DNA Fragments In Agarose Gels Research Articles

Analysis of genotyping features of bovine cattle individuals at the CSN2 locus using ACRS-PCR methods

In the context of solving the problem of obtaining high quality dairy products from livestock, the issue of determining the type of beta-casein (A1 and A2) in the protein fraction of milk becomes essential. Purpose – to analyse the use of ACRS-PCR methods for differentiation of A1 and A2 alleles of bovine beta-casein locus. Genotyping features were analysed using the artificially created restriction site polymerase chain reaction method utilising TaqI and DdeI restriction endonucleases. The electrophoretic distribution of DNA fragments in agarose gels of various concentrations was used to analyse restriction patterns. Based on the results of bioinformatic analysis of the nucleotide reference sequences of the experimental fragment of the beta-casein gene, it was found that the primer system for the ACRS-PCR DdeI method is characterised by higher parameters of flanking efficiency of the target DNA site compared to the ACRS-PCR TaqI system due to significantly greater effectiveness of hybridisation of oligonucleotides on the target DNA. Based on the results of laboratory tests of both methods, it is proposed to use an additional procedure for analysing the fluorescence intensity of individual elements of restriction patterns, which allows reducing the number of false genotyping that occurs in both cases (based on the results of using both methods) due to the appearance of non-specific amplification/restriction fragments within the size of target restrictions. The application of the ACRS-PCR DdeI method provides more differentiated patterns of the corresponding genotypes in agarose gel compared to the ACRS-PCR TaqI method, but leads to higher material costs for conducting research. These disadvantages of using primer systems for ACRS-PCR of the beta-casein locus determine the relevance of developing alternative methods for typing A1 and A2 alleles which include allele-specific PCR. The use of results is promising for solving the problems of genotyping cattle individuals of different breeds by A1 and A2 alleles of the beta-casein locus

中国への渡航者によるパラチフスの集団2事例の分子疫学的解析

We reported two familial clusters of paratyphoid fever after travel to China occurring in the same Yokohama ward from September to October 2002. Six Salmonella enterica serovar Paratyphi A (S. Paratyphi A) strains, 3 each from 2 clusters, were isolated and their characteristics analyzed using phage typing, susceptibility to antibiotics, and patterns of restriction endonuclease-digested DNA fragments in agarose gel following pulsed-field gel electrophoresis (PFGE). Mutations in genes for gyrA and parC, which determine sensitivity to fluoroquinolones, were also investigated. All isolates showed the same characteristics, i.e. "untypable", employing bacteriophages, resistant to antibiotics nalidixic acid and fosfomysin, and decreased susceptibility to fluoroquinolones. No difference was observed in PFGE patterns after digesting with 4 restriction enzymes, Xba I, Bin I, Spe I, and Xho I. We also found that the gyrA gene, which is one of the quinolone-resistance-determining regions (QRDR), was mutated at position 83 from serine to phenylalanine (from TTC to TCC) in all 6 strains. Other QRDR's, parC were not mutated commonly in them. Hearing from patients and family members, it was apparent that these 2 families had been contacted neither in Japan nor in China during ill or incubation period of paratyphoid fever, although a member of one cluster had a familial relationship with one of another family. It was also reported by them that typhoid fever is endemic in both of the areas of their visits. From these results, it was suggested that these 2 cluster cases were infected separately in China with the progeny of the same clone which is endemic in these regions.

HGF protects corneal epithelial cells from apoptosis by the PI-3K/Akt-1/Bad- but not the ERK1/2-mediated signaling pathway.

Cell survival is critical during corneal epithelial regeneration after injury, and growth factors could be fundamental in cytoprotection. The goal of this study was to investigate the involvement of the paracrine hepatocyte growth factor (HGF) in the prevention of corneal epithelial cell apoptosis and to identify signal transducers in this process. Apoptosis in human and rabbit corneal epithelial (HCE and RCE) cells was induced with a nutrient-deprived exhausted medium (ExM) or by treatment with staurosporine (20-100 ng/mL) or the calcium ionophore A23187 (0.5 microM). Apoptotic cells were identified by DNA fragmentation in agarose gels and by Hoechst staining. Active Akt-1 overexpression (Akt-1 pUSEamp cDNA) and small interfering RNA (siRNA) specific for Akt mRNA were used. Immunofluorescence, Western immunoblot analysis, and Akt kinase assays were also used. Staurosporine, ExM, and A23187 induced DNA fragmentation in HCE and RCE cells. HGF (20 ng/mL) in combination with the apoptotic agents greatly reduced DNA breakdown and the number of Hoechst-positive cells. In the presence of phosphatidylinositol-3 kinase (PI-3K) inhibitors (wortmannin and LY294002), HGF did not overcome apoptosis. However, PD98059, the ERK1/2 cascade pathway inhibitor, was ineffective in preventing HGF protection. HGF induced a sustained activation of Akt-1, and overexpression of active Akt-1 reduced apoptosis. HGF stimulated the downstream targets of Akt, glycogen synthase kinase (GSK-3), and Bad, a proapoptotic member of the Bcl-2 family, an effect that was blocked by PI-3K inhibitors but not by ERK1/2 inhibition. Suppressing the expression of Akt by Akt siRNA led to a decrease in the phosphorylation of Bad and GSK-3. Translocation of Bad to the mitochondria, a critical stage in apoptosis, was prevented by HGF when apoptosis was induced. Moreover, in epithelial cells overexpressing active Akt-1, Bad translocation was also prevented. HGF modulates multiple signaling cascades in corneal epithelial cells. The results demonstrated that HGF, in a paracrine fashion, protects cells from apoptosis through a PI-3K/Akt/Bad pathway but not through an ERK1/2 pathway. It was also demonstrated that GSK-3 is a target of PI-3K/Akt-1.

Abdominal temperature induces region-specific p53-independent apoptosis in the cauda epididymidis of the mouse.

It is widely accepted that temperature regulates gene expression and function in the epididymis. However, the significance of reduced temperature of the scrotum in cell survival had not often been examined. Our hypothesis was that the experimental increase of the temperature could induce apoptosis. Using a surgical method that consists of surgically reflecting the cauda epididymidis in the abdomen, we have been able to show that this is the case. Apoptosis was examined by histologic procedures and by visualization of DNA fragmentation in agarose gels. We determined that the apoptosis is region-specific and affects only the principal cells of the proximal region of the cauda. It starts 12 h after surgery and ends by the third day. The apoptotic cells are eliminated by extrusion into the lumen and phagocytosis by adjacent cells. The complete molecular mechanism of apoptosis in this case remains unknown, but we have used the techniques of immunocytochemistry, Western blot, and reverse transcription-polymerase chain reaction to determine the role of some molecules. We have seen no significant role of androgens, the tumor suppressor p53, nor two heat shock proteins, hsp-25 and hsp-70. Nevertheless, we have detected a strong induction of bax and bcl-2 gene products. While the former should be responsible for the apoptosis observed, the latter would promote the survival of most of the cells of the cauda epididymis.

DNA electrophoresis in agarose gels: a simple relation describing the length dependence of mobility.

Electrophoretic mobilities of DNA molecules ranging in length from 100 to 10 000 base pairs (bp) were measured in gels of eleven concentrations of agarose from 0.5 to 1.5%. Excellent fits of the dependence of mobility on DNA length were obtained with the relationship [equation: see text] showing an e(-L/gamma) crossover, where L is the length of a DNA fragment and gamma is a crossover length ranging from 8000 to 12000 bp. The other parameters in the fit are mu(s) the mobility of short DNA with unit charge in the limit as length is extrapolated to zero, and muI, the mobility of long DNA as length is extrapolated to infinity. This exponential relationship should be a useful interpolation function for determining DNA lengths over a wide range. The simplicity of this relationship may be of more fundamental significance and suggests that some common feature dominates the electrophoresis of double stranded DNA fragments in agarose gels, regardless of length.

Human esophageal cancer cell death mediated by apoptosis-inducing nucleosides from CD57+HLA-DRbright natural suppressor cell line.

We approached the induction of apoptosis in human esophageal cancer cells (T.Tn) by apoptosis-inducing nucleosides (AINs) from CD57+HLA-DRbright-natural suppressor (57.DR-NS) cell line originated in decidua. The 57.DR-NS cells generated apoptosis in T.Tn cells by AINs released into the cultures. We isolated a series of AINs by high performance liquid chromatography (HPLC) from 57.DR-NS cell culture fluids. Each AIN and its mixture induced apoptotic cell death in T.Tn cells, detected by DNA fragmentation in agarose gels, terminal deoxynucleotide transferase mediated dUTP-nick end labeling (TUNEL) method and accumulation of sub-G1 DNA content with flow cytometry. Furthermore, we found the occurrence of DNA strand breaks followed by the activation of caspase-3 during AINs-induced apoptosis in T.Tn cells. Thus, we validated that AINs could induce apoptosis in T.Tn cells mediated through DNA strand breaks and activation of caspase-3.

Simvastatin induces apoptosis of cultured rat cardiomyocytes.

Considering the therapeutic effect of statins (3-hydroxy-3-methylglutaryl coenzyme A reductase inhibitors) and simvastatin in patients with coronary heart disease, our first hypothesis was that simvastatin should inhibit apoptosis (programmed cell death) in angiotensin II-treated cultured myocytes. But after realizing that simvastatin stimulates apoptosis, we changed our hypothesis and began to study its apoptotic effect in primary cultured rat cardiomyocytes. We found that simvastatin induced apoptosis in a dose-dependent manner (0.1 to 3 micromol/L), as evidenced by the appearance of increased DNA fragmentation in agarose gels and characteristic apoptotic patterns in nuclei labeled with Hoechst 33342, as well as increased activity of caspase 3. FACS analysis of simvastatin-treated cardiomyocytes showing annexin V binding and propidium iodide exclusion ruled out the possibility of necrosis. Increased intracellular enzymatic activity of creatine phosphokinase, aldolase, and lactic dehydrogenase, markers for normal cell function, could reflect the hypertrophic effect of simvastatin. The results indicate that simvastatin-induced apoptosis in cultured heart cells is concentration-dependent and additive to the apoptotic effect of angiotensin II.

Induction of apoptosis in human mitogen-activated peripheral blood T-lymphocytes by the ether phospholipid ET-18-OCH3: involvement of the Fas receptor/ligand system.

1. Activated T-cells constitute a target for treatment of autoimmune diseases. We have found that the antitumour ether phospholipid 1-O-octadecyl-2-O-methyl-rac-glycero-3-phosphocholine (ET-18-OCH3; edelfosine) induced dose- and time-dependent apoptosis in human mitogen-activated peripheral blood T-lymphocytes, but not in resting T-cells. T-lymphocytes were stimulated with phytohemagglutinin and interleukin-2 or with concanavalin A. Apoptosis was assessed by DNA fragmentation through cell cycle and TUNEL analyses, as well as through visualization of internucleosomal DNA fragmentation in agarose gels. 2. The ET-18-OCH3-mediated apoptotic response in activated T-lymphocytes was less intense than in human leukaemic T cell lines, such as Jurkat cells and Peer cells; namely about 25% apoptosis in activated T-cells versus about 46-61% apoptosis in T leukaemic cells after 24 h treatment with 10 microM ET-18-OCH3. 3. The ET-18-OCH3 thioether analogue BM 41.440 (ilmofosine) showed a similar apoptotic capacity to that found with ET-18-OCH3 in activated T-cells, whereas the phospholipid analogue hexadecylphosphocholine (miltefosine) failed to promote this response. 4. The uptake of [3H]-ET-18-OCH3 was much larger in activated T-cells than in resting lymphocytes. 5. Using a cytofluorimetric approach we have found that ET-18-OCH3 induced disruption of the mitochondrial transmembrane potential and production of reactive oxygen species in activated T-cells, but not in resting lymphocytes. 6. ET-18-OCH3 induced an increase in Fas (APO-1/CD95) ligand mRNA expression in activated T-cells, and incubation with a blocking anti-Fas (APO-1/CD95) antibody partially inhibited the ET-18-OCH3-induced apoptosis of activated T-lymphocytes. 7. These results demonstrate that mitogen-activated T-cells, unlike resting lymphocytes, are able to take up significant amounts of ET-18-OCH3, and are susceptible to undergo apoptosis by the ether lipid via, in part, the Fas (APO-1/CD95) receptor/ligand system. This ET-18-OCH3 apoptotic action can be of importance in the therapeutic action of this ether lipid in certain autoimmune diseases.

Initiation of apoptosis in hepatocytes during prolonged arterial hypotension and postresuscitation period

An increase in activity of Ca2+, Mg2+-dependent endonucleases on the second hour of hypotension coincided with the presence of DNA fragments in agarose gel. A correlation was established between the duration of hypotension, Ca2+, Mg2+-dependent endonuclease activity, and intensity of nuclear DNA fragmention. Apopotosis of hepatocytes is triggered during ischemia and develops during reperfusion.

Abrogation of cisplatin-induced programmed cell death in human breast cancer cells by epidermal growth factor antisense RNA.

Epidermal growth factor receptor (EGF-R) perturbation by receptor ligand(s), e.g., epidermal growth factor (EGF) and transforming growth factor-alpha (TGF-alpha), or receptor-specific antibodies accentuates cisplatin-induced toxicity in tumor cells. This sensitization occurs only in tumor cells with high expression of EGF-R but not in those with low expression of EGF-R. Therefore, we have studied the role of EGF-R expression on cisplatin-mediated cytotoxicity. MDA-468 human breast cancer cells were stably transfected with a p-chloramphenicol acetyl transferase (pact[p]-CAT) vector containing a 4.1-kilobase full-length antisense EGF-R complementary DNA. EGF-R content was assessed by 125I-EGF binding and EGF-R immunoblot assays. Cisplatin sensitivity was evaluated by (a) colony-forming assay in vitro, (b) xenograft growth in nude mice, (c) cell cycle distribution of propidium iodide-labeled DNA, (d) DNA fragmentation in agarose gels, and (e) terminal deoxynucleotidyl transferase (Tdt) fluorescence in situ. Cisplatin uptake was measured by atomic absorption spectroscopy, and the levels of drug-DNA intrastrand adducts were determined by a dissociation-enhanced fluoroimmunoassay that utilizes an antibody against cisplatin-modified DNA. Selected clones (MDA-468/AS-EGFR) exhibited more than 90% loss of both 125I-EGF binding and receptor content determined by western blot analysis, whereas clones transfected with the vector alone (MDA-468/p-CAT) had EGF-R levels similar to those of the parent cells. By use of a colony-forming assay, the 1-hour IC50 (i.e., the concentration of drug required for 1 hour to achieve 50% cell kill) for cisplatin was 2 microM or less for parental and vector-transfected clones (n = 4), whereas it was 25 microM or more for all MDA-468/AS-EGFR clones (n = 3). MDA-468/p-CAT clones exhibited internucleosomal DNA fragmentation, enhanced Tdt-end labeling in situ, and G2 arrest 48 hours after a 1-hour incubation with 3-30 microM cisplatin. Under these conditions, apoptosis and G2 arrest were undetectable in all MDA-468/AS-EGFR clones. An MDA-468 subline selected after long-term treatment with a TGF-alpha-Pseudomonas exotoxin A fusion protein 40 lacked EGF binding and also exhibited cisplatin resistance (1-hour IC50: > 30 microM) compared with parental cells. This EGF-R-dependent difference in cisplatin response was confirmed in a nude mouse xenograft model by use of high- and low-EGF-R-expressing cell clones. Total intracellular drug accumulation after a 1-hour cisplatin exposure, as measured by atomic absorption spectroscopy, was identical in both groups of cells. Intrastrand drug-DNA adducts, however, were statistically higher in high EGF-R expressors than in low-EGF-R-expressing clones. These data indicate that a critical level of EGF-R signaling, which is amplified in some common human cancers, is necessary for cisplatin-mediated apoptosis in tumor cells and suggest an inhibitory effect of this pathway on the repair of cisplatin-damaged DNA.

Complex of osmium tetroxide with 1,10-phenanthroline binds covalently to double-stranded DNA.

Complex of osmium tetroxide with 1,10-phenanthroline (Os,phen) reacts with double-stranded B-DNA in contrast to osmium tetroxide, pyridine and other osmium structural probes which show a strong preference for single-stranded DNA (ssDNA) (Palecek, E. in Abelson, J.N., and Simon, M.I. (eds), Lilley, D.M.J., and Dahlberg, J.E., (volume eds.), Methods in Enzymology, Vol. 212, DNA Structures, part B., Academic Press, 139-155 (1992)). Modification of negatively supercoiled DNA (scDNA) with Os,phen changes the DNA electrophoretic mobility inducing the DNA relaxation at lower degrees of modification followed by formation of positive supercoils at higher modification extents. Electrophoretic mobility of the Os,phen-modified DNA fragments in agarose gel is almost unchanged while a strong retardation of the same fragments is observed in polyacrylamide gels. Os,phen-modified DNA is hypersensitive to nuclease S1. Cleavage of this DNA by restriction enzymes is selectively inhibited showing a preference of Os,phen for TA and AT dinucleotide steps. DNA modification by Os,phen is inhibited by low and moderate concentrations of MgCl2. The covalent binding of Os,phen to double-stranded DNA (dsDNA) is preceded by noncovalent interactions (probably intercalation) inducing DNA structural changes; the shape of the Os,phen-modified DNA molecule appears to be severely deformed.

Transforming growth factor beta abrogates the effects of hematopoietins on eosinophils and induces their apoptosis.

Hematopoietins, interleukin (IL)-3, IL-5, and granulocyte/macrophage colony-stimulating factor (GM-CSF) have previously been shown to prolong eosinophil survival and abrogate apoptosis. The objective of this study was to investigate the effect of transforming growth factor beta (TGF-beta) on eosinophil survival and apoptosis. Eosinophils from peripheral blood of mildly eosinophilic donors were isolated to > 97% purity using discontinuous Percoll density gradient. Eosinophils were cultured with hematopoietins with or without TGF-beta for 4 d and their viability was assessed. We confirmed previous observations that hematopoietins prolonged eosinophil survival and inhibited apoptosis. TGF-beta at concentrations > or = 10(-12) M abrogated the survival-prolonging effects of hematopoietins in a dose-dependent manner and induced apoptosis as determined by DNA fragmentation in agarose gels. The effect of TGF-beta was blocked by an anti-TGF-beta antibody. The anti-TGF-beta antibody also prolonged eosinophil survival on its own. The culture of eosinophils with IL-3 and GM-CSF stimulated the synthesis of GM-CSF and IL-5, respectively, suggesting an autocrine mechanism of growth factor production. TGF-beta inhibited the synthesis of GM-CSF and IL-5 by eosinophils. TGF-beta did not have any effect on the expression of GM-CSF receptors on eosinophils. We also studied the effect of TGF-beta on eosinophil function and found that TGF-beta inhibited the release of eosinophil peroxidase. Thus, TGF-beta seems to inhibit eosinophil survival and function. The inhibition of endogenous synthesis of hematopoietins may be one mechanism by which TGF-beta blocks eosinophil survival and induces apoptosis.

DNA electrophoretic mobility and deformation in agarose gels

Time-dependent electrophoretic mobility, μ, of large DNA fragments in agarose gels and the corresponding conformational changes under an applied electric field can be measured by means of movements of fluorescence pattern after photobleaching (MOFPAP) and transient electric birefringence (TEB), respectively. The short-time (≈ min) averaged electrophoretic mobility initially increased with increasing electric field-on time and finally reached a steady state value. The rate of increase in μ is closely related to the DNA size/gel pore size ratio. The change may also be correlated to the rate of deformation of DNA chains as observed by TEB. The field-free decay for large DNA fragments in agarose gels is very slow, lasting tens of seconds. Coupling of TEB and MOFPAP measurements together with fluorescence microscopy and dichroic measurements should permit us to provide a better description of the short-time averaged mechanisms responsible for polymer chain motions in pulsed field gel electrophoresis.

Effect of ultrasound on the separation of DNA fragments in agarose gel electrophoresis

Since its first use in 1966 interest in and the applications of electrophoresis of DNA fragments in agarose gel have grown rapidly. Nowadays, agarose gel electrophoresis has become a standard technique with high resolving power for the analysis of DNA structure, for example for the determination of the length of DNA fragments obtained by the action of restriction enzymes. The electrophoretic mobility ({mu}) of DNA fragments is influenced by various parameters-molecular weight, gel concentration, temperature, electric field, and DNA-agarose affinity. A comprehensive study of the influence of these main parameters has been reported. In this paper, the authors investigate a new effect on the electrophoretic mobility of DNA fragments in agarose gels, viz. the influence of ultrasound.

Study of large DNA fragments in agarose gels by transient electric birefringence

The pulsed-field gel electrophoresis (PFG) is a newly developing technique used in the fractionation of large DNA fragments. Advances in PFG demand a better understanding in the corresponding mechanisms of DNA dynamics in the gel network. Detailed experiments are needed to verify and to extend existing theoretical predictions as well as to find optimum conditions for efficient separation of large DNA fragments. In the present study, deformation of large DNA fragments (40-70 kilobase pairs) imbedded in agarose gels were investigated by using the transient electric birefringence (TEB) technique under both singular polarity and bipolarity electric pulses at low applied electric field strengths (E less than or equal to 5 V/cm). The steady-state optical retardation (delta s) of DNA molecules is linearly proportional to E2. At a given E, the amplitude of optical retardation [delta(t)] increases monotonically with the pulse width (PW) and then reaches a plateau value [delta(t = 0) = delta s] where t = 0 denotes the time when the applied field is turned off or reversed. The field-free decay time (tau-a few minutes) is several orders of magnitudes slower than that from previous TEB observations using high electric field strengths (E-kV/cm) and short pulse widths (PW-ms). The degree of deformation (stretching and orientation) and the time of restoration to the equilibrium conformation of overall DNA chains have been related to delta and tau. In field inversion measurements, exponentially rising and linearly falling of birefringence signals in the presence of forward/inverse applied fields were observed. The rising and falling of birefringence signals were reproducible under a sequence of alternating pulses. Comparison of our results with literature findings and discussions with theories are presented.

Electrophoresis and movements of fluorescence pattern after photobleaching of large DNA fragments in agarose gels

By combining electrophoresis with movements of fluorescence pattern after photobleaching (MOFPAP), which is abbreviated as EMOFPAP, we are able to measure electrophoretic mobilities of large DNA fragments in an agarose gel within a fairly short time scale (about 10 min or even down to 1 min). The new method represents a significant improvement in experiment time when compared with the time (typically on the order of hours) required to determine the average electrophoretic mobility of large DNA fragments in agarose gels by means of either conventional gel electrophoresis or pulsed-field gel electrophoresis. In this article, we present the EMOFPAP experimental setup and consider optical conditions, including beam profile geometry and fluorescence pattern formation. A realistic formula that can explain the parameters governing the EMOFPAP method using our present optical setup has been derived. A comparison of results between experimental and computer simulation data is made, and an optimization of the EMOFPAP method is proposed.

The electric field dependence of DNA mobilities in agarose gels: A reinvestigation

The electric field dependence of the electrophoretic mobility of linear DNA fragments in agarose gels was reinvestigated in order to correct the observed mobilities for the different temperatures actually present in the gel during electrophoresis in different electric field gradients. When corrected to a common temperature, the electrophoretic mobilities of DNA fragments less than or equal to 1 kilobase pairs (kbp) in size were independent of electric field strength at all field strengths from 0.6 to 4.6 V/cm if the gels contained less than or equal to 1.4% agarose. The mobilities of larger DNA fragments increased approximately linearly with electric field strength. If the agarose concentration was higher than 2%, the mobilities of all DNA fragments increased with increasing electric field strength. The electric field dependence of the mobility was larger in gels cast and run in Tris-borate buffer (TBE) than in gels cast and run in Tris-acetate buffer (TAE), and was more pronounced in gels without ethidium bromide incorporated in the matrix. Ferguson plots were constructed for the various DNA fragments, both with and without extrapolating the temperature-corrected mobilities to zero electric field strength. Linear Ferguson plots were obtained for all fragments less than or equal to 12 kbp in size in agarose gels less than or equal to 1.4% in concentration if the mobilities were first extrapolated to zero electric field strength. Concave upward curvature of the Ferguson plots was observed for DNA fragments greater than or equal to 2 kbp in size at finite electric field strengths. Convex downward curvature of the Ferguson plots was observed for DNA fragments greater than or equal to 1 kbp in size in agarose gels greater than or equal to 2% in concentration. The mobilities of the various DNA fragments, extrapolated to zero agarose concentration and zero electric field strength, decreased with increasing DNA molecular weight; extrapolating to zero molecular weight gave an "intrinsic" DNA mobility of 2.7 x 10(-4) cm2/Vs at 20 degrees C. The pore sizes of LE agarose gels cast and run in TAE and TBE buffers were estimated from the mobility of the DNA fragments.(ABSTRACT TRUNCATED AT 400 WORDS)

Resolution of a paradox in the electrophoresis of DNA in agarose gels

A paradox was observed in a previous study of the electrophoresis of linear DNA fragments in agarose gels (D. L. Holmes and N. C. Stellwagen, Electrophoresis 1990, 11, 5-15). The pore size of the agarose matrix was more accurately determined if the root-mean-square radius of gyration was used to measure DNA macromolecular size. However, the Ogston equations were obeyed and other gel parameters such as the apparent fiber radius and fiber volume appeared to be better described if the geometric mean radius was used to measure DNA size. This paradox can be resolved if relative mobilities (with respect to the smallest DNA molecule in the data set) are used to construct the Ferguson plots, instead of absolute mobilities. Using relative mobilities and the root-mean-square radius of gyration, the Ogston equations are obeyed and the pore size of the matrix is consistent with values determined by other methods.

Measurement of electrophoretic mobility of dye-labeled large DNA fragments in agarose gels by movement of fluorescence pattern after photobleaching.

Measurement of electrophoretic mobility of dye-labeled large DNA fragments in agarose gels by movement of fluorescence pattern after photobleaching.

Two methods to detect DNA fragments produced by restriction enzymes

This report summarizes two methods for detecting limited amounts of DNA from restriction endonuclease digests. The first is a photographic system for visualizing ethidium bromide-stained DNA fragments in agarose gels which can detect as little as 50–100 pg DNA per band. The second technique is direct sulfonation of DNA fragments bound to nylon membranes followed by visualization of the fragments by nonradioactive immunoblot methods. The immunohistochemical staining can detect 10 pg DNA per band. The direct sulfonation technique is not intended to identify specific DNA sequences; DNA-DNA hybridization with sulfonated probes has previously been described (P. Lebacq, D. Squalli, M. Duchenne, P. Poulety, and M. Johannes (1988) J. Biochem. Biophys. Methods 15, 255–266) . Direct sulfonation can be used when samples are relatively free of contaminating nucleic acids and is a useful alternative to end-labeling. These highly sensitive techniques may be suitable when the DNA source is of limited quantity or in instances where radiolabeling is not permitted.