Effects Of DNA Concentration Research Articles

A ring trial to harmonize Toxoplasma gondii microsatellite typing: comparative analysis of results and recommendations for optimization

A ring trial among five European laboratories was organized to reach consistency in microsatellite (MS) typing of the zoonotic parasite Toxoplasma gondii. Three sample sets were circulated and analyzed by each laboratory following a previously published method that is based on fragment length polymorphism of 15 MS markers. The first sample set compared typing results in general and focused on effects of DNA concentration; the second sample set focused on the polymorphic fingerprinting markers that can differentiate T. gondii strains within the same archetypal lineage; and the third set focused on non-archetypal genotypes. Methodological variations between laboratories, including the software programs used to determine MS fragment length, were collated using a questionnaire. Overall, lineage-level typing results reached a high level of agreement, especially in samples with the highest DNA concentrations. However, laboratory-specific differences were observed for particular markers. Major median differences in fragment length, of up to 6 base pairs, were related to the fluorophore used to label fragment-specific primers. In addition, primer pairs with identical sequences obtained from different suppliers resulted in fragments of differing length. Furthermore, differences in the way the sequencing profiles were assessed and interpreted may have led to deviating results in fragment length determination. Harmonization of MS typing, for example, by using the same fluorophores or by numerical adjustments applied to the fragment-lengths determined, could improve the uniformity of the results across laboratories. This is the first interlaboratory comparison, providing guidelines (added as a supplement) for the optimization of this technique.

DNA-assisted synthesis of flower-like ZnO mesocrystal

A flower-like ZnO mesocrystal was fabricated using a DNA template. The structure and morphology of the as-prepared ZnO mesocrystals were correlatively characterized by field emission scanning electron microscopy (FESEM), transmission electron microscopy (TEM), Fourier transform infrared spectroscopy (FTIR), and X-ray diffraction (XRD). The effects of DNA concentration, the ratio of water and glycerin, and the reaction time were studied with respect to the morphology of ZnO mesocrystals. Antibacterial experiments showed that the as-obtained flower-like ZnO mesocrystals exhibit highly effective antibacterial activity against Escherichia coli (E. coli) and Staphylococcus aureus (S. aureus) compared with commercial ZnO nanoparticles (ZnO NPs).

Study of ss-DNA Adsorption and Nano-mechanical Properties on Mica Substrate with Surface Forces Apparatus

Many DNA-based devices need to build stable and controllable DNA films on surfaces. However, the most commonly used method of film characterization, namely, the probe-like microscopes which may destroy the sample and substrate. Surface Forces Apparatus (SFA) technique, specializing in surface interaction studies, is introduced to investigate the effects of DNA concentration on the formation of single-stranded DNA (ss-DNA) film. The result demonstrates that 50 ng/μL is the lowest concentration that ss-DNA construct a dense layer on mica. Besides, it is also indicated that at different DNA concentrations, ss-DNA exhibit diverse morphology: lying flat on surface at 50 ng/μL while forming bilayer or cross-link at 100 ng/μL, and these ss-DNA structures are stable enough due to the repeatability even under the load of 15 mN/m. At the same time, an obvious adhesion force is measured: −6.5 mN/m at 50 ng/μL and −5.3 mN/m at 100 ng/μL, respectively, which is attributed to the ion-correlation effect. Moreover, the atomic force microscopy (AFM) images reveal the entire surface is covered with wormlike ss-DNA and the measured surface roughness (1.8±0.2 nm) also matches well with the film thickness by SFA. The desorption behaviors of ss-DNA layer from mica surface occur by adding sodium salt into gap buffer, which is mainly ascribed to the decreased ion-ion correlation force. This paper employing SFA and AFM techniques to characterize the DNA film with flexibility and stable mechanical ability achieved by ion bridging method, is helpful to fabricate the DNA-based devices in nanoscale.

Biases underlying species detection using fluorescent amplified-fragment length polymorphisms yielded from roots.

BackgroundRoots of different plant species are typically morphologically indistinguishable. Of the DNA-based techniques, fluorescent amplified-fragment length polymorphisms (FAFLPs) are considered reliable, high throughput, inexpensive methods to identify roots from mixed species samples. False-negatives, however, are not uncommon and their underlying causes are poorly understood. We investigated several sources of potential biases originating in DNA extraction and amplification. Specifically, we examined the effects of sample storage, tissue, and species on DNA yield and purity, and the effects of DNA concentration and fragment size on amplification of three non-coding chloroplast regions (trnT-trnL intergenic spacer, trnL intron, and trnL-trnF intergenic spacer).ResultsWe found that sample condition, tissue and species all affected DNA yield. A single freeze–thaw reduces DNA yield, DNA yield is less for roots than shoots, and species vary in the amount of DNA yielded from extractions. The effects of template DNA concentration, species identity, and their interaction on amplicon yield differed across the three chloroplast regions tested. We found that the effect of species identity on amplicon production was generally more pronounced than that of DNA concentration. Though these factors influenced DNA yield, they likely do not have a pronounced effect on detection success of fragments and only underscore the restriction on the use of FAFLPs for measuring species presence rather than their abundance. However, for two of the regions tested—the trnT-trnL intergenic spacer and the trnL intron—size-based fragment competition occurred and the likelihood of detection was higher for smaller than larger fragments. This result reveals a methodological bias when using FAFLPs.ConclusionsTo avoid potential bias with the use of FAFLPs, we recommend users check for the disproportionate absence of species detected belowground versus aboveground as a function of fragment size, and explore other regions, aside from the trnT-trnL intergenic spacer and trnL intron, for amplification.Electronic supplementary materialThe online version of this article (doi:10.1186/s13007-015-0079-1) contains supplementary material, which is available to authorized users.

Study on the adsorption of DNA on Fe3O4 nanoparticles and on ionic liquid-modified Fe3O4 nanoparticles

We have investigated the adsorption of herring sperm DNA on Fe3O4 magnetic nanoparticles (NPs) before and after modification with the ionic liquid 1-hexyl-3-methylimidazolium bromide. Experiments were performed in a batch mode, and the effects of DNA concentration, pH of the sample solution, ionic strength, temperature, and contact time between reagents were optimized. An evaluation of the adsorption isotherm revealed that the Langmuir model better fits the equilibrium data than the Freundlich model. The maximum adsorption capacities of the unmodified and modified NPs, respectively, were found to be 11.8 and 19.8 mg DNA per gram of adsorbent. The adsorption of DNA onto the modified NPs was endothermic, while it was exothermic in the case of the unmodified NPs. The DNA can be desorbed from the modified surfaces of the NPs by using EDTA as the eluent. The NPs were able to adsorb about 90 ± 1.5 % of DNA after being recycled for three times. The method is simple, fast, robust, and does not require organic solvents or sophisticated equipment.

Optimization of polyethylenimine-mediated transient transfection using response surface methodology design

Response surface methodology was undertaken to optimize the polyethylenimine-mediated transient transfection of suspension cultured HEK 293-F cells. A total of 15 combinations were designed according to Box-Behnken design to identify the effects of DNA concentration, polyethylenimine concentration and incubation time on transient transfection efficiency. The highest integral optic density of green fluorescent protein presenting r-protein yield was accessed using a DNA concentration of 1.75 µg/mL, a polyethylenimine concentration of 10.5 µg/mL, and an incubation time of 11.8 min. Analysis of variance demonstrated that the experimental values fit well with a quadratic model. The RSM-optimized transient transfection resulted in greater production of human tissue prokallikrein (TproK) than non-RSM-optimized conditions: protein yield was 32.0 mg/L and the maximum viable cell density reached 3.57 x 10 6 cells/mL in a 5 L stirred-tank bioreactor culture.

Characterization of redox polymer based electrode and electrochemical behavior for DNA detection

Characterization of redox polymer, poly(vinylferrocenium) perchlorate (PVF +ClO 4 −) coated as a film on Pt electrodes, and the detection of DNA based on the electrochemical behavior of the polymer were described in this study. PVF +ClO 4 − modified electrodes were prepared by the electrooxidation of poly(vinylferrocene) (PVF), and DNA immobilized polymer modified electrode was then prepared. The characterization of the polymer modified electrodes were performed by scanning tunneling microscopy (STM), Raman spectroscopy and alternating current (AC) impedance. The effects of DNA concentration, pH, and polymer films in various thicknesses based on the electrode response were also investigated. The electrochemical behavior of DNA modified polymer electrode by using double-stranded DNA (dsDNA) or single-stranded DNA (ssDNA) was compared. DNA hybridization was also investigated.

The effect of DNA concentration on mobility in pulsed field gel electrophoresis.

The effect of DNA concentration on pulsed field gel electrophoretic mobility was studied for human genomic DNA prepared in agarose inserts at 8-800 micrograms/ml and digested to completion with Not I. An eighth of each 100 microliter insert was used to produce DNA loads of 0.1 to 10 micrograms per lane. The mobility of single copy restriction fragments, as detected by hybridization, was largely concentration independent when DNA concentrations were 80 micrograms/ml or less. However, at DNA concentrations of 200 micrograms/ml and greater, dramatic effects of DNA concentration are evident. In the worst case, at 800 micrograms/ml, the apparent size of a DNA fragment is almost 2.5 times its true size. At constant DNA concentrations, increasing the DNA mass loads by loading larger insert slices had no further effect on DNA electrophoretic mobility, although the bands were broader for bigger insert slices. Thus, for precise and accurate sizing in pulsed field gel electrophoresis the DNA concentration in agarose inserts should not be greater than 80 micrograms/ml (10(7) diploid human cells/ml agarose insert).

Regulation of herpes simplex virus immediate-early gene promoters in mouse neuroblastoma cells

The non-permissivity of C1300 mouse neuroblastoma cells for herpes simplex virus (HSV) infection is due to a failure of such cells to transcribe the immediate-early (IE) genes following viral infection. We have transfected both C1300 cells and permissive cells with constructs in which each of the 5 IE promoters drives expression of the readily assayable chloramphenicol acetyl transferase (CAT) gene. These experiments show that the lack of IE gene transcription in C1300 cells is due to the weak activity of the five IE promoters in these cells compared to that observed in a range of permissive cell types. This effect is mediated both by up-stream elements and by sequences present in the minimal promoter. The different effects of DNA concentration on the activities of the minimal and complete promoters suggests that the up-stream sequences act by binding a repressor factor present in C1300 cells whilst the weak activity of the minimal promoter results from the absence of a positive factor in such cells.

Factors affecting the efficiency of introducing foreign DNA into mice by microinjecting eggs.

Microinjection of foreign DNA into fertilized mammalian eggs is a convenient means of introducing genes into the germ line. Some of the more important parameters that influence successful integration of foreign DNA into mouse chromosomes are described. The effects of DNA concentration, size, and form (supercoiled vs. linear with a variety of different ends) are considered as well as the site of injection (male pronucleus, female pronucleus, or cytoplasm) and buffer composition. The optimal conditions for integration entail injection of a few hundred linear molecules into the male pronucleus of fertilized one-cell eggs. Under these conditions about 25% of the mice that develop inherit one or more copies of the microinjected DNA. The overall efficiency also depends on the choice of mouse strains; for example, generating transgenic mice that express foreign growth hormone genes is about eight times easier with C57/BL6 X SJL hybrid mice than with inbred C57/BL6 mice.

The influence of agarose-DNA affinity on the electrophoretic separation of DNA fragments in agarose gels

The effects of DNA concentration, buffer composition, added “carrier” DNA, and chemical modification of agarose on the electrophoretic separation of DNA restriction fragments in agarose gels were tested. Electrophoretic zones of migrating DNA were found to broaden by trailing as sample load was decreased, and this effect was found to be more pronounced for species of higher molecular weight. As DNA sample load was increased, DNA fragments were found to move faster in the direction of electrophoresis (front forward). Sharp, well-resolved electrophoretic zones were obtained at very low DNA loads only when a high-salt, high-pH, high-EDTA buffer was employed or when “carrier DNA” having a broad and uniform molecular weight distribution was included in the sample. Moreover, DNA in high concentration was found to displace DNA in low concentration from a given gel region. Unmodified agaroses were found to differ only slightly in their effectiveness in retarding DNA fragments at a given agarose concentration. However, hydroxyethylated agarose was much more effective in retarding DNA, at a given gel concentration, than the unmodified agaroses tested. These results show that it is useful to consider the agarose gel matrix as possessing the properties of both a molecular sieve and a chromatographic adsorbent when designing electrophoretic separation techniques for DNA. A model for these separations which includes the effects of DNA-agarose interaction and molecular sieving is discussed.

Dielectric relaxation of DNA solutions. III. Effects of DNA concentration, protein contamination, and mixed solvents.

AbstractAs a continuation of previous papers [Biopolymers (1976) 15, 879; (1978) 17, 1508], the low‐frequency dielectric relaxation of DNA solutions was studied with a four‐electrode cell and the simultaneous two‐frequency measurement. Below a critical concentration, the dielectric relaxation time agrees with the rotational relaxation time estimated from the reduced viscosity and is almost independent of DNA concentration Cp, and the dielectric increment is proportional to Cp. The critical concentration is approximately 0.02% of DNA for molecular weight Mr 2 × 106 and 0.2% for Mr 4.5 × 105 in 1 mM NaCl. Dielectric relaxations are compared for samples before and after deproteinization, and the protein contamination is found to have a minor effect on the dipole moment of DNA. The effect of a mixed solvent of water and ethanol on the dielectric relaxation of DNA is well interpreted in terms of changes in viscosity and the dielectric constant of the solvent, assuming that the relaxation arises from rotation of the molecule with a quasi‐permanent dipole due to counterion fluctuation.

The determination of molecular weight of bacterial genome DNA from renaturation rates.

A new method is described for the determination of the total molecular weight of haploid genome DNA. It is based on initial optical renaturation rate measurements of precisely known concentrations of fragmented DNA. The theoretical basis of the measurement is presented. The actual state of replication of the genome has little effect. The exact conditions and the effects of DNA concentration, renaturation time, size of DNA fragments, buffer concentration, optimal temperature and % (G + C) have been determined. Several types of bacterial DNA of known genome size were included as a control. As an application, the DNA genome size have been determined of 40 different bacteria. The method appears to offer advantages by its simplicity, rapidity and reproducibility.