On the movement and alignment of DNA during 120 degrees pulsed-field gel electrophoresis.

The displacement per pulse of lambda, T4, and G DNA during pulsed-field agarose gel electrophoresis has been measured for a fine mesh of pulse durations T between 0.02 and 120 s. The slopes of these curves show that the DNA moves by two distinct processes, designated 1 and 2, depending upon the pulse duration T. Process 1 operates at short T and causes dx/dT to decrease gradually with increasing T. This process is independent of molecular weight M. Process 2 is effective at longer T and causes dx/dT to rise sharply in sigmoidal fashion at a value of T which increases as M1.2, finally reaching a plateau of 1.4 microns/s for E = 4 V/cm. The shape of the dx/dT curve and its dependence on M lead directly to 4 zones of separation in plots of mobility vs M for different T. The alignment of the 3 DNAs during PFGE was measured by fluorescence-detected linear dichroism for E between 4 and 10 V/cm. These results are used in developing a molecular understanding of the mobility data.     

Transient orientation of linear DNA molecules during pulsed-field gel electrophoresis.

The transient orientation of lambda DNA and lambda-DNA oligomers has been measured during pulsed field gel electrophoresis. The DNA becomes substantially aligned parallel to the electric field E. In response to a single rectangular pulse, orientation shows an overshoot with a peak at 1 second, then a small undershoot, and finally a plateau. When the field is turned off, the orientation dissipates in two distinct exponential phases. Field inversion leads to periods of orientation with intervening periods of reduced orientation as the chains reverse direction. Field inversion pulses applied to linear oligomers of lambda-DNA show that orientation responses slow down but increase in amplitude as molecular weight increases, for a given field. Because DNA stretching and alignment parallel to E are expected to correlate with DNA velocity, the velocity in response to a pulsed field is also expected to exhibit an overshoot.     

Fluctuations in the velocity of individual DNA Molecules during agarose gel electrophoresis

The velocity of the center of mass of individual T4 DNA molecules during agarose gel electrophoresis, computed from digitized video-microscopic images, fluctuated between 0 and 4.5 μm/s after a field E = 5 V/cm was applied; the amplitude of the velocity peaks was twice the averaged steady-state velocity. The velocity fluctuations correlated with changes in molecular configuration. The mean velocity (10 molecules) showed a sharp rise in less than 0.2 s, followed by a shallow minimum and a broad peak, before reaching a plateau. The much smaller amplitude of these oscillatory features demonstrated that the velocity fluctuations of individual molecules were largely, but not entirely, uncorrelated with the onset of the field. The components of the shape tensor S of individual chains, which are a measure of the extension of the chains, were also determined for each image sequence. Only the principal component in the direction of E, S_xx, increased.     

Observation of DNA molecules undergoing capillary electrophoresis.

This paper presents a method to observe the motions and configurations of large DNA molecules undergoing capillary electrophoresis (CE). A simple device to perform CE horizontally under microscopic observation is designed and images of single DNA molecules inside the capillary are obtained using an epi-fluorescence microscope. DNA molecules moved towards the negative electrode when an electric field was applied. The mobilities of three types of DNA (T4 and lambda bacteriophage DNA and PBR322 plasmid DNA) were measured at different electric field strength. The mobility vs. electric field strength curves of these three large DNAs showed that the mobility remained constant at high electric field strength (200-600 Volt/cm) and increased significantly at low electric field strength (less than or equal to 50 Volt/cm.). The apparent mobilities of the large DNA molecules were independent of molecular weight. At electric field strengths greater than or equal to 400 Volt/cm., big aggregates (snowballs) of DNA molecules formed and moved upstream towards the positive electrode. When the field was turned off, the aggregates dissociated into a cloud of single DNA molecules, and diffused into the solution.     

Molecular chain orientation of DNA films induced by both the magnetic field and the interfacial effect

DNA films showing highly homogeneous orientation of molecular chains were successfully prepared by drying a semidiluted solution in a horizontal magnetic field. Most of the molecular chain elements in the obtained film were found to be one-dimensionally oriented, as shown by X-ray diffraction, polarization microscopy, and linear dichroism spectroscopy. Because a DNA chain is theoretically expected to orientate only in divergent directions perpendicular to a magnetic field, this result suggests that the DNA chains were aligned not only by a magnetic field but also by the interfacial effect that induced the chains to fit along the air-liquid interface. The descent speed of an air-liquid interface by evaporation was faster than the estimated diffusion rate of DNA, suggesting an emergence of a concentrated layer near the surface. As proved by polarization microscopy, this emergence led to the transitional formation of a nematic-like liquid crystalline phase, which resulted in a DNA film with good chain alignment and unitary orientation. This mechanism underlying chain alignment was supported by molecular weight dependency, in which higher molecular weight DNA is more likely to evince chain alignment that exhibits a higher degree of birefringence. Low molecular weight components have such high thermal motility that it would be difficult to fit them along the air-liquid interface in the early stage of drying. For chain alignment, it was preferable to use an initial concentration of DNA lower than a critical concentration for liquid crystal formation so that the possible diffusion and assembly in a diluted solution would be essential for chain alignment. The DNA film exhibited obvious linear dichroism, indicating the potential for further applications.     

Two-dimensional motion of DNA bands during pulsed-field gel electrophoresis. II. Effect of field angle

In pulsed-field gel electrophoresis, megabase DNAs are well separated if the angle θ between the two electric fields is 120° but not if θ = 90°. To elucidate the molecular basis for this observation, we measured the instantaneous position (x, y) and velocity (v_x, v_y) of a band of G-DNA (670 kb) while the field switched direction, for 90° ≤ θ ≤ 102°. For θ = 120° and long pulse period T. The band retraced the last segment of the preceding pulse before moving in- the new field direction. The retracing wax done at a velocity much greater than the average forward velocity. For θ = 90°, rather than retrace itself, the path during one pulse appeared to originate from a point beyond that reached in the previous pulse, end the velocity showed only a brief backward spike. A Monte Carlo simulation that included tube-length fluctuations and hernias was carried out for a model DNA chain moving through a three-dimensional network of interconnected pores, with parameters corresponding to the DNA size, agarose concentration, and field strength of the experiments, Both the xy path and the instantaneous velocities of the simulation were in excellent agreement with experiment for 90° ≤ θ ≤ 120°. When the field changed direction in the simulation, hernias often advanced from both ends in the new field direction. In the 120° case, those near the erstwhile trailing segments of the chain soon established superiority because chain tension and a component of the new field aided their growth. For θ = 90° and long T, however, segments from the head end were more likely to continue to lead because there was often an excess of relaxed segments there, and no component of the field aided either end. © 1995 John Wiley & Sons, Inc.     

A quantitative study of electroporation showing a plateau in net molecular transport.

Electroporation is believed to involve a temporary structural rearrangement of lipid bilayer membranes, which results in ion and molecular transport across the membrane. The results of a quantitative study of molecular transport due to electroporation caused by a single exponential pulse are presented; transport of four molecules of different physical characteristics across erythrocyte ghost membranes is examined as a function of applied field strength. Flow cytometry is used to quantitatively measure the number of molecules transported for 10(4) to 10(5) individual ghosts for each condition. This study has four major findings: 1) Net transport first increases with field strength, but reaches a plateau at higher field strengths. Significant transport is found at or below 1 kV/cm, and transport plateaus begin at field strengths between 2 and 5 kV/cm depending on the molecule transported. 2) A single population of ghosts generally exists, but exhibits a wide distribution in the amount of molecular transport. 3) Under the conditions used, the direction of transport across the ghost membrane does not appear to affect molecular transport significantly. 4) Large numbers of ghosts may be destroyed by the electroporation procedure.     

Uptake of bacteriophage λ DNA in Escherichia coli by electroporation: An alternative to in vitro packaging

Summary By using a high field strength DC pulse of 15 kV/cm and a pulse duration of 5 ms for the transfection of E. coli by bacteriophage DNA, we obtained efficiencies of 1.1 × 10⁶ (pfu/g bacteriophage , DNA). This represents a 100-fold improvement over the traditional CaCl₂/heat shock method and is a viable alternative to the more costly in vitro packaging of recombinant bacteriophage DNA for the production of cDNA and genomic libraries.     

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.     

Effects of supercoiling in electrophoretic trapping of circular DNA in polyacrylamide gels.

Electrophoretic velocity and orientation have been used to study the electric-field-induced trapping of supercoiled and relaxed circular DNA (2926 and 5386 bp) in polyacrylamide gels (5% T, 3.3% C) at 7.5-22.5 V/cm, using as controls linear molecules of either the same contour length or the same radius of gyration. The circle-specific trapping is reversible. From the duration of the reverse pulse needed to detrap the molecules, the average trap depth is estimated to be 90 A, which is consistent with the molecular charge and the field strengths needed to keep molecules trapped. Trapped circles exhibit a strong field alignment compared to the linear form, and there is a good correlation between the enhanced field alignment for the circles and the onset of trapping in both constant and pulsed fields. The circles do not exhibit the orientation overshoot response to a field pulse seen with linear DNA, and the rate of orientation growth scales as E(-2+/-0.1) with the field, as opposed to E(-1.1+/-0.1) for the linear form. These results show that the linear form migrates by cyclic reptation, whereas the circles most likely are trapped by impalement on gel fibers. This proposal is supported by very similar velocity and orientation behavior of circular DNA in agarose gels, where impalement has been deemed more likely because of stiffer gel fibers. The trapping efficiency is sensitive to DNA topology, as expected for impalement. In polyacrylamide the supercoiled form (superhelical density sigma = -0.05) has a two- to fourfold lower probability of trapping than the corresponding relaxed species, whereas in agarose gels the supercoiled form is not trapped at all. These results are consistent with existing data on the average holes in the plectonemic supercoiled structures and the fiber thicknesses in the two gel types. On the basis of the topology effect, it is argued that impalement during pulsed-field electrophoresis in polyacrylamide gels may be useful for the separation of more intricate DNA structures such as knots. The results also indicate that linear dichroism on field-aligned molecules can be used to measure the supercoiling angle, if relaxed DNA circles are used as controls for the global degree of orientation.     

Effects of pulse length and pulse strength on transfection by electroporation

The relative importance of pulse field strength E and pulse length tau 1/2 (half decay time of an exponential decay pulse) on the stable transfection frequency for HeLa or HUT-78 cells was investigated. Cells were transfected with plasmids containing the promoter and drug resistant genes pRSVgpt or pRSVneo by electroporation. The stable transfection frequency was assayed using the marker rescue technique. The transfection frequency increases with increasing values of E tau 1/2. For a given pulse length, the transfection frequency is proportional to the power of the pulse (E2 tau 1/2). Pulses with half decay times of 2.2 to 4.6 ms appear to be more efficient than 0.275 to 0.31 ms for stable transfection of HeLa cells.     

Early stage shape change of human erythrocytes after application of electric field pulses.

Erythrocytes which receive electric field pulses are subject to poration, fusion and shape changes due to electrodynamic forces, aminophospholipid perturbation and influences on the normal flip-flop process. The shape change characteristics of cells suspended in different media were analysed after application of rectangular electric field pulses from t=11-44 micros and from E=4-8 kV/cm. Albumin is shown to decelerate the echinocyte shape change within the first few seconds after pulse application. The addition of fluoride and vanadate accelerates the shape change due to their inhibiting influence on the aminophospholipid translocase. For both the duration of the field pulse and its field strength, there exist lower threshold values under which no early stage shape change is observable. The activation energy calculated from the dissipative influence of the electric field alone is smaller than expected, indicating the electrodynamic influence on the flip-flop process. Cell shapes were additionally analysed by contour tracing to focus on the echinocyte spicule distribution after pulse application. This image analysis revealed that, with an increase of both pulse duration and field strength, the shape change velocity and the shape change intensity increase.     

Verification of a decrease in the rigidity of the phage lambda DNA polymeric chain in low ionic strength aqueous solutions by testing the polymer-polymer interlink interactions

Changes in the rigidity of the polymetric chain of phage lambda double-strand DNA have been studied by laser correlation spectroscopy. It was shown that, as the ionic strength increases, the effect of the screening of the hydrodynamic interaction of the links of the polymeric chain specific for polymeric coils arises in a DNA solution. It is assumed that the screening occurs when the threshold of the overlapping of DNA coils is achieved. The overlapping of coils is the result of a previously observed significant rise of DNA coil size from abnormally small DNA coils in low ionic strength buffers (about 10(-2) M Na+ or less) to maximum possible large coils in the 5SSC and 5SSC-like buffers. Further analysis of the far interlink interactions in linear lambda phage DNA coils in similar buffers at pH 7 and 4 confirms the earlier proposal about the role of H+ ions in the appearance of abnormally small DNA coils. The abnormal decrease in the DNA coil size in low ionic strength buffers is not a specific feature of lambda phage DNA only.     

Kinetics of sterilization of Lactobacillus brevis cells by the application of high voltage pulses

The technique of irreversible electroporation has been successfully applied to cause a lethal effect on Lactobacillus brevis cells suspended in phosphate buffer solution, Na(2)HPO(4)/NaH(2)PO(4) . H(2)O (0.845/0.186 mM) between parallel plane electrodes. Tests were carried out at different temperatures (24,45,60, and 80 degrees C) to determine if there was a synergistic effect of temperature and electric pulse treatment on the destruction of L. brevis. Experimental results indicate that the viability (log N/N(0); where N(0) and N are the number of cells survived per milliliter before and after pulse voltage application, respectively) of L. brevis decreased with electric field strength E and temperature T and treatment time t(t). The relations between log(N/N(0)) and t(t) and log(N/N(0)) and E indicate that higher field strengths are more effective than higher treatment times in causing destruction of L. brevis cells. It was also found that as the temperature of the liquid medium containing L. brevis cells increased from 24 to 60 degrees C, the death rate of L. brevis cells increased with a decrease in the total treatment time t(t) (pulse width x number of pulses applied). The application of an electric field strength E = 25 kV/cm at 60 degrees C and treatment time t(t) = 10 ms resulted in very high destruction levels of L. brevis cells (N/N(0) = 10(-9)). In comparison with existing steam sterilization technology, this new method of sterilization using relatively low temperature and short treatment time could prove to be an excellent method to minimize thermal denaturation of important nutrient components in liquid media. (c) John Wiley & Sons, Inc.     

A Chlamydomonas outer arm dynein mutant with a truncated beta heavy chain

A new allele of the Chlamydomonas oda4 flagellar mutant (oda4-s7) possessing abnormal outer dynein arms was isolated. Unlike the previously described oda4 axoneme lacking all three (alpha, beta, and gamma) outer-arm dynein heavy chains, the oda4-s7 axoneme contains the alpha and gamma heavy chains and a novel peptide with a molecular mass of approximately 160 kD. The peptide reacts with a mAb (18 beta B) that recognizes an epitope on the NH2-terminal part of the beta heavy chain. These observations indicate that this mutant has a truncated beta heavy chain, and that the NH2-terminal part of the beta heavy chain is important for the stable assembly of the outer arms. In averaged electron microscopic images of outer arms from cross sections of axonemes, the mutant outer arm lacks its mid-portion, producing a forked appearance. Together with our previous finding that the mutant oda11 lacks the alpha heavy chain and the outermost portion of the arm (Sakakibara, H., D. R. Mitchell, and R. Kamiya. 1991. J. Cell Biol. 113:615-622), this result defines the approximate locations of the three outer arm heavy chains in the axonemal cross section. The swimming velocity of oda4-s7 is 65 +/- 8 microns/s, close to that of oda4 which lacks the entire outer arm (62 +/- 8 microns/s) but significantly lower than the velocities of wild type (194 +/- 23 microns/s) and oda11 (119 +/- 17 microns/s). Thus, the lack of the beta heavy chain impairs outer-arm function more seriously than does the lack of the alpha heavy chain, suggesting that the alpha and beta chains play different roles in outer arm function.     

Cloning and expression of the 3' portion of the T4 denV gene as a lacZ fusion gene

Polyclonal antibodies have been raised against endonuclease V from the bacteriophage T4. This rabbit serum, from which endemic E. coli antibodies have been removed, reacts with a single protein from T4-infected E. coli with a molecular weight of 16078 dalton. It was confirmed that these antibodies were directed against endonuclease V through the inhibition of the pyrimidine dimer specific nicking activity of endonuclease V in an in vitro nicking assay. A phage lambda gt11 T4 dC DNA library was screened for phage which produced a beta-galactosidase-endonuclease V fusion protein. Immunopositive clones were detected at a frequency of 0.25% of the plaques in the library. Restriction enzyme analyses of the DNA from 45 of these phage showed that all contained a 1.8 kb T4 EcoRI fragment which had been inserted within lambda gt11 in a single orientation. Western analysis of proteins which were produced from an induction of lysogens made from these phage reveals a single fusion protein band with a molecular weight slightly larger than native beta-galactosidase.     

Orientation of DNA in agarose gels.

An orientation of the lambda DNA during the electrophoresis in agarose gels was measured by a microscopic linear dichroism technique. The method involved staining the DNA with the dye ethidium bromide and measuring under the microscope the polarization properties of the fluorescence field around the electrophoretic band containing the nucleic acid. It was first established that the fluorescence properties of the ethidium bromide-DNA complex were the same in agarose gel and in a solution. Then the linear dichroism method was used to measure the dichroism of the absorption dipole of EB dye bound to lambda DNA. In a typical experiment the orientation of two-tenth of a picogram (2 x 10(-13)g) of DNA was measured. When the electric field was turned on, the dichroism developed rapidly and assumed a steady state value which increased with the strength of the field and with the size of DNA. A linear dichroism equation related the measured dichroism of fluorescence to the mean orientation of the absorption dipole of ethidium bromide and to an extent to which the orientation of this dipole deviated from the mean. The observed development of dichroism in the presence of an electric field was interpreted as an alignment of DNA along the direction of the field. The increase in the steady state value of dichroism with the rise in the strength of the field and with the increase of the size of DNA was interpreted as a better alignment of DNA along the direction of the field and as a smaller deviation from its mean orientation.     

Induction of T4 DNA ligase in a recombinant strain of Escherichia coli

The kinetics of cell growth and foreign protein production, as well as factors affecting protein stability, were studied and optimized in batch and fed-batch fermentations of a recombinant strain of Escherichia coli. The pL promoter from bacteriophage lambda under the control of a temperature-sensitive cl represser, with the entire construct integrated into the E. coli chromosome through the use of a defective bacteriophage lambda lysogen, was used to direct the synthesis of T4 DNA ligase. The biphasic fermentations consisted of a primary growth phase at 30 degrees C followed by an induction phase which was initiated by shifting the temperature to 42 degrees C. In the fed-batch fermentations, additional nutrients were added at the time of initiating induction. Maintenance of sufficiently high concentrations of the organic substrates (glucose and casamino acids) during the induction phase was required for continued cell growth at 42 degrees C. Such growth was essential for T4 DNA ligase formation and in vivo stability. Hence, fed-batch fermentations produced the highest yield of the foreign protein Commensurate with providing lower total amounts of substrates. In such cases, high cell densities (6 g dry wt/L) with substantial intracellular levels of T4 DNA ligase (4.6% total cellular protein, or 2.7% of the dry biomass) were achieved.