A semiautomated system for the production and analysis of sucrose density gradients

Effect of alkali on the size dispersity of mammalian DNA measured by filter elution

DNA from unirradiated and irradiated cultured 9L rat brain tumor cells was held for varying times in low ionic strength solutions at pH 11.0, 12.3, or 12.9. The effect of this exposure to alkali on the DNA size distribution was determined by comparing the DNA filter elution profiles obtained experimentally with those theoretically predicted for monodispersed and random distributions. At pH 12.3 or 12.9, DNA from cells irradiated with 300 rad eluted with first-order kinetics corresponding to a random DNA size distribution. The median size of the distribution decreased if the irradiated DNA was exposed to pH 12.3 for 24 h. At pH 12.3 or 12.9, DNA from unirradiated cells eluted initially with complex kinetics that later became linear (18-21 h for pH 12.3 or 13-15 h for pH 12.9), characteristic of a monodispersed DNA size distribution. Holding either unirradiated or irradiated DNA at pH 11.0, below the critical unwinding pH, produced no effect on the elution profiles. Analysis of these filter elution data indicated that after sufficient exposure to pH 12.3 or 12.9, undamaged DNA molecules from mammalian cells elute as a single-stranded monodispersed size distribution of approximately 1 X 10(10) daltons. While the possibility cannot be completely eliminated that this monodispersed size represents an upper limit determined by physical forces, these results, in conjunction with those obtained using other techniques, lend credence to the existence of a nonrandom higher-order structure in mammalian chromosomal DNA.

Characterization of density gradients prepared by freezing and thawing a sucrose solution

Density gradients of sucrose can be prepared in large numbers by successive freezing and thawing of sucrose solutions. Gradients of other solute molecules, such as salt and detergents, also form and this could affect subsequent sedimentation behavior of some molecules. However, the sedimentation behavior of native and denatured DNA of bacteriophage lambda was essentially isokinetic under the conditions used thus making these gradients comparable with ones prepared manually, at least for preparative sedimentation work with nucleic acids.

The repair of double-strand breaks in the nuclear DNA of Saccharomyces cerevisiae and its genetic control

With the use of neutral sucrose sedimentation techniques, the size of unirradiated nuclear DNA and the repair of double-strand breaks induced in it by ionizing radiation have been determined in both wild-type and homozygous rad52 diploids of the yeast Saccharomyces cerevisiae. The number average molecular weight of unirradiated DNA in these experiments is 3.0 X 10(8)+/-0.3 Daltons. Double-strand breaks are induced with a frequency of 0.58 X 10(-10) per Daltonkrad in the range of 25 to 100 krad. Since repair at low doses is observed in wild-type but not homozygous rad52 strains, the corresponding rad52 gene product is concluded to have a role in the repair process. Cycloheximide was also observed to inhibit repair to a limited extent indicating a requirement for protein synthesis. Based on the sensitivity of various mutants and the induction frequency of double-strand breaks, it is concluded that there are 1 to 2 double-strand breaks per lethal event in diploid cells incapable of repairing these breaks.

The repair of DNA double-strand breaks in mammalian cells and the organization of the DNA in their chromosomes

The molecular weight of native DNA has been accurately determined by the use of a semiautomated sucrose gradient system. A mondisperse size distribution (speed dependence free) of eighth-of-a-chromatid pieces [1.7 S 10(10) daltons, with 95% confidence (fiducial) limits of +/- 48%] was found. This size has been confirmed by viscoelastometry. Ionizing radiation rapidly breaks each of these pieces into about 21 subunits (again monodisperse) of 8 X 10(8) daltons each. With increaseing dose (greater than 2 krad) the subunits are themselves randomly broken down into even smaller pieces. Postirradiation incubation at 37 degrees C permits the cells to repair both DNA double-strand breaks and intersubunit linkages at the same dose-independent rate (T37) of about 55 min, the same rate as found in Micrococcus radiodurans. The repair data are compatible with a first-order-kinetics repair system, analogous to the post-UV excision-repair system, which becomes saturated at high doses (greater than 60 krad). Specially constructed "enzyme" gradients show that the linkages contain at least two protein molecules each covalently bound to the end of a subunit and linking the subunits together by a disulfide bond(s). Correlation of cell survival and DNA break kinetics yields two possible models. These are that the two-thirds of the lethal events which are due to improperly or unrepaired double-strand breaks result from either (1) a misrepair frequency of 3.5 X 10(-3) (rather high for a mutation frequency) or (2) the induction of a double-strand break in a single eighth-of-a-chromatid unit which is essential for survival but which cannot be repaired, possibly because the unit contains the double-strand break repair system gene(s).