DNA elimination and its relation to quantities in the macronucleus of Tetrahymena

The macronucleus of Tetrahymena contains a large number of DNA molecules of subchromosomal size. They belong to about 270 species each one occurring at an average number of 45 copies Macronuclei divide unequally and nothing is known of segregation control. This and the elimination and degradation of DNA during macronuclear amitosis make the clonal stability of macronuclei a problem of qualitative and quantitative control on a subchromosomal level. We studied the contribution of DNA elimination to the quantitative composition of the macronucleus cytophotometrically in single cells of different strains. This was done under standard conditions and under conditions known to influence the amount of macronuclear DNA. The following results were found: Elimination of DNA occurs at almost every division. The size of the elimination body is highly variable but still positively correlated with the macronuclear DNA content. In T. thermophila the amount of eliminated DNA is 2.5% of the G2 content and is not dependent on the growth state. It varies with species, amounting to as much as 8% in T pigmentosa. During conditions which increase the macronuclear DNA content, very little DNA is eliminate. On the other hand, large amounts are eliminated under other conditions causing the macronuclear DNA content to decrease. DNA to be eliminated at division is synthesized at the same time as bulk DNA. We developed a computer program which helps us study the effects of DNA elimination and unequal divisions upon the copy numbers of subchromosomal DNA classes. The result indicates that in a given cell line at least one of the DNA molecules becoms extinct after 60 generations which we expect would cause the cell's extinction and restrict a clone's life to 60 generations. As this does not happen in nature, there must be some control of the copy numbers preventing their extinction during vegetative multiplication. Whether elimination increases or decreases the imbalance of genes remains to be investigated. © 1992 Wiley-Liss, Inc.     

DNA elimination and its relation to quantities in the macronucleus of Tetrahymena.

The macronucleus of Tetrahymena contains a large number of DNA molecules of subchromosomal size. They belong to about 270 species each one occurring at an average number of 45 copies. Macronuclei divide unequally and nothing is known of segregation control. This and the elimination and degradation of DNA during macronuclear amitosis make the clonal stability of macronuclei a problem of qualitative and quantitative control on a subchromosomal level. We studied the contribution of DNA elimination to the quantitative composition of the macronucleus cytophotometrically in single cells of different strains. This was done under standard conditions and under conditions known to influence the amount of macronuclear DNA. The following results were found: Elimination of DNA occurs at almost every division. The size of the elimination body is highly variable but still positively correlated with the macronuclear DNA content. In T. thermophila the amount of eliminated DNA is 2.5% of the G2 content and is not dependent on the growth state. It varies with species, amounting to as much as 8% in T. pigmentosa. During conditions which increase the macronuclear DNA content, very little DNA is eliminated. On the other hand, large amounts are eliminated under other conditions causing the macronuclear DNA content to decrease. DNA to be eliminated at division is synthesized at the same time as bulk DNA. We developed a computer program which helps us study the effects of DNA elimination and unequal divisions upon the copy numbers of subchromosomal DNA classes.(ABSTRACT TRUNCATED AT 250 WORDS)     

Preparation of multimilligram quantities of large, linear DNA molecules for structural studies

We describe a method for preparing large, linear DNA molecules in amounts that are suitable for structural studies. The procedure employs self-primed DNA amplification on a starting molecule that consists of the sequence of interest flanked by the cohesive end sequences from bacteriophage lambda as well as endonuclease recognition sites. Amplification produces long polymers of DNA, tens of kilobases in length, which harbor many copies of the sequence of interest. Endonuclease digestion of these polymers, followed by chromatographic purification, yields high-quality preparations of the DNA molecule of interest. Reliance on the cohesive end sequences to initiate self-primed amplification effectively enables the synthesis of DNA molecules of interest with minimal restriction on length and sequence.     

Assay for nanogram quantities of DNA in cellular homogenates.

The DNA concentration of a crude cellular homogenate can be measured accurately in the nanogram range using the fluorescence enhancement of 4′,6-diamidino-2-phenylindole (DAPI) or bisbenzimidazole (Hoechst H 33258) complexed with DNA. A simple assay has been devised including an internal standard, which allows reliable measurement and compensates for any quenching due to cellular components or buffer. The fluorescence enhancement is highly specific for DNA; no other cell component produces significant fluorescence. The response is linear over a broad dynamic range making the measurement of unknown DNA concentrations convenient.     

Stability of DNA/Td3717 complexes for gene transfection,defined by the size and polydispersity of the complex

The amphiphilic α-helical peptide, Td3717, is a bi-functional synthetic peptide that acts as both a polycation for DNA binding and a ligand for targeted delivery to tumor cells. Td3717 forms a stable complex with plasmid DNA, and the complex maintained high transfection efficiency after storage at 4 °C for six months and after four freeze/thaw cycles. During the storage and freeze/thaw cycling, the particle size of the DNA/Td3717 complex remained less than 100 nm. The size of the complex is an important factor for its internalization into cells via the endocytosis pathway; therefore, the stability of the particles will strongly contribute to high transfection efficiencies after storage and repeated freezing/thawing.     

Dendritic star polymers for efficient DNA binding and stimulus-dependent DNA release

Water-soluble core-shell star polymers consisting of a dendritic polyphenylene core and an outer shell containing a defined number of amino groups have been synthesized via atom transfer radical polymerization (ATRP). All macromolecules efficiently interacted with a diverse set of DNA fragments, and stable complexes were formed and visualized by atomic force microscopy. The observed tight binding of DNA, which was found in the sub-nanomolar range, was mainly attributed to strong electrostatic interactions. Complex stoichiometries between the polyelectrolytes were controlled via the number of amino groups of the star polymers, and well-defined nanoscopic architectures were formed. DNA was released from the complexes after treatment with high concentrations of sodium chloride in aqueous solution. Such star polymers, which allow the binding and release of DNA, represent attractive candidates for the development of novel anion-exchange resins for DNA purification or as nonviral vector systems for gene delivery.     

Pentalysine-grafted ROMP polymers for DNA complexation and delivery

Amphiphilic graft polymers, containing oligolysine groups pendent to a hydrophobic polycyclooctene backbone, were used to form polyplexes with plasmid DNA pZsGreen1-N1. These poly(cyclooctene- graft-pentalysine) structures were found to be effective transfection reagents for COS-1 and HeLa cells. In the case of polymer 1e (average degree of polymerization of 206), protein expression levels 48 h post-transfection were found to be comparable to, or better than, commercial transfection reagents jetPEI and SuperFect. With HeLa cells, GFP expression levels were better than Lipofectamine 2000. Of particular interest was the excellent cell viability seen in experiments with polyplexes formed from the pentalysine-grafted polymers. In the example of the highest molecular weight graft copolymer, polymer 1e, cell viability relative to untreated cells was 99% with COS-1 cells and 92% with HeLa cells in contrast to the commercial reagents, which gave 67-80% with COS-1 cells and 17-52% with HeLa cells. The effectiveness of these polyolefin- graft-pentalysine structures as DNA delivery vehicles is attributed to their amphiphilic nature and branched architecture.     

A rapid colorimetric assay for the estimation of microgram quantities of DNA

The thiobarbituric acid assay, routinely employed for the quantification of sialic acids, has been modified for the estimation of DNA in the range 0.5–500 μg. Neither RNA nor protein interfere in this procedure. The assay, as described, is more sensitive and less time consuming than the diphenylamine reaction.     

Cytosine methylation and hydroxymethylation mark DNA for elimination in Oxytricha trifallax

Background

Cytosine methylation of DNA is conserved across eukaryotes and plays important functional roles regulating gene expression during differentiation and development in animals, plants and fungi. Hydroxymethylation was recently identified as another epigenetic modification marking genes important for pluripotency in embryonic stem cells.

Results

Here we describe de novo cytosine methylation and hydroxymethylation in the ciliate Oxytricha trifallax. These DNA modifications occur only during nuclear development and programmed genome rearrangement. We detect methylcytosine and hydroxymethylcytosine directly by high-resolution nano-flow UPLC mass spectrometry, and indirectly by immunofluorescence, methyl-DNA immunoprecipitation and bisulfite sequencing. We describe these modifications in three classes of eliminated DNA: germline-limited transposons and satellite repeats, aberrant DNA rearrangements, and DNA from the parental genome undergoing degradation. Methylation and hydroxymethylation generally occur on the same sequence elements, modifying cytosines in all sequence contexts. We show that the DNA methyltransferase-inhibiting drugs azacitidine and decitabine induce demethylation of both somatic and germline sequence elements during genome rearrangements, with consequent elevated levels of germline-limited repetitive elements in exconjugant cells.

Conclusions

These data strongly support a functional link between cytosine DNA methylation/hydroxymethylation and DNA elimination. We identify a motif strongly enriched in methylated/hydroxymethylated regions, and we propose that this motif recruits DNA modification machinery to specific chromosomes in the parental macronucleus. No recognizable methyltransferase enzyme has yet been described in O. trifallax, raising the possibility that it might employ a novel cytosine methylation machinery to mark DNA sequences for elimination during genome rearrangements.     

Antimicrobial polymers: mechanism of action,factors of activity,and applications

Complex epidemiological situation, nosocomial infections, microbial contamination, and infection risks in hospital and dental equipment have led to an ever-growing need for prevention of microbial infection in these various areas. Macromolecular systems, due to their properties, allow one to efficiently use them in various fields, including the creation of polymers with the antimicrobial activity. In the past decade, the intensive development of a large class of antimicrobial macromolecular systems, polymers, and copolymers, either quaternized or functionalized with bioactive groups, has been continued, and they have been successfully used as biocides. Various permanent microbicidal surfaces with non-leaching polymer antimicrobial coatings have been designed. Along with these trends, new moderately hydrophobic polymer structures have been synthesized and studied, which contain protonated primary or secondary/tertiary amine groups that exhibited rather high antimicrobial activity, often unlike their quaternary analogues. This mini-review briefly highlights and summarizes the results of studies during the past decade and especially in recent years, which concern the mechanism of action of different antimicrobial polymers and non-leaching microbicidal surfaces, and factors influencing their activity and toxicity, as well as major applications of antimicrobial polymers.     

High-efficiency preparation of DNA from limiting quantities of eukaryotic cells for hybridization analysis

This report describes a DNA preparation method which allows the detection of single-copy genes in samples of as few as 6000 eukaryotic cells. The technique uses proteinase K digestion in detergent and low-gelation-temperature agarose followed by solidification of the agarose and removal of the detergent by diffusion. RNase and restriction enzyme digestion are carried out in solution after remelting the agarose. The procedure can be performed successfully with mammalian cells in suspension, with parasitic protozoa and with pieces of mammalian tissue weighing less than 1 mg. Numerous samples can be processed simultaneously using frozen as well as fresh material.     

Characteristic distribution of L-tuple for DNA primary sequence

We consider construction of a characteristic distribution of an L-tuple in a DNA sequence. The mathematical characteristic of the characteristic distribution is selected as invariant to characterize the L-tuple. With the invariant, we can perform the sequence comparison. The graphs of characteristic distributions of dinucleotide GC for the coding sequences of the first exon of beta-globin gene of eleven different species and the construction of phylogenetic tree of twenty four coronavirus genomes illustrate the utility of the approach.     

Molecular modeling of temperature dependence of solubility parameters for amorphous polymers

A molecular modeling strategy is proposed to describe the temperature (T) dependence of solubility parameter (δ) for the amorphous polymers which exhibit glass-rubber transition behavior. The commercial forcefield "COMPASS" is used to support the atomistic simulations of the polymer. The temperature dependence behavior of δ for the polymer is modeled by running molecular dynamics (MD) simulation at temperatures ranging from 250 up to 650 K. Comparing the MD predicted δ value at 298 K and the glass transition temperature (T(g)) of the polymer determined from δ-T curve with the experimental value confirm the accuracy of our method. The MD modeled relationship between δ and T agrees well with the previous theoretical works. We also observe the specific volume (v), cohesive energy (U(coh)), cohesive energy density (E(CED)) and δ shows a similar temperature dependence characteristics and a drastic change around the T(g). Meanwhile, the applications of δ and its temperature dependence property are addressed and discussed.