• The Transactions of the Korean Institute of Electrical Engineers C
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• v.52 no.8
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• pp.365-370
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• 2003

This research aims to develop an indicator-free DNA chip using micro-fabrication technology. At first, we fabricated a DNA microarray by lithography technology. Several probe DNAs consisting of thiol group at their 5-end were immobilized on the gold electrodes. Then indicator-free target DNA was hybridized by an electrical force and measured electrochemically in potassium ferricyanide solution. Redox peak of cyclic-voltammogram showed a difference between target DNA and mismatched DNA in an anodic peak current. Therefore, it is able to detect various genes electrochemically after immobilization of various probe DNAs and hybridization of indicator-free DNA on the electrodes simultaneously It suggested that this DNA chip could recognize the sequence specific genes.

• Bulletin of the Korean Chemical Society
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• v.33 no.11
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• pp.3719-3726
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• 2012

Formation of Z-DNA, a left-handed double helix, from B-DNA, the canonical right-handed double helix, occurs during important biological processes such as gene expression and DNA transcription. Such B-Z transitions can also be induced by high salt concentration in vitro, but the changes in the relative stability of B-DNA and Z-DNA with salt concentration have not been fully explained despite numerous attempts. For example, electrostatic effects alone could not account for salt-induced B-Z transitions in previous studies. In this paper, we propose that the B-Z transition can be explained if counterion entropy is considered along with the electrostatic interactions. This can be achieved by conducting all-atom, explicit-solvent MD simulations followed by MM-PBSA and molecular DFT calculations. Our MD simulations show that counterions tend to bind at specific sites in B-DNA and Z-DNA, and that more ions cluster near Z-DNA than near B-DNA. Moreover, the difference in counterion ordering near B-DNA and Z-DNA is larger at a low salt concentration than at a high concentration. The results imply that the exclusion of counterions by Z-DNA-binding proteins may facilitate Z-DNA formation under physiological conditions.

• Applied Biological Chemistry
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• v.48 no.4
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• pp.331-334
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• 2005

In this study, the effects of five extraction methods for raw and processed corns were compared with respect to the integrity, yields and quality of DNA extracted from them and the results were assessed by PCR analysis. From the comparison of five extraction methods, DNA integrity showed a similar pattern. Amounts of genomic DNA obtained from the five extraction methods varies from $0.25{\mu}g\;to\;234{\mu}g$ per 1 g sample. The DNA yield extracted with CTAB method and DNeasy Plant Maxi kit is greater than that obtained from other extraction methods. These results would be applicable for the selection of an adequate extraction method for specific samples.

• Proceedings of the Acoustical Society of Korea Conference
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• spring
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• pp.319-322
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• 2004

본 연구에서는 DNA의 상보적인 결합을 이용하여 DNA 혼성화 반응을 감지할 수 있는 SH형 SAW 센서를 개발하였다. 측정에 사용된 DNA는 15개의 염기를 가진 올리고 뉴클레오티드를 사용하였으며 이에 대해 상보적 결합이 가능한 염기서열을 가진 것과 그렇지 않은 미스매치 형태의 DNA 올리고뉴클레오티드를 이용하여 DNA 혼성화 반응 특성을 측정하였다. SH형 SAW 센서는 압전 단결정 $LiTaO_{3}$를 사용하여 100 MHz 발진되는 형태로 제작하였으며, 센서의 지연선 위에 Ti/Au 층을 증착하여 SH기가 수식된 탐침 DNA의 고정화가 가능하게 하였다. 제작된 센서는 Au가 증착된 박막위에 탐침 DNA를 SAM 방법으로 고정화 시켰을 경우와 고정화된 탐침 DNA와 표적 DNA와의 혼성화 반응을 시키고 난 후의 센서의 주파수 변화를 각각 측정하였다. 개발된 DNA 혼성화 반응 측정용 SH형 SAW센서는 DNA 혼성화 특성에 기인한 질량하중 효과에 따른 안정적인 주파수 변화를 나타내었다.

• Environmental Analysis Health and Toxicology
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• v.29
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• pp.7.1-7.8
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• 2014

Objectives The present study was designed to systematically characterize the denaturation and the renaturation of double stranded DNA (dsDNA), which is suitable for DNA hybridization. Methods A series of physical and chemical denaturation methods were implemented on well-defined 86-bp dsDNA fragment. The degree of each denaturation was measured and the most suitable denaturation method was determined. DNA renaturation tendency was also investigated for the suggested denaturation method. Results Heating, beads mill, and sonication bath did not show any denaturation for 30 minutes. However probe sonication fully denatured DNA in 5 minutes. 1 mol/L sodium hydroxide (alkaline treatment) and 60% dimethyl sulfoxide (DMSO) treatment fully denatured DNA in 2-5 minutes. Conclusions Among all the physical methods applied, the direct probe sonication was the most effective way to denature the DNA fragments. Among chemical methods, 60% DMSO was the most adequate denaturation method since it does not cause full renaturation during DNA hybridization.

• Bulletin of the Korean Chemical Society
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• v.24 no.5
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• pp.579-582
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• 2003

Norfloxacin, that inhibits the action of topoisomerase Ⅱ, binds to wide variety of DNA. The binding mode of this drug to double- and super-coiled DNA (ds- and scDNA) is compared in this study by various spectroscopic methods, including absorption, fluorescence, and circular dichroism(CD) spectroscopy. Hypochromism in the absorption band, negative and positive induced CD bands (respectively in 240-260 nm and 270-300 nm region) are apparent for the norfloxacin that bound to both the dsDNA and scDNA. A decrease in fluorescence is also noticed in the presence of both DNAs. Since the spectroscopic characteristics are the same for both complexes, it is imperative that the binding mode of the norfloxacin is similar in ds- and scDNA. In the presence of $Mg^{2+}$, which is a cofactor in the topoisomerase Ⅱ action, the fluorescence intensity of the scDNA-norfloxacin complex increased and the resulting fluorescence intensity and shape was identical to that in the absence of scDNA. Therefore, the addition of an excess amount of $Mg^{2+}$ may result in the extrusion of norfloxacin from scDNA.

• Animal cells and systems
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• v.7 no.1
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• pp.81-87
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• 2003

While screening proteins that interact with DnaA protein, the initiator protein for Escherichia coil chromosomal DNA replication, we found a 52-kD sized protein which bound to DnaA protein in a salt-dependent manner. This protein was identified as trigger factor, a ribosome-associated peptidyl-prolyl- cisltrans isomerase with chaperone activity. Trigger factor was overproduced and purified to near homogeneity, and its effect on the function of DnaA protein was examined, Enhanced binding of DnaA protein to DnaA box with no apparent supershift in the gel-shift experiments suggested that trigger factor, by virtue of its chaperone activity, exerts a change on DnaA protein thus increasing its binding affinity for DnaA box.

• Journal of Microbiology and Biotechnology
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• v.8 no.1
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• pp.89-91
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• 1998

Cryptotanshinone induced topoisomerase I-mediated DNA cleavage in vitro as strongly as camptothecin, whereas topoisomerase II-mediated DNA cleavage was not induced by this agent. In DNA relaxation assay using calf thymus DNA topoisomerase I and supercoiled pBR322 DNA, cryptotanshinone inhibited topoisomerase I-mediated DNA relaxation in a dose-dependent manner. In unwinding assay, cryptotanshinone ($50{\mu}M$) did not shift the topoisomers of DNA. These results suggest that cryptotanshinone exerted a preferential inhibition of topoisomerase I without intercalating into DNA.

• Analytical Science and Technology
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• v.12 no.1
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• pp.80-83
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• 1999

Recently, it has been possible to the alphoid gene, which has X and Y specificity, and determine the sex from human physical evidence using PCR methods. Samples from single sources, PCR method applied to the alphoid gene results in highly sensitive and accurate results even when only 60 pg of the genomic DNA was available for sex determination. Even for samples containing DNA from more than one gender source where the female DNA was present in the amount 10 times than that of the male, sex determination was possible. Therefore, this result suggests that alphoid gene, which has X and Y specificity, could be used effectively for sex determination in case of mixed DNA samples from biological evidence.

• Journal of Microbiology
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• v.34 no.3
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• pp.229-235
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• 1996

Microgram quantities of DNA per gram soil were recovered with SDS- based and freeze-and thaw procedures. The average DNA fragment size was > 23 Kb. This method generated minimal shearing of extracted DNA. However, the DNA extracts still contained considerable amounts of humic impurities sufficient to inhibit PCR. Several approaches were used to reduce the interferences with the PCR (use of CTAF in extraction step, Elutip-d column purification, addition of BSA to PCR buffer) to accomplish PCR with DNA extract as a template. Most of the DNA extracts were not digested completely by restriction endonuclease, and CTAB-TREATED ane Elutip-d column purified DNA extracts were partially digested. Regarding as restriction enzyme digestion, all PCRs failed to amplify 16S rRNA gene fragments in the DNA extracts. In the case of DNA extracts only where BSA was added to PCR buffer, PCR was successfully conducted whether the DNA extracts were treated with CTAB or purified with columns. However, these two treatments were indispensable for humic impurity-rich DNA extracts to generate the PCR-compatible DNA samples. Direct extraction of DNA, coupled with these procedures to remove and relieve interferences by humic impurities and followed by the PCR, can be rapid and simple method for molecular microbiological study on soil microorganisms.