Effects of DNA topology, temperature and solvent viscosity on DNA retardation in slalom chromatography

Slalom chromatography is a unique size-fractionation method applicable to large DNA molecules [>5 kilobase pairs (kbp)]. The method was first developed by using columns packed with microbeads (diameter, <20 microm) used for high-performance liquid chromatography and by applying a relatively fast flow-rate (>0.3 ml/min). Previous studies suggested that the separation is attributed to a hydrodynamic rather than to an equilibrium phenomenon (J. Hirabayashi and K. Kasai, Anal. Biochem. 178 (1989) 336; J. Hirabayashi, N. Itoh, K. Noguchi and K. Kasai, Biochemistry, 29 (1990) 9515). In the present report, the results of a systematic study on the effects of DNA topology, temperature, and solvent viscosity on DNA retardation are described. Firstly, the behaviour of circular (super-coiled) and linearized forms of charomid DNAs (20-42 kbp) was studied. Circular-form DNA molecules were found to be fractionated size-dependently similarly to linear forms in a flow-rate dependent manner. However, the extent of retardation of the circular form DNA was apparently less than that of the corresponding linear forms. Circular DNAs showed almost the same retardation (e.g., 42 kbp) as DNA fragments (e.g., 20 kbp) having approximately half of the size of the former. This observation indicates that DNA retardation is basically related to physical length, not to mass. Secondly, to study the effect of temperature with special reference to solvent viscosity, we carried out chromatographic analysis at various temperatures ranging from 6 to 65 degrees C in both the absence and presence of sucrose (10 or 20%, w/v). The results showed that it is the solvent viscosity that determines the extent of retardation. Taken together, all of physicochemical parameters that define hydrodynamic properties, i.e., particle size, flow-rate and solvent viscosity, proved to be critical in slalom chromatography as well as the potential physical length of the DNA, thus supporting the concept that slalom chromatography is based on a hydrodynamic principle.     

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.     

Studying the mechanism of RNA separations using RNA chromatography and its application in the analysis of ribosomal RNA and RNA:RNA interactions

DNA/RNA chromatography presents a versatile platform for the analysis of nucleic acids. Although the mechanism of separation of double stranded (ds) DNA fragments is largely understood, the mechanism by which RNA is separated appears more complicated. To further understand the separation mechanisms of RNA using ion pair reverse phase liquid chromatography, we have analysed a number of dsRNA and single stranded (ss) RNA fragments. The high-resolution separation of dsRNA was observed, in a similar manner to dsDNA under non-denaturing conditions. Moreover, the high-resolution separation of ssRNA was observed at high temperatures (75 °C) in contrast to ssDNA. It is proposed that the presence of duplex regions/secondary structures within the RNA remain at such temperatures, resulting in high-resolution RNA separations. The retention time of the nucleic acids reflects the relative hydrophobicity, through contributions of the nucleic sequence and the degree of secondary structure present. In addition, the analysis of RNA using such approaches was extended to enable the discrimination of bacterial 16S rRNA fragments and as an aid to conformational analysis of RNA. RNA:RNA interactions of the human telomerase RNA component (hTR) were analysed in conjunction with the incorporation of Mg²⁺ during chromatography. This novel chromatographic procedure permits analysis of the temperature dependent formation of dimeric RNA species.     

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.     

Chromatographic behaviour and purification of linear lambda phage and plasmid DNA molecules on 2-hydroxyethyl methacrylate-ethylene dimethacrylate-based supports

The HEMA-BIO 1000 support, which is based on a copolymer of 2-hydroxyethyl methacrylate and ethylene dimethacrylate, was used for separation of lambda DNA and its fragments and plasmid pBR322 DNA. The separation of fragments greater than 6.6 kbp was demonstrated according to the slalom chromatography mechanism on column for size-exclusion chromatography in the case of linear lambda DNA fragments. The influence of particle size of column packing, mobile phase rate, and KCl concentration in mobile phase is discussed. The purification of plasmid DNA pBR322 using size-exclusion chromatography was more rapid compared to gel electrophoresis. The presence of salts in the eluate is not disadvantageous. DNA can be recovered from the eluate by ethanol precipitation. Plasmid DNA pBR322 isolated in this way was suitable for different biological applications (cleavage with restrictases, electrotransformation into bacterial cells).     

Effects of sequence and structure in the separation of nucleic acids using ion pair reverse phase liquid chromatography

Ion pair reverse phase high performance liquid chromatography on non-porous alkylated poly(styrene-divinylbenzene) particles enables the high resolution separation of double stranded DNA fragments. To further understand the separation mechanisms involved in ion pair reverse phase liquid chromatography we have analysed the effects of curved or "bent" DNA fragments with respect to their separation using both gel electrophoresis and ion pair reverse phase liquid chromatography. Size dependent separations of curved DNA fragments that migrate anomalously during gel electrophoresis were observed using ion pair reverse phase liquid chromatography. To further study the sequence effect and resulting changes in hydrophobicity of the duplex DNA, PCR fragments were generated that contain uracil in place of thymine. The resulting fragments were shown to elute with shorter retention times, demonstrating that sequence-specific effects can alter the retention of duplex DNA. The study was extended to the investigation of non-canonical B-DNA structures (Holliday junctions) under various chromatographic conditions, demonstrating that the coaxial stacking of the helices in such structures, in the presence of magnesium causes a change in retention.     

Activation energy of single-stranded DNA moving through cross-linked polyacrylamide gels at 300 V/cm effect of temperature on sequencing rate in high-electric-field capillary gel electrophoresis

In DNA sequencing, single-stranded DNA fragments are separated by gel electrophoresis. This separation is based on a sieving mechanism where DNA fragments are retarded as they pass through pores in the gel. In this paper, we present the mobility of DNA sequencing fragments as a function of temperature; mobility is determined in 4% T LongRanger gels at an electric field of 300 V/cm. The temperature dependence is compared with the predictions of the biased reptation model. The model predicts that the fragment length for the onset of biased reptation with stretching increases with the square of temperature; the data show that the onset of biased reptation with stretching decreases with temperature. Biased reptation fails to model accurately the temperature dependence of mobility. We analyzed the data and extracted the activation energy for passage of sequencing fragments through the gel. For fragments containing less than ca. 200 bases, the activation energy increases linearly with the number of bases at a rate of 25 J/mol per base; for longer fragments, the activation energy increases at a rate of 6.5 J/mol per base. This transition in the activation energy presumably reflects a change in conformation of the DNA fragments; small fragments exist in a random coil configuration and larger fragments migrate in an elongated configuration.     

Simultaneously Sizing and Quantitating Zeptomole‐Level DNA at High Throughput in Free Solution

Determining the sizes and measuring the quantities of DNA molecules are fundamental tasks in molecular biology. DNA sizes are usually evaluated by gel electrophoresis, but this method cannot simultaneously size and quantitate a DNA at low zeptomole (zmol) levels of concentration. We have recently developed a new technique, called bare‐narrow‐capillary/hydrodynamic‐chromatography or BaNC‐HDC, for resolving DNA based on their sizes without using any sieving matrices. In this report, we utilize BaNC‐HDC for measuring the sizes and quantities of DNA fragments at zmol to several‐molecule levels of concentration. DNA ranging from a few base pairs to dozens of kilo base pairs are accurately sized and quantitated at a throughput of 15 samples per hour, and each sample contains dozens of DNA strands of different lengths. BaNC‐HDC can be a cost‐effective means and an excellent tool for high‐throughput DNA sizing and quantitation at extremely low quantity level.     

DNA migration regimes in hydrodynamic chromatography and slalom chromatography: evidence for a transition

Recently, we hypothesized that DNA separation mechanisms in slalom chromatography (SC) and packed column hydrodynamic chromatography (HDC) could be connected and simultaneously observed 'J. Chromatogr. A 886 (2000) 1'. The present paper describes the migration of various circular and linear double-stranded DNAs in a chromatographic system using a C1 stationary phase and an acetonitrile-phosphate buffer mixture as a mobile phase. The migration dependence on the flow rate for the different species showed the relative contribution of both the SC and HDC separation mechanisms. A transition between the SC and HDC regimes was demonstrated for the first time. In addition, the data were analyzed in terms of polymer migration in a dense structure. Three different behaviors were distinguished in relation to the size and the compactness of the nucleic acid.     

Water-organic solvent systems in countercurrent chromatography: Liquid stationary phase retention and solvent polarity

Countercurrent chromatography (CCC) is a separation technique in which the stationary phase is a liquid. The liquid stationary phase retention is a critical problem in CCC. The retention of 18 organic solvents in a hydrodynamic CCC apparatus was measured with an aqueous mobile phase, the centrifuge spin rate and the mobile phase flow rate being constant, 800 rpm and 2 ml/min, respectively. Conversely, water retention was measured when the 18 solvents were the mobile phases. A direct relationship between the liquid stationary phase retention and the phase density difference was found. The liquid phase density difference is the most important parameter for stationary phase retention in a hydrodynamic CCC apparatus with coiled tubes. The chromatographic retention of formanilide was measured in biphasic systems and expressed as the formanilide partition coefficient. It is shown that the partition coefficient correlates with the Reichardt polarity index of the organic solvent when the liquid stationary phase retention volume does not.     

Rapid high-performance liquid chromatography of nucleic acids with polystyrene-based micropellicular anion exchangers

Nucleic acids were separated by ion-exchange chromatography on 30 x 4.6 and 100 x 4.6 mm columns packed with a micropellicular anion exchanger made of 3-microns rigid polystyrene-based non-porous microspheres with a covalently bound hydrophilic layer and DEAE functional groups at the surface. The stationary phase particles showed negligible swelling in methanol according to permeability measurements with water and methanol. Nucleic acids and their fragments including synthetic single-stranded oligonucleotides, linear, nicked and supercoiled DNAs as well as DNA restriction fragments were separated in less than 5 min, a time scale that is much smaller than that of conventional high-performance liquid chromatographic analysis for such samples. When only buffer and sodium chloride were used in the eluent for the separation of double-stranded DNA restriction fragments pGEM-3Z/Taq I, electrophoretic analysis of the effluent revealed the presence of smaller fragments in the bands of the larger ones. Upon addition of ethylenediaminetetraacetic (EDTA) salt to the eluent, however, such contamination by shorter fragments was no longer observed. In the absence of EDTA, magnesium chloride in the eluent at a concentration of 1 mM precluded the separation of the restriction fragments under otherwise identical chromatographic conditions.     

Supercoiled circular DNA retention in nonequilibrium chromatography: viscosity and velocity dependence--behavior difference with proteins

This study demonstrates that the retention behavior of various circular double-stranded DNA molecules (3, 5, and 10 kb) increases over the entire flow-rate range (0.02-1.8 mL/min) at all the mobile phase viscosities (h). The transition between the two well-known nonequilibrium chromatography methods (slalom and hydrodynamic chromatography) is clearly visualized for proteins and does not appear for plasmids because of their strong compact structure. Also, the optimal conditions for F and h are determined to obtain the most efficient separation of these three plasmids in a minimum analysis time.     

Mass transfer characteristics of plasmids in monoliths

The hydrodynamic properties and pore-structure of monoliths based on functionalized poly(glycidyl methacrylate-ethylene dimethacrylate) were characterised by pulse response experiments using different probes representing a wide range of molecular mass. On a small scale, band spreading was found to be caused to the extent of more than 90% by extra-column effects. These monoliths have large channel diameters, providing a suitable chromatography adsorbent for processing of large molecules. Dynamic and static binding capacity for plasmid DNA was investigated. For our model plasmid, consisting of 4.9 kbp, a capacity of 7 mg/mL was observed in comparison to 0.3 mg/mL for a conventional medium designed for protein separation. When plasmids were loaded on the monolith a gradual increase in pressure drop was observed. The channels filled up and the cross-sectional area available for liquid flow decreased. Therefore, a higher pressure drop was observed during elution. This is caused by (i) shrinking of the channels as effect of the high salt concentration, (ii) high viscosity of the mobile phase due to high concentration of plasmids, and (iii) an increase of the hydrodynamic radius of the plasmid with salt concentration from 45 nm at 150 mM to 70 nm at 2 M NaCl, as measured by dynamic light scattering. These types of monoliths are considered to be the preferred adsorbents for plasmid separation.     

Electric and hydrodynamic stretching of DNA-polymer conjugates in free-solution electrophoresis

The conjugation of an uncharged polymer to DNA fragments makes it possible to separate DNA by free-solution electrophoresis. This end-labeled free-solution electrophoresis method has been shown to successfully separate ssDNA with single monomer resolution up to about 110 bases. It is the aim of this paper to investigate in more detail the coupled hydrodynamic and electrophoretic deformation of the ssDNA-label conjugate at fields below 400 V/cm. Our model is an extension of the theoretical approach originally developed by Stigter and Bustamante [Biophys. J. 75, 1197 (1998)] to investigate the problems of a tethered chain stretching in a hydrodynamic flow and of the electrophoretic stretch of a tethered polyelectrolyte. These two separate models are now used together since the charged DNA is "tethered" to the uncharged polymer (and vice versa), and the resulting self-consistent model is used to predict the deformation and the electrophoretic velocity for the hybrid molecule. Our theoretical and experimental results are in good qualitative agreement.     

Experimental observations of the hydrodynamic behavior of solvent systems in high-speed counter-current chromatography. III. Effects of physical properties of the solvent systems and operating temperature on the distribution of two-phase solvent systems

Statistical studies were made to correlate the hydrodynamic behavior of two-phase solvent system in counter-current chromatography (CCC) to their physical properties including interfacial tension, viscosity, and the difference in density of the two phases. Settling time measured under unit gravity provided a reliable numerical index for the hydrodynamic behavior of the solvent systems in a centrifugal force field. Viscosity and settling time were strongly correlated (correlation coefficient, r = +0.88) while interfacial tension (r = -0.65) and phase density difference (r = -0.45) showed moderate and weak correlation, respectively. Studies of the effect of temperature on settling time as well as a preliminary apparatus operated at higher temperature show that raising the temperature will improve the performance of high-speed CCC.     

Mobile phase viscosity and velocity dependence on protein retention using nonequilibrium chromatographic techniques

Nonequilibrium chromatography (NEC) is an alternative chromatographic procedure for the separation of macromolecules. The retardation of a protein series is studied using a phosphate buffer as a mobile phase with various concentrations of glycerol fraction (used as a viscosity modifier) at different mobile phase velocities and a C1 column with a very low packing particle diameter as a stationary phase. It is shown that the two factors (viscosity and velocity) of the mobile phase constituted important parameters in the retention mechanism of the proteins in NEC. The retardation velocity domain is divided into two regions. For low velocity regions, the protein retention decreased with a mobile phase velocity increase. This retention is enhanced above a critical value of the mobile phase velocity. The transition between the two well-known NEC methods, slalom chromatography and hydrodynamic chromatography, is clearly visualized for the first time for the protein retention of particular values of the mobile phase velocity.     

CE of Small DNA Fragments Using Linear Polyacrylamide Matrices

Mutations at codons 248 and 249 of p53 gene showed a relatively high incidence in gastric cancer patients. Development of novel methods for the detection of codon mutations is of great importance for gastric cancer research. Studies have showed that the separation matrix can significantly influence the separation efficiency and resolution of small DNA fragments in CE. In order to achieve baseline separation of PCR-amplified products of small DNA fragments from gastric cancer tissue, linear polyacrylamides (LPA I and LPAII) were designed and synthesized in the current study. LPAI and LPAII were used as separation matrixes to separate small size fragments (less than 70 bp) of pBR322/BsuRI DNA Marker and the separation conditions were optimized. Optimum separations were performed at 25 kV in reversed-polarity mode with capillary temperature set at 15 °C. The signal of DNA fragments was detected using laser-induced fluorescence detector, with an argon ion laser as the excitation source that emits at 488 nm. A 520 nm bandpass filter was used as an emission cut-off filter. The resolution of small DNA fragments was higher when LPAI was used as separation matrix compared to LPAII, accompanied with longer migration time. The results indicated that LPAI as separation matrix was more efficient for the separation of small DNA fragments (less than 70 bp) than other LPAs. A rapid and sensitive analysis method for the separation and detection of small DNA fragments (less than 70 bp) was established in this study. The method was successfully applied to detect the mutations at codons 248 and 249 in p53 gene from gastric cancer tissues.     

The interaction of copper-bipyridyl complex with DNA and cleavage to DNA.

The interaction of a copper-bipyridyl (bpy) complex with CT-DNA was investigated by voltammetry, absorption and fluorescence spectrophotometry. The binding constant of the Cu(bpy)2(2+) complex interacting with DNA was 3.24 x 10(4) L/mol and the ability binding of Cu(bpy)2(2+) to DNA was 1.3-times as large as that of Cu(bpy)2+ to DNA. DNA could be efficiently cleaved by a potential-modulated method in the presence of the Cu(bpy)2(2+) complex. The fragments of the cleaved DNA were separated by high-performance liquid chromatography (HPLC). The experimental results revealed that the proposed method for DNA cleavage is highly efficient.     

Influence of the order parameter and of the director orientation on the surface tension of free nematic films

A radial hydrodynamic flow in the nematic phase of free, suspended cylindrical films of 4-n-heptyl- and decyloxybenzoic acid and in 4,4'-di-n-heptyl-oxyazoxybenzene has been observed. The flow starts about 7°C before the phase transition into the smectic C phase. Under the same experimental conditions such a hydrodynamic flow is not established in free nematic films of 4-n-heptyl-and octyloxy-4'-cyanobiphenyl, 4,4'-dimethoxyazoxybenzene and N-(4-ethoxybenzylidene)-4'-n-butylaniline after the completion of the transition from the isotropic liquid to the nematic phase. The observed hydrodynamic flow is explained by a non-linear temperature dependence of the surface tension.