• BMB Reports
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• v.34 no.6
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• pp.489-495
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• 2001

DNA damage by UV and environmental agents are the major cause of genomic instability that needs to be repaired, otherwise it give rise to cancer. Accordingly, mammalian cells operate several DNA repair pathways that are not only responsible for identifying various types of DNA damage but also involved in removing DNA damage. In mammals, nucleotide excision repair (NER) machinery is responsible for most, if not all, of the bulky adducts caused by UV and chemical agents. Although most of the proteins involved in NER pathway have been identified, only recently have we begun to gain some insight into the mechanism by which proteins recognize damaged DNA. Binding of Xeroderma pigmentosum group C protein (XPC)-hHR23B complex to damaged DNA is the initial damage recognition step in NER, which leads to the recruitment of XPA and RPA to form a damage recognition complex. Formation of damage recognition complex not only stabilizes low affinity binding of XPA to the damaged DNA, but also induces structural distortion, both of which are likely necessary for the recruitment of TFIIH and two structure-specific endonucleases for dual incision.

• Proceedings of the Korean Institute of Intelligent Systems Conference
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• 2002.12a
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• pp.383-386
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• 2002

In this paper, we investigated the pattern recognition performance of the numeric patterns (from 0 to 9) using DNA coding method. The pattern recognition performance of the DNA coding method is compared to the that of the GA(Genetic Algorithm). GA searches effectively an optimal solution via the artificial evolution of individual group of binary string using binary coding, while DNA coding method uses four-type bases denoted by A(Adenine), C(Cytosine), G(Guanine) and T(Thymine), The pattern recognition performance of GA and DNA coding method is evaluated by using the same genetic operators(crossover and mutation) and the crossover probability and mutation probability are set the same value to the both methods. The DNA coding method has better characteristics over genetic algorithms (GA). The reasons for this outstanding performance is multiple possible solution presentation in one string and variable solution string length.

• The KIPS Transactions:PartB
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• v.10B no.7
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• pp.769-776
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• 2003

DNA computing has used to solve MCP (Maximal Clique Problem). However, when current DNA computing is applied to MCP. it can't efficiently express vertices and edges and it has a problem that can't look for solutions, by misusing wrong restriction enzyme. In this paper we proposed ACO (Algorithm for Code Optimization) that applies DNA coding method to DNA computing to solve MCP's problem. We applied ACO to MCP and as a result ACO could express DNA codes of variable lengths and generate codes without unnecessary vertices than Adleman's DNA computing algorithm could. In addition, compared to Adleman's DNA computing algorithm, ACO could get about four times as many as Adleman's final solutions by reducing search time and biological error rate by 15%.

• Journal of the Korean Institute of Intelligent Systems
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• v.13 no.1
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• pp.37-44
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• 2003

In this paper, we investigated the performance of both DNA coding method and Genetic Algorithm(GA) in numeric pattern (from 0 to 9) recognition. The performance of the DNA coding method is compared to the that of the GA. GA searches effectively an optimal solution via the artificial evolution of individual group of binary string using binary coding, while DNA coding method uses four-type bases denoted by Adenine(A), Cytosine(C), Guanine(G) and Thymine(T). To compare the performance of both method, the same genetic operators(crossover and mutation) are applied and the probabilities of crossover and mutation are set the same values. The results show that the DNA coding method has better performance over GA. The reasons for this outstanding performance are multiple candidate solution presentation in one string and variable solution string length.

• Proceedings of the Microbiological Society of Korea Conference
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• 2000.10a
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• pp.15-23
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• 2000

The subcellular localization of the SopB protein, which is encoded by the Escherichia coli F plasmid and is involved in the partition of the single-copy plasmid, was directly visualized through the expression of the protein fused to the jellyfish green fluorescent protein (GFP). The fusion protein was found to localize to positions close but not at the poles of exponentially growing cells. Examination of derivatives of the fusion protein lacking various regions of SopB suggests that the signal for the cellular localization of SopB resides in a region close to its N terminus. Overexpression of SopB led to silencing of genes linked to, but well-separated from, a cluster of SopB-binding sites termed sopC. In this SopB-mediated repression of sopC-linked genes, all but the N-terminal 82 amino acids of SopB can be replaced by the DNA-binding domain of a sequence-specific DNA -binding protein, provided that the sopC locus is also replaced by the recognition sequence of the DNA-binding domain. These results suggest a mechanism of gene silencing: patches of closely packed DNA-binding protein is localized to specific cellular sites; such a patch can capture a DNA carrying the recognition site of the DNA -binding domain and sequestrate genes adjacent to the recognition site through nonspecific binding of DNA.

• Journal of KIISE:Software and Applications
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• v.26 no.11
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• pp.1350-1358
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• 1999

이 논문에서는 유전밴드 영상신호에 포함되어 있는 지형적 특징을 이용하여 밝기의 변화가 일정하지 않은 유전밴드를 인식하는 방법을 연구하였다. 유전밴드는 동일인을 식별하는데 있어서 지문보다 높은 신뢰성을 가지고 있으므로, 유전밴드 영상에서 유전밴드의 유무와 위치를 자동적으로 검출하는 것은 매우 중요하다. 레인내의 밝기의 변화가 일정한 유전밴드는 미분연산자에 의해 검출할 수 있지만, 밝기의 변화가 일정하지 않은 레인내의 유전밴드는 일반적인 인식방법에 의해서는 검출하기 어렵다. 따라서 유전밴드 영상으로부터 지형적 특징을 추출하고, 이것으로부터 계산한 곡률(curvature)의 크기에 의해 유전밴드를 인식함으로써 레인의 밝기가 변화하는 경우에도 효과적으로 인식하였다.Abstract This paper presents recognition of DNA band using the topographical features of DNA band images. The DNA band provides a more reliable way of identification than fingerprints. Recognition based on differentiation operators can easily detect the DNA band if the brightness of lane in the image is almost uniform. When the brightness of the lane changes gradually, the DNA bands are hard to be recognized. Using the curvature magnitude of the lane computed from topographic features extracted from DNA images, the DNA bands are efficiently recognized in the lane whose brightness changes.

• Bulletin of the Korean Chemical Society
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• v.31 no.9
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• pp.2724-2726
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• 2010

• Smart Structures and Systems
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• v.12 no.1
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• pp.73-95
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• 2013

Nine deoxyribonucleic acid (DNA) sequences were used to functionalize single-walled carbon nanotube (SWNT) sensors to detect the trace amount of methanol, acetone, and HCl in vapor. DNA 24 Ma (24 randomly arranged nitrogenous bases with one amine at each end of it) decorated SWNT sensor and DNA 24 A (only adenine (A) base with a length of 24) decorated SWNT sensor have demonstrated the largest sensing responses towards acetone and HCl, respectively. On the other hand, for the DNA GT decorated SWNT sensors with different sequence lengths, the optimum DNA sequence length for acetone and HCl sensing is 32 and 8, separately. The detection of methanol, acetone, and HCl have identified that DNA functionalized SWNT sensors exhibit great selectivity, sensitivity, and repeatability with an accuracy of more than 90%. Further, a sensor array composed of SWNT functionalized with various DNA sequences was utilized to identify acetone and HCl through pattern recognition. The sensor array is a combination of four different DNA functionalized SWNT sensors and two bare SWNT sensors (work as reference). This wireless sensing system has enabled real-time gas monitoring and air quality assurance for safety and security.

• The Plant Pathology Journal
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• v.37 no.3
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• pp.291-298
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• 2021

False smut caused by Ustilaginoidea virens is an important rice fungal disease that significantly decreases its production. In the recent past, conventional methods have been developed for its detection that is time-consuming and need high-cost equipments. The research and development in nanotechnology have made it possible to assemble efficient recognition interfaces in biosensors. In this study, we present a simple, sensitive, and selective oxidized graphene-based geno-biosensor for the detection of rice false smut. The biosensor has been developed using a probe DNA as a biological recognition element on paper electrodes, and oxidized graphene to enhance the limit of detection and sensitivity of the sensor. Probe single-stranded DNA (ssDNA) and target ssDNA hybridization on the interface surface has been quantitatively measured with the electrochemical analysis tools namely, cyclic voltammetry, and linear sweep voltammetry. To confirm the selectivity of the device, probe hybridization with non-complementary ssDNA target has been studied. In our study, the developed sensor was able to detect up to 10 fM of target ssDNA. The paper electrodes were employed to produce an effective and cost-effective platform for the immobilization of the DNA and can be extended to design low-cost biosensors for the detection of the other plant pathogens.

• Proceedings of the Korean Biophysical Society Conference
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• 1998.06a
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• pp.11-11
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• 1998

Zinc fingers of Cys$_2$His$_2$ class constitute one of the most common DNA binding motifs in eukaryotes. Unlike other DNA binding motifs, zinc finger proteins recognize very diverse DNA sites, and their sequence specificities can be systematically changed by phage display.(omitted)