DNA interactive property of poly-L-lysine induces apoptosis in MCF-7 cells through DNA interaction

Poly-L-lysine (PLL) is known to be an encapsulating agent in drug formulation and delivery. PLL also has apoptotic and antiproliferative activities that enable blocking of the tumorigenesis process. However, the dose-selective activities of PLL in exerting apoptosis against cancer are unclear. Therefore, this study has been designed to explore the potential role and dose of PLL in apoptosis, if any. For this, PLL was administered at several doses in cancer cell lines and was found to be more potent against MCF-7 cells. PLL causes mitochondria-mediated apoptotic death through the upregulation of cleaved caspase-3. To investigate the mechanism responsible for this activity, we have analyzed if PLL could have the DNA interactive property or not. For this, molecular docking analysis was carried out to prove whether it has the property to bind with DNA or not. Studies have revealed that PLL is a potent DNA binder and it probably performs such apoptotic activities through the binding of cellular DNA early in an exposure. Simultaneous upregulation of both ROS-mediated stress and also in key protein expressions like γ-H2AX could also help us to confirm that PLL induces apoptosis through DNA interaction. This finding leads us to believe that PLL could play an interfering role with other chemotherapeutic compounds when used as a drug-coating material as it exerts an apoptotic effect on cancer cells, which should be avoided by using a much lower concentration.     

A Quantitative Microtiter Plate Nuclease Assay Based on Ethidium/DNA Fluorescence

A microtiter plate assay was developed to quantitate the nuclease activity of the extracellularSerratia marcescensendonuclease under different buffer conditions. Substrate cleavage was followed as decrease in ethidium/DNA fluorescence using a uv-transilluminator and a video documentation system. Time courses of DNA cleavage were recorded and cleavage rates determined very precisely within a factor of 1.2. The assay has a linear dynamic range covering three orders of magnitude of nuclease activity and can be carried out very quickly within a few minutes. It can also be used with RNA as substrate. With appropriate modifications it should be possible to adapt this assay for other enzymatic reactions which are accompanied by changes in absorbance or fluorescence.     

In vitro effects of low-level, low-frequency electromagnetic fields on DNA damage in human leucocytes by comet assay

The sources for the effects of electromagnetic fields (EMFs) have been traced to time-varying as well as steady electric and magnetic fields, both at low and high to ultra high frequencies. Of these, the effects of low-frequency (50/60 HZ) magnetic fields, directly related to time-varying currents, are of particular interest as exposure to some fields may be commonly experienced. In the present study, investigations have been carried out at low-level (mT) and low-frequency (50 Hz) electromagnetic fields in healthy human volunteers. Their peripheral blood samples were exposed to 5 doses of electromagnetic fields (2,3,5,7 and 10mT at 50 Hz) and analysed by comet assay. The results were compared to those obtained from unexposed samples from the same subjects. 50 cells per treatment per individual were scored for comet-tail length which is an estimate of DNA damage. Data from observations among males were pooled for each flux density for analysis. At each flux density, with one exception, there was a significant increase in the DNA damage from the control value. When compared with a similar study on females carried out by us earlier, the DNA damage level was significantly higher in the females as compared to the males for each flux density.     

Biochemical properties of a plastidial DNA polymerase of rice

Plastids are organelles unique to plant cells and are responsible for photosynthesis and other metabolic functions. Despite their important cellular roles, relatively little is known about the mechanism of plastidial DNA replication and repair. Recently, we identified a novel DNA polymerase in Oryza Sativa L. (OsPOLP1, formerly termed OsPolI-like) that is homologous to prokaryotic DNA polymerase Is (PolIs), and suggested that this polymerase might be involved in plastidial DNA replication and repair. Here, we propose to rename the plant PolI homologs as DNA polymerase π (POLP), and investigate the biochemical properties of full-length OsPOLP1. The purified OsPOLP1 elongated both DNA and RNA primer hybridized to a DNA template, and possessed a 3′ exonuclease activity. Moreover, OsPOLP1 displayed high processivity and fidelity, indicating that this polymerase has the biochemical characteristics appropriate for DNA replication. We found that POLPs have two extra sequences in the polymerase domain that are absent in prokaryotic PolIs. Deletion of either insert from OsPOLP1 caused a decrease in DNA synthetic activity, processivity, and DNA binding activity. In addition, OsPOLP1 efficiently catalyzed strand displacement on nicked DNA with a 5′-deoxyribose phosphate, suggesting that this enzyme might be involved in a repair pathway similar to long-patch base excision repair. These results provide insights into the possible role of POLPs in plastidial DNA replication and repair. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Antimutator variants of DNA polymerases

Evolution balances DNA replication speed and accuracy to optimize replicative fitness and genetic stability. There is no selective pressure to improve DNA replication fidelity beyond the background mutation rate from other sources, such as DNA damage. However, DNA polymerases remain amenable to amino acid substitutions that lower intrinsic error rates. Here, we review these ‘antimutagenic’ changes in DNA polymerases and discuss what they reveal about mechanisms of replication fidelity. Pioneering studies with bacteriophage T4 DNA polymerase (T4 Pol) established the paradigm that antimutator amino acid substitutions reduce replication errors by increasing proofreading efficiency at the expense of polymerase processivity. The discoveries of antimutator substitutions in proofreading-deficient ‘mutator’ derivatives of bacterial Pols I and III and yeast Pol δ suggest there must be additional antimutagenic mechanisms. Remarkably, many of the affected amino acid positions from Pol I, Pol III, and Pol δ are similar to the original T4 Pol substitutions. The locations of antimutator substitutions within DNA polymerase structures suggest that they may increase nucleotide selectivity and/or promote dissociation of primer termini from polymerases poised for misincorporation, leading to expulsion of incorrect nucleotides. If misincorporation occurs, enhanced primer dissociation from polymerase domains may improve proofreading in cis by an intrinsic exonuclease or in trans by alternate cellular proofreading activities. Together, these studies reveal that natural selection can readily restore replication error rates to sustainable levels following an adaptive mutator phenotype.     

Testing and using complete plastomes and ribosomal DNA sequences as the next generation DNA barcodes in Panax (Araliaceae)

Complete plastid genome (plastome) sequences and nuclear ribosomal DNA (nrDNA) regions have been proposed as candidates for the next generation of DNA barcodes for plant species discrimination. However, the efficacy of this approach still lacks comprehensive evaluation. We carried out a case study in the economically important but phylogenetically and taxonomically difficult genus Panax (Araliaceae). We generated a large data set of plastomes and nrDNA sequences from multiple accessions per species. Our data improved the phylogenetic resolution and levels of species discrimination in Panax, compared to any previous studies using standard DNA barcodes. This provides new insights into the speciation, lineage diversification and biogeography of the genus. However, both plastome and nrDNA failed to completely resolve the phylogenetic relationships in the Panax bipinnatifidus species complex, and only half of the species within it were recovered as monophyletic units. The results suggest that complete plastome and ribosomal DNA sequences can substantially increase species discriminatory power in plants, but they are not powerful enough to fully resolve phylogenetic relationships and discriminate all species, particularly in evolutionarily young and complex plant groups. To gain further resolving power for closely related species, the addition of substantial numbers of nuclear markers is likely to be required.     

Nuclear DNA changes within Helianthus annuus L.: origin and control mechanism

Summary Previous results suggested that the amount of nuclear DNA varies in one and the same progeny of Helianthus annuus, depending on the head portion in which seeds have developed. Accordingly, cytophotometric determinations were carried out in a selfed line, after Feulgen-staining, to obtain information on the developmental stages at which DNA changes are produced and on the mechanism controlling the variation. It was found that the Feulgen absorption values of mitotic prophases in immature anthers and pistils and of meiotic prophases I are the same in any flower of the head. In contrast, the Feulgen/DNA contents of early prophases in heart-shaped embryos differ significantly, increasing from those developing at the centre of the head to those developing at its periphery, and remaining unchanged in each embryo during further development and seed germination. Variations in the number of chromosomes do not account for the differences observed in nuclear DNA contents in which sequences comprised in heterochromatic nuclear regions are involved. The Feulgen absorption values of seedlings obtained from seeds developed in different portions of single heads increase or diminish starting from those found in the mother plant. This depends on whether these latter are relatively low or high and on the gradient of seed location in the head. The variation occurring within each single progeny covers the whole range existing within the line.     

Metabolism and distribution of yolk DNA in embryos ofOphryotrocha labronica La Greca and Bacci

Summary Exposure of the polychaeteOphryotrocha labronica to³H-thymidine during vitellogenesis leads to substantial incorporation of label in the ooplasm, especially in yolk granule DNA. In embryos from oocytes labelled in this way it was possible to follow the amount and localization of the labelled material (DNA) throughout early development by means of light microscopical and electron microscopical autoradiography; liquid scintillation measurements also were carried out.Within the embryonic cells the bulk of the labelled DNA was localized in the yolk granules and noticeable amounts were associated with minor structural elements, whereas mitochondria and lipid droplets were only slightly labelled. Nuclear labelling was weak. Early development was found to be characterized by rapid loss of labelled DNA, so that larvae, ready to leave the egg packs, retained only about 30% of the amount originally present.It was concluded that yolk granule DNA cannot be a store of precursor material for nuclear DNA synthesis, as has been suggested sometimes, but most likely represents an informative DNA which upon release from the yolk granules is rapidly metabolized. Possible roles for yolk granule DNA is discussed.The excellent technical assistance of Mrs. Siv Nilsson and Mrs. Annagreta Petersen is gratefully acknowledged. This work has been supported by the Swedish Natural Science Research Council and Kungliga Fysiografiska Sällskapet, Lund.     

Analysis of DNA fragmentation in mouse embryos exposed to an extremely low-frequency electromagnetic field

Effects of extremely low-frequency electromagnetic fields (ELF-EMFs) on DNA damage in biological systems are still a matter of dispute. The aim of the present study was to investigate the possible effect of electromagnetic field exposure on DNA fragmentation in cells (blastomers) of mouse blastocysts.

Eighty female NMRI mice were randomly divided into 2 groups of 40 animals each. The control group was left unexposed whereas the animals in the EMF-group were exposed to a 50-Hz EMF at 0.5 mT 4 h per day, 6 days a week for a duration of 2 weeks. After the 8^th day of exposure, the female mice in both groups were superovulated (with injections of pregnant mare serum gonadotropin and human chorionic gonadotropin) and then mated overnight. At approximately 4 days after mating (102 h after the human chorionic gonadotropin treatment), blastocysts were obtained by flushing the uterus horns. The mean numbers of pregnant mice, blastocysts after flushing, blastomers within the blastocysts, and the DNA fragmentation index following staining in both groups were compared using statistical methods (SPSS, the Chi-square test, the Student's t-test and the Mann-Whitney U-test, P < 0.05). The results showed that the mean number of blastocysts after flushing was significantly decreased in the EMF-group compared to that of the control group (P < 0.03). The DNA fragmentation index was significantly increased in the EMF-group compared to control (10.53% vs. 7.14%; P < 0.001). However, there was no significant difference in the mean numbers of blastomers and numbers of pregnant mice between the EMF-exposed and control group. Our findings indicate that the EMF exposure in preimplantation stage could have detrimental effects on female mouse fertility and embryo development by decreasing the number of blastocysts and increasing the blastocysts DNA fragmentation.     

Fetal DNA detection in maternal plasma throughout gestation

The presence of fetal DNA in maternal plasma may represent a source of genetic material which can be obtained noninvasively. We wanted to assess whether fetal DNA is detectable in all pregnant women, to define the range and distribution of fetal DNA concentration at different gestational ages, to identify the optimal period to obtain a maternal blood sample yielding an adequate amount of fetal DNA for prenatal diagnosis, and to evaluate accuracy and predictive values of this approach. This information is crucial to develop safe and reliable non-invasive genetic testing in early pregnancy and monitoring of pregnancy complications in late gestation. Fetal DNA quantification in maternal plasma was carried out by real-time PCR on the SRY gene in male-bearing pregnancies to distinguish between maternal and fetal DNA. A cohort of 1,837 pregnant women was investigated. Fetal DNA could be detected from the sixth week and could be retrieved at any gestational week. No false-positive results were obtained in 163 women with previous embryo loss or previous male babies. Fetal DNA analysis performed blindly on a subset of 464 women displayed 99.4, 97.8 and 100% accuracy in fetal gender determination during the first, second, and third trimester of pregnancy, respectively. No SRY amplification was obtained in seven out of the 246 (2.8%) male-bearing pregnancies. Fetal DNA from maternal plasma seems to be an adequate and reliable source of genetic material for a noninvasive prenatal diagnostic approach.     

Nucleotide excision repair and anti-cancer chemotherapy

DNA repair is an important effector of anti-cancer drug resistance. In recent years, it has become apparent that DNA repair is an extremely complex process. Processes within DNA repair that may contribute to one or more drug resistance phenotypes include; O-6-alkyltransferase activity, base excision repair, mismatch repair, nucleotide excision repair, and gene specific repair. Clearly, several of these processes may show increased activity within any single cell, or tumor, at any one time. This review attempts to touch briefly upon the question of the distinctions between each of these specific pathways; and then seeks to expand on nucleotide excision repair as a possible effector of cellular and clinical resistance to platinum-based anticancer therapy. This revised version was published online in August 2006 with corrections to the Cover Date.     

DNA ANALYSIS OF EUKARYOTIC ALGAL SPECIES1

Plastid genomes of algae resemble those of terrestrial plants in form, size, and rate of nucleotide sequence change. They are circular and range in size from 73 kilobases (kb) to over 400 kb. Their many copies per cell can compose >15% of total cell DNA. Mitochondrial genomes, like plastid genomes, are present in high copy number in preparations of total algal cell DNA. Almost all known algal mitochondrial DNA genomes are relatively small, <50 kb; in some species they are linear, whereas in others they are circular. One of the persistent perplexities for phycologists is the question of what relationship two clones or two groups of organisms bear to each other. Several relatively simple techniques can reveal whether or not two organisms belong to the same clone. Total mitochondrial genome size can be compared directly between isolates, although identity in size does not necessarily mean identity in sequence. Restriction endonuclease digestion combined with probing permits comparison of DNA fragment patterns to see if there is identity or near identity between two samples. This methodology can be applied both to organelle genomes and to nuclear genomes. So far, restriction endonucleases cleave plastid and mitochondrial DNA of organisms belonging to the same gene pool into nearly identical fragment patterns, whereas organisms nearly or totally incapable of interbreeding display patterns wherein ? 50% of restriction fragments differ in position on an agarose gel after electrophoresis. Thus, organelle genomes may be the first choice for comparing both total size and restriction endonuclease fragment patterns to obtain an indication of whether two organisms are closely related. This methodology can be applied both to organisms in which interbreeding is easy to test and to the many algae in which homothallism or lack of sexual clones has precluded standard breeding analyses. With further data on variability levels within and between fertile populations, it may be possible to state with confidence whether a sample of morphologically similar organisms shares a common gene pool, even if their breeding cannot be manipulated experimentally.     

Nontemplate Polymerization of Free Nucleotides Into Genetic Elements by Thermophilic DNA Polymerase in vitro

DNA synthesis is the cornerstone of all life forms and is required to replicate and restore the genetic information. Usually, DNA synthesis is carried out only by DNA polymerases semiconservatively to copy preexisting DNA templates. We report here that DNA strands were synthesized ab initio in the absence of any DNA or RNA template by thermophilic DNA polymerases at (a) a constant high temperature (74°C), (b) alternating temperatures (94°C/60°C/74°C), or (c) physiological temperatures (37°C). The majority of the ab initio synthesized DNA represented short sequence blocks, repeated sequences, intergenic spacers, and other unknown genetic elements. These results suggest that novel DNA elements could be synthesized in the absence of a nucleic acid template by thermophilic DNA polymerases in vitro. Biogenesis of genetic information by thermophilic DNA polymerase-mediated nontemplate DNA synthesis may explain the origin of genetic information and could serve as a new way of biosynthesis of genetic information that may have facilitated the evolution of life.

Supplemental materials are available for this article. Go to the publisher's online edition of Nucleosides, Nucleotides, and Nucleic Acids to view the free supplemental file.     

Condensin minimizes topoisomerase II‐mediated entanglements of DNA in vivo

The juxtaposition of intracellular DNA segments, together with the DNA‐passage activity of topoisomerase II, leads to the formation of DNA knots and interlinks, which jeopardize chromatin structure and gene expression. Recent studies in budding yeast have shown that some mechanism minimizes the knotting probability of intracellular DNA. Here, we tested whether this is achieved via the intrinsic capacity of topoisomerase II for simplifying the equilibrium topology of DNA; or whether it is mediated by SMC (structural maintenance of chromosomes) protein complexes like condensin or cohesin, whose capacity to extrude DNA loops could enforce dissolution of DNA knots by topoisomerase II. We show that the low knotting probability of DNA does not depend on the simplification capacity of topoisomerase II nor on the activities of cohesin or Smc5/6 complexes. However, inactivation of condensin increases the occurrence of DNA knots throughout the cell cycle. These results suggest an in vivo role for the DNA loop extrusion activity of condensin and may explain why condensin disruption produces a variety of alterations in interphase chromatin, in addition to persistent sister chromatid interlinks in mitotic chromatin.     

DNA‐PK suppresses a p53‐independent apoptotic response to DNA damage

p53 is required for DNA damage‐induced apoptosis, which is central to its function as a tumour suppressor. Here, we show that the apoptotic defect of p53‐deficient cells is nearly completely rescued by inactivation of any of the three subunits of the DNA repair holoenzyme DNA‐dependent protein kinase (DNA‐PK). Intestinal crypt cells from p53 nullizygous mice were resistant to radiation‐induced apoptosis, whereas apoptosis in DNA‐PK_cs/p53, Ku80/p53 and Ku70/p53 double‐null mice was quantitatively equivalent to that seen in wild‐type mice. This p53‐independent apoptotic response was specific to the loss of DNA‐PK, as it was not seen in ligase IV (Lig4)/p53 or ataxia telangiectasia mutated (Atm)/p53 double‐null mice. Furthermore, it was associated with an increase in phospho‐checkpoint kinase 2 (CHK2), and cleaved caspases 3 and 9, the latter indicating engagement of the intrinsic apoptotic pathway. This shows that there are two separate, but equally effective, apoptotic responses to DNA damage: one is p53 dependent and the other, engaged in the absence of DNA‐PK, does not require p53.     

New phthalimide‐appended Schiff bases: Studies of DNA binding,molecular docking and antioxidant activities

Herein, we investigated new phthalimide‐based Schiff base molecules as promising DNA‐binding and free radical scavenging agents. Physicochemical properties of these molecules were demonstrated on the basis of elemental analysis, ultraviolet–visible (UV–Vis), infra‐red (IR), ¹H and ¹³C nuclear magnetic resonance (NMR) spectroscopy. All spectral data are agreed well with the proposed Schiff base framework. The DNA‐binding potential of synthesized compounds were investigated by means of UV–visible, fluorescence, iodide quenching, circular dichroism, viscosity and thermal denaturation studies. The intrinsic binding constants (K _b) were calculated from absorption studies were found to be 1.1 × 10⁴ and 1.0 × 10⁴ M^?1 for compounds 2a and 2b suggesting that compound 2a binding abilities with DNA were stronger than the compound 2b. Our studies showed that the presented compounds interact with DNA through groove binding. Molecular docking studies were carried out to predict the binding between Ct‐DNA and test compounds. Interestingly, in silico predictions were corroborated with in vitro DNA‐binding conclusions. Furthermore, the title compounds displayed remarkable antioxidant activity compared with reference standard.     

DNA ligases from thermophilic bacteria enhance PCR amplification of long DNA sequences

Bacterial NAD-dependent Taq and Tth DNA ligases are capable of significantly increasing the yield of long PCR products when the amplification is carried out using bacterial family A DNA polymerases, e.g. Taq or Tth DNA polymerases, or with enzymatic blends containing these polymerases. We also show that Taq and Tth DNA ligases improve the results of PCR in the absence of NAD and therefore in the absence of DNA ligase activity. These observations suggest that bacterial DNA ligases can interact with these DNA polymerases, presumably as accessory proteins, thereby enhancing the efficiency of DNA polymerization. Published in Russian in Biokhimiya, 2009, Vol. 74, No. 5, pp. 685–690.