• Biotechnology and Bioprocess Engineering:BBE
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• v.11 no.3
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• pp.179-186
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• 2006

End-Labeled Free-Solution Electrophoresis (ELFSE) is a new technique that is a promising bioconjugate method for DNA sequencing (or separation) and genotyping by both capillary and microfluidic device electrophoresis. Because ELFSE enables high-resolution electrophoretic separation in aqueous buffer alone (i.e., without a polymer matrix), it eliminates the need to load viscous polymer networks into electrophoresis microchannels. To achieve microchannel DNA separations with high performance, ELFSE requires monodisperse perturbing entities (i.e., drag-tags), which create a large amount of frictional drag when pulled behind DNA during free-solution electrophoresis, and which have other properties suitable for microchannel electrophoresis. In this article, the theoretical concepts of ELFSE and the required characteristics of the drag-tag molecules for the ultimate performance of ELFSE are reviewed. Additionally, the merits and limitations of current drag-tags are also discussed in the context of recent experimental data of ELFSE separation (or sequencing).

• Korean Journal of Veterinary Research
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• v.33 no.1
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• pp.81-85
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• 1993

Gel electrophoresis has proven to be one of the most useful of DNA separation and purification. The new technique of pulsed field gel electrophoresis (PFGE) is high resolution separation of large size DNA moleculs. Conventional continuous gel electrophresis can not be separation of large DNA fragments(20~50 k base). Field inversion gel electrophoresis(FIGE) is very useful for large DNA molecules. We have found that a pulse ratio ; 2 : 1, time ; 24hrs., volts ; $10^{volts}/_{cm}$, start ; 0.45sec, end ; 1sec, is most effectively resolves DNA fragment in the 6~50k base.

• Transactions of the Korean Society of Mechanical Engineers A
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• v.30 no.1 s.244
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• pp.26-31
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• 2006

This paper reports low-cost PDMS/glass based DNA microbiochip for the restriction enzyme reaction and its products detection using the capillary electrophoresis. The microbiochip ($25mm{\times}75mm$) has the heater integrated reactor ($5{\mu}{\ell}$) for DNA restriction enzyme reaction at $37^{\circ}C$ and the microchannel ($80\;{\mu}m{\times}100\;{\mu}m{\times}58mm$) for the capillary electrophoresis detection. It is experimentally confirmed that the digestion of the plasmid ($pGEM^{(R)}-4Z$) by the enzyme (Hind III and Sca I) is performed for less than 10 min and its electrophoresis detection is able to sequentially on the fabricated microbiochip.

• Environmental Mutagens and Carcinogens
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• v.17 no.2
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• pp.71-77
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• 1997

The single cell gel electrophoressis(SCGE) assay, also known as the comet assay, is a rapid, simple, visual and sensitive technique for measuring and analysing DNA breakage in mammalian cells. The SCGE or comet assay is a promising test for the detection of DNA damage and repair in individnal cells. It has widespread potential applications in DNA damage and repair studies, genotoxicity testing and biomonitoring. In this microgel electrophoresis technique, cells are embedded in agarose gel on microscope slides, iysed and electrophoresed under alkaline conditions. Cells with increased DNA damage display increased migration of DNA from the nucleus towards the anode. The length of DNA migration indicates the amount of DNA breakage in the cell. The comet assay is also capable of identifying apoptotic cells which contain highly fragmented DNA. Here we review the development of the SCGE assay, existing protocols for the detection and analysis of comets, the relevant underlying principles determining the behaviour of DNA and the potential applications of the technique.

• BMB Reports
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• v.31 no.4
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• pp.384-390
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• 1998

DNA fragments (51-587 bp) were separated by capillary electrophoresis using entangled polymer, hydroxyethylcellulose, in uncoated fused silica capillary columns. The factors affecting the separation of DNA fragments with hydroxyethylcellulose media were evaluated, i.e., the concentration of buffer and entangled polymer, effects of additives (methanol, ethidium bromide, EDTA), temperature, and injection methods. Maximum performance was obtained by adding 5% methanol in 0.5% hydroxyethylcellulose solution at $30^{\circ}C$. Addition of methanol in polymer media increased the resolution of small size DNA fragments (< 100 bp). On the other hand, addition of ethidium bromide and EDTA, which are commonly used in conventional DNA separation, reduced the resolution of DNA fragments in the polymer solution. It turns out that the separation behavior of DNA in entangled polymer is more sensitive to the running condition compared to that in polyacrylamide gel-filled capillary, but the reproducibility of DNA separation in entangled polymer is reliable.

• Environmental Mutagens and Carcinogens
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• v.18 no.2
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• pp.83-88
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• 1998

To detect the mutation in a given sequence, there are variety of methods developed by use of the gel electrophoresis. One of the methods, TGGE (Temperature Gradient Gel Electrophoresis), is a popular technique because it can detect mutations in DNA fragment with ease and at low cost. This study used 200 bp BamHI-digested DNA fragment containing the human $\varepsilon$-globin promoter which was mutated[$\varepsilon$ F1*(-141), GATA- I*(-163), and GATA-1* & $\varepsilon$F1]. This BamHI-digested DNA fragment was directly used to detect the mutated DNA fragment on 50% denaturant gel with temperature gradient of 45$^{\circ}C$ through $53^{\circ}C$. In agreement with the theoretical result of MELTSCAN program (Brossette and Wallet, 1994) the mobilities of mutated DNA fragments were shown to be nearly distinguished on the temperature gradient gel. In contrast to the above result the heteroduplex analysis under the temperature gradient condition was shown to detect the mutated DNA fragments through the heteroduplex formation between strands of mutated DNA and wild-type DNA.

• KSBB Journal
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• v.17 no.1
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• pp.106-109
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• 2002

Gel electrophoresis of DNA is a well known technique in molecular biology. This technique is simple, rapid to perform, and capable of adequately separating fragments of DNA. A number of mixtures of DNA fragments ("DNA size markers") are frequently employed in a purpose of extrapolating the sizes or the amount of DNA molecules during gel electrophoresis. DNA size markers are constructed by digesting plasmid DNA, bacteriophage DNA, or recombinant DNA molecules with one or more restriction enzymes. However, liquid suspension containing DNA size marker needs to be kept at a low temperature during storage and shipping. In an attempt to maintain the DNA samples at room temperature for extended period of time, lyophilization of DNA with addition of nuclease inhibitor was studied. Gel loading buffer was also added to the lyophilized DNA to provide additional convenience such that DNA size marker was the "ready-to-use" followed by simply reconstituting with distilled water.

• Bulletin of the Korean Chemical Society
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• v.24 no.7
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• pp.943-947
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• 2003

We have studied the migration behavior of single-stranded DNA using capillary gel electrophoresis under various conditions. It was found that optimum electric fields should be less than 150 V/cm for the good tradeoff between the separation time and the resolution. It seems that the gel matrix with the combination of different polymer average molecular weights is important to extend the maximum readable DNA bases. The total gel concentration less than 3.1% in the mixed gel system showed good separation efficiency up to 600 bases. The best result was obtained with the poy(ethylene)oxide (PEO) gel concentration of 1.2% of Mr 8,000,000 and 1.8% of Mr 600,000. We observed that the capillary length between 50 cm to 100 cm (effective length) should be employed for the optimization between the total DNA migration time and the maximum readable length. A trizma base-boric acid-ethlyenediaminetetraacetic acid (EDTA) (TBE) buffer was commonly used for DNA sequencing, but we found that 3-[tris(hydroxymethyl)methyl amino]-1-propane sulfonic acid (TAPS) buffer worked as well for the single-stranded DNA separation. Especially, TAPS buffer showed a good resolution for very short DNA bases (1 to 30 bases).

• Bulletin of the Korean Chemical Society
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• v.32 no.12
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• pp.4316-4320
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• 2011

The effects of various hydroxide compounds on base stacking (BS) were investigated for pre-concentration of DNA molecules in capillary electrophoresis (CE). In BS, hydroxide ions ($OH^-$) were electrokinetically introduced after DNA sample injection. A neutralization reaction occurred between the $OH^-$ and $Tris^+$ of the running buffer, which resulted in a zone of lower conductivity. Within the low conductivity zone of the high electric field, the DNA molecules moved more rapidly and were concentrated in front of the low conductivity zone. At the same BS conditions of CE, the enhanced sensitivity of the DNA samples was dependent on the kind of multivalent cations in the hydroxide compounds. Except for LiOH, the hydroxide compounds with monovalent cations showed more effective BS than those with divalent cations because of solubility, ionic strength and electronegativity. The order of hydroxide compounds that enhance the detection sensitivity of DNA molecules was as follows: NaOH > $NH_4OH$ > KOH > $Ba(OH)_2$ > $Sr(OH)_2$ > LiOH > $Ca(OH)_2$ > $Mg(OH)_2$. $NH_4OH$, KOH and $Ba(OH)_2$ proved to be efficient hydroxide compounds to use as effective BS reagents in CE instead of NaOH.

• Environmental Mutagens and Carcinogens
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• v.21 no.2
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• pp.89-94
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• 2001

Recently, single cell gel electrophoresis, also known as comet assay, is widely used for the detection and measurement of DNA strand breaks in vitro and in vivo in many toxicological fields such as radiation exposure, human monitoring and toxicity evaluation. As well defined, comet assay is a sensitive, rapid and visual method for the detection of DNA strand breaks in individual cells. Briefly, a small number of damaged cells suspended in a thin agarose gel on a microscope slide were lysed, unwinded, electrophoresed, and stained with a fluorescent DNA binding dye. The electric current pulled the charged DNA from the nucleus such that relaxed and broken DNA fragments migrated further. The resulting images which were subsequently named for their appearance as comets, were measured to determine the extent of DNA damages. However, some variations could be occurred in procedures, laboratories's conditions and kind of cells used. Hence, to overcome and to harmonize these matters in comet assay, International Workshop on Genotoxicity Test Procedure (IWGTP) was held with several topics including comet assay at Washington D.C. on March, 1999. In spite of some consensus in procedures and conditions in IWGTP, there are some problems still remained to be solved. In this respect, we attempted to set the practical optimal conditions in the experimental procedures such as lysis, unwinding, electrophoresis and neutralization conditions and so on. First of all, we determined optimal lysis and unwinding time by using 150 $\mu$M methyl methanesulfonate (MMS) which is usually used concentration. And then, we determined optimal positive control concentrations of benzo(a)pyrene (BaP) and MMS in the presence and absence of S9 metabolic activation system, respectively.