Correction of the ultraviolet light induced DNA-repair defect in xeroderma pigmentosum cells by electroporation of a normal human endonuclease

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The construction of an individually addressable cell array for selective patterning and electroporation

In basic cell biology research and drug discovery, it is important to rapidly introduce genes, proteins or drug compounds into cells without permanent damage. Here, we report a three dimensional SU-8 micro-well structure sandwiched with an indium tin oxide (ITO) electrode-covered slide from the top and an individually addressable array of microelectrodes on the bottom to allow parallel delivery of exogenous molecules into various cells in a spatially specific manner. A positive dielectrophoretic force was selectively applied by energizing appropriate electrodes to capture the dispersed cells at the bottom electrode, while the micro-wells were designed to confine cells in situ when the positive dielectrophoretic force is removed. The combination of spatial positive dielectrophoresis (pDEP) and micro-wells made it possible to construct cell microarrays with specific patterns. Once the cells become attached to the electrodes, different plasmids can be introduced sequentially for selective electroporation. The present cell arraying-assisted electroporation chip integrates a pDEP-assisted cell positioning function with selective electroporation to provide a simple and efficient method for gene transfer. This platform is ideal for high throughput screening of compounds in parallel and thus holds promise for applications in cellular and molecular research.

Damage-resistant DNA synthesis in Fanconi anemia cells treated with a DNA cross-linking agent

Fanconi anemia (FA) is a recessive disorder associated with diverse congenital anomalies, progressive bone marrow failure, and a marked predisposition to develop cancer. At the cellular level, FA is characterized by a prolonged G(2) phase in proliferating cells and a marked hypersensitivity to both the cytotoxic and the clastogenic effects of agents which produce DNA interstrand cross-links. Treatment with these agents leads to even further prolongation of the G(2) phase in FA cells. We now show that FA cells, from four different complementation groups, fail to decrease their rates of replicative DNA synthesis, as do normal cells, following treatment with a DNA cross-linking agent. This may be responsible for the prolongation of the G2 phase seen in these cells, and suggests that the fundamental defect in response of FA cells to DNA cross-linking agents may be in the S phase, rather than the G(2) phase, of the cell cycle.

DNA repair and chromatin structure in genetic diseases

Interaction of DNA repair proteins with damaged DNA in eukaryotic cells is influenced by the packaging of DNA into chromatin. The basic repeating unit of chromatin, the nucleosome, plays an important role in regulating accessibility of repair proteins to sites of damage in DNA. There are a number of different pathways fundamental to the DNA repair process. Elucidation of the proteins involved in these pathways and the mechanisms they utilize for interacting with damaged nucleosomal and nonnucleosomal DNA has been aided by studies of genetic diseases where there are defects in the DNA repair process. Two of these diseases are xeroderma pigmentosum (XP) and Fanconi anemia (FA). Cells from patients with these disorders are similar in that they have defects in the initial steps of the repair process. However, there are a number of important differences in the nature of these defects. One of these is in the ability of repair proteins from XP and FA cells to interact with damaged nucleosomal DNA. In XP complementation group A (XPA) cells, for example, endonucleases present in a chromatin-associated protein complex involved in the initial steps in the repair process are defective in their ability to incise damaged nucleosomal DNA, but, like the normal complexes, can incise damaged naked DNA. In contrast, in FA complementation group A (FA-A) cells, these complexes are equally deficient in their ability to incise damaged naked and similarly damaged nucleosomal DNA. This ability to interact with damaged nucleosomal DNA correlates with the mechanism of action these endonucleases use for locating sites of damage. Whereas the FA-A and normal endonucleases act by a processive mechanism of action, the XPA endonucleases locate sites of damage distributively. Thus the mechanism of action utilized by a DNA repair enzyme may be of critical importance in its ability to interact with damaged nucleosomal DNA.

Quantification of XPA gene expression levels in human and mouse cell lines by competitive RT-PCR

Expression of the mammalian photoproduct-specific DNA-binding protein XPA has been quantified by competitive reverse transcription-polymerase chain reaction, a method that provides relative numbers of mRNA molecules per cell. Human primary and simian virus (SV)40-transformed fibroblasts had 4.8 and 8.4 transcripts per cell, respectively; mouse embryonic and SV40-transformed fibroblasts had 6.7 and 5.5 transcripts per cell, respectively. None of these differences are significant, and the mean value of 5 to 8 transcripts per cell indicates that XPA is expressed as a low-abundance mRNA. Two cell lines transfected with XPA on a conditional promoter showed different numbers of XPA mRNA molecules, consistent with their respective responses to an inducer and their sensitivity to ultraviolet light. The similarity of results in human and mouse cells shows that a difference in XPA expression cannot account for the greater repair of nontranscribed DNA in human cells.

Human endonucleolytic incision of DNA 3' and 5' to a site-directed psoralen monoadduct and interstrand cross-link

Human chromatin-associated protein extracts were examined for endonucleolytic activity on a defined 132-base pair DNA substrate containing a single, site-specific 4,5'-8-trimethylpsoralen plus long wavelength ultraviolet light-induced furan side or pyrone side monoadduct or interstrand cross-link. These extracts produced incisions on both the 3' and 5' sides of each of these lesions. The distance between the 3' and 5' incisions at sites of a furan side monoadduct or cross-link was 9 nucleotides, and at sites of a pyrone side monoadduct or cross-link it was 17 nucleotides. Incisions on the 3' side of both types of furan side and pyrone side adducts were similar and were either at the fourth or fifth phosphodiester bond from the adducted thymine, depending upon the adduct. However, greater differences were observed between sites of 5' incision. This incision occurred at the fifth and sixth phosphodiester bonds from the adducted thymine at sites of furan side monoadducts and cross-links, respectively, and at the 13th and 14th phosphodiester bonds at sites of pyrone side monoadducts and cross-links, respectively. Thus, direct analysis of sites of endonucleolytic incision reveals that the location of sites of incision on TMP-adducted substrates depends upon the type of adduct present.

Mutation and expression of the XPA gene in revertants and hybrids of a xeroderma pigmentosum cell line

A series of ultraviolet (UV)-resistant cell lines have been generated from a UV-sensitive XP group A cell line homozygous for a stop codon (TGA) in the chromosome 9 XPA gene. Three lines generated by chemical mutagenesis acquired the ability to excise (6-4) photoproducts but not cyclobutane dimers from the whole genome; two lines generated by a fusion procedure with hamster cells acquired the ability to excise both (6-4) photoproducts and cyclobutane dimers from the whole genome. A central region of the hamster XPA gene was cloned and sequenced. With the use of species-specific primers in the polymerase chain reaction, we found that the hybrid cell lines do not contain a hamster XPA gene. Sequence analysis showed that all of the UV-resistant cell lines contain reversions of the human stop codon, resulting in missense mutations (glycine or leucine for arginine) or wild-type sequences. The concentration of XPA protein in revertant cell lines was about one-half that in normal cells, which would be expected from heterozygous cells; there was no evidence that the mutant proteins were less stable than the wild-type proteins. These results are consistent with the idea that the XPA protein initiates repair by binding to damaged sites with various affinities, depending on the photoproduct and the transcriptional state of the region. A concentration of XPA protein near 50% is needed before repair can proceed into nontranscribed regions of the genome. The revertant cell lines represent a class of missense mutations in the XPA gene that may have altered specificity and that can be used to understand some of the regulatory differences in repair of photoproducts in various regions of the genome.

Cell electropermeabilization: a new tool for biochemical and pharmacological studies

Cell electropermeabilization is the transient permeabilization of the plasma membrane by means of short and intense electric pulses. Under optimized conditions, electropermeabilization is compatible with cell survival. It provides a direct access into the cytosol to ions, small molecules, exogenous drugs and macromolecules. As cells remain functional, a large variety of cell biology questions can be addressed. Such 'in situ biochemistry' opens new possibilities beside the more classical studies dealing with unpermeabilized cells or subcellular extracts. Electropermeabilization also allows pharmacological studies with cells, cultured monolayers and in vivo tissues as well as the design of drug controlled-release systems.

Co-recessive inheritance: A model for DNA repair and other surveillance genes in higher eukaryotes

The co-recessive inheritance hypothesis proposes that certain recessively inherited diseases require homozygosity and/or hemizygosity for defective alleles at more than one locus simultaneously for the trait to be expressed. Although this hypothesis was originally proposed in the context of defective alleles for genes coding for DNA-repair functions, it need not be limited to this context, and genetic selection pressure may favor this model for genes involved in surveillance of any type. The co-recessive inheritance hypothesis also predicts extremely high carrier frequencies, likely affecting much of the general population, for defective alleles associated with these rare recessive diseases. The model predicts much lower rates of consanguinity between the parents of affected individuals than autosomal recessive inheritance, allowing it to be tested epidemiologically, and recent data suggest that the hypothesis may be valid for some cases of ataxia telangiectasia and xeroderma pigmentosum. The model provides possible explanations for a number of otherwise puzzling findings in several diseases associated with defective DNA repair.