Conformational transitions in closed circular DNA molecules. II. Biological implications

Elastic torsional strain in DNA within a fraction of SV40 minichromosomes: relation to transcriptionally active chromatin

After treatment of SV40 minichromosomes with DNA topoisomerase I, the superhelicity in the bulk of the DNA extracted from minichromosomes is known to remain unchanged. However, we found that the DNA extracted from a small fraction of SV40 minichromosomes (2-5%), was almost completely relaxed, and covalently closed as shown by agarose gel electrophoresis. Thus, the DNA in these 2-5% of SV40 minichromosomes was probably torsionally strained (TS). The proportion of such TS minichromosomes is close to the estimated proportion of transcriptionally active minichromosomes. The distribution of the TS minichromosomes in sucrose gradient coincided with the distribution of transcriptionally active complexes. Both sedimented faster than the majority of minichromosomes. Furthermore, after treatment with topoisomerase I the relaxed minichromosomes could be quantitatively separated from the bulk of material by recentrifugation in a sucrose gradient. A major part of the endogenous RNA polymerase activity was recovered in the relaxed fraction. These data suggest that TS-minichromosomes correspond to transcriptionally active chromatin. After relaxation with topoisomerase I the TS minichromosomes lacked histones.

DNA topological linking numbers in malignantly transformed Syrian hamster cells

The topological linking numbers in closed superhelical loops of nuclear DNA were measured as the density of DNA topological turns ('titratable superhelical turns') per unit length of DNA by means of sedimentation of superhelical DNA (in nucleoids) in gradients of 15-30% sucrose containing 1.95 M NaCl and various concentrations of ethidium bromide. In four malignantly transformed Syrian hamster cell lines (three SV40-transformed and one spontaneous) the density of DNA topological turns was equal to or higher than the density of DNA topological turns in early passage embryonal Syrian hamster cells (/delta/ greater than or equal to 0.076) and, in contrast to normal cells, the malignant ones did not decrease the density of their DNA topological turns upon cultivation. It is proposed that the persistence of high densities of DNA topological turns in malignant cells is responsible for activation of transcription of a number of genes during malignant transformation.

Extremely underwound chromosomal DNA in nucleoids of mouse sarcoma cells

The superhelical properties of chromosomal DNA from cells of a mouse sarcoma were investigated in neutral sucrose gradients containing ethidium bromide. Removal of negative supercoiling from the DNA of the sarcoma cells required a substantially higher dye concentration than was necessary in the case of DNA from cultured mouse fibroblasts. The calculated value of the mean superhelical density in malignant cells (sigma = -0.14) appears abnormally high compared with the value (sigma = -0.09) obtained for DNA of mouse fibroblasts. Chromosomal DNA from mouse sarcoma cells is therefore concluded to be highly deficient in helical turns.

Decrease in the number of DNA topological turns during Friend erythroleukemia differentiation

Murine erythroleukemia cells were induced to undergo erythroid differentiation by growing in presence of dimethylsulfoxide, butyric acid or actinomycin D. topological linking numbers in closed loops of nuclear DNA were measured by means of centrifugation of nucleoids containing superhelical DNA in sucrose gradients containing varying concentrations of ethidium bromide. All cells were grown to G1 stage of the cell cycle. It was found that the mean density of the DNA topological linking number decreases from 0.076 turns per 10 nucleotide pairs in non-differentiated cells to 0.062 turns in the cells induced to differentiate. This decrease in topological linking number of DNA loops is quite sufficient for the change in the DNA double helix secondary structure which in turn may be responsible for coordinate switch in transcription of genes which control cellular differentiation (Luchnik, 1980a, b).

Conformational transitions in closed circular DNA molecules. I. Topological and energetical considerations

A theory of conformational transitions in closed circular DNA as a function of topological linking number of the molecule (alpha) is elaborated taking into account topological and energetical considerations. The theory predicts a step-like dependence of a number of superhelical turns in DNA molecules (tau) on delta alpha. Thus, the number of superhelical turns tau = delta alpha for small values of delta alpha. For a large delta alpha (when conformational begin to occur) tau = delta alpha - sigma phi ij, where sigma phi ij is the total angle of conformational transitions for a given delta alpha. This prediction is in good agreement with published data on the dependence of the sedimentation coefficient of circular DNA molecules on their topological linking number. The results also allow to explain the disagreement between a number of titratable superhelical turns in circular DNA molecules and a number of supercoiles seen on electron micrographs for molecules with sufficiently large delta alpha.