• BMB Reports
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• v.38 no.1
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• pp.97-103
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• 2005

Under the condition of expression of $\lambda$ P protein at lethal level, the oriC DNA-binding activity is significantly affected in wild-type E. coli but not in the rpl mutant. In purified system, the $\lambda$ P protein inhibits the binding of both oriC DNA and ATP to the wild-type DnaA protein but not to the rpl DnaA protein. We conclude that the $\lambda$ P protein inhibits the binding of oriC DNA and ATP to the wild-type DnaA protein, which causes the inhibition of host DNA synthesis initiation that ultimately leads to bacterial death. A possible beneficial effect of this interaction of $\lambda$ P protein with E. coli DNA initiator protein DnaA for phage DNA replication has been proposed.

• Journal of Microbiology
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• v.44 no.5
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• pp.508-514
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• 2006

In this study, the double-stranded DNA-dependent activities of Deinococcus radiodurans RecA protein (Dr RecA) were characterized. The interactions of the Dr RecA protein with double-stranded DNA were determined, especially dsDNA-dependent ATP hydrolysis by the Dr RecA protein and the DNA strand exchange reaction, in which multiple branch points exist on a single RecA protein-DNA complex. A nucleotide cofactor (ATP or dATP ) was required for the Dr RecA protein binding to duplex DNA. In the presence of dATP, the nucleation step in the binding process occurred more rapidly than in the presence of ATP. Salts inhibited the binding of the Dr RecA protein to double-stranded DNA. Double-stranded DNA-dependent ATPase activities showed a different sensitivity to anion species. Glutamate had only a minimal effect on the double-stranded DNA-dependent ATPase activities, up to a concentration of 0.7 M. In the competition experiment for Dr RecA protein binding, the Dr RecA protein manifested a higher affinity to double-stranded DNA than was observed for single-stranded 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.

• KIEE International Transactions on Electrophysics and Applications
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• v.4C no.4
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• pp.133-136
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• 2004

This research aims to develop a DNA chip array without an indicator. We fabricated a microelectrode array through photolithography technology. Several DNA probes were immobilized on an electrode. Then, target DNA was hybridized and measured electrochemically. Cyclic-voltammograms (CVs) showed a difference between the DNA probe and mismatched DNA in an anodic peak. This indicator-free DNA chip resulted in a sequence-specific detection of the target DNA.

• Journal of the Korea Computer Graphics Society
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• v.2 no.2
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• pp.61-68
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• 1996

In this paper we propose a new visualization technique to characterize qualitative information of a large DNA sequence. While a long DNA sequence has huge information, it is not easy to obtain genetic information from the DNA sequence. We transform DNA sequences into a polygon to compute their homology in image domain rather than text domain. Our program visualizes DNA sequences with colored random walk plots and simplify them k-convex hulls. A random walk plot represents DNA sequence as a curve in a plane. A k-convex hull simplifies a random work plot by removing some parts of its insignificant information. This technique gives a biologist an insight to detect and classify DNA sequences with easy. Experiments with real genome data proves our approach gives a good visual forms for long DNA sequences for homology analysis.

• Journal of the Korean Institute of Intelligent Systems
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• v.16 no.2
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• pp.222-227
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• 2006

Recently the research for Traveling Salesman Problem (TSP) using DNA computing with massive parallelism has been. However, there were difficulties in real biological experiments because the conventional method didn't reflect the precise characteristics of DNA when it express graph. Therefore, we need DNA sequence generation algorithm which can reflect DNA features and reduce biological experiment error. In this paper we proposed a DNA sequence generation algorithm that applied DNA coding method of evolution model to DNA computing. The algorithm was applied to TSP, and compared with a simple genetic algorithm. As a result, the algorithm could generate good sequences which minimize error and reduce the biologic experiment error rate.

• Biomedical Science Letters
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• v.26 no.4
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• pp.275-287
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• 2020

Since its introduction in the forensic field, quantitative PCR (qPCR) has played an essential role in DNA analysis. Quality of DNA should be evaluated before short tandem repeat (STR) profiling to obtain reliable results and reduce unnecessary costs. To this end, various human DNA quantification kits have been developed. Among these kits, the PowerQunat® System was designed not only to determine the total amount of human DNA and human male DNA from a forensic evidence item, but also to offer data about degradation of DNA samples. However, a crucial limitation of the PowerQunat® System is its high cost. Therefore, to minimize the cost of DNA quantification, we evaluated kit performance using a reduced volume of reagents (1/2-volume) using DNA samples of varying types and concentrations. Our results demonstrated that the low-volume method has almost comparable performance to the manufacturer's method for human DNA quantification, human male DNA quantification, and DNA degradation index. Furthermore, using a reduced volume of regents, it is possible to run 2 times more reactions per kit. We expect the proposed low-volume method to cut costs in half for laboratories dealing with large numbers of DNA samples.

• Biomedical Science Letters
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• v.28 no.3
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• pp.157-169
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• 2022

DNA typing is the typical technology in the forensic science and plays a significant role in the personal identification of victims and suspects. Short tandem repeat (STR) is the short tandemly repeated DNA sequence consisting of 2~7 bp DNA units in specific loci. It is disseminated across the human genome and represents polymorphism among individuals. Because polymorphism is a key feature of the application of DNA typing STR analysis, STR analysis becomes the standard technology in forensics. Therefore, the DNA database (DNA-DB) was first introduced with 4 essential STR markers for the application of forensic science; however, the number of STR markers was expanded from 4 to 13 and 13 to 20 later to counteract the continuously increased DNA profile and other needed situations. After applying expanded STR markers to the South Korean DNA-DB system, it positively affected to low copy number analysis that had a high possibility of partial DNA profiles, and especially contributed to the theft cases due to the high portion of touch DNA evidence in the theft case. Furthermore, STR marker expansion not only contributed to the resolution of cold cases but also increased kinship index indicating the potential for improved kinship test accuracy using extended STR markers. Collectively, the expansion of the STR locus was considered to be necessary to keep pace with the continuously increasing DNA profile, and to improve the data integrity of the DNA-DB.

• Korean Journal of Microbiology
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• v.43 no.4
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• pp.250-255
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• 2007

The RecA protein of Deinococcus radiodurans is essential for the extreme radiation resistance of this organism. The central steps involved in recombinational DNA repair require DNA-dependent ATP hydrolysis by recA protein. Key feature of RecA protein-mediated activities is the interactions with ssDNA and dsDNA. The ssDNA is the site where RecA protein filament formation nucleates and where initiation of DNA strand exchange takes place. The effect of sequence heterogeneity of ssDNA was examined in this experiment. The rate of homopolymeric synthetic ssDNA-dependent ATP hydrolysis was constant or nearly so over a broader range of pHs. For poly(dT)-dependent ATP or dATP hydrolysis, rates were generally faster, with a broader optimum between pH 7.0 and 8.0. Activities of RecA protein were affected by the ionic environment. The ATPase activity was shown to have different sensitivity to anionic species. The presence of glutamate seemed to slimulate the hydrolytic activity. Dr RecA protein was shown to require $Mg^{2+}$ ion greater than 2 mM for binding to etheno ssDNA and the binding stoichiometry of 3 nucleotide for RecA protein monomer.

• The Transactions of the Korean Institute of Electrical Engineers C
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• v.51 no.2
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• pp.92-97
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• 2002

One of the important roles of a DNA chip is the capability of detecting genetic diseases and mutations by analyzing DNA sequence. For a successful electrochemical genotyping, several aspects should be considered including the chemical treatment of electrode surface, DNA immobilization on electrode, hybridization, choice of an intercalator to be selectively bound to double standee DNA, and an equipment for detecting and analyzing the output signal. Au was used as the electrode material, 2-mercaptoethanol was used for linking DNA to Au electrode, and methylene blue was used as an indicator that can be bound to a double stranded DNA selectively. From the analysis of reductive current of this indicator that was bound to a double stranded DNA on an electrode, a normal double stranded DNA was able to be distinguished from a single stranded DNA in just a few seconds. Also, it was found that the peak reduction current of indicator is proportional to the concentration of target DNA to be hybridized with probe DNA. Therefore, it is possible to realize a sim71e and cheats DNA sensor using the electrochemical measurement for genotyping.