Measurement of DNA mismatch repair activity in live cells

Loss of DNA mismatch repair (MMR) function leads to the development and progression of certain cancers. Currently, assays for DNA MMR activity involve the use of cell extracts and are technically challenging and costly. Here, we report a rapid, less labor-intensive method that can quantitatively measure MMR activity in live cells. A G–G or T–G mismatch was introduced into the ATG start codon of the enhanced green fluorescent protein (EGFP) gene. Repair of the G–G or T–G mismatch to G–C or T–A, respectively, in the heteroduplex plasmid generates a functional EGFP gene expression. The heteroduplex plasmid and a similarly constructed homoduplex plasmid were transfected in parallel into the same cell line and the number of green cells counted by flow cytometry. Relative EGFP expression was calculated as the total fluorescence intensity of cells transfected with the heteroduplex construct divided by that of cells transfected with the homoduplex construct. We have tested several cell lines from both MMR-deficient and MMR-proficient groups using this method, including a colon carcinoma cell line HCT116 with defective hMLH1 gene and a derivative complemented by transient transfection with hMLH1 cDNA. Results show that MMR-proficient cells have significantly higher EGFP expression than MMR-deficient cells, and that transient expression of hMLH1 alone can elevate MMR activity in HCT116 cells. This method is potentially useful in comparing and monitoring MMR activity in live cells under various growth conditions.     

Comparison of three DNA fluorochromes for flow cytometric estimation of nuclear DNA content in plants

Flow cytometric estimation of nuclear DNA content was performed in six plant species employing three fluorochromes showing different DNA base preferences: propidium iodide (no base preference), 4',6-diamidino-2-phenylindole (DAPI; AT preference), and mithramycin (GC preference). Nuclei isolated from human leukocytes were used as a primary reference standard. While nuclear DNA contents estimated using propidium iodide were in agreement with published data obtained using other techniques, the values obtained using fluorochromes showing base preference were significantly different. It was found that the differences were caused by the differences in overall AT/GC ratios, and by the species-specific differences in binding of these fluorochromes to DNA. It was concluded that nuclear DNA content estimations performed with fluorochromes showing base preference should be interpreted with caution even when AT/GC ratios of the reference and the sample are equal. The use of intercalting dyes (e.g. propidium iodide) is recommended for this purpose. On the other hand, comparison of the staining behaviour of intercalating dyes with that of dyes showing base preference may give additional information on chromatin structural differences and arrangement of molecule pairs in DNA.     

Labelling of live cells using fluorescent aptamers: binding reversal with DNA nucleases

A reversible cell labelling method has been developed for non-destructive and non-invasive cell labelling and purification. Our method uses high affinity single strand DNA (ssDNA) aptamers against surface exposed target molecules on cells. The aptamers are subsequently removed from the cell surface using DNase nuclease treatment. We exemplified our method by labelling human acute lymphoblastic leukemia cells with Qdot-ssDNA aptamers, and restoring them to the label-free condition by treatment with Benzonase. Binding of the fluorescent-aptamers to the cells was evaluated by measuring fluorescence intensity and was further confirmed using flow cytometry. Removal of the aptamers can be achieved in ~10 min by the DNase nuclease digestion. Incubation of cells with aptamers or with the nucleases results in no apparent damage to the cells and does not affect their growth rates. The latter were equivalent to the rates measured for the untreated cells. Our method provides an alternative to traditional antibody-based techniques and could be especially suitable for non-invasive reversible cell labelling and cell separations where maintaining native cell activity is needed.     

Measurement of DNA damage in mammalian cells using flow cytometry

A technique for the detection of DNA damage induced by radiation insult has been developed. Cells were lysed with a buffer containing 2 M sodium chloride to release the DNA in a supercoiled form, the nucleoid. These were stained with the DNA intercalating dye, ethidium bromide, and exposed to laser light within a flow cytometer. Scattered and fluorescent light was analyzed from the laser/nucleoid interaction following irradiation of viable cells with gamma rays. The addition of ethidium bromide to prepared nucleoids caused a reduction in scattered light due to condensation of the nucleoid. Irradiation of cells prior to nucleoid production and ethidium bromide treatment restricted this condensation and produced a dose-dependent increase in laser scatter. Nucleoids derived from human lymphocytes showed enhanced light scatter from 5 Gy, compared to Chinese hamster ovary (CHO) fibroblasts where doses above 10 Gy were required. Up to 30 Gy CHO nucleoids showed a dose-dependent reduction in the ethidium bromide fluorescence. This technique allows detection of altered light scattering and fluorescent behavior of nucleoids after cellular irradiation; these may be related to structural changes within the nucleus induced by the radiation. The use of flow cytometry compared to other methods allows a rapid analysis of nuclear damage within individual cells.     

Unstainable DNA in cell nuclei. Comparison of ten different fluorochromes

Ten fluorochromes with specificity for DNA were used to compare the stainability of nuclei of exponentially growing, nondifferentiated Friend leukemia (FL) cells with that of dimethylsulfoxide-induced, fully differentiated FL cell nuclei. Decreased accessibility of DNA to several dyes, particularly pronounced in the case of some intercalators, was observed in differentiated cells. Dye binding was also compared for both sets of nuclei following extraction of nuclear proteins, mostly histones, with 0.1-N HCl. Acid extraction of nuclear proteins increased the accessibility of DNA to varying degrees, depending upon the fluorochrome. In most cases, the differences in fluorescence between differentiated and nondifferentiated nuclei stained with most intercalating dyes was abolished by acid treatment. The results are discussed in terms of the mode of interaction between DNA and the various fluorochromes and the factors associated with chromatin structure, which may affect or be associated with different degrees of proliferative activity.     

Efficient expression of an Epstein-Barr nuclear antigen in Drosophila cells transfected with Epstein-Barr virus DNA.

In a search for exogenous promoters which function in cultured Drosophila cells, we have co-transfected a D. melanogaster cell line with an Epstein-Barr virus (EBV) cosmid clone which encodes the Epstein-Barr nuclear antigen (EBNA-1). Here we report that Drosophila cells containing stably integrated copies of EBNA-1 encoding DNA synthesise a polypeptide of mol. wt. identical to that of authentic EBNA-1, which is detectable with EBNA-positive but not EBNA-negative human serum. As in EBV-transformed lymphoblastoid cells, this neo-antigen is associated with the nucleus of transfected cells suggesting that cellular localisation signals which operate in mammalian cells are also recognised in insect cells.     

DNA sequencing of four bases using three lanes.

A three-lane DNA sequencing strategy is described which is based on redundant binary coding principles from communications theory. Three-lane sequencing is an efficient, accurate, and flexible strategy, suitable for large-scale automated DNA sequencing. Communications theory and algebraic coding principles can also be applied to sequencing other informational macromolecules.     

Hepatitis B surface antigen expression in NT-1 cells of tobacco using different expression cassettes

Nicotiana tabacum 1 (NT-1) cells were transformed with four different expression cassettes of hepatitis B surface antigen (HBsAg). The transformed nature of the cells was confirmed by polymerase chain reaction (PCR). The expression levels were assayed by enzyme linked immunosorbent assay (ELISA). The expressivities varied among the different cassettes and the maximum expression of 16.6 ng g⁻¹(f.m.) of cells was noted in pEFEHER transformed cells. Salicylic acid (100 μM) treatment resulted in 1.8 fold increase of expression in pEFEHBS transformed cells. The effect of different concentrations of kanamycin and geneticin was studied on the growth of transformed cells and HBsAg expression. The cell growth was optimum at lower concentrations of the antibiotics, and the maximum expression was noted at 200 mg dm⁻³ of kanamycin.     

Use of caged fluorochromes to track macromolecular movement in living cells.

One way to visualize and track the movement of macromolecules in the living cell is to follow their movement after tagging the molecule with a 'caged' or chemically masked fluorochrome. The fluorochrome does not fluoresce until the caging group is released by spot photoactivation, and the bright fluorescent signal can then be tracked as it moves into the dark surrounding area of the cell. When coupled with rapid imaging microscopy, it is possible to measure rates of movement as fast as macromolecular diffusion. This article describes the use of photoactivatable fluorochromes to track the intracellular movement of both proteins and nucleic acids and to track cell lineages.     

Studies of three Amerindian populations using nuclear DNA polymorphisms.

Three Amerindian populations, two from Rond?nia, Brazil (Karitiana and Rond?nia Suruí), and one from Campeche, Mexico (Mayan), were typed for up to 30 nuclear restriction fragment length polymorphisms (RFLPs). Heterozygosities, both observed and expected, were compared with those of Europeans. Average heterozygosity is reduced among these Amerindians (relative to that of Europeans) by 7.0% (Mayan) to 27.1% (Karitiana). This amount of heterozygosity in the nuclear DNA is nevertheless high enough that it is unlikely that there was a severe or prolonged bottleneck.     

DNA sequence analysis of the C4 antigen WH: evidence for two mechanisms of expression

 Amino acid and protein analyses have allowed the construction of a model for the C4-based Rodgers and Chido blood group antigens. The single low-frequency allele (WH) in this blood group system, however, has not been characterized at the molecular level. Two WH⁺ donors were studied by C4 agarose gel electrophoreses, immunoblot studies using monoclonal anti-Rg: 1 or anti-Ch: 1, serological phenotyping, polymerase chain reaction-restriction fragment length polymorphism of their C4 genes, and DNA sequencing of the WH allele. The first donor had the C4A1, A3 phenotype; the C4A1 carried Ch: 1, 3, 6 (thus exhibiting reversed antigenicity) and the C4A3 carried the WH antigen. The amino acid sequence of the WH allele was PCPVLD at positions 1101 – 1106, S at position 1157, and VDLL at positions 1188 – 1191. A second donor typed as C4A2, A4, B1 and was also WH⁺. Immunoblot analysis showed that a C4B1 protein expressed Rg: 1. Sequence analysis of the C4B genes showed the amino acids LSPVIH at positions 1101 – 1106, S at position 1157, and ADLR at positions 1188 – 1191. Thus, the WH antigen is a conformational epitope that can arise through different mechanisms on either a C4A or C4B gene. Received: 22 November 1995 / Revised: 19 February 1996     

DNA stainability in aneuploid breast tumors: comparison of four DNA fluorochromes differing in binding properties.

The aim of this study was to evaluate whether or not the differences in chromatin structure between diploid stromal cells or lymphocytes, which are often used as DNA ploidy standard, and aneuploid breast tumor cells can significantly affect the estimates of the DNA index of these tumors. To this end, the DNA content estimates of 34 aneuploid breast tumors, differing in size, degree of differentiation, and presence or absence of estrogen and progesterone receptors and metastases, were compared using four common DNA fluorochromes: DAPI, Hoechst 33342, propidium iodide, and acridine orange. These dyes differ in their mode of interaction with DNA (binding to minor groove or intercalation) and for each of them binding to DNA is restricted to a different degree by nuclear proteins. It was expected, therefore, that if differences in chromatin structure play a role in DNA content estimates, the DNA index of the measured tumors may vary depending on the dye. The cell nuclei were isolated from the tumors using a detergent-based procedure and stained with each of the dyes and the DNA index was estimated using peripheral blood lymphocytes as a DNA content standard. For each of the tumors, the DNA index estimates with all four dyes correlated very well. When the results obtained with individual dyes were compared in pairs, the correlation coefficients (r) of DNA indices were all above 0.96 (correlation at p less than 0.001). The best concordance was seen between specimens stained with Hoechst 33342 and DAPI (r = 0.99), and the least between those stained with Hoechst 33342 and propidium iodide (r = 0.96). The data indicate that DNA content analysis of unfixed nuclei, utilizing the above fluorochromes, is not significantly biased by differences in chromatin structure of the measured cells.     

Tracking molecular particles in live cells using fuzzy rule-based system.

Recent development of detection techniques of molecular particles in live cells has stimulated interest in developing the new powerful techniques to track the molecular particles in live cells. One special type of cellular microscopy images is about the formation and transportation of clathrin-coated pits and vesicles. Clathrin-coated pits are very important in studying the behavior of proteins and lipids in live cells. To answer the question, whether there exist "hot spots" for the formation of Clathrin-coated pits or the pits and arrays formed randomly on the plasma membrane, it is necessary to track many hundreds of individual pits dynamically in live-cell microscope movies to capture and monitor how pits and vesicles were formed. Therefore, a motion correspondence algorithm based on fuzzy rule-based system is proposed to resolve the problem of ambiguous association encountered in these dynamic, live-cell images of clathrin assemblies. Results show that this method can accurately track most of the particles in the high volume images.     

New fluorescence reactions in DNA cytochemistry. 1. Microscopic and spectroscopic studies on nonrigid fluorochromes

Some nonrigid DNA-binding antibiotics and fluorochromes that recognize adenine-thymine (AT) sequences are widely applied in biomedical research, but the microscopic use, spectral characteristics and DNA binding modes of other similar compounds have been overlooked or scarcely explored. After treatment with thioflavine T, auramine O and G, curcumin, bis-aminophenyl-oxadiazol, berenil and distamycin A, a bright DNA-dependent fluorescence reaction was found in the chromatin of interphase nuclei, meiotic and polytene chromosomes, spermatozoa heads and kinetoplasts of Trypanosoma cruzi epimastigotes. Nucleoli and basophilic cytoplasm showed low or no fluorescence; the highest emission occurred in the AT-rich kinetoplast DNA. When bound to DNA or in the presence of alpha-cyclodextrin and viscous solvents or cosolutes, nonrigid compounds revealed a striking enhancement of fluorescence. The results indicate that these new or poorly known fluorochromes bind selectively to DNA-containing structures and that the minor groove from AT-rich DNA regions could represent the specific and highly fluorescent binding site.     

Evaluation of DNA vaccination with recombinant adenoviruses using bioluminescence imaging of antigen expression: impact of application routes and delivery with dendritic cells

Recombinant DNA vaccines are able to induce strong CD8+ T cell mediated immunity and have become increasingly attractive for the prevention and treatment of infectious diseases and cancer. Dendritic cells (DC), which critically control cellular immune responses, have been transduced with antigen ex vivo and used as 'nature's adjuvant' to enhance vaccine efficacy. The impact of the application route on the in vivo distribution of antigen and the stimulation of CD8+ T cells have been subjects of considerable debate. Here we report the construction of vectors expressing a fusion protein between EGFP, the H2-K(b)-binding peptide OVA(aa257-264) and green click beetle luciferase as a model antigen which allows for simultaneous quantitative assessment of antigen expression using fluorescence and bioluminescence imaging in correlation with CD8+ T cell stimulation in vivo. We applied this construct to evaluate DNA vaccination with recombinant adenoviral vectors, assess the impact of using cultured DC for vaccine delivery and investigate different application routes. Antigen expression was non-invasively followed in vivo by visualizing bioluminescence with an ultrasensitive CCD camera. CD8+ T cell stimulation was detected with H2-K(b)-OVA(aa257-264) tetramers. We found that intravenous injection of adenovirus-transduced DC stimulated the strongest OVA(aa257-264)-specific cytotoxic T-lymphocyte (CTL) responses although it delivered two orders of magnitude less antigen in vivo when compared to direct injection of recombinant adenovirus. We believe that our experimental approach has the potential to facilitate translational development of improved genetic immunization strategies targeting DC directly in vivo.     

DNA profiling in a genetically isolated population using three hypervariable DNA markers.

We determined the allele frequencies for three hypervariable DNA loci D2S44, D1S7 and D7S21 using the probes YNH24, MS1 and MS31 in the genetically isolated Finnish population. The allelic length ranges were 1.7- < 6.0 kb for YNH24, 1.7- < 18.0 kb for MS1 and 3.2- < 12.0 kb for MS31. High heterozygosity rates (0.94-0.96) were detected for all three probes. In 48 mother-child pairs no mutations were found using the probes YNH24 and MS31, whereas a mutation rate of 0.064 was observed for probe MS1. In addition, an unexpected four-band pattern was detected in 1 out of 170 individuals using the probe MS1, suggesting complex DNA polymorphism based on both a variable number of tandem repeats and restriction site polymorphism. Our findings also show that all three probes are valuable in individual identification in this genetically isolated population.