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At least 1,135 records · Page 63Linked to original sources
PubMed1977

Biosynthesis of mitochondrial DNA. Is 8 S DNA an artifact?

Sucrose density gradient fractionation of isolated rat liver mitochondrial DNA ordinarily yields two peaks, one at 39 S, the other at 27 S. However, when these mitochondria are first incubated with a labeled DNA precursor, a labeled peak at about 8 S is also observed. Is this low molecular weight 8 S DNA merely an artifact of contamination or breakdown, or is it a functioning part of the mitochondrial genome? That it is not a nuclear contaminant is shown by: (a) the absence of nuclei or nuclear fragments in active mitochondrial preparations; (b) the insensitivity of 8 S DNA synthesis to treatment of mitochondria with DNase and RNase; (c) the ability of inner membrane preparations to synthesize this DNA; (d) the ability of atractyloside to inhibit incorporation of [3H]dATP into 8 S and 39 S or 27 S DNA equally; (e) the labeling of 8 S DNA (as well as 39 S and 27 S DNA) but not of nuclear DNA after the administration in vivo of [3H]thymidine. The evidence that 8 S DNA is not an artifact resulting from DNA breakdown during mitochondrial incubation or DNA isolation is as follows: (a) 8 S DNA can be isolated from unincubated mitochondrial; (b) 8 S DNA becomes labeled when labeled DNA precursors are administered in vivo; (c) 8 S DNA biosynthesis continues in the complete absence of labeled 39 S or 27 S DNA (whose synthesis is repressed by ethidium bromide), making it unlikely that 8 S DNA is formed from the breakdown of 39 S or 27 S DNA; (d) substitution of milder methods of DNA extraction does not decrease 8 S DNA labeling; moreover, the usual conditions of extraction, when applied to purified 39 S and 27 S DNA, do not generate 8 S DNA, nor does an additional mitochondrial washing cycle; (e) the specific radioactivity of 8 S DNA is higher than that of 39 S or 27 S DNA, making it improbable that the latter forms are precursors of 8 S DNA. Since 8 S DNA is double-stranded, it is not identical to the 7 S fragment of D loop DNA. The hypothesis that the artifactual nicking of those DNA molecules which contain opposing D loops leads to the release of double-stranded fragments was tested. The DNA which was released was predominantly (and probably completely) single-stranded. We conclude that 8 S DNA is probably not an artifact and studies are in progress on its function.

Animals↗
PubMed2005

DNA extraction from low-biomass carbonate rock: an improved method with reduced contamination and the low-biomass contaminant database.

Caves represent a unique environment in which to study subsurface geomicrobial interactions and processes. One of the primary techniques used to study such geologic samples is molecular phylogenetic analysis, but this technique is hampered by low microbial biomass and calcium in the host rock, often leading to poor and irreproducible DNA extraction. We describe an improved protocol to recover extremely low amounts of DNA from calcium-rich geologic samples. This protocol relies on the use of the synthetic DNA molecule poly-dIdC, to act both as blocking agent and carrier molecule to increase the yield of DNA, and dialysis to remove calcium inhibitors of PCR amplification. Further, we demonstrate that many traditionally used laboratory substrates contain microbial DNA that can be amplified through the polymerase chain reaction (PCR) and contaminate molecular phylogenetic profiles. While the number of potential contaminants can be minimized, it cannot be eliminated from extraction techniques. We have therefore established the low-biomass contaminant (LBC) database, which contains the 16S rRNA gene sequences of species that have been identified as common laboratory contaminants. These identified contaminants provide a reference database to allow investigators to critically evaluate certain species identified within their phylogenetic profile when examining such low-biomass environments.

Base Sequence↗
PubMed1994

The generation of DNA single-strand breaks during the reduction of chromate by ascorbic acid and/or glutathione in vitro.

The potential role of iron and copper and the involvement of hydroxyl radicals in the DNA cleavage caused by chromate and glutathione (GSH) has been investigated. We have also studied the ability of chromate, on reaction with ascorbate as well as in mixed solutions of ascorbate and GSH, to cause DNA strand breaks. In both fully demetalated and conventional (i.e., metal contaminated) systems, chromate and GSH induced similar numbers of DNA strand breaks. This observation suggests that traces of iron or copper contaminating the reaction mixtures do not play a major role in the DNA cleavage caused by chromate and GSH. A series of hydroxyl radical scavengers exhibited a protective influence on the induction of DNA strand breaks. However, glucose and sucrose, both strong hydroxyl radical scavengers, showed no concentration-dependent inhibition of DNA cleavage. Competition kinetics studies yielded apparent rate constants that were not consistent with hydroxyl radicals being the species responsible for DNA strand breaks. Ascorbate in combination with chromate was also found to induce strand breaks in DNA; this damage could be attributed to reactive intermediates generated during the reduction. When mixed systems of ascorbate and GSH in the presence of chromate were investigated, there were clearly interactions between the two reductants.

Ascorbic Acid↗
PubMed1975

Studies on the fate of homologous DNA applied to seedlings of Matthiola incana.

Seedlings of Matthiola incana (crucifer) are able to take up exogenous homologous DNA by the roots. DNA homogenously labelled with [3H]adenine and 5-bromodeoxyuridine is incorporated into the plants in a macromolecular form. Intact donor DNA and a fraction with a buoyant density intermediate between that of the donor and the recipient DNA can be recovered. Analysis of this intermediate fraction by ultrasonication and alkali treatment allows the suggestion that homologous DNA is integrated as a double-stranded DNA which becomes covalently linked to the recipient DNA. Control experiments in which seedlings were incubated in a mixture simulating donor DNA degradation products in the presence and absence of unlabelled competitors suggest that these results are not due to the breakdown of donor DNA and reincorporation of the products during DNA synthesis in the recipient plants. When ultrasonicated or thermally denatured DNA is applied to the plants it may be degraded and reused for recipient DNA synthesis but it is not recovered in a macromolecular form. The possibility that the intermediate DNA fraction arises by bacterial contamination of the plants can be excluded by several arguments. Autoradiographic studies show that at least part of the radioactivity of the donor DNA taken up by the plants is associated with the cell nucleus.

Adenine↗
PubMed1996

Validation of probe EFD52 (D17S26) for forensic DNA analysis.

Validation studies that meet TWGDAM (The Working Group on DNA Analysis Methods) and CAC (California Association of Criminalists) guidelines for RFLP (restriction fragment length polymorphism) analysis were performed with the DNA probe EFD52 (D17S26). These studies demonstrate that the probe EFD52 is suitable for forensic casework. No unexpected DNA banding patterns were obtained from controlled studies examining various tissues, sample consistency over many gels, mixtures of body fluids, various substrates, various contaminants and non-human DNA sources. Of all the animal DNAs tested, only one higher primate yielded a single band to EFD52 hybridization. The sensitivity of EFD52 was shown to be comparable to that of other forensic probes. Population frequency distribution tables were prepared from over 4000 alleles and two-locus studies were conducted on nine forensically useful probes. Black, White, Hispanic and Lumbee Indian populations were found to be in Hardy-Weinberg and linkage equilibrium. Comparisons between victim blood standards and epithelial fractions of mixed strains from sexual assault cases were used to demonstrate the robustness of the EFD52 probe in forensic casework.

Asian People↗
PubMed1976

Identification of DNA in the core component of avian myeloblastosis virus.

Avian myeloblastosis virus (AMV) was found to contain DNA associated with the virion. The viral envelope was removed by treating the virus with a nonionic detergent and the DNA was found in the core fraction. These experiments indicate that the DNA associated with tumor virus is not contaminant associated with the viral envelope and suggest that the DNA is part of the internal core component. The DNA from avian myeloblastosis virus has a density of 1.70 g/cm3.

Avian Leukosis Virus↗
PubMed1991

Capture PCR: efficient amplification of DNA fragments adjacent to a known sequence in human and YAC DNA.

We have devised a procedure, termed capture PCR (CPCR), that permits the rapid isolation of DNA segments situated adjacent to a characterized nucleotide sequence. In this procedure, a DNA sample is restriction-digested and a linker, comprising two base-paired oligonucleotides, is added to the ends by ligation. Multiple extension reactions are performed using a biotinylated primer derived from the known sequence, permitting the subsequent isolation of extension products on a streptavidin-coated support. The enriched fragments are amplified exponentially using another specific oligonucleotide, hybridizing 3' to the biotinylated primer in combination with one of the linker oligonucleotides, now functioning as a PCR primer. The convenience of CPCR is greatly enhanced by using a novel streptavidin-coated manifold, which is constructed so that it projects into each individual well of a microtiter plate. The procedure permits the simultaneous isolation of fragments from large numbers of DNA samples and minimizes the risk of contamination between reactions. We have applied this method to identify DNA sequences located downstream of known sequences in the human genome. The technique has also been used to identify end fragments of sequences cloned in a yeast artificial chromosome (YAC) vector. The reactions can be initiated directly from yeast colonies and provide access to DNA sequence information for these end fragments in a minimal number of steps. With the aid of the present technique, we have isolated over 100 end fragments from YACs derived from the human X chromosome. Isolated end sequences have been used to order YAC clones into a contig.

Base Sequence↗
PubMed1998

Methods for microbial DNA extraction from soil for PCR amplification.

Amplification of DNA from soil is often inhibited by co-purified contaminants. A rapid, inexpensive, large-scale DNA extraction method involving minimal purification has been developed that is applicable to various soil types (1). DNA is also suitable for PCR amplification using various DNA targets. DNA was extracted from 100g of soil using direct lysis with glass beads and SDS followed by potassium acetate precipitation, polyethylene glycol precipitation, phenol extraction and isopropanol precipitation. This method was compared to other DNA extraction methods with regard to DNA purity and size.

Journal Article↗
PubMed1992

Enzymatic purification of plasmid DNA.

A novel method for plasmid DNA purification using enzymes that degrade all major types of contaminating nucleic acids present in crude plasmid DNA mixtures (but not plasmid DNA) has been devised. This method is quick (can be accomplished in two hours), requires no expensive laboratory equipment (an ultracentrifuge is not necessary) and is inexpensive. Plasmid DNA purified by this methodology can be used in a variety of molecular biological techniques including restriction enzyme digestions, subcloning, sequencing, nick translation and end labeling. This plasmid purification technique will be very useful for the molecular biologist performing cloning experiments.

DNA↗
PubMed2006

Selective purification of supercoiled plasmid DNA from clarified cell lysates with a single histidine-agarose chromatography step.

The ability to isolate sc (supercoiled) pDNA (plasmid DNA) isoform should be one of the features of a pDNA purification process, eliminating sample contaminants such as RNA, gDNA (genomic DNA), proteins and endotoxins. A process is described that uses a single histidine-agarose chromatography step to purify sc pDNA from other isoforms and Escherichia coli impurities present in a clarified lysate. The histidine-agarose support combines the mild hydrophobic characteristics of an epoxy spacer arm with a pseudo-affinity histidine ligand. The 6 kb DNA vaccine backbone pVAX1-LacZ was used as a model target. Following loading at high salt [2.3 M (NH4)2SO4], the different species were eluted by a series of reverse salt step gradients (2.0, 1.5 and 0 M (NH4)2SO4). Open circular pDNA and gDNA was eluted at 2.3 M, sc pDNA was isolated as a single peak at 2.0 M and RNA was eluted at 1.5 M (NH4)2SO4 and lower. The underlying mechanism is thought to involve not only hydrophobic interactions between the support and pDNA molecules, but also non-specific biorecognition of nucleic acid bases by the histidine ligand. Control analysis showed that the isolated sc pDNA conforms to specifications in terms of gDNA (3.4 ng/microg of pDNA), endotoxins (0.02 endotoxin unit/microg of pDNA), RNA and proteins (undetectable) and pDNA homogeneity (approximately 100% sc). Furthermore, the transfection efficiency of Chinese-hamster ovary cells (50%) was significantly higher when compared with the efficiency (25%) of a pDNA control. The present study confirms the possibility of using a single histidine-agarose chromatography step to purify sc pDNA from other isoforms and host contaminants present in a clarified E. coli lysate.

Chromatography, Affinity↗
PubMedDate not supplied

Genetic approaches to the detection of contaminants in Escherichia coli fermentations.

In facilities which cultivate more than one rDNA organism, contamination by the same species is difficult to detect. Since the same species may be producing a different product in an adjacent fermentor or in the same vessel in a subsequent procedure, the possibility of cross-product contamination must be considered. Here we describe a simple, sensitive, and reliable technique for the detection of same-species contamination. The assay uses negative genetic markers such as the inability to use a carbohydrate, e.g., ribose. When the facility is managed to use the ribose marker for only one product, this culture can be plated on ribose minimal medium to allow rapid and sensitive detection of contaminants. If the facility is used for several rDNA products, multiple carbohydrate markers per strain can be used so that a limited number of markers can differentiate among larger host collections. The approach was developed and tested using Escherichia coli as the host organism. If hosts with auxotrophies, e.g., for amino acids, are used in the facility, the plate medium can be supplemented. When this technique is combined with existing methods for detecting different species and bacteriophage contamination, all three classes of biological contamination can be detected.

DNA, Bacterial↗
PubMed1989

Genetic analysis of DNA from single human oocytes: a model for preimplantation diagnosis of cystic fibrosis.

Gene sequences in human oocytes were studied to investigate the possibility of diagnosing inherited or sporadic genetic disease before implantation after in vitro fertilisation. By specific amplification the possibility of analysing the DNA from single human oocytes for a specific gene was shown, and genotypes for markers closely linked to cystic fibrosis and Duchenne muscular dystrophy were determined. Single oocytes were used to approximate the total amount of DNA present in a single cell taken for biopsy from a 4-16 cell blastocyst. With a new technique for specific DNA amplification, the polymerase chain reaction, these data can be obtained within several hours of cell isolation. Extreme care must be taken to avoid any contamination of the sample with DNA from other sources. With this technique genotyping for single gene disorders is feasible with an accuracy and on a time scale that would allow implantation of the zygote after in vitro fertilisation without freezing.

Base Sequence↗
PubMed1999

[Influence of sample dilution on separation and detection of DNA fragments by capillary electrophoresis].

Capillary electrophoresis has become an important and useful method to separate and determine DNA fragments. In molecular biochemistry, the volume of DNA sample is very small (microL level) and DNA sample is liable to be contaminated and degraded. According to theoretical inference and experiments, we propose that dilution of DNA sample solution can increase separation efficiency and resolution without evidently reducing height of peaks. By this method, the usage efficiency of DNA sample can be improved. It is also demonstrated the separation and detection of DNA fragments by capillary electrophoresis with hydroxyethyl cellulose non-gel sieving matrix and with laser-induced fluorescence charge-coupled device as detector. By using lower concentration non-gel matrix (0.4%), all 8 larger size fragments of lambda DNA/Hind III (125 bp-23 130 bp) can be completely separated. Twenty smaller size fragments of pBR322-Hae III DNA (18 bp-587 bp) can be separated by higher concentration (1.6%) non-gel matrix. As ratio of sample dilution is 10, two adjacent fragment (123 bp and 124 bp) of pBR322-Hae III DNA can be separated.

DNA↗
PubMed2000

[Analysis of Amomun villosum species and some adulterants of zingiberaceae by RAPD].

Different Amomum villosum Lour. species and some their adulterants of Zingiberaceae were researched using RAPD. The PCR indicates favourable differentiation of the reaction. The Amomum villosum Lour. species have the similar DNA fingerprints while it is obviously differ from adulterants. There are 12.17 percent of primers which appear polymorphism. We can identify different species according to these dissimilarity. We also construct the tree of the molecular evolution through NJ software, the hereditary distance of the graph shows different relationships between Amomum villosum Lour. species and their adulterants. The result created by software is analogous the traditional methods.

Amomum↗
PubMed2000

[Influences of counterfeits on RAPD results of Semen Cuscutae].

Compared the differences of the RAPD results between pure Semen Cuscutae and 12 commercial samples, it comes into the conclusion that the exiting other sample influences the RAPD results when its content is over 60% and the results is same as its content being under 60%.

Cuscuta↗
PubMed1998

Characterization of wild-type adeno-associated virus type 2-like particles generated during recombinant viral vector production and strategies for their elimination.

The pSub201-pAAV/Ad plasmid cotransfection system was developed to eliminate homologous recombination which leads to generation of the wild-type (wt) adeno-associated virus type 2 (AAV) during recombinant vector production. The extent of contamination with wt AAV has been documented to range between 0.01 and 10%. However, the precise mechanism of generation of the contaminating wt AAV remains unclear. To characterize the wt AAV genomes, recombinant viral stocks were used to infect human 293 cells in the presence of adenovirus. Southern blot analyses of viral replicative DNA intermediates revealed that the contaminating AAV genomes were not authentic wt but rather wt AAV-like sequences derived from recombination between (i) AAV inverted terminal repeats (ITRs) in the recombinant plasmid and (ii) AAV sequences in the helper plasmid. Replicative AAV DNA fragments, isolated following amplification through four successive rounds of amplification in adenovirus-infected 293 cells, were molecularly cloned and subjected to nucleotide sequencing to identify the recombinant junctions. Following sequence analyses of 31 different ends of AAV-like genomes derived from two different recombinant vector stocks, we observed that all recombination events involved 10 nucleotides in the AAV D sequence distal to viral hairpin structures. We have recently documented that the first 10 nucleotides in the D sequence proximal to the AAV hairpin structures are essential for successful replication and encapsidation of the viral genome (X.-S. Wang et al., J. Virol. 71:3077-3082, 1997), and it was noteworthy that in each recombinant junction sequenced, the same 10 nucleotides were retained. We also observed that adenovirus ITRs in the helper plasmid were involved in illegitimate recombination with AAV ITRs, deletions of which significantly reduced the extent of wt AAV-like particles. Furthermore, the combined use of recombinant AAV plasmids lacking the distal 10 nucleotides in the D sequence and helper plasmids lacking the adenovirus ITRs led to complete elimination of replication-competent wt AAV-like particles in recombinant vector stocks. These strategies should be useful in producing clinical-grade AAV vectors suitable for human gene therapy.

Base Sequence↗