Capturing the variant surface glycoprotein repertoire (the VSGnome) of Trypanosoma brucei Lister 427

Trypanosoma brucei evades the adaptive immune response through the expression of antigenically distinct Variant Surface Glycoprotein (VSG) coats. To understand the progression and mechanisms of VSG switching, and to identify the VSGs expressed in populations of trypanosomes, it is desirable to predetermine the available repertoire of VSG genes (the 'VSGnome'). To date, the catalog of VSG genes present in any strain is far from complete and the majority of current information regarding VSGs is derived from the TREU927 strain that is not commonly used as an experimental model. We have assembled, annotated and analyzed 2563 distinct and previously unsequenced genes encoding complete and partial VSGs of the widely used Lister 427 strain of T. brucei. Around 80% of the VSGnome consists of incomplete genes or pseudogenes. Read-depth analysis demonstrated that most VSGs exist as single copies, but 360 exist as two or more indistinguishable copies. The assembled regions include five functional metacyclic VSG expression sites. One third of minichromosome sub-telomeres contain a VSG (64-67 VSGs on ∼96 minichromosomes), of which 85% appear to be functionally competent. The minichromosomal repertoire is very dynamic, differing among clones of the same strain. Few VSGs are unique along their entire length: frequent recombination events are likely to have shaped (and to continue to shape) the repertoire. In spite of their low sequence conservation and short window of expression, VSGs show evidence of purifying selection, with ∼40% of non-synonymous mutations being removed from the population. VSGs show a strong codon-usage bias that is distinct from that of any other group of trypanosome genes. VSG sequences are generally very divergent between Lister 427 and TREU927 strains of T. brucei, but those that are highly similar are not found in 'protected' genomic environments, but may reflect genetic exchange among populations.

Quantifying DNA damage by gel electrophoresis, electronic imaging and number-average length analysis

DNA damages that can be converted to single- or double strand breaks can be quantified by separating DNA by gel electrophoresis and obtaining a quantitative image of the resulting distribution of DNA in the gel. We review the theory of this method and discuss its implementation, including the charge-coupled device (CCD) camera systems we developed to acquire images of fluorophore labeled DNA.

Pulsed-field gel electrophoresis

Pulsed-field gel electrophoresis (PFGE) was originally developed as a technique for providing electrophoretic karyotypes of micro-organisms. Since then the technique has evolved and diversified in many new directions. This review traces the evolution of PFGE, summarizes our understanding of its theoretical basis, and provides a comprehensive description of the methodology. Established and novel applications are explored and the reader is provided with an extensive list of references.

Electrophoretic separation of the three Rhizobium meliloti replicons

The megaplasmids and the chromosome from the bacterium Rhizobium meliloti 1021 were separated in preparative quantities by using transverse alternating-field gel electrophoresis. The genetic content of each electrophoretically separated band was determined by Southern hybridization with replicon-specific probes and by comparison with Agrobacterium tumefaciens transconjugants harboring either pSym-a or pSym-b megaplasmids. Pulsed-field gel electrophoresis analyses of PacI (5'-TTAATTAA-3') and SwaI (5'-ATTTAAAT-3') digests of the whole genome and of the separated replicons were used to calculate genome sizes in two R. meliloti strains. In these strains, PacI digestion yielded only four fragments for the entire genome. The sizes of the PacI fragments from R. meliloti 1021 in megabase pairs (Mb) were 3.32 +/- 0.30, 1.42 +/- 0.13, 1.21 +/- 0.10, and 0.55 +/- 0.08, for a total genome size of 6.50 +/- 0.61 Mb. Southern hybridization with replicon-specific probes assigned one PacI fragment to the chromosome of R. meliloti 1021, one to pRme1021a, and two to pRme1021b. PacI digestion of A. tumefaciens pTi-cured, pSym transconjugants confirmed these assignments. In agreement with PacI data, the addition of the six SwaI fragments from R. meliloti 1021 gave a genome size of 6.54 +/- 0.43 Mb. pRme1021a was calculated to be 1.42 +/- 0.13 Mb, 1.34 +/- 0.09 Mb, and 1.38 +/- 0.12 Mb on the basis of PacI digestion, SwaI digestion, and the migration of uncut pRme1021a, respectively. pRme1021b was calculated to be 1.76 +/- 0.18 Mb, 1.65 +/- 0.10 Mb, and 1.74 +/- 0.13 Mb on the basis of PacI digestion, SwaI digestion, and the migration of uncut pRme1021B, respectively. The R. meliloti 1021 chromosome was calculated to be 3.32 +/- 0.30 Mb, 3.55 +/- 0.24 Mb, and 3.26 +/- 0.46 Mb on the basis of PacI data, SwaI data, and the migration of uncut chromosome, respectively.

Microscopic behaviour of DNA during electrophoresis: electrophoretic orientation

The study of the behaviour of DNA when subjected to electric fields poses several intriguing problems of fundamental physico-chemical importance. Electric field (Kerr effect) orientation of DNA in free solution as well as migration of DNA in gel electrophoresis are two well-established, but so far rather separate, research fields. Whereas the first one has been generally concerned with basic structural and dynamical properties of DNA (Charney, 1988), the second is closely related to techniques of molecular biology (for a review on DNA electrophoresis, see stellwagen 1987).

An angle-variable three-dimensional pulsed field gel electrophoresis system

A three-dimensional pulsed field electrophoretic method based on the simultaneous application of fixed and cyclically alternating polarity fields at a right angle is described. Requiring only minimal electronic hardware it provides highly homogeneous field conditions over a large gel area and the versatility to vary the pulse vector angle. The electrophoretic parameters critical to achieve fast high resolution separation over a wide range of molecular sizes have been optimized and applied to megabase-size chromosomal DNA molecules. The empirical relationships between pulse time, field strength conditions, and resolution limits derived allow selection of coordinated experimental conditions for the separation of specific DNA size ranges.

Electric birefringence of dilute agarose solutions

The technique of transient electric birefringence was used to investigate the orientation of agarose solutions in pulsed electric fields. If the agarose was dissolved in deionized water, the sign of the birefringence was positive when the electric field was small, indicating that the agarose molecules were orienting parallel to the electric field lines. The decay of the birefringence was rapid, consistent with the orientation of individual agarose helices. The amplitude of the birefringence, but not the birefringence decay times, increased as the agarose solution aged, suggesting that the helices formed slowly from the sol state. Increasing the amplitude or duration of the pulsed electric field caused additional negative, and then positive, birefringence signals to appear, characterized by much slower rise and decay times, consistent with the formation of aggregates. The slowest decay times ranged from 7.5-9.0 s, suggesting that the aggregates were several microns in size. When agarose was dissolved in dilute Tris buffer instead of deionized water, the fast positive birefringence signal was not observed, suggesting that individual helices were not present in solutions containing dilute buffer.

Semiconductor-controlled contour-clamped homogeneous electric field apparatus

The design and construction of a transistor-driven hexagonal contour-clamped homogeneous electric field (CHEF) apparatus is discussed in detail. The addition of computer control of pulsed-field timings and experiment duration gives rise to an efficient electrophoresis tool designed to achieve separation of DNA molecules in different size groupings. In particular, pulse time regimes which lead to the monotonic separation of DNA molecules ranging from 90 kbp to over a megabase pair are demonstrated. Theoretical treatment of electric field clamping with transistor-driven multiple electrodes is supported by measurements and by the actual performance of electrophoretic separation of yeast chromosomes. The large sample capacity of gels run in this apparatus coupled with the modest power requirements necessary to provide a homogeneous electric field offer significant advantages over earlier CHEF designs.

Recent developments in electrophoretic methods

13. Given the recent extended review by Vesterberg [J. Chromatogr., 480 (1989) 3-19] of electrokinetic methods, this survey has been restricted to the last decade, which has seen tremendous progress in several fields. DNA electrophoresis has experienced strong developments, both in the sequencing strategies (which have been largely automated with the use of fluorescent probes) and in pulsed field analysis of mega-DNA fragments, which has seen such developments as inverse-field, contour-clamped and rotating gel platforms, all allowing for straight band migration in each lane. Chromosome size mapping has now become a reality. Two-dimensional (2D) maps have also shown a dramatic improvement in performance, largely through the development of immobilized pH gradients, giving highly reproducible protein spots in the 2D plane and allowing the exploration of very narrow pH regions. Blotting techniques, combined with 2D mapping, allow sequence analysis and fingerprinting of a single polypeptide spot in a complex sample without resorting to lengthy chromatographic purification steps. Chromatophoresis generates a novel type of 2D mapping, based on hydrophobicity vs. size, rather than on charge vs. size, by direct coupling of a reversed-phase high-performance liquid chromatographic (HPLC) eluate to sodium dodecyl sulphate electrophoresis. The new rising star, capillary zone electrophoresis, offers speed, a large number of theoretical plates, selectivity and small sample requirements in a highly automated equipment.

Genetic control of capsid length in bacteriophage T4. VII. A model of length regulation based on DNA size

Four models for head length regulation in bacteriophage T4 are described and discussed. Several length mutants in the major capsid protein gene (23) were studied by sucrose gradient analysis, rotating gel analysis of DNA length, and by mixed infection gene dosage experiments with T4 amber mutants in gene 24. The results show that head length variation is quantized and highly specific, in that certain amino acid changes in gp23 results in reproducible and well-defined head length phenotypes. These data are presented as being most consistent with a vernier-type of head length control mechanism.

Quantized viral DNA packaging revealed by rotating gel electrophoresis

Two classes of missense mutations in the bacteriophage T4 gene coding for the major head protein produce phage with different length heads. The pt (petite) mutations produce phage with normal, intermediate, and isometric heads, whereas ptg (petite and giant) mutations also produce greatly elongated (giant) heads. DNA from petite, normal, and giant particles was clearly resolved by discontinuous rotating gel electrophoresis, and several new species of headful length DNA were found. These results confirm the idea that the major stop points for head length regulation are at Q = 13, 17, and 21, and also show that minor stop points exist at Q = 16, 18 and 20. The existence of these well-defined classes of DNA that correlate with capsid structure suggest that a structural relationship between the scaffold protein and the capsid protein determines head length and thus DNA length.

Computer-controlled discontinuous rotating gel electrophoresis for separation of very large DNA molecules

The newly designed equipment for alternating field gel electrophoresis which permits the separation of very large DNA molecules and the simultaneous analysis of up to 35 samples is described. The field alternation is effected by intermittently rotating the submerged agarose gel by optitional angles. The time intervals between changes of position are controlled by a computer program driving a simple switching device which was designed to suit any technique using periodic switching or inversion of the electrical field. Because the electrophoresis unit provides an absolutely homogeneous electrical field, no distortion of migration lanes occurs and the resolution is very good. Moreover, by using a switching time interval gradient an almost perfect linear relationship between migration distances and molecule sizes in the range of about 100-1250 kilobase pairs is observed. In two-dimensional separations, different switching time programs for the first and second dimension allow maximum resolution of selected size ranges. Field inversion gel electrophoresis is possible as well. The performance of the method is demonstrated by comparing the chromosome sizes of different yeast strains.

Separation of large DNA molecules by pulsed-field gel electrophoresis. A review of the basic phenomenology

Pulsed-field gel electrophoresis is a method of separating large DNA molecules. The distinctive feature of this method is that the direction of the electric field is changed periodically. During the five years since Schwartz and Cantor introduced this technique, there has been dramatic progress in pulsed-field instrumentation and in associated electrophoretic methods. Progress has been driven by practical experience with little guidance from theory. In this review, the basic phenomenology of pulsed-field gel electrophoresis is summarized and some speculations are advanced about possible molecular mechanisms.

Reptation-breathing theory of pulsed electrophoresis: dynamic regimes, antiresonance and symmetry breakdown effects

We apply the concepts of tube and reptation to the pulsed electrophoresis of DNA, considering both biased reptation and "breathing" modes (internal modes of the chain). Using suitable preaveraging approximations, analytical expressions are derived which relate displacement in crossed field electrophoresis to molecular weight, field strength, field period, pore size of the gel, and the angle between the field. These expressions provide scaling laws for the change of mobility when one (or more) of the parameters is varied as well as "universal" velocity versus molecular weight versus pulse time curves. These results are quantitatively compared with experiments. At some point which depends on field angle, field strength and chain length, however, we predict a failure of this model due to symmetry breakdown and loss of ergodicity. Qualitatively, this should lead to considerable band spreading and/or splitting of the highest DNA bands into two bands migrating sideways from the diagonal. The case of field inversion is also investigated. It is shown that only breathing modes can explain the strong differences in mobility experienced by chains of different length when opposite fields of equal amplitude are applied: the "trapping" of chains in conformations of low mobility is associated with an antiresonance-like coupling between the external field and the internal modes.

Gel electrophoresis method for quantitation of gamma ray induced single- and double-strand breaks in DNA irradiated in vitro

We describe a method based on gel electrophoresis for the quantitation of strand breaks in DNA and demonstrate its application to the measurement of single- and double-strand breaks formed by gamma-rays for DNA irradiated in vitro. For single-strand breaks, our data span the dose range from 0.1 to 1 Gy, while for double-strand breaks doses were from 3 to 15 Gy. In agreement with results obtained using other techniques, we find that the dose response function for single-strand breaks is linear while the dose response function for double-strand breaks is curved, indicating that it is the sum of both linear and quadratic components. We discuss factors that determine the sensitivity of the method and indicate approaches to make possible the quantitation of strand breaks in the DNA of cells irradiated with sublethal doses.

Separation of chromosomal length DNA molecules: pneumatic apparatus for rotating gels during electrophoresis

The maximum length of DNA molecules that can be separated by gel electrophoresis can be increased greatly by periodically altering the direction of the electric field with respect to the gel by an angle that exceeds 90 degrees. One method involves rotating the gel by the desired angle in alternate directions periodically during electrophoresis. We describe a modification of the rotating gel electrophoresis apparatus developed by Serwer (Electrophoresis 1987, 8, 301-304) that uses a pneumatic rotary actuator instead of a stepping motor, hence reducing the cost by about 50%. Other advantages of our design are a lower center of gravity that makes the apparatus more stable and the removal of all electrical power from beneath the fluid-filled electrophoresis chamber. We present data demonstrating the separation of chromosomal length DNA molecules from Saccharomyces cerevisiae strain 334 into 14 resolved bands in parallel lanes.

Pulsed field gel electrophoresis: studies of DNA migration made with the programmable, autonomously-controlled electrode electrophoresis system

We have studied the migration of DNA in pulsed field agarose gels under a variety of electrophoresis conditions. We have made use of an instrument which can generate electric fields of any orientation, magnitude, or duration to compare different separation techniques for DNA molecules of from 1 to several thousand kilobase pairs. We discuss the capabilities of the system and present results of gel runs in which electrophoresis conditions were changed individually or in combination. The mobility of DNA in pulsed field gels is shown to reflect a number of interdependent physical parameters.

Mobility surfaces for field-inversion gel electrophoresis of linear DNA

The mobility of linear DNA during field-inversion gel electrophoresis was measured as a function of molecular weight Mr, pulse time t, and field strength E. Values of Mr between 48.5 and 194 kilobase pairs (kb), E from 5 to 14 V/cm and pulse times of 0.3 to 12 s were used. The data are presented as three-dimensional surfaces of mobility: E:t for fixed Mr or graphs of mobility: Mr:t for fixed E. The surfaces are not smoothly increasing functions of E, Mr, or t but instead show a valley with minimum mobility and a steep rise in mobility as t increases. For a field of 10 V/cm, 1% agarose gels, and 3:1 ratio of forward:back pulse time, the forward switching time t* at which the mobility changes most rapidly is given by t* = (0.034 +/- 0.003) Mr for Mr in kb and t* in seconds. The data and equations delineate the best conditions to achieve a particular separation.

Sieving of double-stranded DNA during agarose gel electrophoresis

Agarose gel electrophoresis is used to fractionate linear, double-stranded DNA by its length. Sieving of the gel is the cause of this fractionation and has been investigated by developing theoretical models and by quantifying sieving observed during electrophoresis. Here are reviewed the following aspects of the fractionation of linear, double-stranded DNA by agarose gel electrophoresis: (1) the basic observations that qualitatively characterize these fractionations, (2) evidence for the deformation of DNA's random coil, (3) quantitative analysis of the relationship of observed electrophoretic mobility to the DNA's length, (4) theoretical models that have been developed to explain data presented in Sections 1-3, (5) observations not yet quantitatively explained by models, and (6) some aspects of the use of a variable electrical field (pulsed-field gel electrophoresis) to improve separations.

Effect of nonparallel alternating fields on the mobility of DNA in the biased reptation model of gel electrophoresis

Chromosome-size DNA molecules can now be separated using a variety of pulsed field gel electrophoresis techniques. In this article, we study the predictions of the biased reptation model concerning the effect of two pulsed fields, making an arbitrary angle, on the power of separation of gel electrophoresis. Separation is predicted to be largely enhanced for obtuse angles, in agreement with experiments. Interestingly, very large molecules, which are not separated by pulsed fields, are predicted not to migrate along the gel diagonal for fairly long periods of time. Finally, we discuss the optimization of these techniques using the results of the theory, and the limitations of the latter when fluctuations and intramolecular modes probably dominate the system.

Generalized tube model of biased reptation for gel electrophoresis of DNA

A theoretical analysis of the reptational motion of DNA in a gel that includes the effects of molecular fluctuations has been used to explain the main features found in experiments involving periodic inversion of the electric field. The resonance-like decrease of the electrophoretic mobility as a function of pulse duration is related to transient "undershoots" in the orientation of the molecule, in agreement with recent experimental data. These features arise from a delicate interplay of internal and center of mass motion of the molecules under pulsed field conditions, and are important for the separation of DNA molecules in the size range 0.2 to 10 million base pairs.

High-resolution separation and accurate size determination in pulsed-field gel electrophoresis of DNA. 3. Effect of electrical field shape

The resolution of pulsed-field gel electrophoresis is dramatically affected by the number and configuration of the electrodes used, because these alter the shape of the applied electrical fields. Here we present calculations and experiments on the effect of electrode position in one of the most commonly used pulsed-field gel electrophoresis configurations. The goal was to explore which aspects of the electrical field shape correlate with improved electrophoretic resolution. The most critical variable appears to be the angle between the alternate electrical fields. The most effective electrode configurations yield angles of more than 110 degrees. A continually increasing angle between the fields produces band sharpening that greatly enhances the resolution.

Electric field gradients and band sharpening in DNA gel electrophoresis

A mathematical study of the effect of non-uniform electric fields on the width of DNA electrophoretic bands is presented. Using a simple model, we show that field gradients sharpen these bands during an experiment if the corresponding gradient of electrophoretic velocity is large enough. This is in agreement with experimental results indicating that narrower bands form when pulsed field electrophoresis is carried out in the presence of field gradients. Moreover, it is shown that there is in fact an optimal experimental duration that maximizes separation. Finally, gradients are also predicted to reduce the relative mobilities of the DNA fragments, which is a serious drawback of this technique.

A novel instrument for separating large DNA molecules with pulsed homogeneous electric fields

A new instrument has been developed for the electrophoretic separation of large DNA molecules that can independently regulate the voltage of each of 24 electrodes and allow the magnitude, orientation, homogeneity, and duration of the electric field to be precisely controlled. Each parameter can be varied at any time during the electrophoretic process. Thus distinct sets of conditions can be combined to optimize the separation of various fragment sizes in a single run. Independent control of electrode voltage allows all of the fields to be generated with electrodes arranged in a closed contour, independent of a particular geometry. This device increases both the resolution in any size range and the speed of separation, especially for DNA molecules larger than 3 megabases.

Concatemerization and packaging of bacteriophage T7 DNA in vitro: determination of the concatemers' length and appearance kinetics by use of rotating gel electrophoresis

During its morphogenesis both in intact infected cells (in vivo) and in lysates of infected cells (in vitro), bacteriophage T7 forms end-to-end concatemers of its mature DNA, a linear, nonpermuted, terminally repetitious DNA. During morphogenesis, in vivo T7 concatemers are packaged in preformed capsids and cut to mature size. In the present study the lengths and appearance kinetics of concatemers formed in vitro from mature T7 DNA have been determined. The following procedures are used here for the first time: (a) 20-35% efficient in vitro concatemerization and packaging of T7 DNA; the mixture used for packaging contained two lysates that together had all T7 gene products, and (b) fractionation of concatemers by rotating gel electrophorsis (RGE), which improves the resolution by length of concatemer-length DNA. Concatemerization at 30 degrees was so fast that some other process must be rate limiting for packaging. The concatemers formed were linear and joined left-end to right-end by complementary base pairing, not by blunt-end ligation. Concatemers formed at 30 degrees were reconverted to mature DNA by packaging in vitro. Reducing the temperature to 0 degrees both slowed concatemerization to the time scale (minutes) needed for control of the extent of concatemerization and reduced packaging to insignificant levels, thereby also uncoupling packaging from concatemerization. At both 30 degrees and 0 degrees bands of discrete-length concatemers were observed by RGE. The lengths were n times the length of mature T7 DNA; n was found to be any integer from 2 to 15. The bands were stronger at 0 degrees than they were at 30 degrees in comparison to a background of heterogeneous DNA. No evidence for the favoring of any value of n was found. In addition, it was found by two-dimensional agarose gel electrophoresis that a comparatively small amount of circular DNA was produced in vitro.