The superhelical density of nuclear DNA from human cells

Formation of G-quadruplex structure in supercoiled DNA under molecularly crowded conditions

G-quadruplex is a secondary structure of nucleic acids that plays crucial roles in many significant biological processes. Potential G-quadruplex-forming sequences exist widely in various regions of the genome such as telomeres and gene promoters. In spite of the fact that G-quadruplex can be readily assembled from a single-stranded segment of DNA, its formation from duplex DNA is very difficult under physiological conditions because Watson–Crick interactions in guanine rich segments need to be weakened first. It is demonstrated in our studies that intrastrand G-quadruplex generated from a perfectly matched guanine-rich duplex in a circular DNA as a result of significant quadruplex stabilization and duplex destabilization created by the combined actions of negative DNA supercoiling and molecular crowding conditions.

It is demonstrated that G-quadruplex generated from G-rich duplex in a circular DNA as a result of quadruplex stabilization and duplex destabilization created by the combined actions of negative DNA supercoiling and molecular crowding condition.

A Biophysical Model of CRISPR/Cas9 Activity for Rational Design of Genome Editing and Gene Regulation

The ability to precisely modify genomes and regulate specific genes will greatly accelerate several medical and engineering applications. The CRISPR/Cas9 (Type II) system binds and cuts DNA using guide RNAs, though the variables that control its on-target and off-target activity remain poorly characterized. Here, we develop and parameterize a system-wide biophysical model of Cas9-based genome editing and gene regulation to predict how changing guide RNA sequences, DNA superhelical densities, Cas9 and crRNA expression levels, organisms and growth conditions, and experimental conditions collectively control the dynamics of dCas9-based binding and Cas9-based cleavage at all DNA sites with both canonical and non-canonical PAMs. We combine statistical thermodynamics and kinetics to model Cas9:crRNA complex formation, diffusion, site selection, reversible R-loop formation, and cleavage, using large amounts of structural, biochemical, expression, and next-generation sequencing data to determine kinetic parameters and develop free energy models. Our results identify DNA supercoiling as a novel mechanism controlling Cas9 binding. Using the model, we predict Cas9 off-target binding frequencies across the lambdaphage and human genomes, and explain why Cas9's off-target activity can be so high. With this improved understanding, we propose several rules for designing experiments for minimizing off-target activity. We also discuss the implications for engineering dCas9-based genetic circuits.

Toxicological and mutagenic analysis of Artemisia dracunculus (tarragon) extract

Mutagenicity and liver toxicity of the herb tarragon (Artemisia dracunculus) were evaluated using single cell gel (comet) electrophoresis. Ten microlitres aliquots of peripheral venous human blood were incubated with tarragon extract, saline, or the mutagen sodium dichromate. Cell suspensions dispersed in low-melting agarose were electrophoresed in ethidium bromide. The resulting DNA migration trails were obtained using fluorescent microscopy at 400× magnification, and graded according to the mutagenicity index (MI) for each cell incubation condition. The in vivo liver toxicity of Artemisia dracunculus was assessed in the blood of mice treated orally with the extract of the herb, using alanine aminotransferase (ALT) and aspartate aminotransferase (AST) as liver function indicators. Liver morphology was assessed using hematoxylin and eosin (HE) staining of liver tissue. The present study demonstrated a direct correlation between tarragon extract dosage and three major outcome variables: MI; serum liver enzyme activity; and liver histopathology. These outcomes are possibly due to the presence in tarragon of methylchavicol and other genotoxic compounds. These findings provide a preliminary guide for risk assessment of tarragon in diet and in possible therapeutic applications.

The fast-halo assay for the assessment of DNA damage at the single-cell level

The detection of breaks in mammalian cell DNA and the measurement of their repair represent primary endpoints for genotoxicity testing. Over the past three decades many techniques sensitive to the presence of DNA breaks have been developed: their availability significantly increased the knowledge in the area of genetic toxicology. In general, these techniques have evolved to become more sensitive and flexible as well as less complicated. The fast-halo assay (FHA) is a very recent method to detect DNA-strand breakage induced either by various genotoxic agents or secondary to apoptotic DNA cleavage, and to study the repair of primary DNA breaks at the single-cell level. In FHA, damaged DNA is separated from intact one by means of solvent gradient, stained with ethidium bromide and visualized under a fluorescence microscope. The level of DNA breaks is then determined with an image analysis software. FHA is as sensitive, reliable, and flexible as the well-established comet assay, but it has the advantage of being, as compared to any other existing method, the most rapid and less expensive one. Taken collectively, these unique features render FHA the ideal method to perform a large number of genotoxicity tests on mammalian cells in a particularly cost-effective and time-saving manner.

The fast halo assay: an improved method to quantify genomic DNA strand breakage at the single-cell level

The present study describes the improvement of a technique, the alkaline-halo assay (AHA), for the assessment of DNA single-strand breakage at the single-cell level. AHA involves a series of sequential steps in which cells are embedded in melted agarose and spread onto microscope slides, incubated in a high-salt alkaline lysis solution, then in a hypotonic alkaline solution and, finally, stained with ethidium bromide (EB). Under these conditions, single-stranded DNA fragments diffuse radially from the nuclear cage and generate a fluorescent image that resembles a halo concentric to the nuclear remnants: the area of the halo is a direct function of the extent of DNA strand scission. These phenomena can be conveniently monitored with a fluorescence microscope and quantified by image-processing analysis. The behaviour of single-stranded DNA fragments under the conditions of the modified assay, called fast halo assay (FHA), is essentially the same as in AHA. The modifications consist in the simplification of the lysis, denaturation and staining procedures, and allow, as compared with AHA, the preparation of samples within 15 min, with a two-third reduction in total processing time, using only two reagents to promote DNA extraction and staining: NaOH and EB. A variation of the FHA operating at non-denaturing conditions to discriminate apoptotic cells from non-apoptotic cells bearing DNA single-strand breaks is also illustrated. To benchmark FHA sensitivity and reliability, the DNA single-strand breaks (SSBs) resulting either from exposure of cultured mammalian cells to different DNA-damaging agents or from secondary apoptotic DNA cleavage, have been quantified and results compared with the outcomes of reference techniques run in parallel, namely AHA, comet assay and Hoechst 33342 staining. The results indicate that FHA has the same reliability and sensitivity of the reference assays, but presents the additional advantages of being inexpensive, more rapid and strikingly simple.

Changes in DNA supercoiling during repair of gamma-radiation-induced damage

Enriched human B-lymphocyte and T-lymphocyte subpopulations were isolated by means of two Percoll density gradient centrifugation steps. Strand-break repair kinetics of 60Co gamma-irradiation-damaged DNA were obtained by applying a modified nucleoid sedimentation technique. Although no variations in the strand-break repair patterns of B-cells and T-cells within an individual could be detected, variations between individuals were evident. Changes in DNA supercoiling during the repair process were studied by means of ethidium bromide intercalation. The supercoiled conformation of DNA in peripheral lymphocyte subpopulations displayed similar undulating patterns within an individual, variations occurring between individuals. The results of this study indicate that alterations to the higher-order structure (supercoiling) of DNA are integral to the repair process.

Eukaryotic genome: model considerations

The paper presents a new model of chromosome structure based on the assumption that multiple circular subunits of DNA exist. The essential difference with previously described models is the circular DNA unit forms a central chromosome axis. Chromosome configurations during various phases of the cell cycle depend on the various conformations of this central integrating unit. The described model can be generalized for all haploid set of eukaryotic nucleus. Some aspects of the chromosome structure and their functions have been discussed.

Fanconi's anemia: anomaly of enzyme passage through the nuclear membrane? Anomalous intracellular distribution of topoisomerase activity in placental extracts in a case of Fanconi's anemia

In cells of Fanconi's anemia (FA) spontaneous breakage of chromosomes was first recognized by Schroeder et al. (1964). Sensitivity to bivalent alkylants has been found to be a constant feature, whereas low levels of several repair-related enzymes have been described in different FA cell lines. In a family with known FA, during a further pregnancy the prenatal diagnosis of the disease was made by cytogenetic analysis of amniotic cells. After birth the fresh placenta was extracted for further enzymologic analysis. An unusual distribution of DNA topoisomerase activity was noted: high in the cytoplasm and only a little activity in the nuclear sap. This contrasts with findings in normal placentae. Since amniotic cells, lymphocytes, and fibroblasts of this child exhibited both high spontaneous breakage of chromosomes and sensitivity to the bivalent alkylant, diepoxybutane, a correlation between the findings on cytogenetic and enzymologic levels is assumed. Whereas in other published cases, a true reduction of activities of enzymes involved in DNA replication and repair has been found, the present results suggest the interpretation that in our patient the genetic anomaly does not affect the level of synthesis of the enzyme itself, but the passage of the enzyme from the place of synthesis (the cytoplasm) to the substrate (inside the nucleus). A genetic anomaly of the nuclear membrane might be a possible explanation, or alternatively, a structural mutation of the enzyme at a site not affecting the catalytic activity, but affecting the membrane passage or intranuclear accumulation. Meanwhile, placentae of two other cases gave similar results, thus supporting our findings.

Spectrofluorometric measurement of the binding of ethidium to superhelical DNA from cell nuclei

Structures retaining many of the morphological features of nuclei may be released by lysing HeLa cells in solutions containing non-ionic detergents and high concentrations of salt. These nucleoids contain few chromatin proteins. We have shown that the DNA of nucleoids is quasicircular and supercoiled by measure spectrofluorometrically the amount of the intercalating dye, ethidium, bound to unirradiated and gamma-irradiated nucleoids. Ethidium binds to nucleoids in the manner characteristic of the binding to superhelical DNA: at low concentrations more ethidium binds to unirradiated nucleoids than to their gamma-irradiated counterparts with broken DNA, and at higher concentrations less ethidium binds to the unirradiated nucleoids. The quasi-circles in nucleoids are 22 times less sensitive to gamma-irradiation than are circles of pure PM2 DNA: they must contain about 2.2 X 10(5) base pairs. The constraints that maintain the quasi-circularity of nucleoid DNA are very resistant to extremes of temperature and alkali; some remain under conditions in which the duplex is denatured. The constraints are destabilised by ethidium suggesting that they are stabilised by free energy of supercoiling. Proteolytic enzymes, but not ribonucleases, remove the constraints. Possible structures for the constraining mechanism are discussed.