Physico-chemical model for DNA alkaline elution: new experimental evidence and differential role of DNA length, chain flexibility and superpacking

The Filter Does Not Act as a DNA Size Discriminator in the Neutral Filter Elution Technique

Various types of filters were used with the neutral filter elution technique. No significant differences in elution rate or curve shapes were found. Therefore we assume that the release of DNA fragments from the DNA gel formed by lysis of cells is the rate-determining event in elution and not the rate of migration through the filter. We suggest that the filter only serves as a support for the DNA gel.

Fluid mechanics of DNA double-strand filter elution

Measurement of infrequent DNA double-strand breaks (DSB) in mammalian cells is essential for the understanding of cell damage by ionizing radiation and many DNA-reactive drugs. One of the most important assays for measuring DSB in cellular DNA is filter elution. This study is an attempt to determine whether standard concepts of fluid mechanics can yield a self-consistent model of this process. Major assumptions of the analysis are reptation through a channel formed by surrounding strands, with only strand ends captured by filter pores. Both viscosity and entanglement with surrounding strands are considered to determine the resistance to this motion. One important result is that the average elution time of a strand depends not only on its length, but also on the size distribution of the surrounding strands. This model is consistent with experimental observations, such as the dependence of elution kinetics upon radiation dose, but independence from the size of the DNA sample up to a critical filter loading, and possible overlap of elution times for strands of different length. It indicates how the dependence of elution time on the flow rate could reveal the relative importance of viscous and entanglement resistance, and also predicts the consequences of using different filters.

Nuclear structure and higher order gene structure: their role in the control of chemically-induced neoplastic transformation

An overview is hereby given of the physical and physicochemical alterations at the level of nuclear structures in rat liver cells, following a chemically-induced neoplastic transformation. These alterations refer to chromatin-DNA structure, from secondary (B- versus A- and Z-form) to tertiary-quanternary up to quinternary (in situ), and to the physical state of water. Possible molecular mechanisms-linking global chromatin changes to single gene expression in the control of neoplastic transformation-are discussed in terms of the degree of negative superhelicity of fibrosomes, recently identified single repeating structural subunits and hereby associated with single functional genes.

Mapping of peroxyl radical induced damage on genomic DNA

We have examined the DNA damage produced by reaction of peroxyl radicals with human fibroblast DNA. DNA damage consisted of both strand breaks and base modifications. The extent of strand breaks and base modifications induced as a function of peroxyl radical concentration was determined by quantitation of fragment size distributions using denaturing glyoxal-agarose gel electrophoresis. Both strand breaks and base modifications increased in a log linear fashion with respect to peroxyl radical concentration. Oxidative base modifications were observed to occur to a greater extent than strand breaks at every concentration measured. The sequence-specific distribution of peroxyl radical induced base damage was mapped for 803 nucleotide positions using the method of ligation mediated PCR. A total of 87% of all guanine positions in the examined sequences was found to be significantly oxidized. The order of reactivity of DNA bases toward oxidation by peroxyl radicals was found to be G >> C > T. Adenine is essentially unreactive. The yield of oxidative base modifications at guanines and cytosines by peroxyl radicals depends on the exact specification of 5' and 3' flanking bases in a polarity dependent manner. Every guanine in the 5'XGC3' motif was found to be oxidized, where X is any 5' neighbor. In contrast, 5' and 3' purine flanks drastically reduced the extent of peroxyl radical G oxidation. The pattern of base modification and the influence of nearest neighbors differs substantially from that previously reported for hydrogen peroxide damage mediated by low valent transition metal ions for the identical DNA sequences.

Size distribution of DNA molecules recovered from non-denaturing filter elution

DNA fragments removed from the filter during non-denaturing filter elution were collected and loaded on top of neutral sucrose gradients. Their size distribution was determined by low-speed centrifugation in neutral sucrose gradients. The average size of eluted DNA was found to be approximately 110 S, yet the average size of DNA collected after short elution times was found to be slightly larger than that after long elution times. It is concluded that the size of eluted DNA fragments is not correlated with their elution rate, and it is proposed that shear forces generated at the pores of the filter cause degradation of the DNA. A comparison of the sedimentation profiles of carefully prepared cellular DNA before and after elution revealed that the generated shear forces during elution break down the DNA to an extent equivalent to around 20,000 DNA double-strand breaks (dsb) per G1 cell. The size of DNA fragments decreased with increasing radiation dose; however, five times more dsb were found than expected after exposure to radiation alone. It is proposed that this excess of dsb may derive from the transformation of other radiation-induced lesions to dsb under the action of the shear forces generated during elution.

Principles and practice of DNA filter elution

DNA filter elution assays have proved useful in studies of DNA strand breaks and crosslinks produced in mammalian cells or tissues by a wide variety of carcinogenic and cancer chemotherapeutic agents. The basic types of DNA lesions that can be measured include single and double-strand breaks, interstrand crosslinks and DNA-protein crosslinks. DNA filter elution has also been adapted to the assay of other lesions such as alkali-labile sites and the protein-associated strand breaks of topoisomerase DNA cleavage complexes. The essential concepts and theory of the technique are discussed and the applications of the technique to various types of studies are critically reviewed.

Non-linear dose-effect curve for DNA double-strand breaks by low LET radiation: the effect of eluting buffer composition on the measurement of breaks by the filter elution technique

Chinese hamster V79 cells were irradiated with 250 kVp X-rays and analysed for the presence of DNA double-strand breaks using filter elution. Changing the pH of the elution and lysis buffers from pH 9.6 to 7.2 leads to a decreased rate of elution of the DNA from the filters and a small difference in the dose-effect relationship obtained. In both cases the dose-effect curves were non-linear. When cells are irradiated with 238Pu alpha-particles a difference in the rate of elution of the DNA is also observed between the two pH values, although the dose-effect curves are linear. These findings suggest that there may be qualitative differences in the types of lesions being induced by low-LET radiation and being scored as dsb in the filter elution assay at pH 9.6. However, carrying out elution at pH 7.2 does not eliminate the nonlinear response measured after X-irradiation.

Techniques to measure DNA single-strand breaks in cells: a review

Alkaline sucrose sedimentation was for a number of years the standard procedure for the measurement of single-strand breaks. Some years ago a number of new techniques with improved sensitivity were introduced. The following techniques are presented and discussed: alkaline unwinding, alkaline filter elution, nucleoid sedimentation, viscoelastometry, microelectrophoresis of single cells, DNA precipitation, pulse field gel electrophoresis, fluctuation spectroscopy and nick translation.

The dose-response for low-LET radiation-induced DNA double-strand breakage: methods of measurement and implications for radiation action models

There is considerable controversy over the form of the dose-response for DNA double-strand breakage (dsb) induction in mammalian cells by low-LET type radiation. This controversy centres on the techniques used for measuring DNA dsb. The applications and shortcomings of the four major techniques for estimating DNA size--sedimentation, viscoelastometry, electrophoresis, and non-denaturing filter elution--are examined. In particular, the criticisms of the results obtained using the non-denaturing filter elution technique, which have suggested that the DNA dsb dose-response is non-linear, are discussed. It is concluded that these results may require a re-evaluation of the basic assumptions of many radiation action models.

A simple model for DNA elution from filters

DNA chain scission, induced both in vitro and in vivo by various agents, is an event of great biological relevance. The damage is currently evaluated by empirical membrane separation techniques; the results are quite reproducible and the sensitivity higher than 1 single strand break per 10(9) Daltons. We outline a simple theory of the filtration of coiled macrosolutes, having a random size distribution, through porous membranes, considered as being in quasi-steady flow. The basic transport equation Jj = cj (1 - sigma)Jv is solved by considering that the value of sigma j, the reflection coefficient of component j, (1 less than or equal to j less than or equal to N), is given by (1 - KjRj), where Kj is the partition constant between pore and solution, a function of the conformational entropy loss of the coil, and Rj accounts for the frictional force experienced by a particle moving along the pore. The problem of evaluating the volume Vs filled up with solute has been approached according to a simplified theory of the excluded volume for flexible polymers; the result is Vs = sigma nj4/3 pi(rGj)3 where rGj is the jth radius of gyration. The solution of the resulting set of N differential equations gives nj, the number of molecules of component j remaining on the filter, as a function of the elution volume V. The theory demonstrates that the process is governed by the average dimensions of the coil, so affording a universal calibration of filter elution methods, in excellent agreement with the experiments.

Studies on DNA damage: discordant responses of rate of DNA disentanglement (viscosimetrically evaluated) and alkaline elution rate, obtained for several compounds. Possible explanations of the discrepancies

Alkaline elution is a well-known method for detecting DNA damage. Recently we have developed a viscosimetric method that is even more sensitive than alkaline elution. Here we report that the two methods, although apparently both revealing alkaline DNA fragmentation, can give dramatically different results for a significant series of compounds. We suspect that alkaline elution might reveal not only DNA fragmentation but also the extent of disentanglement of chromatin structure, whereas this DNA disentanglement rate, when evaluated viscosimetrically , is more strictly correlated with the initiation of DNA unwinding.