Computer analysis of Feulgen hydrolysis kinetics

Summary A least squares fit of Feulgen hydrolysis time curves to the Bateman function is performed using an especially adapted parameter transformation together with a standard conjugate gradients iteration procedure. The method has been applied to a large number of measured data, and the use and limits of the computer evaluation are discussed.     

Computer analysis of Feulgen hydrolysis kinetics.

A least squares fit of Feulgen hydrolysis time curves to the Bateman function is performed using an especially adapted parameter transformation together with a standard conjugate gradients iteration procedure. The method has been applied to a large number of measured data, and the use and limits of the computer evaluation are discussed.     

Comparative studies of Feulgen hydrolysis for DNA

Summary We compared the Feulgen hydrolysis curves (37° C, 5 M HCl) of human blood lymphocytes fixed by the following four methods: 96% ethanol, 60 min at 20° C; ethanol-acetone, 11, 120 min at 4° C; ethanolglacial acetic acid mixture (31), containing 2% of formaldehyde (EAF), 90 min at 20° C; and ethanol-glacial acetic acid (31), 60 min followed by 5% chrome alum solution for 360 min at 20° C. The best results were obtained with EAF-fixation, with respect to the highest amount of DNA-Schiff complex at the peak point of the curve, the longest plateau region and the smallest scattering of DNA-Schiff amount values along the plateau. With other types of fixation the addition of polyethylene glycol (PEG) 6,000 to the hydrolysis solution resulted in modification of the shape of the hydrolysis curve so that it became nearly similar to the EAF-curve. The effect of PEG₆₀₀₀ on the EAF-curve was minimal. Slides fixed by ethanol were used for a comparison of polyethylene glycols with m.w. 1,500, 6,000 and 20,000. The longest plateau was obtained with PEG₆₀₀₀. The only effect of PEG₁₅₀₀ was a dramatic increase of DNA-Schiff amount at the peak point. PEG₂₀₀₀₀ had no significant effect on the shape of the hydrolysis curve. The results are discussed in terms of Kjellstrand's chain with a stable structure model of Feulgen hydrolysis.     

Repetitive DNA and Feulgen hydrolysis kinetics in three species of Bufo.

Two North American species of the genus Bufo (Bufo cognatus and Bufo boreas, 2n = 22) and one African species (Bufo regularis, 2n = 20) were analyzed with respect to their repetitive DNA fractions and the behaviour of their chromatin to the acid hydrolysis at different times. The mean melting point of the total isolated DNA decreased from 89 degrees C to 87 degrees C with a genome size increase from 4.4 to 7.5 pg. The differences in genome size can only partly be explained on the basis of repetitive DNA fractions (renaturing up to Cot 10 in 0.12 M phosphate buffer). Several fractions in this repetitive range behave independently in the three species and the spectrum of repetitive fractions in the African Bufo regularis differs distinctly from those of the American toads. When fixed chromatin of these species in histochemical preparations is hydrolyzed with 5N HCl during the Feulgen reaction, the kinetics of depurination are equal in all species, while hydrolytic DNA breakdown proceeds distinctly more slowly in Bufo reularis as compared to the other species.     

A study of DNA depolymerisation during Feulgen acid hydrolysis.

The binding of Schiff dye molecules after acid hydrolysis (1 M HCl) for varying lengths of time was studied in ascites tumour cells. The amount of dye bound to the tumour cells closely followed the number of aldehyde groups, calculated from the extraction of radioactive nucleotides. This constant dye to aldehyde ratio did not change when the hydrolysis was performed at a lower acid concentration (0.3 M HCl). The conclusion drawn is that Feulgen dye measurements represent, in a constant way, the number of aldehydes on DNA at any given time during hydrolysis. The alteration of the hydrolysis pattern of chromatin fixed in formalin was found to be due to a slower extraction of DNA depolymerisation products, the purine liberation being unaffected. A similar explanation is offered for the extreme pattern obtained from hydrolysis of bull spermatozoa chromatin.     

Quantitative detection of DNA damage in the neuronal cells of the cerebellum and cerebrum by the analysis of Feulgen hydrolysis curves

Touch smears of the cerebellum and cerebrum of ageing rats were fixed with methanol, hydrolyzed with 2 N HCl at various temperatures and for various periods, and stained with pararosaniline-Schiff reagent. The hydrolysis curves were determined by fluorescence cytophotometry and were computer fitted to the Bateman function to determine the kinetic parameters, the initial yield of apurinic acid or single-stranded DNA (y0), and the rate constants for depurination or denaturation (k1) and depolymerization (k2). The values for k1 (1/k1 is correlated with the degree of chromatin condensation) and k2 (which reflects the degree of DNA instability) steadily increased with age. The values for y0, which may indicate the degree of DNA denaturation or damage present before acid hydrolysis, also increased with age in both the cerebellum and cerebrum; however, this value was lower in the cerebellum until 15 weeks, with the situation being reversed after 35 weeks, the cross-over time being at about 25 weeks. The values of lnk1 and lnk2 were plotted as the function of the reciprocal of the absolute temperature (T) (Arrhenius plot) for both the cerebellum and cerebrum of 15- and 74-week-old rats, and the activation energies (E) for depurination and depolymerization were calculated from the slopes. In particular, the values of E for k2 decreased much more quickly with age and were smaller in cerebellum. In conclusion, the degree of DNA damage and DNA instability steadily increases in both the cerebellum and cerebrum of ageing rats, and this process is much faster in the cerebellum.     

Quantitative detection of DNA damage in the neuronal cells of the cerebellum and cerebrum by the analysis of Feulgen hydrolysis curves

Summary Touch smears of the cerebellum and cerebrum of ageing rats were fixed with methanol, hydrolyzed with 2N HCl at various temperatures and for various periods, and stained with pararosaniline-Schiff reagent. The hydrolysis curves were determined by fluorescence cytophotometry and were computer fitted to the Bateman function to determine the kinetic parameters, the initial yield of apurinic acid or single-stranded DNA (y ₀), and the rate constants for depurination or denaturation (k ₁) and depolymerization (k ₂). The values for k ₁ (1/k ₁ is correlated with the degree of chromatin condensation) and k ₂ (which reflects the degree of DNA instability) steadily increased with age. The values for y ₀, which may indicate the degree of DNA denaturation or damage present before acid hydrolysis, also increased with age in both the cerebellum and cerebrum; however, this value was lower in the cerebellum untill 15 weeks, with the situation being reversed after 35 weeks, the cross-over time being at about 25 weeks. The values of lnk ₁ and lnk ₂ were plotted as the function of the reciprocal of the absolute temperature (T) (Arrhenius plot) for both the cerebellum and cerebrum of 15- and 74-week-old rats, and the activation energies (E) for depurination and depolymerization were calculated from the slopes. In particular, the values of E for k ₂ decreased much more quickly with age and were smaller in cerebellum. In conclusion, the degree of DNA damage and DNA instability steadily increases in both the cerebellum and cerebrum of ageing rats, and this process is much faster in the cerebellum.In honour of Prof. P. van Duijn     

Factors affecting the course of DNA acid hydrolysis in carrying out the Feulgen reaction]

Literature data concerning acid hydrolysis of DNA during the Feulgen procedure are reviewed, with emphasis being made on the dependence of Schiff-apurinic acid binding on the fixation technique, the temperature of hydrolysis and acid concentration, the rate of extraction of depolymerized DNA fragments, the nucleotide composition of DNA, the chromatin state, and on the composition of nucleoprotein. Some practical considerations for optimization of the Feulgen procedure for a precise quantitative determination of DNA amount are given.     

The effect of sodium chloride on the extraction of DNA fragments during Feulgen acid hydrolysis

Synopsis Feulgen acid hydrolysis was performed on ascites tumour cells labelled with radioactive DNA-precursors. The development of fragments of apurinic acid and the extraction of purines were studied by monitoring the variations in the extraction rate during the hydrolysis when sodium chloride was either present or absent from the hydrolysis solution. The changes in the rate of extraction of purines and the alterations in the initial retardation of the apurinic acid extracting process followed approximately the same pattern. The extractability of apurinic acid fragments during hydrolysis in 0.3m HCl was found to be a maximum when the sodium chloride concentration was about 1m. Sudden exchange experiments, in which acid was substituted for sodium chloride after various times of hydrolysis, revealed a successive shortening of the extractable fragments during the low acid concentration hydrolysis. The results strengthen the view that, during hydrolysis, apurinic acid is lost from the cells through a reaction whose form is determined, first, by an initial retardation of the depolymerization, second, by the maximum length at which fragments developed through the depolymerization become soluble and are lost by diffusion, and last, at low acid concentrations, by a mechanism whose influence is equivalent to the presence of bonds between the fragments and an unextractable stable structure.     

Comparative studies of Feulgen hydrolysis for DNA. I. Influence of different fixatives and polyethylene glycols

We compared the Feulgen hydrolysis curves (37 degrees C, 5 M HCl) of human blood lymphocytes fixed by the following four methods: 96% ethanol, 60 min at 20 degrees C; ethanol-acetone, 1:1, 120 min at 4 degrees C; ethanol-glacial acetic acid mixture (3:1), containing 2% of formaldehyde (EAF), 90 min at 20 degrees C; and ethanol-glacial acetic acid (3:1), 60 min followed by 5% chrome alum solution for 360 min at 20 degrees C. The best results were obtained with EAF-fixation, with respect to the highest amount of DNA-Schiff complex at the peak point of the curve, the longest "plateau" region and the smallest scattering of DNA-Schiff amount values along the "plateau". With other types of fixation the addition of polyethylene glycol (PEG) 6,000 to the hydrolysis solution resulted in modification of the shape of the hydrolysis curve so that it became nearly similar to the EAF-curve. The effect of PEG6000 on the EAF-curve was minimal. Slides fixed by ethanol were used for a comparison of polyethylene glycols with m.w. 1,500, 6,000 and 20,000. The longest "plateau" was obtained with PEG6000. The only effect of PEG1500 was a dramatic increase of DNA-Schiff amount at the peak point. PEG20000 had no significant effect on the shape of the hydrolysis curve. The results are discussed in terms of Kjellstrand's "chain with a stable structure" model of Feulgen hydrolysis.     

Kinetics of DNA alkylation, depurination and hydrolysis of anti diol epoxide of benzo(a)pyrene and the effect of cadmium on DNA alkylation

Anti benzo[a]pyrene diol epoxide (BPDE) alkylates guanines of DNA at N7 in the major groove and at the exocyclic amino group in the minor groove. In this report we investigated the rates of BPDE hydrolysis, DNA alkylation and subsequent depurination of BPDE-adducted pBR322 DNA fragment using polyacrylamide gel electrophoresis. Preincubation studies showed that it hydrolyzed completely in triethanolamine buffer in <2 min. The depurination kinetics showed that a fraction of the N7 alkylated guanine depurinated rapidly; however a significant amount of N7 guanine alkylation remained stable to spontaneous depurination over a 4-h period. Similar results were obtained for the hydrolysis and alkylation rates of syn isomer but it required nearly 500 times more concentration to induce similar levels of N7 guanine alkylation. Cadmium ion strongly inhibited the N7 guanine alkylation of both isomers. But the minor groove alkylation was not affected as demonstrated by postlabeling assay which confirmed the presence of heat-and cadmium-stable minor groove adducts in BPDE-treated calf thymus DNA. Based on these and our earlier findings, we propose a mechanism for the synergistic effect of cadmium in chemically induced carcinogenesis.     

Feulgen hydrolysis and chromosome banding in Chilocorus (Coleoptera: Coccinellidae).

Prolonged Feulgen hydrolysis of chromosomes of Chilocorus orbus Csy. and C. stigma Say produces banding patterns that are the reverse of those revealed with quinacrine; brightly fluorescing regions are unstained, but nonfluorescent regions remain relatively darkly stained. This differential reactivity at hydrolysis times that otherwise yield intense Feulgen staining confirms the need for caution in the determination of DNA values with the Feulgen reaction in material with well-defined quinacrine bands. The coincidence of DNA-specific Feulgen bands with Q-, G-, and C-bands supports the view that, in Chilocorus at least, bands reflect differences in DNA composition along the chromosome.     

Acid hydrolysis characteristics of spleen colony cells under Feulgen staining

A cytophotometrical determination of DNA content was performed in cells of murine spleen colonies originating from bone marrow and in lymphocytes of axillary lymph nodes under various temperatures (22, 25 and 37 degrees C) of hydrolysis (5N HCl). It is shown that acid hydrolysis at 20 and 25 degrees C is most-preferable for proliferated cells of spleen clones and for non-proliferated lymphocytes. It is concluded that hydrolysis curves for clonal cell nuclei in different phases of mitotic cycle practically coincided.     

Temperature and acid concentration in the search for optimum Feulgen hydrolysis conditions.

Exposure and removal of aldehyde groups during Feulgen acid hydrolysis were studied at a wide range of temperature and acid concentrations. Temperatures between 9 and 75degreesC were found to influence only the rate of the hydrolysis reaction over the entire range from high (6 M) to low (0.05 M) HCl concentrations. The temperature dependence was high, and around +5degreesC was sufficient to double the reaction rate. The influence of acid concentrations between 0.02 and 6 M was studied, and the extraction rates that determine the peak values of the Feulgen hydrolysis curve were found to depend in the same way on the (H+) concentration. A diagram is given that makes it possible to determine the time to reach the point during hydrolysis where the maximum amount of aldehyde groups are developed for a wide range of temperatures and acid concentrations. Temperatures slightly above room temperature in combination with high acid concentration is recommended for Feulgen hydrolysis.     

Effects of depurination on the fidelity of DNA synthesis.

The effect of depurination of polynucleotide templates on the fidelity of DNA synthesis in vitro has been determined. The fidelity of DNA synthesis with Escherichia coli DNA polymerase I, avian myeloblastosis virus DNA polymerase and human placenta DNA polymerase-β is decreased as a result of depurination of the poly[d(A-T)], poly[d(G-C)]and poly[d(A)]templates. The error rate with poly[d(A-T)]increased from $\text{1}\text{17,500}$ to $\text{1}\text{2100}$ using E. coli Pol I, and from $\text{1}\text{4100}$ to $\text{1}\text{1500}$ using the myeloblastosis virus DNA polymerase. Depurination of poly[d(A)]increased the error rate from $\text{1}\text{21,000}$ to $\text{1}\text{6500}$ using E. coli Pol I, and from $\text{1}\text{19,300}$ to $\text{1}\text{6100}$ using the DNA polymerase-β from human placenta. Depurination of poly[d(G-C)]resulted in an increase in the error rate with E. coli Pol I from $\text{1}\text{9200}$ to $\text{1}\text{2200}$, and with the virus DNA polymerase from $\text{1}\text{2400}$ to $\text{1}\text{1300}$. This misincorporation is shown to be directly proportional to the extent of depurination. Deletion experiments and alkaline sucrose gradient analyses suggest that the incorporation of complementary and non-complementary nucleotides is dependent on polymerization, and occurs in the same newly synthesized product. Kinetic studies and nearest-neighbor analyses indicate that the incorporation of non-complementary nucleotides occurs randomly as single-base substitutions. The nearest-neighbor studies also suggest that any of the four deoxynucleotides can be incorporated opposite apurinic sites. The number of each nucleotide incorporated relative to the number of apurinic sites was determined to be $\text{1}\text{490}$ for dGTP, $\text{1}\text{115}$ for dCTP, $\text{1}\text{2·5}$ for dATP and $\text{1}\text{1·7}$ for dTTP with both the poly[d(A-T)] and poly[d(A)] templates. The frequencies of misincorporation relative to the number of apurinic sites with the poly[d(G-C)]template were $\text{1}\text{230}$ for dATP, $\text{1}\text{120}$ for dTTP, $\text{1}\text{2·4}$ for dGTP and $\text{1}\text{1·8}$ for dCTP. Hydrolysis at the apurinic sites by alkali treatment reversed the effects of depurination on fidelity. The error rates with the depurinated templates were reduced to within 2% of those obtained prior to depurination, providing additional evidence that the misincorporation after depurination results from apurinic sites on the template. These results suggest a possible relationship between depurination of DNA and errors in DNA replication and/or repair.