the cells. The possibility that they are generated by errors in DNA replication is discussed.

Adenoviruses, Human↗
PubMed1988

Preferential uptake of restriction fragments from a gonococcal cryptic plasmid by competent Neisseria gonorrhoeae.

Factors involved in the specificity of DNA uptake by competent Neisseria gonorrhoeae were examined. Host-controlled modification did not affect uptake. Certain restriction fragments of the 4.2 kb gonococcal cryptic plasmid pFA1 and of the replicative form of the bacteriophage M13 were taken up in preference to others, independent of differences in fragment size. A 600 bp fragment from the 4.2 kb plasmid was cloned into pLES2, a gonococcal-Escherichia coli shuttle vector; the 600 bp fragment was taken up into a DNAase-I-resistant state in preference to the vector fragment. A second 370 bp fragment in pFA1 was also taken up preferentially. The 600 bp and 370 bp fragments share a 10 bp sequence, which is found in pFA1 only on fragments that were taken up readily. However, a fragment from M13 which was efficiently taken up did not contain this 10 bp sequence. In addition, this sequence was not sufficient to direct preferential DNA uptake by gonococci, since a recombinant plasmid containing this 10 bp sequence was not taken up appreciably better than the vector plasmid or another recombinant plasmid containing an unrelated 10 bp sequence. Sequence comparisons of the three restriction fragments which were preferentially taken up did not yield any consensus sequences greater than 7 bp. Although it is likely that efficient uptake of DNA by gonococci is determined by DNA structure, a single short sequence could not be found that accounted for specific uptake.

Base Sequence↗
PubMed1993

Analysis of DNA fragmentation in human uterine cervix carcinoma HeLa S3 cells treated with duocarmycins or other antitumor agents by pulse field gel electrophoresis.

Pulse field gel electrophoresis using a contour-clamped homogeneous electric field was applied for the analysis of DNA-fragmenting activity of antitumor agents towards human uterine cervix carcinoma HeLa S3 cells. Duocarmycins (DUMs), novel antitumor antibiotics with ultrapotent cell growth-inhibitory activities, caused DNA fragmentation at 10 times their IC50 values at 2 h exposure. At 100 times their IC50 values, the size of the smallest fragments was about 245 kilobase pairs (kbp). DUMA, DUMB1 and DUMB2 exhibited similar DNA fragmentation patterns, suggesting similar action mechanisms. DNA fragmentation was also detected in cells treated with radical producers, intercalators and topoisomerase inhibitors. Two bands of about 1800 and 1500 kbp were commonly detected in the cells treated with DUMs and these agents. In addition, fragments of about 900 kbp were detected in the cells treated with a topoisomerase inhibitor, 4'-(9-acridinylamino)methane-sulfon-m-anisidine, and fragments in the broad size range between 700 and 245 kbp in the cells treated with radical producers, bleomycin and neocarzinostatin. DUMs showed a characteristic DNA fragmentation pattern, since both types of fragments induced by the topoisomerase inhibitor and the radical producers were simultaneously detected, suggesting a novel mode of interaction with DNA. DNA-crosslinking agents and mitotic inhibitors did not induce DNA fragmentation under these conditions. The pulse field gel electrophoresis is potentially useful for characterizing DNA-cleaving activity of various antitumor agents at the cellular level.

Antibiotics, Antineoplastic↗