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1.
Kan CW  Barron AE 《Electrophoresis》2003,24(1-2):55-62
We present a "proof-of-concept" study showing that a blend of thermo-responsive and nonthermo-responsive polymers can be used to create a DNA sieving matrix with a thermally tunable mesh size, or "dynamic porosity". Various blends of two well-studied sieving polymers for CE, including hydroxypropylcellulose (HPC), a thermo-responsive polymer, and hydroxyethylcellulose (HEC), a nonthermo-responsive polymer, were used to separate a double-stranded DNA restriction digest (Phi X174-HaeIII). HPC exhibits a volume-phase transition in aqueous solution which results in a collapse in polymer coil volume at approximately 39 degrees C. Utilizing a blend of HPC and HEC in a ratio of 1:5 by weight, we investigated the effects of changing mesh size on DNA separation, as controlled by temperature. High-resolution DNA separations were obtained with the blended matrix at temperatures ranging from 25 degrees C to 38 degrees C. We evaluated changes in the selectivity of DNA separation with increasing temperature for certain pairs of small and large fragments. A pure HEC (nonthermo-responsive) matrix was used over the same temperature range as a negative control. In the blended matrix, we observe a maximum in selectivity at approximately 31 degrees C for small DNA, while a significant increase in the selectivity of large-DNA separation occurs at approximately 36 degrees C as the polymer mesh "opens". We also demonstrate, through a temperature ramping experiment, that this matrix can be utilized to obtain high-resolution separation of both small and large DNA fragments simultaneously in a single CE run. Blended polymer matrices with "dynamic porosity" have the potential to provide enhanced genomic analysis by capillary array or microchip electrophoresis in microfluidic devices with advanced temperature control.  相似文献   

2.
Xu F  Baba Y 《Electrophoresis》2004,25(14):2332-2345
We give an overview of recent development of low-viscosity polymer solutions and entropic trapping networks for double-stranded DNA (dsDNA) separations by conventional capillary electrophoresis and microchip electrophoresis. Theoretical models for describing separation mechanisms, commonly used noncross-linked polymer solutions, thermoresponsive (viscosity-adjustable) polymer solutions, and novel entropic trapping networks are included. The thermoresponsive polymer solutions can be loaded at one temperature into microchannels at lower viscosities, and used in separation at another temperature at entanglement threshold concentrations and higher viscosities. The entropic-based separations use only arrays of regular obstacles acting as size-separations and do not need viscous polymer solutions. These progresses have potential in integration to automated capillary and microfluidic chip systems, enabling better reusability of separation microchannels, much shorter DNA separation times, and higher reproducibility due to less matrix degradation.  相似文献   

3.
Sun M  Lin JS  Barron AE 《Electrophoresis》2011,32(22):3233-3240
Double-stranded (ds) DNA fragments over a wide size range were successfully separated in blended polymer matrices by microfluidic chip electrophoresis. Novel blended polymer matrices composed of two types of polymers with three different molar masses were developed to provide improved separations of large dsDNA without negatively impacting the separation of small dsDNA. Hydroxyethyl celluloses with average molar masses of ~27 kDa and ~1 MDa were blended with a second class of polymer, high-molar mass (~7 MDa) linear polyacrylamide. Fast and highly efficient separations of commercially available DNA ladders were achieved on a borosilicate glass microchip. A distinct separation of a 1-kb DNA extension ladder (200-40,000 bp) was completed in 2 min. An orthogonal design of experiments was used to optimize experimental parameters for DNA separations over a wide size range. We find that the two dominant factors are the applied electric field strength and the inclusion of a high concentration of low-molar mass polymer in the matrix solution. These two factors exerted different effects on the separations of small dsDNA fragments below 1 kbp, medium dsDNA fragments between 1 and 10 kbp, and large dsDNA fragments above 10 kbp.  相似文献   

4.
A temperature sensitive dopamine-imprinted polymer was prepared in 80% aqueous methanol solution by free-radical cross-linking co-polymerisation of methacrylic acid and acrylamide at 60 degrees C in the presence of N,N-methylene-bis-acrylamide as the cross-linker and dopamine hydrochloride as template molecule. The resulting molecularly imprinted polymer (MIP) formed temperature responsive materials, which could be used for the selective separation of appropriate dopamine and adrenergic compounds from a liquid matrix at ambient temperatures. The thermoresponsive MIP exhibited a swelling-deswelling transition in 80% aqueous methanol solution at about 35 degrees C. The capacity of the thermoresponsive MIP to recognise the template molecule when present in aqueous methanol solution changed with temperature, with the highest selectivity found at 35 degrees C. Additionally, binding parameters obtained from Scatchard analyses indicate that increasing temperature resulted in an increased affinity and binding capacity of specific binding sites, but had less effect on non-selective binding sites. Subsequently, the thermoresponsive MIP was tested for its application as a sorbent material, utilisable in the selective solid-phase extraction (SPE) of dopamine and other adrenergic compounds (epinephrine, isoproterenol, salbutamol and serotonin) from urine samples. It was shown that the compounds that were structurally related to dopamine could be removed by elution, while dopamine and serotonin, the analytes of interest, remained strongly adsorbed to the adsorbent during SPE applications. The thermoresponsive MIP displayed different efficiency in clean-up and enrichments using the SPE protocol at different temperatures.  相似文献   

5.
Read length in DNA sequencing by capillary electrophoresis at elevated temperatures is shown to be greatly affected by the extent of hydrophobicity of the polymer separation matrix. At column temperatures of up to 80 degrees C, hydrophilic linear polyacrylamide (LPA) provides superior read length and separation speed compared to poly(N,N-dimethylacrylamide) (PDMA) and a 70:30 copolymer of N,N-dimethylacrylamide and N,N-diethylacrylamide (PDEA30). DNA-polymer and polymer intramolecular interactions are presumed to be a major cause of band broadening and the subsequent loss of separation efficiency with the more hydrophobic polymers at higher column temperatures. With LPA, these interactions were reduced, and a read length of 1000 bases at an optimum temperature of 70 degrees -75 degrees C was achieved in less than 59 min. By comparison, PDMA produced a read length of roughly 800 bases at 50 degrees C, which was close to the read length attained in LPA at the same temperature; however, the migration time was approximately 20% longer, mainly because of the higher polymer concentration required. At 60 degrees C, the maximum read length was 850 bases for PDMA, while at higher temperatures, read lengths for this polymer were substantially lower. With the copolymer DEA30, read length was 650 bases at the optimum temperature of 50 degrees C. Molecular masses of these polymers were determined by tandem gel permeation chromatography-multiangle laser light scattering method (GPC-MALLS). The results indicate that for long read, rapid DNA sequencing and analysis, hydrophilic polymers such as LPA provide the best overall performance.  相似文献   

6.
建立一种毛细管电泳快速高效检测限制性内切酶酶切产物的方法, 使其更好地用于基因诊断. 以甲基纤维素(Methyl cellulose, MC)为筛分介质, 用pUC19 DNA/Msp I (Hpa II) Marker标准DNA片段为实验对象, 通过考察筛分介质的浓度、pH值、毛细管的温度和运行电压优化出分离小于600 bp的双链DNA片段的最适条件, 并将此方法应用于临床59例胃癌患者肿瘤组织H-ras基因12位密码子点突变情况的检测. MC是一种良好的筛分介质, 运用其进行毛细管电泳对于遗传性疾病的诊断将更加快速、准确、简便、灵敏.  相似文献   

7.
Griess GA  Hardies SC  Serwer P 《Electrophoresis》2005,26(23):4440-4448
A previous study shows that electrophoretic preconditioning of a commercial polymer solution increases the spacing and resolution of DNA fragments fractionated in this solution by CE at 50 degrees C (Griess, G. A. et al., Electrophoresis 2005, 26, 102). The present study shows that this preconditioning effect on peak spacing progressively increases when the temperature of preconditioning increases to 70 degrees C, though fractionation is still performed at 50 degrees C. An increase in peak sharpness accompanies the increase in peak separation for DNA fragments longer than 200 bases. Changing the preconditioning temperature from 50 to 70 degrees C optimally improves resolution of fragment analysis in the range of 600-2000 nucleotides. When DNA sequencing is performed with automated base calling and 70 degrees C preconditioning at 319 V/cm (47 cm long capillary, Applied Biosystems 310 apparatus), the range of high-quality base calls is increased by 25% to 750; the range of low-quality base calls is increased by about 100% to 1200 in comparison to DNA sequencing without preconditioning.  相似文献   

8.
Positive ion electrospray ionization mass spectra of 16 base-pair double-stranded (ds)DNA have been obtained with essentially no ions from single-stranded DNA present. Single-stranded DNA was minimized by: (1) careful choice of DNA sequences; (2) the use of a relatively high salt concentration (0.1 M ammonium acetate, pH 8.5), and, (3) a low desolvation temperature (40 degrees C). Similarly, ESI-MS complexes of dsDNA with cisplatin, daunomycin and distamycin were obtained that contained only negligible amounts of single-stranded DNA. The complexes with daunomycin and distamycin were more stable to strand separation in the gas phase than dsDNA alone. This is in agreement with solution studies and with other recent gas phase results. These data contrast with many earlier ESI-MS studies of dsDNA and DNA/drug complexes in which ions from ssDNA are also normally observed.  相似文献   

9.
Physically adsorbed (dynamic) polymeric wall coatings for microchannel electrophoresis have distinct advantages over covalently linked coatings. In order to determine the critical factors that control the formation of dynamic wall coatings, we have created a set of model polymers and copolymers based on N,N-dimethylacrylamide (DMA) and N,N-diethylacrylamide (DEA), and studied their adsorption behavior from aqueous solution as well as their performance for microchannel electrophoresis of DNA. This study is revealing in terms of the polymer properties that help create an "ideal" wall coating. Our measurements indicate that the chemical nature of the coating polymer strongly impacts its electroosmotic flow (EOF) suppression capabilities. Additionally, we find that a critical polymer chain length is required for polymers of this type to perform effectively as microchannel wall coatings. The effective mobilities of double-stranded (dsDNA) fragments within dynamically coated capillaries were determined in order to correlate polymer hydrophobicity with separation performance. Even for dsDNA, which is not expected to be a strongly adsorbing analyte, wall coating hydrophobicity has a deleterious influence on separation performance.  相似文献   

10.
A three‐dimensional DNA hydrogel was generated by self‐assembly of short linear double‐stranded DNA (dsDNA) building blocks equipped with sticky ends. The resulting DNA hydrogel is thermoresponsive and the length of the supramolecular dsDNA structures varies with temperature. The average diffusion coefficients of the supramolecular dsDNA structures formed by self‐assembly were determined by diffusion‐ordered NMR spectroscopy (DOSY NMR) for temperatures higher than 60 °C. Temperature‐dependent rheological measurements revealed a gel point of 42±1 °C. Below this temperature, the resulting material behaved as a true gel of high viscosity with values for the storage modulus G′ being significantly larger than that for the loss modulus G′′. Frequency‐dependent rheological measurements at 20 °C revealed a mesh size (ξ) of 15 nm. AFM analysis of the diluted hydrogel in the dry state showed densely packed structures of entangled chains, which are also expected to contain multiple interlocked rings and catenanes.  相似文献   

11.
To elucidate the impact of matrix chemical and physical properties on DNA sequencing separations by capillary electrophoresis (CE), we have synthesized, characterized and tested a controlled set of different polymer formulations for this application. Homopolymers of acrylamide and N,N-dimethylacrylamide (DMA) and copolymers of DMA and N,N-diethylacrylamide (DEA) were synthesized by free radical polymerization and purified. Polymer molar mass distributions were characterized by tandem gel permeation chromatography - laser light scattering. Polymers with different chemical compositions and similar molar mass distributions were selected and employed at the same concentration so that the variables of comparison between them were hydrophobicity and average coil size in aqueous solution. We find that the low-shear viscosities of 7% w/v polymer solutions decrease by orders of magnitude with increasing polymer hydrophobicity, while hydrophilic polymers exhibit more pronounced reductions in viscosity with increased shear. The performance of the different matrices for DNA sequencing was compared with the same sample under identical CE conditions. The longest read length was produced with linear polyacrylamide (LPA) while linear poly-N,N-dimethylacrylamide (PDMA) gave approximately 100 fewer readable bases. Read lengths with DMA/DEA copolymers were lower, and decreased with increasing DEA content. This study highlights the importance of polymer hydrophilicity for high-performance DNA sequencing matrices, through the formation of robust, highly-entangled polymer networks and the minimization of hydrophobic interactions between polymers and fluorescently-labeled DNA molecules. However, the results also show that more hydrophobic matrices offer much lower viscosities, enabling easier microchannel loading at low applied pressures.  相似文献   

12.
The retention mechanism of acids and bases in reversed-phase liquid chromatography (RPLC) has been experimentally studied by examining the temperature dependence of retention, with emphasis on the role of the buffer ionization equilibria in the retention and selectivity. Retention factors of several ionizable compounds in a typical octadecylsilica column and using buffers dissolved in 50% (w/w) methanol as eluents at three temperatures in the range of 25-50 degrees C were measured. Two pairs of buffer solutions were prepared by a close adjusting of their pH at 25 degrees C; differences in their ionization enthalpies determined a different degree of ionization when temperature was raised and, as a consequence, a different shift in the eluent pH. Predictive equations of retention that take into account the temperature effect on both the transfer and the ionization processes are proposed. This study demonstrates the significant role that the selected buffer would have in retention and selectivity in RPLC at temperatures higher than 25 degrees C, particularly for co-eluted solutes.  相似文献   

13.
Wang Y  Liang D  Hao J  Fang D  Chu B 《Electrophoresis》2002,23(10):1460-1466
A noncross-linked interpenetrating polymer network (IPN), consisting of poly(N,N-dimethylacrylamide) (PDMA) and polyvinylpyrrolidone (PVP, weight-average molecular weight M(w) = 1 x 10(6) g/mol) was synthesized by polymerizing N,N-dimethylacrylamide (DMA) monomers directly in PVP buffer solution and tested as a separation medium for double-stranded (ds)DNA analysis without further purification. Due to the incompatibility of PVP and PDMA, a simple solution mixture could incur a microphase separation and showed poor performance on dsDNA separation. However, a dramatic improvement was achieved by the formation of an IPN. We attributed the high sieving ability of IPN as due to an increase in the number of entanglements by the more extended polymer chains. Apparent viscosity studies showed that the IPN had a much higher viscosity than the simple mixture containing the same amount of PDMA and PVP. In 1 x Tris-borate-EDTA (TBE) buffer, the concentration ratio of PDMA and PVP had a great effect on the DNA separation. At optimal conditions, the 22 fragments in pBR322/HaeIII DNA were successfully separated within 15 min, with a resolution of better than 1.0 for 123/124 bp.  相似文献   

14.
We report the changes in the structure and thermoresponsive behavior of poly(N-isopropylacrylamide) (PNIPAm) hydrogels when gold nanostructures are synthesized in situ within the hydrogel matrix. Cross-linked PNIPAm hydrogels were synthesized using NIPAm and 0.00-3.50% (w/w versus NIPAm) of N,N'-methylenebisacrylamide (MBAm) and/or N,N'-cystaminebisacrylamide (CBAm) as cross-linking agents. The hydrogels were soaked in potassium tetrachloroaurate to introduce gold ions. The hydrogels containing Au3+ were then immersed in a sodium borohydride solution to reduce the gold ions. Infrared spectroscopy, UV-visible spectroscopy, and equilibrium swelling were used to examine the structural/physical differences between gels of different compositions; UV-visible spectroscopy and mass measurements were used to observe the kinetics and thermodynamics of the hydrogel volume phase transition. These studies revealed several differences in the physical characteristics and thermoresponsive behavior of hydrogels based on cross-linker identity and the presence or absence of gold nanostructures. Hydrogels with gold nanostructures and high CBAm and low MBAm content have equilibrium swelling masses 3-20 times their native analogues. In comparison, gold-containing hydrogels with high MBAm and low CBAm content have swelling masses that are equal to their native analogues. Additionally, the gold-containing PNIPAm hydrogels cross-linked with only CBAm have a deswelling temperature of approximately 40 degrees C, approximately 8 degrees C above the samples cross-linked with only MBAm. Varying the CBAm content and introducing gold enables tuning of the deswelling temperature.  相似文献   

15.
Kotler L  He H  Miller AW  Karger BL 《Electrophoresis》2002,23(17):3062-3070
The goal of this work was to reduce the capillary electrophoresis (CE) separation time of DNA sequencing fragments with linear polyacrylamide solutions while maintaining the previously achieved long read lengths of 1000 bases. Separation speed can be increased while maintaining long read lengths by reducing the separation matrix viscosity and/or raising the column temperature. As urea is a major contributor to the separation buffer viscosity, reducing its concentration is desirable both for increase in the separation speed and easier solution replacement from the capillary. However, at urea concentrations below 6 M, the denaturing capacity of the separation buffer is not sufficient for accurate base-calling. To restore the denaturing properties of the buffer, a small amount of an organic solvent was added to the formulation. We found that a mixture of 2 M urea with 5% v/w of dimethyl sulfoxide (DMSO) resulted in 975 bases being sequenced at 70 degrees C in 40 min with 98.5% accuracy. To achieve this result, the software was modified to perform base-calling at a peak resolution as low as 0.24. It is also demonstrated that the products of thermal decomposition of urea had a deleterious effect on the separation performance at temperatures above 70 degrees C. With total replacement of urea with DMSO, at a concentration of 5% v/w in the same linear polyacrylamide (LPA)-containing buffer, it was possible to increase the column temperature up to 90 degrees C. At this temperature, up to 951 bases with 98.5% accuracy could be read in only 32 min of separation. However, with DMSO alone, some groups of C-terminated peaks remained compressed, and column temperature at this level cannot at present be utilized with existing commercial instrumentation.  相似文献   

16.
Poly(N-isopropylacrylamide) (PIPAAm) of controlled molecular weight was densely grafted onto glass capillary lumenal surfaces using surface-initiated atom transfer radical polymerization (ATRP). Temperature-dependent changes of these thermoresponsive brush surfaces with hydrophobic steroids were investigated by exploiting thermoresponsive aqueous wettability changes of the polymer-modified surfaces in microfluidic systems. IPAAm was polymerized on ATRP initiator-immobilized glass surfaces using CuCl/CuCl(2)/tris(dimethylaminoethyl)amine (Me(6)TREN) as an ATRP catalyst in water at 25 degrees C. PIPAAm graft layer thickness and its homogeneity on glass surfaces are controlled by changing ATRP reaction time. Aqueous wettability changes of PIPAAm-grafted surfaces responses drastically changed to both grafted polymer layer thickness and temperature, especially at lower temperatures. Temperature-responsive surface properties of these PIPAAm brushes within capillary inner wall surfaces were then investigated using capillary chromatography. Effective interaction of hydrophobic steroids with dehydrated, hydrophobized PIPAAm-grafted capillary surfaces was observed above 30 degrees C without any column packing materials. Steroid elution behavior from PIPAAm-grafted capillaries contrasted sharply with that from PIPAAm hydrogel-grafted porous monolithic silica capillaries prepared by electron beam (EB) irradiation wherein significant peak broadening was observed at high-temperature regardless of sample hydrophobicity factors (log P values), indicating multistep separation modes in coated monolithic silica capillaries. In conclusion, thermoresponsive polymer-grafted capillary inner wall surfaces prepared by ATRP exhibit useful temperature-dependent surface property alterations effective to regulate interactions with biomolecules without requirements for separation bed packing materials within the capillary lumen.  相似文献   

17.
We have studied the separation of a double stranded DNA (dsDNA), which is driven by either the temperature or force. By monitoring the probability of opening of entire base pairs along the chain, we show that the opening of a dsDNA depends not only on the sequence but also on the constraints on the chain in the experimental setups. Our results clearly demonstrate that the force-induced melting of dsDNA, whose one of the ends is constrained, is significantly different from the thermal melting, when both ends are free.  相似文献   

18.
2-(2,3-anthracenedicarboximido)cyclohexane derivatives (AC) have been known as the evolutionary diastereomerizing reagents for enantiomer discrimination in HPLC with ODS. However, a substantial separation of diastereomers can be observed only at lower temperatures, such as -40 degrees C. Therefore, in this work, poly(octadecyl acrylate)-grafted silica, ODAn was applied as an alternative stationary phase to ODS for the separation of AC-derived diastereomers. As a result, complete separation was achieved even under the conventional condition: for example, methanol as the mobile phase and 0 degrees C as the column temperature. An investigation on the temperature dependency of the selectivity demonstrated that ODAn shows a remarkable increase in selectivity at temperatures below 30 degrees C, which almost agreed with the peak-top temperature of the endothermic peak in a DSC thermogram for ODA35 immersed in a mobile phase. The better separation would be derived from a highly ordered structure of ODAn and a carbonyl-pi interaction with AC-derived diastereomers.  相似文献   

19.
Wang Q  Xu X  Dai L 《Electrophoresis》2006,27(9):1749-1757
The preparation of a new separation matrix, quasi-interpenetrating networks (quasi-IPNs) formed by poly(N-acryloyl-Tris) (poly(tris-A)) and PVP, and its application for dsDNA and ssDNA fragments separation by CE with UV detection, are presented. This new quasi-IPN exhibited high sieving performance, good dynamic coating ability, and low viscosity. Single-base resolutions of dsDNA fragments (Rs = 0.92 for 123/124 bp) and ssDNA fragments (Rs = 0.65 for 123/124 base, Rs = 0.48 for 309/310 base) were achieved by using the quasi-IPN of poly(tris-A)/PVP (2% + 2%) solution in a 31 cm effective length linear polyacrylamide (LPA)-coated column. Single-base separation of dsDNA fragments (Rs = 0.92 for 123/124 bp) was also obtained within 28 min in a 46.7 cm effective length bare column at higher 160 V/cm electric field strength by using the same quasi-IPN solution. The RSD of the migration time measured for each DNA fragments was less than 1.5% in the bare column for nine continuous runs. The effects of temperature and electric field strength on the DNA separation were also investigated.  相似文献   

20.
Shell cross-linked (SCL) micelles with hydroxy-functional coronas have been constructed in aqueous solution by exploiting the micellar self-assembly behavior of a new thermoresponsive ABC triblock copolymer. This copolymer was prepared via atom transfer radical polymerization in a convenient one-pot synthesis and comprised a thermoresponsive core-forming poly(propylene oxide) (PPO) block, a cross-linkable central poly(2-(dimethylamino)ethyl methacrylate) (DMA) block, and a hydroxy-functional outer block based on poly(glycerol monomethacrylate) (GMA). DMF GPC analysis confirmed a unimodal molecular weight distribution for the PPO-PDMA-PGMA triblock copolymer precursor, with an M(n) of 12 100 and a polydispersity of approximately 1.26. This copolymer dissolved molecularly in aqueous solution at 5 degrees C but formed micelles with hydroxy-functional coronas above a critical micelle temperature of around 12 degrees C, which corresponded closely to the cloud point of the PPO macroinitiator. Cross-linking of the DMA residues using 1,2-bis(2-iodoethoxy)ethane produced SCL micelles that remained intact at 5 degrees C, i.e., below the cloud point of the core-forming PPO block. Dynamic light scattering studies confirmed that the SCL micelle diameter could be varied depending on the temperature employed for cross-linking: smaller, more compact SCL micelles were formed at higher temperatures, as expected. Since cross-linking involved quaternization of the DMA residues, the SCL micelles acquired cationic surface charge as judged by aqueous electrophoresis studies. These cationic SCL micelles were adsorbed onto near-monodisperse anionic silica sols, which were used as a model colloidal substrate. Thermogravimetric analyses indicated a SCL micelle mass loading of 2.5-4.4%, depending on the silica sol diameter and the initial micelle concentration. Aqueous electrophoresis measurements confirmed that surface charge reversal occurred after adsorption of the SCL micelles, and scanning electron microscopy studies revealed a uniform coating of SCL micelles on the silica particles.  相似文献   

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