Separation of different physical forms of plasmid DNA using a combination of low electric field strength and flow in porous media: effect of different field gradients and porosity of the media

The retention of different physical forms of DNA by an electric field in a chromatography system was studied. We were able to effectively separate the supercoiled and the open circular forms of plasmid DNA using this type of electrochromatography system. Chromatography columns were packed with porous beads, and an axial electric field was applied so that convective buffer flow opposed the direction of electrophoresis of the DNA. A model system composed of approximately equal amounts of the super-coiled and open circular forms of the plasmid pBR 322 (4322 base pairs) was used to test the separation. Chromatography beads (agarose-based) with different porosities were used to determine the effect of the stationary phase on the separation. The porous media did not have a major effect on the separation, but the best separations were obtained using porous chromatography media made with the highest agarose concentration (10% agarose). Selective elution of plasmid DNA with different forms was obtained by either increasing the flow rates or decreasing the electric field strength (by steps or a gradient). In all the separations, the more compact supercoiled form of the plasmid was retained less strongly than either the open circular form (nicked) or the linear form. High molecular weight host genomic DNA was more strongly retained than the plasmid DNA. Increasing the ionic strength of the buffer improved resolution and capacity. The capacity of the separation was determined by injecting increasing amounts of plasmid DNA. Satisfactory separation was obtained at sample loading of up to 360 microg of total DNA on a column with dimensions of 2.5 by 11 cm (bed volume of 54 mL). The retention of DNA depends upon a counter-current flow of electrophoresis and convective flow and could be regarded as a type of field flow fractionation. The retention of the DNA by the electric field and flow is discussed in relation to the diffusion coefficients of the DNA.     

样品稀释对毛细管电泳分离检测DNA片段的影响

通过理论推导和实验验证表明;适当稀释DNA样品溶液,采用流体力学进样或电动进样都不会较大地减低峰高,而DNA片段毛细管电泳的分离效率和分离度还能有所提高。采用稀释样品的方法可提高DNA样品的使用效率。采用羟乙基纤维素无胶筛分介质分离了DNA片段。用激光诱导荧光（氩离子激光器,488nm）电荷耦合器件检测。用低浓度的筛分介质（0．4％）分离了分子质量较大的ADNA－HindⅢ全部8个片段（12bp～23130bP）。用高浓度的筛分介质（1．6％）分离分子质量较小的pBR322－HaeⅢ22个片段（18bp～587bp）。     

Anion-exchange chromatography of DNA restriction fragments.

The abilities of several high-performance liquid chromatography (HPLC) anion-exchange packings to separate DNA restriction fragments, ranging in size from 50 to 23,000 base pairs, were studied. The ion exchangers investigated include the porous packings Protein-Pak DEAE-5PW, Nucleogen-DEAE 4000-7, Poros-Q and BakerBond WP-PEI, and the non-porous packings TSK Gel DEAE-NPR, Gen-Pak FAX, and ProPac PA1. The results indicated that the non-porous packings could separate all 18 fragments (less than 600 base pairs) in a pBR322 DNA-HaeIII digest, while of the porous packings, only Nucleogen-DEAE 4000-7 could resolve DNA fragments in this size range. Only Gen-Pak FAX and TSK Gel DEAE-NPR could significantly resolve the very large DNA fragments (125-23,000 base pairs) of a lambda DNA-HindIII digest. The chromatographic parameters governing this separation by Gen-Pak FAX were optimized so that six of eight fragments were resolved. Split-peak phenomena were observed at low flow-rates when employing non-poros packings, but were eliminated by the incorporation of organic modifiers or surfactants, suggesting that, under certain conditions, hydrophobicity may play a significant role in separations on this packing. Gen-Pak FAX also separated 21 of 23 fragments in a 1000-base pair DNA ladder, a performance which, in addition to the quantitative capabilities of HPLC, makes anion-exchange chromatography a powerful method complementary to slab-gel electrophoresis, and perhaps preferable over agarose gel electrophoresis for applications such as the confirmation of plasmid integrity.     

Identifying the orientation of DNA fragment in recombinant plasmid by capillary electrophoresis with a non-gel sieving solution.

It was demonstrated that a capillary electrophoresis (CE) method with a non-gel sieving solution has been developed to identify the orientation of DNA fragments in recombinant plasmids in molecular biology. The influences of the concentration of sieving polymer HEC, the applied electric field strength and sampling on CE separation were analyzed concerning the optimization of separation. YO-PRO-1 was used as a DNA intercalating reagent to facilitate fluorescence detection. Under the chosen conditions (buffer, 1 x TBE containing 1 microM YO-PRO-1 and 1.2% HEC; applied electric field strength, 200 V/cm; electrokinetic sampling: time, 5 s; voltage, -6 kV), three DNA markers (phi 174/HaeIII, pBR322/HaeIII and lambda DNA/HindIII) were tested for further evaluating the relationship between the DNA size and the mobility. The established CE method conjugated with the enzymatic approach was successfully applied to identifying the DNA orientation of recombinant plasmid in transgene operations of a newly cloned gene from Arabidopsis Thaliana.     

Effect of temperature on DNA fractionation in slalom chromatography

Slalom chromatography is an alternative chromatographic procedure for the analysis of relatively large double-stranded DNA molecules and is based on a hydrodynamic principle. The retardation of the DNA fragments from the cleavage of the Lambda DNA by the KpnI restriction enzyme was studied using an acetonitrile-phosphate buffer as a mobile phase (flow rate equal to 0.3 ml/min) and a C1 column as a stationary phase at various temperatures. It was shown that the temperature constituted an important parameter for the separation of the DNA fragments in slalom chromatography. The DNA hydrodynamic behavior with the temperature was related to the variation in the fluid viscosity and the modification of the elastic properties of the biopolyrner.     

Mobile-phase-viscosity dependence on DNA separation in slalom chromatography

Slalom chromatography (SC) is an alternative chromatographic procedure for the separation of relatively large double-stranded DNA molecules and is based on a new principle. The retardation of the DNA fragments from the cleavage of the Lambda DNA by the KpnI restriction enzyme was studied using an acetonitrile-phosphate buffer as a mobile phase with various concentrations of viscosity modifier (i.e. glycerol) and a C1 column as a stationary phase. The DNA molecule retention was accurately described over the glycerol concentration range using a model previously established. It was shown that the eluent viscosity increase enhanced the slalom chromatographic capacity to separate the DNA fragments. A connection between SC and 'hydrodynamic chromatography' processes was predicted to link the two processes in a global separation mechanism based on a non-equilibrium principle.     

Molecular mass distribution analysis of ethyl(hydroxyethyl)cellulose by size-exclusion chromatography with dual light-scattering and refractometric detection

Dual low-angle light scattering and refractometric detection coupled to size-exclusion chromatography provided proof for the presence of a low amount of stable aggregates/particles in ethyl(hydroxyethyl)cellulose. Unlike the correct size-exclusion chromatographic behavior of the parent polysaccharide itself, the aggregates exhibit variable size-dependent weak retention as a function of flow-rate and of ionic strength of the aqueous mobile phase. Therefore, determination of the molecular mass of non-aggregated polymer is possible in aqueous mobile phase containing 0.1 M NaCl under conditions at which aggregates are completely adsorbed on the column packing irrespective of the flow-rate used. Flow-rate and ionic strength-dependent variations of aggregate behavior as well as model size-exclusion experiments with latex particles indicate that they partly carry a minute charge and have a compact structure. Their weak retention under the separation conditions used suggests a difference in their surface chemistry when compared with the dissolved polymer coils which exhibit a correct size-exclusion behavior.     

Fractionation of apple procyanidins by size-exclusion chromatography.

Oligomeric constituents of apple procyanidins were fractionated by size-exclusion chromatography using a TSKgel Toyopearl HW-40F column. The best separation was obtained using a mobile phase of acetone-8 M urea (6:4; adjusted to pH 2) at a flow-rate of 1.0 ml/min. In this chromatographic system, the use of 8 M urea in the mobile phase resulted in a molecular sieve effect without any surface affinity interaction between the gel beads and the procyanidin molecules. Each fraction obtained was examined by reversed-phase high-performance liquid chromatography and time-of-flight mass spectrometry. The order of elution of the procyanidins from the column was coincident with their degree of polymerization.     

Comparison of the separation of proteins of wide-ranging molecular weight via trilobal polypropylene capillary-channeled polymer fiber,commercial superficiously porous,and commercial size exclusion columns

Reversed phase and size-exclusion chromatography methods are commonly used for protein separations, although they are based on distinctly different principles. Reversed phase methods yield hydrophobicity-based (loosely-termed) separation of proteins on porous supports, but tend to be limited to proteins with modest molecular weights based on mass transfer limitations. Alternatively, size-exclusion provides complementary benefits in the separation of higher mass proteins based on entropic, not enthalpic, processes, but tend to yield limited peak capacities. In this study, microbore columns packed with a novel trilobal polypropylene capillary-channeled polymer fiber were used in a reversed phase modality for the separation of polypeptides and proteins of molecular weights ranging from 1.4 to 660 kDa. Chromatographic parameters including gradient times, flow rates, and trifluoroacetic acid concentrations in the mobile phase were optimized to maximize resolution and throughput. Following optimization, the performance of the trilobal fiber column was compared to two commercial-sourced columns, a superficially porous C4-derivatized silica and size exclusion, both of which are sold specifically for protein separations and operated according to the manufacturer-specified conditions. In comparison to the commercial columns, the fiber-based column yielded better separation performance across the entirety of the suite, at much lower cost and shorter separation times.     

High-performance liquid chromatography of nucleic acid constituents: Chromatographic examination of novel stationary phases

Summary Silica-bonded stationary phases were developed for the separation of nucleic acid constituents and their properties investigated with homologous oligoriboadenylic acids in electrostatic interaction chromatography and with alkylbenzenes in reversed-phase chromatography. Analysis of retention data confirmed the stratified molecular structure of the surface which consist of a layer of propyl chains anchoredvia siloxane bridges to the silica surface proper and of polar moieties attached to the hydrocarbonaceous functions. The polar top layer contains weak cationic and/or hydrophobic binding sites, is strongly hydrated in contact with aqueous eluents and bars the access by large biopolymers to the hydrocarbonaceous sublayer. In reversed-phase chromatography of small non polar molecules with hydro-organic eluents, however, this layer is accessible and engenders a retentive behavior typical for weak hydro-carbonaceous bonded phases. As a result the stationary phases, depending on the nature of the sample and the mobile phase, exhibit the properties of "soft" phases for the chromatography of biopolymers under mild elution conditions and those of "hard" phases for the separation of small non-polar molecules under conditions generally employed in reversed-phase chromatography. The retention of nucleic acid constituents on most of the stationary phases investigated subject to a dual mechanism as a result of the interplay of electrostatic and hydrophobic interactions between the eluites and the binding sites on the stationary phase surface. Siliceous stationary phases having surface morphology described above are suitable for the separation of nucleic acid constituents having widely ranging molecular weights up to 3 × 10⁶ Daltons provided the support has appropriate pore dimensions. This is demonstrated by the separation of mixtures arising from digesting t-RNA^pha or polyadenylic acids as well as those of ribosomal RNA’s and different forms of the plasmid pBR322 DNA. Presented at the 15th International Symposium on Chromatography, Nürnberg, October 1984     

Poppe plots for size-exclusion chromatography

Poppe plots provide a clear and unambiguous way to discuss the performance limits of separation systems. The effects of particle size, pressure drop and column permeability can be illustrated using such plots. The performance limits of size-exclusion chromatography are of interest, due to developments in combinatorial chemistry and high-throughput experimentation. In these fields, fast separations of high-molecular-weight analytes are required. In this paper, Poppe plots will be presented for size-exclusion chromatography. Because of the very high-reduced velocities encountered, the Poppe plots are found to be significantly different from those commonly observed in HPLC. Fast separations in size-exclusion chromatography are not as unfavourable as suggested by conventional theory. The results are based on experimental data obtained for a wide range of polystyrenes (1.7-3.25 kDa) using THF as mobile phase, but may be equally valid in other cases.     

Separation of tanshinones from Salvia miltiorrhiza bunge by multidimensional counter-current chromatography

Non-equilibrium chromatography (NEC) is a chromatographic mode for the rapid separation of polymers. The retention behavior of various proteins (human, chicken, bovine serum albumin) and supercoiled circular double-stranded DNA (plasmids) was investigated using a phosphate buffer as a mobile phase at different velocities and column temperatures with a C₁ column with very low-packing particle diameter as a stationary phase. It was shown that the two factors (temperature and velocity) constituted important parameters in the retention mechanism of plasmids and proteins in NEC. The protein was retained more than the plasmid. At all the temperatures (5, 10, 15, 20, 25 °C) the plasmid retention increased over the entire flow-rate range (0.02–1.8 ml/min). For the protein, the retention curve presented a decrease in the relative retention time until a critical value of the mobile phase flow-rate, followed by an increase. The transition between the two well known NEC methods, slalom chromatography and hydrodynamic chromatography was clearly visualized for proteins at the lowest temperature, but did not appear for plasmids due to their strong compact structure.     

Micellar gradients in size-exclusion simulated moving bed chromatography

The selectivity of size-exclusion chromatography (SEC) can be modified by adding non-ionic micelles to the mobile phase. Surfactant-aided size-exclusion chromatography (SASEC) can therefore very well be performed in a gradient mode on an SMB, as is reported in this paper. A method has been developed for correctly positioning a micellar gradient over an SMB. The method is applied for size-exclusion chromatography with the non-ionic surfactant C12E23 as gradient forming solute, and demonstrated by applying it to a relevant chromatographic protein separation problem.     

Fast size-exclusion chromatography at high temperature

We report on the size-exclusion chromatography (SEC) operated at high column temperature to reduce the analysis time. The column temperature was raised beyond the normal boiling point of the eluent and a sufficient column backpressure was applied to prevent the mobile phase from boiling by inserting a narrow bore tubing between the separation column and the detector. The narrow bore tubing also functions to cool the effluent down to the room temperature before it reaches the detector. Therefore, normal SEC detectors can be used without any modification. It was confirmed that the SEC analysis time could be shortened significantly by the high-temperature operation without serious deterioration in the resolution.     

Retention mechanism of poly(ethylene oxide) in reversed-phase and normal-phase liquid chromatography

The retention behavior of low- and high-molecular-mass poly(ethylene oxide) (PEO) in reversed-phase (RP) and normal-phase (NP) liquid chromatography was investigated. In RPLC using a C18 bonded silica stationary phase and an acetonitrile-water mixture mobile phase, the sorption process of PEO to the stationary phase showed deltaH(o) > 0 and deltaS(o) > 0. Therefore, PEO retention in RPLC separation is an energetically unfavorable, entropy-driven process, which results in an increase of PEO retention as the temperature increases. In addition, at the enthalpy-entropy compensation point the elution volume of PEO was very different from the column void volume. These observations are quite different from the RPLC retention behavior of many organic polymers. The peculiar retention behavior of PEO in RPLC separation can be understood in terms of the hydrophobic interaction of this class of typical amphiphilic compounds with the non-polar stationary phase, on the one hand, and with the aqueous mobile phase, on the other. The entropy gain due to the release of the solvated water molecules from the PEO chain and the stationary phase is believed to be responsible for the entropy-driven separation process. On the other hand, in NPLC using an amino-bonded silica stationary phase and an acetonitrile-water mixture mobile phase, PEO showed normal enthalpy-driven retention behavior: deltaH(o) < 0 and deltaS(o) < 0, with the retention decreasing with increasing temperature and PEO eluting near the column void volume at the enthalpy-entropy compensation point. Therefore, high-resolution temperature gradient NPLC separation of high-molecular-mass PEO samples can be achieved with relative ease. The molecular mass distribution of high-molecular-mass PEO was found to be much narrower than that measured by size-exclusion chromatography.     

Resolution of circular, nicked circular and linear DNA, 4.4 kb in length, by electrophoresis in polyacrylamide solutions.

Circular DNA of more than 1,400 bp in size is known not to migrate into polyacrylamide gels. The migration of supercoiled plasmid pBR322 DNA (4,363 by) into uncrosslinked polyacrylamide (Mw 5 x 10(6)) solutions and its separation, on the basis of conformation, from its nicked form is demonstrated in this study. Migration of the supercoiled, nicked circular and linear forms of the plasmid DNA is retarded in proportion to the concentration of uncrosslinked polyacrylamide, the degree of retardation being highest for the nicked circular form. Decreasing the level of supercoiling of the covalently closed circular form by decreasing the concentration of the intercalating dye (ethidium homodimer) shows that the degree of retardation decreases in proportion to the superhelix density.     

Preparative size-exclusion chromatography for purification and characterization of colloidal quantum dots bound by chromophore-labeled polymers and low-molecular-weight chromophores

We explore the use of preparative size-exclusion chromatography (SEC) and high-performance liquid chromatography (HPLC) to purify quantum dots (QDs) after surface modification. In one example, in which Bio-Beads (S-X1) were used as the packing material for the preparative SEC column, CdSe QDs treated with a functional coumarin dye could be separated from the excess free dye by using tetrahydrofuran (THF) as the mobile phase. This column was unable to separate polymer-coated QDs from free polymer (M ∼ 8000) because of the relatively low cutoff mass of the column. Here a preparative HPLC column packed with TOYOPEARL gel allowed the effective separation of polymer-bound QDs from the excess free polymer by using N-methyl-2-pyrrolidinone (NMP) as the mobile phase. When other solvents such as absolute ethanol, acetonitrile, THF, and THF–triethylamine mixtures were used as the eluent, QDs stuck to the column. While NMP was an effective medium to remove excess free polymer from the QDs, it was difficult to transfer the purified QDs to more volatile solvents and maintain colloidal stability.     

Selectivity in preparative separations of inorganic electrolytes by size-exclusion chromatography on hypercrosslinked polystyrene and microporous carbons

Preparative-scale separation of concentrated solutions of simplest mineral electrolytes by size-exclusion chromatography was performed on three samples of commercially available microporous hypercrosslinked polystyrene sorbents "Macronet Hypersol" and two experimental samples of activated carbons. Selectivity of separation of a pair of electrolytes was found to be determined by the largest ions in each pair. Fortunately, selectivity rises at higher concentrations of electrolytes, which was explained by exclusion of smaller species from the concentrated solution, i.e., mobile phase, into small pores of the column packing that are inaccessible to large species. The separation of concentrated mixtures revealed another remarkable advantage of the new process - self-concentrating of each of two separated components in the corresponding fractions. Self-concentration is more pronounced for the minor component that occupied less space in the initial mixture. The new method may prove productive in processing pickle bath solutions.     

Use of hydrophilic hydroxypropyl methacrylate/ethylene glycol methacrylate packing material in size-exclusion chromatography

Spherical particles of hydroxypropyl methacrylate/ethylene glycol methacrylate copolymer were synthesized in-house for use in size-exclusion chromatography. The porous hydrophilic material was packed in glass and stainless steel columns to evaluate their chromatographic performance. The support particles were small (approximately 20 A), and the average pore size was in the low range of mesopores (approximately 100 A). The packed columns were calibrated by using polysaccharide dextrans, showing a good range of separation for molecular weights between 10000 and 600000 daltons. The packing material appears to separate the large molecules through the size-exclusion mechanism. Polysaccharides and polypeptides dissolved in adequate mobile phases were injected into the packed column. The separation of the macromolecules was consistent with the size-exclusion mechanism. Application of the packing material to the separation of small molecules (alkyl alcohols) was also investigated.     

CU(II) SENSITIZES pBR322 PLASMID DNA TO INACTIVATION BY UV-B(280–315 nm)

Abstract— Copper(II), in the presence of UV-B radiation(280–315 nm), can generate single-strand breaks in the sugar-phosphate backbone of pBR322 plasmid DNA. A low level of single-strand backbone breaks occurs in the presence of Cu(II) alone, but UV-B irradiation increases the rate by the more than 100-fold. Concomitant with the damage to the DNA backbone is a loss of transforming activity. Oxygen is required for generation of the single-strand breaks but not for the loss of transforming activity. A DNA glycosylase (Fpg), which participates in the repair of certain DNA nitrogenous base damage, does not repair plasmid DNA damaged by Cu(II). The hydroxyl radical scavenging compound DMSO is only somewhat effective at protecting the physical and biological properties of the DNA. These results with Cu(II) are compared to those obtained previously with pBR322 plasmid DNA in the presence of Fe(III) and UV-A.