Reexamination of the effect of endotoxin on cell proliferation and transfection efficiency

Plasmid DNA purified from bacterial cells can be contaminated with endotoxin to different extents, depending on the purification method. Earlier reports indicate that endotoxin can decrease transfection efficiency in many eukaryotic cell lines; however, the amount of endotoxin required for inhibition is unclear. We determined endotoxin effects in several cell lines and observed that endotoxin levels greater than or equal to 10,000 endotoxin units (EU) were needed to significantly affect cell proliferation and viability; levels greater than 2000 EU/mu g DNA were required to significantly inhibit transfection for all but one (Huh-7) of the cell lines tested. These endotoxin levels are significantly higher than endotoxin contamination in plasmid DNA purified by anion exchange, CsCl2 gradient and endotoxin-free purification technology, but not as high as a crude alkaline lysis preparatory method. Plasmid DNA prepared using anion exchange technology was comparable to endotoxin-free technology in terms of transfection efficiency. Even Huh-7 cells, which are markedly more sensitive to endotoxins, have comparable transfection efficiencies using plasmid DNA purified by either of these two methods. We conclude that for those cell lines commonly used for transfection studies, endotoxin-free, quality DNA is not necessary because significantly higher levels of bacterial endotoxins are required to inhibit either cell proliferation or transfection.     

Nonlinear electrophoresis for purification of soil DNA for metagenomics

Purification of microbial DNA from soil is challenging due to the co-extraction of humic acids and associated phenolic compounds that inhibit subsequent cloning, amplification or sequencing. Removal of these contaminants is critical for the success of metagenomic library construction and high-throughput sequencing of extracted DNA. Using three different composite soil samples, we compared a novel DNA purification technique using nonlinear electrophoresis on the synchronous coefficient of drag alteration (SCODA) instrument with alternate purification methods such as direct current (DC) agarose gel electrophoresis followed by gel filtration or anion exchange chromatography, Wizard DNA Clean-Up System, and the PowerSoil DNA Isolation kit. Both nonlinear and DC electrophoresis were effective at retrieving high-molecular weight DNA with high purity, suitable for construction of large-insert libraries. The PowerSoil DNA Isolation kit and the nonlinear electrophoresis had high recovery of high purity DNA suitable for sequencing purposes. All methods demonstrated high consistency in the bacterial community profiles generated from the DNA extracts. Nonlinear electrophoresis using the SCODA instrument was the ideal methodology for the preparation of soil DNA samples suitable for both high-throughput sequencing and large-insert cloning applications.     

Imaging of chemiluminescent signals with cooled CCD camera systems

We investigated imaging of chemiluminescent signals from 1,2-dioxetanes with cooled CCD cameras. Non-radioactive detection methods for biomolecules utilizing these chemiluminescent substrates for alkaline phosphatase have been developed. Applications which have been successfully adapted to this technology include Southern and Northern blotting, immunoblotting, ELISA methods and DNA sequencing. Dephosphorylation of the dioxetane CSPD by alkaline phosphatase generates an unstable anion that decomposes resulting in light production. The wavelength of the emitted light is approximately 460nm. We have utilized Photometrics Star and MXC 200L cooled CCD cameras for direct imaging of chemiluminescent signals. Benefits of utilizing a CCD detector include rapid data digitization and more accurate quantitation of chemiluminescent signals compred to film-based densitometry owing to the significantly greater dynamic range. Chemiluminescent images from dot blots of biotinylated DNA, Southern blots and DNA sequencing gel blots were obtained. In a chemiluminescent microtitre plate assay, serial dilutions of alkaline phosphatase spanning four orders of magnitude can be detected. Our results indicate that the digitization of chemiluminescent signal data with cooled CCD cameras is an excellent alternative to ³²P detection methods utilizing storage phosphor screen imaging systems.     

Development of a purification process for adenovirus: controlling virus aggregation to improve the clearance of host cell DNA

The clearance of host cell DNA is a critical goal for purification process development for recombinant Ad5 (rAd5) based vaccines and gene therapy products. We have evaluated the clearance of DNA by a rAd5 purification process utilizing nuclease digestion, ultrafiltration, and anion exchange (AEX) chromatography and found residual host cell DNA to consistently reach a limiting value of about 100 pg/10(11) rAd5 particles. Characterization of the purified rAd5 product using serial AEX chromatography, hydroxyapatite chromatography, or nuclease treatment with and without particle disruption showed that the residual DNA was associated with virus particles. Using a variety of additional physical characterization methods, a population of rAd5 virus in an aggregated state was detected. Aggregation was eliminated using nonionic detergents to attenuate hydrophobic interactions and sodium chloride to attenuate electrostatic interactions. After implementation of these modifications, the process was able to consistently reduce host cell DNA to levels at or below 5 pg/10(11) rAd5 particles, suggesting that molecular interactions between cellular DNA and rAd5 are important determinants of process DNA clearance capability and that the co-purifying DNA was not encapsidated.     

Yeast RNA polymerase III. Chromatographic, catalytic and DNA-binding properties are highly dependent on the type of anion

The chromatographic, catalytic and DNA-binding properties of yeast RNA polymerase III are highly affected by both concentration and type of salt. The type of anion is an especially important modulating factor for the enzymological properties of the enzyme. When acetate or sulfate anions are substituted for chloride anions, RNA polymerase III exhibits a higher affinity for DEAE-Sephadex A25, becomes able to transcribe DNA at relatively high ionic strength and shows a significant increase in the binding strength to DNA. A quantitative analysis of the binding of the enzyme to single-stranded DNA shows that the number of ionic contacts in the complex is not affected by the type of anion, but the nonionic contribution to the binding constant is significantly increased when acetate is substituted for chloride.     

Metallothionein inhibits peroxynitrite-induced DNA and lipoprotein damage

Previous studies have demonstrated that metallothionein functions as an antioxidant that protects against oxidative DNA, protein, and lipid damage induced by superoxide anion, hydrogen peroxide, hydroxyl radical, and nitric oxide. The present study was undertaken to test the hypothesis that metallothionein also protects from DNA and lipoprotein damage induced by peroxynitrite, an important reactive nitrogen species that causes a diversity of pathological processes. A cell-free system was used. DNA damage was detected by the mobility of plasmid DNA in electrophoresis. Oxidation of low density lipoprotein was measured by a thiobarbituric acid-reactive substance, which was confirmed by lipid hydroperoxide assay. Plasmid DNA damage and low density lipoprotein oxidation were induced by 3-morpholinosydnomine, which produces peroxynitrite through the reaction between nitric oxide and superoxide anion or by synthesized peroxynitrite directly. DNA damage by 3-morpholinosydnomine was prevented by both metallothionein and superoxide dismutase, whereas the damage caused by peroxynitrite was prevented by metallothionein only. The oxidation of low density lipoprotein by 3-morpholinosydnomine and peroxynitrite was also significantly inhibited by metallothionein. This study thus demonstrates that metallothionein may react directly with peroxynitrite to prevent DNA and lipoprotein damage induced by this pathological reactive nitrogen species.     

Assay for the quantification of small-sized fragmented genomic DNA

This paper presents a simple assay for the direct quantification of small-sized (up to 1000 bp) fragmented DNA based on the differential separation between large- and small-sized DNA by polyethylene glycol precipitation. The assay can be applied to as low as 1 microg ml(-1) DNA and has a very low DNA detection limit (0.01 microg ml(-1) fragmented DNA), which can be further lowered at least 10-fold with anion exchange chromatography. The assay quantifies for the first time a more direct indicator of the extent of DNA damage than the usually assessed DNA nicks and base modifications, since small-sized fragmented DNA represents an unrepairable DNA damage of necrotic and apoptotic events that are related to normal and abnormal biological conditions.     

Low-energy (5-40 eV) electron-stimulated desorption of anions from physisorbed DNA bases

We present the results of experiments on anion desorption from the physisorbed DNA bases adenine, thymine, guanine and cytosine induced by the impact of low-energy (5-40 eV) electrons. Electron bombardment of DNA base films induces ring fragmentation and desorption of H(-), O(-), OH(-), CN(-), OCN(- ) and CH(2)(-) anions through either single or complex multibond dissociation. We designate the variation of the yield of an anion with electron energy as the yield function. Below 15 eV incident electron energy, bond cleavage is controlled mainly by dissociative electron attachment. Above 15 eV, the portion of a yield function that increases linearly is attributed to nonresonant processes, such as dipolar dissociation. A resonant structure is superimposed on this signal around 20 eV in the anion yield functions. This structure implicates dissociative electron attachment and/or resonant decay of the transient anion into the dipolar dissociation channel, with a minimal contribution from multiple inelastic electron scattering. The yields of all desorbing anions clearly show that electron resonances contribute to the damage of all DNA bases bombarded with 5-40 eV electrons. Comparison of the ion yields indicates that adenine is the least sensitive base to slow electron attack. Electron-irradiated guanine films exhibit the largest yields of desorbed anions.     

Separation of plasmid DNA from protein and bacterial lipopolysaccharides using displacement chromatography

The preparation of plasmid DNA at large scale constitutes a pressing problem in bioseparation. This paper describes a first investigation of displacement chromatography as a means to separate plasmid DNA (4.7 kb) from E. coli lipopolysaccharides and protein (holo transferrin), respectively. Displacement chromatography has advantages in this regard, since the substance mixture is resolved into rectangular zones of the individual components rather than into peaks. Thus a higher total concentration can be maintained in the pooled product fractions. Hydroxyapatite (type I and II) and anion exchange stationary phases were included in the experiments. In addition to a conventional anion exchange column packed with porous particles, the recently introduced continuous bed UNOTM anion exchange column was investigated. No DNA purification was possible with either hydroxyapatite material. Conventional particle based columns in general were not suited to the separation of any two substances varying considerably in molecular mass, e.g. plasmid DNA and standard protein. Presumably, the direct competition for the binding sites, which is essential in displacement chromatography, was restricted by the size dependency of the accessible stationary phase surface area in this case. Better results were obtained with the continuous bed column, in which the adsorptive surface coincides with the walls of the flow through pores. As a result the accessible surface does not vary as much with the size of the interacting molecules as for the conventional stationary phase materials. Sharper transitions were also observed between substance zones recovered from the UNOTM column. The steric mass action model was used to aid method development in case of the anion exchange approach. While further research in obviously necessary, displacement chromatography on continuous bed columns has been shown to be capable of separating plasmid DNA from typical impurities. This revised version was published online in July 2006 with corrections to the Cover Date.     

Effects of pH,conductivity, host cell protein,and DNA size distribution on DNA clearance in anion exchange chromatography media

Flowthrough anion exchange chromatography is commonly used as a polishing step in downstream processing of monoclonal antibodies and other therapeutic proteins to remove process‐related impurities and contaminants such as host cell DNA, host cell proteins, endotoxin, and viruses. DNA with a wide range of molecular weight distributions derived from Chinese Hamster Ovary cells was used to advance the understanding of DNA binding behavior in selected anion exchange media using the resin (Toyopearl SuperQ‐650M) and membranes (Mustang® Q and Sartobind® Q) through DNA spiking studies. The impacts of the process parameters pH (6–8), conductivity (2–15 mS/cm), and the potential binding competition between host cell proteins and host cell DNA were studied. Studies were conducted at the least and most favorable experimental conditions for DNA binding based on the anticipated electrostatic interactions between the host cell DNA and the resin ligand. The resin showed 50% higher DNA binding capacity compared to the membrane media. Spiking host cell proteins in the load material showed no impact on the DNA clearance capability of the anion exchange media. DNA size distributions were characterized based on a “size exclusion qPCR assay.” Results showed preferential binding of larger DNA fragments (>409 base pairs). © 2017 The Authors Biotechnology Progress published by Wiley Periodicals, Inc. on behalf of American Institute of Chemical Engineers Biotechnol. Prog., 34:141–149, 2018     

No detectable reaction of the anion radical metabolite of nitrofurans with reduced glutathione or macro-molecules

The initial metabolite formed by most mammalian nitroreductases is the nitro anion free radical. We, as well as others, have proposed that nitroheterocyclic anion radicals covalently bind to protein, DNA, or thiol compounds such as reduced glutathione (GSH). Our results indicate that even at 100 mM GSH does not affect the steady-state concentration of the nitro anion free radical of N-[4-(5-nitro-2-furyl)-2-thiazolyl]acetamide (NFTA) in rat hepatic microsomal or xanthine oxidase incubations. The steady-state ESR amplitude of the anion radical is also unchanged by the addition of BSA or DNA. Similar results are obtained with nitrofurazone and nitrofurantoin. The reactive chemical species which binds to tissue macromolecules and GSH upon the reduction of nitrofurans remains unknown, but the anion free radical metabolite can be excluded from consideration.     

Photodegradation of DNA with fluorescent light in the presence of riboflavin, and photoprotection by flavin triplet-state quenchers

Superoxide anion was photogenerated upon illumination of nucleic acids with fluorescent light in a solution containing phosphate buffer, pH 7.8 and riboflavin. DNA was a better reducing substrate for this reaction than was RNA. A similar riboflavin-sensitized photoreaction caused single- and double-strand scissions of supercoiled PM2 DNA as detected by electrophoresis in agarose gels. None of specific scavengers or quenchers for superoxide anion and other active oxygen species prevented the DNA strand breaks. However, among the flavin triplet-state quenchers, potassium iodide, butylated hydroxyanisole, and ferricytochrome c protected the supercoiled DNA from photodegradation; butylated hydroxytoluene, alpha-tocopherol, tyrosine and hemoglobin did not have any protective effect. These results indicate that triplet-state riboflavin or a derivative formed from it participate directly in the observed riboflavin-sensitized DNA photodegradation and that active oxygen species are not directly involved.     

Inhibition of chick embryo DNA ligase by dATP: its use in enzyme purification.

Highly purified chick embryo DNA ligase (EC.6.5.1.1) obtained in our laboratory using classical methods, mainly column chromatographies shows a bimodal pH activity and an high affinity inhibition by dATP. A single step passage of crude extract containing DNA ligase through an anion exchange resin (Dowex AG₁X₂) saturated with dATP allows an important purification of the enzyme retained on the column at pH 7.5 and eluted at pH 8.6. Specific activity of the purified enzyme preparation is more than 600 fold higher than that of the crude extract. Analysis of the eluant by polyacrylamide gel electrophoresis shows a main protein containing the enzyme activity.     

Purification of single stranded DNA from asymmetric PCR product using the SMART system

A method has been developed using the SMART system for the purification of single stranded DNA from a mixture containing single- and double-stranded DNA amplified using asymmetric PCR. The asymmetric PCR product was separated into single- and double-stranded DNA using an anion exchange column which took 15 min. Compared to another method in which biotinylated symmetric PCR products were applied to an immobilized streptavidin column, this method was simple and could purify single- and double-stranded DNA. © Rapid Science Ltd. 1998     

Oxidative damage of DNA by the reaction of amino acid with methylglyoxal in the presence of Fe(III)

Methylglyoxal (MG) is an endogenous metabolite which is present in increased concentrations in diabetics and reacts with amino acids to form advanced glycation end products. DNA cleavage induced by the reaction of MG with lysine in the presence of Fe3+ was investigated. When plasmid DNA was incubated with MG and lysine in the presence of Fe3+, DNA strand breakage was proportional to MG and lysine concentrations. The formation of superoxide anion was detected during this reaction, and catalase, hydroxyl radical scavengers and iron chelator, desferrioxamine inhibited DNA cleavage. Deoxyribose assays showed that hydroxyl radicals were generated during the MG/lysine/Fe3+ reaction. These results suggest that superoxide anion and H2O2 may be generated from the glycation reaction between lysine with MG, and that Fe3+ probably participates in a Fenton's type reaction to produce hydroxyl radicals, which may cause DNA cleavage. This mechanism, in part, may provide an explanation for the deterioration of organs under diabetic conditions.     

Na2CO3 influence on DNA double helix stability: strong anion destabilizing effect

Addition of Na(2)CO(3) to almost salt-free DNA solution (5.10(-5)M EDTA, pH=5.7, T(m)=26.5 degrees C) elevates both pH and the DNA melting temperature (T(m)) if Na(2)CO(3) concentration is less than 0.004 M. For 0.004 M Na(2)CO(3), T(m)=58 degrees C is maximal and pH=10.56. Further increase in concentration gives rise to a monotonous decrease in T(m) to 37 degrees C for 1M Na(2)CO(3) (pH=10.57). Increase in pH is also not monotonous. The highest pH=10.87 is reached at 0.04 M Na(2)CO(3) (T(m)=48.3 degrees C). To reveal the cause of this DNA destabilization, which happens in a narrow pH interval (10.56/10.87) and a wide Na(2)CO(3) concentration interval (0.004/1M), a procedure has been developed for determining the separate influences on T(m) of Na(+), pH, and anions formed by Na(2)CO(3) (HCO(3)(-) and CO(3)(2-)). Comparison of influence of anions formed by Na(2)CO(3) on DNA stability with Cl(-) (anion inert to DNA stability), ClO(4)(-) (strong DNA destabilizing "chaotropic" anion) and OH(-) has been carried out. It has been shown that only Na(+) and pH influence T(m) in Na(2)CO(3) solution at concentrations lower than 0.001 M. However, the T(m) decrease with concentration for [Na(2)CO(3)]>/=0.004 M is only partly caused by high pH=10.7. Na(2)CO(3) anions also exert a strong destabilizing influence at these concentrations. For 0.1M Na(2)CO(3) (pH=10.84, [Na(+)]=0.2M, T(m)=42.7 degrees C), the anion destabilizing effect is higher 20 degrees C. For NaClO(4) (ClO(4)(-) is a strong "chaotropic" anion), an equal anion effect occurs at much higher concentrations approximately 3M. This means that Na(2)CO(3) gives rise to a much stronger anion effect than other salts. The effect is pH dependent. It decreases fivefold at neutral pH after addition of HCl to 0.1M Na(2)CO(3) as well as after addition of NaOH for pH greater than 11.2.     

Production of plasmid DNA for human gene therapy using modified alkaline cell lysis and expanded bed anion exchange chromatography

We describe a process for the commercial manufacture of therapeutic grade plasmid DNA. The industrially scaleable unit operations employed in this process are: (i) optimized alkaline lysis; (ii) bag filtration; (iii) expanded bed anion exchange chromatography; (iv) ultrafiltration, and (v) size exclusion chromatography. These steps are scaleable alternatives to current approaches to plasmid DNA isolation such as high speed centrifugation for feedstock clarification and solvent precipitation for plasmid concentration, and an efficient alternative to conventional low through-put packed bed chromatography.The process produces plasmid DNA characterized by low level chromosomal DNA, RNA and endotoxin contamination without the use of flammable solvents or toxic reagents and is suitable for therapeutic administration.     

Synthesis, characterization, DNA binding, and cytotoxic studies of some mixed-ligand palladium(II) and platinum(II) complexes of alpha-diimine and amino acids

The syntheses of nine palladium(II) complexes of type [Pd(phen)(AA)]+ (where AA is an anion of glycine, L-alanine, L-leucine, L-phenylalanine, L-tyrosine, L-tryptophan, L-valine, L-proline, or L-serine) have been achieved. These palladium(II) complexes have been characterized by ultraviolet-visible, infrared, and 1H NMR spectroscopy. The binding studies of several complexes [M(NN)(AA)]+ (where M is Pd(II) as Pt(II), NN is 2,2'-bipyridine or 1,10-phenanthrodine, and AA is an anion of amino acid) with calf thymus DNA have been carried out using UV difference absorption and fluorescence spectroscopy. The mode of binding of the above complexes to DNA suggests the involvement of the hydrogen bonding between them. Several complexes [M(phen)(AA)]+ (where M is Pd(II) or Pt(II) and AA is an anion of amino acid) have also been screened for cytotoxicity in P388 lymphocytic cells. Of them, only two complexes, [Pd(Phen)(Gly)]+ and [Pd(phen)(Val)]+, show comparable cytotoxicity, as cisplatin does.     

A method for the isolation of cross-linked nucleosides from DNA: application to cross-links induced by nitrous acid.

A procedure is reported for the isolation of cross-linked nucleosides from nitrous acid-treated calf thymus DNA. Cross-linked DNA was hydrolyzed enzymatically with deoxyribonuclease I and snake venom phosphodiesterase and fractionated on a DEAE-Sephadex column. After desalting, the fractions were characterized by ultraviolet spectroscopy, anion exchange high pressure liquid chromatography, gel filtration, and two dimensional thin layer chromatography. A cross-linked dinucleotide, and a series of oligonucleotides were isolated. The oligomers, which had resisted digestion by the above enzyme system, were digested to the nucleoside level by a spleen phosphodiesterase-alkaline phosphatase combination. A second cross-linked product was isolated from this mixture. The cross-linked nucleosides were less than 0.17% of the total nucleotides of the DNA. The methods developed here are recommended for the isolation of products from DNA treated with other cross-linking agents.     

Control of antibody-antigen interaction using anion-induced conformational change in antigen peptide

The binding of a monoclonal antibody to an epitope peptide was controlled by the conformational change of the epitope peptide induced by anions. We synthesized peptides in which the epitope sequence DTYRYI for the monoclonal antibody AU1 is located between amphiphilic peptides (KKLL)n and (LLKK)n. In the absence of an appropriate anion, the peptide was in a random coil state and the epitope was linear. In contrast, in the presence of an appropriate anion, the peptide exhibited an anti-parallel alpha-helical structure and the epitope was subsequently 'bent'. In the presence of 41 microM triphosphate, the association constant between the antibody and the peptide was decreased by one order of magnitude in the case of n = 3 and at least three orders of magnitude in the case of n = 4 or 5. Oligo-DNAs, as anions, dissociated the antibody-peptide complex, whereas triphosphate did not. The DNA concentrations required for 50% dissociation of the antibody-peptide complex at pH 7.5 were 4x10(-8), 1x10(-7) and 6x10(-6) M for decamer, octamer and hexamer DNA, respectively.